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Infant in arms: Some thoughts from a father traveling solo with an infant

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Brief Context

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As a scientist, I often attend conferences/meetings/etc. +Making this work as a childless, married academic husband was reasonably straightforward for my wife and me. +However, things changed in April of 2018 when our daughter was born. +Finding a way to integrate our daughter into this schedule is important because academic life bleeds heavily into times that are normally reserved for family life (weekends, evenings). +Many academic conferences and events are scheduled over a weekend or involve weekend travel. +What works for us is that I will take the baby with me when I travel for trips where it makes sense for both of our schedules. +In our daughter’s first six months, I traveled roughly 25,000 miles with her via air, car, and Amtrak. +Here I’m compiling some observations from my travel that may be informative or helpful to others.

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+ + Visiting the Broad Institute on the first solo trip I took with our daughter, which we did via Amtrak. + + +
+ Visiting the Broad Institute on the first solo trip I took with our daughter, which we did via Amtrak. + +
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Travel Supplies

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A good backpack beats a diaper bag. +I received an Aer Travel Pack 2 as a gift and used it as a travel backpack for some time before our daughter was born. +It was fine for that, but it makes a great travel diaper bag. +The features that I have found most important are that 1) electronics get stored in a separate, padded compartment; 2) the separate “shoe compartment” can be used for soiled clothes (or diapers if you haven’t found a place to dispose of them) wrapped in a plastic bag; 3) it opens like a clamshell, so you can access different contents easily: I store diapers and wipes at the bottom, a couple changes of clothes above that, and then bottles, formula, and toys at the top; and 4) it fits under the seats of nearly all aircraft (there are a few aircraft types that have very narrow underseat storage for the aisle seat where it won’t fit).

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+ + Napping on the Boppy pillow. + + +
+ Napping on the Boppy pillow. + +
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Have a support for the baby on your lap. +I’ve had good success with a Boppy pillow. +These things look like a huge neck pillow for the waist. +I’ve found this helps with feeding, but it also gives our baby something to sleep on during the flight. +For me, it reduces the discomfort from having her on my lap for long stretches.

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+ + Everything’s a toy! This cup was a big hit with me in Houston. + + +
+ Everything’s a toy! This cup was a big hit with me in Houston. + +
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Bring a few toys, but find a bunch more. +Our baby’s philosophy seems to be that an object is just a toy she hasn’t figured out how to have fun with yet. +Travel leads to lots of new objects. +We’ve had fun with snack mix bags, plastic cups, spoons, and many other items. +I’ve had good luck bringing a few toys and planning to find more along the way.

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+ + Car seat, stroller, Boppy in the walking-through-the-airport configuration. + + +
+ Car seat, stroller, Boppy in the walking-through-the-airport configuration. + +
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My travel go-to items for baby moving are an Ergobaby carrier, travel stroller, and car seat. +I like a travel stroller that the car seat gets attached to via a strap that goes where the seat belt would be. +In general, I use these as one would expect. +The best way I’ve found to board a plane solo is to, a few minutes before boarding begins, put the baby into the ergobaby. +Wheel the stroller with the car seat inside down the ramp. +Fold the stroller and place both the stroller and the car seat at the end of the ramp for the ground crew. +For deplaning, I do this in reverse. +Finding a routine that works has helped me to keep everything together in some hectic situations. +The one caveat of going this route is to note that you need two gate-check tags - one for the stroller and a second one for the car seat.

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Feeding

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Traveling with formula was the best option for me. +I traveled with a cooler of breastmilk for the first trip I took with our baby, which was via Amtrak. +It dramatically increased how much I needed to carry, the logistics involved with timing, and meant that I needed to make absolutely sure that the hotel would have a suitably cold fridge (and freezer) on arrival. +It is something that is possible to do via train. +I only did this for the first trip, though I looked at what it would take to pack for travel via air and decided against for subsequent trips. +Formula is easier for me since I can easily pack it or buy it upon arrival.

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Feed when the baby is hungry, and stay consistent in the size of the bottle. +For the first trips I had planned out when our baby would be hungry based on her normal schedule, and so I knew where I would be for each one. +Unfortunately, travel seems to alter babies eating schedules in unpredictable ways. +I tried to compensate by feeding an “interim” bottle that was half-size to tide her over to the planned feeding time, but I have found this to be a path straight to a fussy baby and don’t recommend it.

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Whenever I find the perfect size cups, I ask for a few. +When I travel with room-temperature formula and happen across paper cups for hot drinks that hold the bottle plus a roughly equal amount of water, I snag a few. +When I ask for water to heat up formula on a plane, I usually get near-boiling water (when I use this water to heat formula, I let the water cool just a little bit, and then swirl the formula pretty quickly while it’s warming - I didn’t do this the first time, cooked the formula, and had to throw it out and start over). +I’ve found that with the rate of heat loss from such cups, equal amounts of formula and water is about the right size to get a suitably warm bottle of formula for our baby. +If the volume of the cup is too large the formula ends up too hot and I increase the risk of cooking it. +If it’s too low, our baby won’t drink it.

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In Air and Airport

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Flights with a connection are better for longer itineraries. +When I traveled alone, I preferred the direct flight. +I’ve found that when traveling with a baby, the opportunity to disembark, walk around a little bit, feed and change the baby in a less cramped space, and then continue to the destination is far more compatible with the happiness of me and our baby. +As a side benefit, these flights are often a bit cheaper than direct ones.

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+ + Snack mix bags crinkle, and wow that is fun! + + +
+ Snack mix bags crinkle, and wow that is fun! + +
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Airline club membership is helpful when traveling with an infant. +In 2017, I flew enough that I had complimentary access to Delta’s Sky Clubs in 2018. +The ability to take my stuff and baby in, set the stuff down, get a bite of food and some water, eat, feed the baby, change the baby, and get to the next flight made all of this far more pleasant.

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+ + Skyclub membership was helpful. This one in SLC let us put our stuff down and recharge mid-itinerary. + + +
+ Skyclub membership was helpful. This one in SLC let us put our stuff down and recharge mid-itinerary. + +
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Certain aircraft do not have changing tables in the restrooms. +Delta flies a number of older aircraft (MD-88s, MD-90s, and 717s) and they use them heavily for flights to Philadelphia. +The existence of changing tables on these aircraft has been hit or miss. +If they do have changing tables, they’re usually in one of the economy restrooms in the tail. +At least on Delta, you won’t know this when you book - only when you look. +You probably want to check all three restrooms unless you are comfortable changing an infant who you are holding vertically. +I’ve had to change three blowouts while holding our baby vertically in these aircraft without any tables. +It’s something you get ok at. +I highly recommend traveling with the baby in either kimono-style onesies or zippy jamz pajamas. +Anything that goes over the head is bad news for a standing blowout change.

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+ + Even as our daughter has grown, the Boppy pillow remains a favorite in the air. + + +
+ Even as our daughter has grown, the Boppy pillow remains a favorite in the air. + +
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Ask for more cabin comfort. +The time that this most comes to mind for me was an early morning flight out of Houston’s Hobby Airport. +We’d gotten up around 4AM to catch a 6AM flight, and the aircraft was inordinately warm when we boarded. +My daughter actually did ok during the boarding process, but the flight continued to warm up on ascent. +My daughter started crying and was very difficult to console. +I thought the heat might be an issue, but it also could have been the early wake-up or something else. +I waited until the drink service to ask if the cabin could be cooled down. +After service, the flight attendants must have asked the cockpit to reduce the temperature. +As soon as it started cooling down, she went to sleep and slept the rest of the flight. +If I’d used the call button before service, I could have saved everyone a half-hour of listening to a crying baby.

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Hotels

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For our baby at least, the first night in each new hotel room was a rough one. +I usually had at least a few wake-ups at unusual times in addition to the usual ones. +I haven’t found a solution to this, but at least I’m now aware of what it’ll be like.

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Don’t expect a crib in the room when you arrive. +I don’t care how many times you call the hotel. +I don’t care if it’s the AAA four-diamond rated Fairmont Orchid and you noted it on your reservation, confirmed again a week before, and confirmed at the desk when you checked in. +Do not expect it to be there. +Expect it to take at least an hour and three calls to the service desk after you arrive (at 10 PM Hawaii time after traveling from the east coast - I’m still glaring at you Fairmont Orchid). +We occasionally found the crib we had asked for (every time for our hotels in Japan, almost never anywhere else). +But this seems to be something hotels in the US are more or less terrible at, so I’d say just imagine it won’t be there. +We did purchase a travel crib, which we have used when my wife and I have traveled together. +My daughter sleeps better in this, but the weight and added item makes it too cumbersome for me to take when it’s just me.

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Other Venue Notes

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Some places have been remarkably wonderful to work with. +In particular, the folks who scheduled the Annual Keck Center Research Conference for the Gulf Coast Consortia were incredible. +I was invited to speak at this event and initially declined because it was the day after a previously-scheduled return flight from Japan. +After some discussion with the organizers, I decided to skip my final Detroit to Philadelphia leg and fly to Houston for the event before returning home. +While in Japan, we found it hard to get liquid formula that we’d need for the Houston part of the trip. +When I asked for suggestions of a place to buy formula near the airport or hotel, the folks from the event put enough bottles of formula at the hotel check-in that we were able to make it through the first night. +Then I just had to walk to a store to buy formula before the meeting the next day. +I also want to give a shout out to the folks from Northwestern Mutual’s HQ in Milwaukee. +They hosted ALSF’s Young Investigator Summit and made traveling with the baby a breeze.

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+ + Speaker dinner for the Keck Center Research Conference. + + +
+ Speaker dinner for the Keck Center Research Conference. + +
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Traveling with an infant may cost you some opportunities. +I was invited to give talks both during a symposium and for the community in my area of expertise at the University of Oslo that would have involved weekend travel. +When I asked the organizers to ask the hotel to add a crib to the room during the reservation process, this led to some red flags that ultimately led to the decision to find another speaker for their event and seminar series. +The advice that I’ve gotten from folks on social media who traveled to work-related seminars where they needed to take their kids was to not give organizers a heads up and to deal directly with the hotel for a crib. +If it’s an opportunity you can’t afford to miss, it sounds like this is still the way to go in 2018. +However, if missing the event wouldn’t be hugely costly, I’ve found other places to be helpful and willing to ask the hotel for a crib when they make the reservation.

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+ + Our daughter spending lunch with me at PSB. + + +
+ Our daughter spending lunch with me at PSB. + +
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Certain conferences and meetings also have very restrictive policies on children, so before you go it’s probably good to see where your society falls. +I mentioned to a colleague that I would be at the American Association for Cancer Research (AACR) meeting with our daughter, and they mentioned that they had seen a scientist barred from the meeting because they were with a child. +It turns out that AACR bans children from exhibit halls, poster sessions, and scientific sessions at their annual meeting though it does provide a childcare option that might work for some. +The American Society for Clinical Oncology (ASCO) also bans children at their annual meeting and has not generally provided childcare for attendees. +In 2019 both of these meetings include a weekend, making the policies even more family-unfriendly. +On the other hand, the American Society for Cell Biology (ASCB) has clear, inclusive policies during the meeting. +The Pacific Symposium on Biocomputing (PSB), a computational biology conference, has been family friendly for as long as I can remember. +The American Society for Human Genetics (ASHG) and International Society for Computational Biology (ISCB) get special shoutouts for both providing childcare options and allowing children at the meeting itself providing parents with the flexibility they need.

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Closing thoughts

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I’ve enjoyed traveling with our daughter during this time. +For fathers who are considering traveling with their infants to a conference or symposium, I’ve found that it is very practical to do so. +I would be remiss not to note that we give women traveling with a baby far less support than men. +There have been numerous situations throughout my time traveling that have made this clear to me. +On multiple flights, attendants have offered to hold my daughter if I needed to go to the restroom. +I haven’t seen the same level of support for women traveling alone with their babies. +In one case, a flight attendant walked my daughter up and down the aisle of the aircraft to calm her. +Even fellow passengers seemed less irritated by a fussy infant with me: in all of this travel I can only think of one dirty look that I got from a fellow passenger while I was traveling alone with my daughter. +When you travel, offer assistance and understanding to women who need it as well.

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+ + The Harassment Tax + + +
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The Harassment Tax

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TL;DR: This twitter thread from Michael Hendricks is on the money.

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In a recent article in Science about the National Academies developing a procedure to expel sexual harassers, Dr. Robert Weinberg (Member, Whitehead Institute; and Daniel K. Ludwig Professor for Cancer Research in the Department of Biology at MIT) was quoted as saying, “Before there is a mad rush to approve such an ejection procedure, it might be useful to ask whether sexual harassment by a member has anything whatsoever to do with their credibility as a scientist and the soundness of their research accomplishments—the criteria that were used to elect them in the first place.” +When scientists reach these milestones by imposing costs on others through falsification, harassment, or other means they are externalizing costs onto the rest of the field. +We shouldn’t honor that.

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We might be tempted to buy into a lone genius model of science. +In popular media, scientists are sometimes presented as brilliant folks who toil in isolation and only emerge when they have some deep, self-evident insight that nobody can disagree with. +However, this model is a myth and nothing could be further from the truth. +Science is a messy, community-based process. +The scientist toiling long hours in the lab has based work on the findings of others. +That scientist has had ideas honed by a mentor, feedback from others in the research group, and directly or indirectly by external peers. +For the work to be convincing and impactful, the scientist will need to rule out additional models raised by the community by performing more experiments. +The ultimate trajectory of a research program and its influence is shaped by others.

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As soon as one leaves the lone genius myth behind, it is obvious why harassers should not be admitted to the National Academies and should be expelled if they already have been admitted. +Unfortunately, harassment is all too common in academia, with fifty-eight percent of female faculty and staff in academia reporting behaviors that constitute harassment. +Scientists who are harassed have their time and attention unfairly taken from them. +They may leave one field and transition to another to escape their harasser(s) – requiring them to spend time gaining additional skills and knowledge – or even leave science entirely (see the NASEM report on Sexual Harassment of Women, Chapter 4). +Those who support such scientists (for example Dr. BethAnn McLaughlin, founder of #MeTooSTEM) are also taxed for their own time and attention. +Too often, these may be ghost mentors who receive little or no credit for their efforts.*

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Harassment taxes the harassed scientist’s time, attention and resources, as well as those of other scientists. +It weakens the community: by promoting a homogeneity of experiences and backgrounds it reduces the effectiveness of scientific inquiry. +In short, it imposes the costs for the failings of the harasser on others. +Revisiting Dr. Weinberg’s question of whether or not sexual harassment has anything to do with a perpetrator’s credibility and research accomplishments, my answer is an emphatic “Yes!”

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It’s clear that the National Academies can be a force for good: see, for example, their own report on the impact of Sexual Harassment. +If the National Academies fail to pass this policy during the vote on April 30th, then they will have failed the scientific community. +Other organizations, for example the Wellcome Trusts, are moving ahead with policies to reduce harassment in science. +Every time that the National Academies fail to expel harassers, they look more like relics of a bygone age. +This diminishes the relevance of the Academies to the future of science and the honor associated with membership.

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* Take Dr. McLaughlin for example: her work is more widely cited than mine, she’s received more NIH funding than I have (in addition to other federal funding), and she’s clearly had a larger impact on the practice of science than I have (AAAS and NAS among many others). +It’s clear that she is far more qualified to be a tenured faculty member than I am. +In a seemingly absurd decision, Vanderbilt denied her tenure case after the dean of VUMC, Jeffrey Balser, had her case reconsidered by a committee that included a faculty member now on leave for sexual misconduct (David Sweatt). +The committee in question was overturning two initial favorable tenure decisions. +The Chancellor of Vanderbilt University, Nick Zeppos, has failed to support her tenure case, though he has published a blog post on the importance of women at Vanderbilt. +It conspicuously ignores Dr. McLaughlin, a winner of the MIT Disobedience Prize.

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P.S. I gave a talk at UAB recently, where I included some slides (+ a new bonus slide with Dr. Weinberg’s quotation for a seminar I’m giving at NYU on Monday, April 8). +You are welcome to use them in your own talks (note the arrangement, which is my own, is CC0 licensed, but certain content is by others and not openly licensed and so uses of those portions must fall under fair use).

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+ + Infant in arms: Some thoughts from a father traveling solo with an infant + + +
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+ + Why do we have application fees? + + +
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Why do we have application fees?

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Context

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I’m considering this question in regards to PhD programs in the biological sciences. +For a brief bit of context, these are programs where trainees, once they join a program, have their tuition paid for and also receive a stipend. +The funds to offer the stipend and tuition coverage primarily come from an institution, from training grants (which are given to an individual or institution to support training in areas of need), and from research project grants (which are given to an institution for the purposes of carrying out a specific research project). +In short, the training program includes classwork, which is an investment that the institution makes in each student, as well as a research component, which involves the trainee carrying out a project that also benefits the institution.

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What are the application fees?

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When students want to apply to one of these programs, they are often required to pay a fee to have their application considered. +The fee to apply to our Genomics and Computational Biology (GCB) program for the 2019 class year was $80. +This means that we raise from applicants, at most (see the bit on fee waivers below), about $16000 per year if we assume roughly 200 applications. +A student applying to 10 PhD programs would spend roughly $800 with the hopes of matriculating into one.

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What are the arguments in favor of application fees?

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I’ve heard a few arguments for fees. +I can continue to add to this list if folks provide new reasons (mention @greenescientist on twitter or email greenescientist@gmail.com). +If you want to add a reason, please keep it to a few sentences or provide a link to a twitter thread / blog post / something else that I can link to.

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What are my concerns with application fees?

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I worry that the fees present barriers for reasons that I’ll detail below. +I can also continue to add to this list if folks provide new reasons (mention @greenescientist on twitter or email greenescientist@gmail.com). +If you want to add a reason, please keep it to a few sentences or provide a link to a twitter thread / blog post / something else that I can link to.

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What could the next steps be?

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I have been made aware that at Penn we looked into the effect of application fees and little evidence was found that our fees were a barrier. I did look through the peer-reviewed literature a bit, and I couldn’t find data on the results of a complete elimination of application fees. I did find results that suggested that granting fee waivers as a matter of routine could be helpful. It seems that perhaps there isn’t evidence simply because the experiment hasn’t been done.

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I hope that one or more graduate programs at an institution will run an experiment with the complete elimination of application fees. It is probably best, from an experimental design point of view, to eliminate fees for randomly selected set of programs while leaving other programs at the institution’s application fee unchanged. Interesting outcomes to examine would include committee-assigned scores for applicants invited to interview; the number of first generation, low income, and underrepresented minority scientists invited to interview; and the yield from the interview process. I had hoped that we would be able to run such an evaluation at Penn, but this will not come to pass. +I am posting this to the blog in the hopes that another institution will find the question to be worth asking.

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Update 5/1/19:

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After posting, I was pointed to CMU’s Department of Philosophy’s elimination of application fees in 2017.

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+ + + Previous post
+ + The Harassment Tax + + +
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+ + Deep Learning in Biology Workshop + + +
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Deep Learning in Biology Workshop

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Discovering the beauty of math and the fun of computer science

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My mother saw math in everything around us; in the geometry of a bridge we drove across, in the permutations of numbers that make up my birthday. +Growing up she would get excited as she explained the solution to a math problem. +She would tell me that math is beautiful. +As a high school student, I remember thinking that math was simply a graduation requirement. +However my understanding and appreciation for math soon changed. +After taking an applied mathematics course in college (Bryn Mawr College), I discovered how math paired with computer science could be used to model and solve real world problems such as predicting the spread of influenza virus through a population given different control measures such as antiviral drugs. +This course introduced me to mathematical concepts that allowed me to make quasi-discoveries within a simplified dynamical system. +I found the beauty in math was combining it with computer science to translate science and research to clinical applications – It was exciting that I could make discoveries about seal populations with a few lines of code and some math equations!

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I started to actively pursue opportunities to continue applying computational methods to science problems. +This eventually lead to me to start a graduate degree program in Genomics and Computational Biology at the University of Pennsylvania in 2017. +In 2018, I joined Casey Greene’s lab, which has a lot of expertise in using deep learning methods to study biology. +Despite having a computational background, I had a lot to learn about what deep learning was. +Additionally, my educational background was purely computational and so I also needed to learn biology – in my first graduate course I remember my first question was “what is a gene?”

+ +

After a long journey, I have published a paper using a generative multi-layer neural network to simulate compendia of gene expression experiments from large-scale microbial and human datasets. +I have contributed to a community-written manuscript about tips for using deep learning in biology. +Overall, my dissertation research has focused on using deep learning methods to extract patterns from large-scale gene expression datasets. +I am currently applying these methods to understand mechanisms of P.aeruginosa infection. +My goal is to develop methods that help gain insight into the complexities of disease traits. +You can find my current research projects on my github page.

+
+ + + + + +
+ + +

Deep learning in biology workshop

+ +

To celebrate and pass on the knowledge, my lab mate, Ben Heil and I are hosting a “Deep Learning for Biologists Workshop”.

+ +

For biologists with no computational background, we hope that after this course:

+ +
    +
  1. You will have an idea of what deep learning is
  2. +
  3. You will be inspired to find applications of deep learning in your own research
  4. +
+ +

For those with some computational background, you will also gain an intuitive sense for how these methods work with a little bit of math (what else would you expect from a former math major).

+ +

We know the idea of deep learning feels very daunting, but we know that you can learn this too!

+ +

Come join us Thursday, October 29 at 11am - 2pm EST.

+ +

Registration can be found here

+ +
+ + figure image + + +
+ +
+ + figure image + + +
+
+ + + + + +
+ + + +
+ + + Previous post
+ + Why do we have application fees? + + +
+ + + +
+
+ + +
+ + + + + + + diff --git a/preview/pr-117/404.html b/preview/pr-117/404.html new file mode 100644 index 00000000..37808a0b --- /dev/null +++ b/preview/pr-117/404.html @@ -0,0 +1,742 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +404 | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+

+ Page Not Found

+ +

Try searching the whole site for the content you want:

+ +
+ + +
+
+ + +
+ + + + + + + diff --git a/preview/pr-117/_scripts/anchors.js b/preview/pr-117/_scripts/anchors.js new file mode 100644 index 00000000..904edf9c --- /dev/null +++ b/preview/pr-117/_scripts/anchors.js @@ -0,0 +1,47 @@ +/* + creates link next to each heading that links to that section. +*/ + +{ + const onLoad = () => { + // for each heading + const headings = document.querySelectorAll( + "h1[id], h2[id], h3[id], h4[id]" + ); + for (const heading of headings) { + // create anchor link + const link = document.createElement("a"); + link.classList.add("icon", "fa-solid", "fa-link", "anchor"); + link.href = "#" + heading.id; + link.setAttribute("aria-label", "link to this section"); + heading.append(link); + + // if first heading in the section, move id to parent section + if (heading.matches("section > :first-child")) { + heading.parentElement.id = heading.id; + heading.removeAttribute("id"); + } + } + }; + + // scroll to target of url hash + const scrollToTarget = () => { + const id = window.location.hash.replace("#", ""); + const target = document.getElementById(id); + + if (!target) return; + const offset = document.querySelector("header").clientHeight || 0; + window.scrollTo({ + top: target.getBoundingClientRect().top + window.scrollY - offset, + behavior: "smooth", + }); + }; + + // after page loads + window.addEventListener("load", onLoad); + window.addEventListener("load", scrollToTarget); + window.addEventListener("tagsfetched", scrollToTarget); + + // when hash nav happens + window.addEventListener("hashchange", scrollToTarget); +} diff --git a/preview/pr-117/_scripts/dark-mode.js b/preview/pr-117/_scripts/dark-mode.js new file mode 100644 index 00000000..b0124d94 --- /dev/null +++ b/preview/pr-117/_scripts/dark-mode.js @@ -0,0 +1,28 @@ +/* + manages light/dark mode. +*/ + +{ + // save/load user's dark mode preference from local storage + const loadDark = () => window.localStorage.getItem("dark-mode") === "true"; + const saveDark = (value) => window.localStorage.setItem("dark-mode", value); + + // immediately load saved mode before page renders + document.documentElement.dataset.dark = loadDark(); + + const onLoad = () => { + // update toggle button to match loaded mode + document.querySelector(".dark-toggle").checked = + document.documentElement.dataset.dark === "true"; + }; + + // after page loads + window.addEventListener("load", onLoad); + + // when user toggles mode button + window.onDarkToggleChange = (event) => { + const value = event.target.checked; + document.documentElement.dataset.dark = value; + saveDark(value); + }; +} diff --git a/preview/pr-117/_scripts/fetch-tags.js b/preview/pr-117/_scripts/fetch-tags.js new file mode 100644 index 00000000..c843b67f --- /dev/null +++ b/preview/pr-117/_scripts/fetch-tags.js @@ -0,0 +1,67 @@ +/* + fetches tags (aka "topics") from a given GitHub repo and adds them to row of + tag buttons. specify repo in data-repo attribute on row. +*/ + +{ + const onLoad = async () => { + // get tag rows with specified repos + const rows = document.querySelectorAll("[data-repo]"); + + // for each repo + for (const row of rows) { + // get props from tag row + const repo = row.dataset.repo.trim(); + const link = row.dataset.link.trim(); + + // get tags from github + if (!repo) continue; + let tags = await fetchTags(repo); + + // filter out tags already present in row + let existing = [...row.querySelectorAll(".tag")].map((tag) => + window.normalizeTag(tag.innerText) + ); + tags = tags.filter((tag) => !existing.includes(normalizeTag(tag))); + + // add tags to row + for (const tag of tags) { + const a = document.createElement("a"); + a.classList.add("tag"); + a.innerHTML = tag; + a.href = `${link}?search="tag: ${tag}"`; + a.dataset.tooltip = `Show items with the tag "${tag}"`; + row.append(a); + } + + // delete tags container if empty + if (!row.innerText.trim()) row.remove(); + } + + // emit "tags done" event for other scripts to listen for + window.dispatchEvent(new Event("tagsfetched")); + }; + + // after page loads + window.addEventListener("load", onLoad); + + // GitHub topics endpoint + const api = "https://api.github.com/repos/REPO/topics"; + const headers = new Headers(); + headers.set("Accept", "application/vnd.github+json"); + + // get tags from GitHub based on repo name + const fetchTags = async (repo) => { + const url = api.replace("REPO", repo); + try { + const response = await (await fetch(url)).json(); + if (response.names) return response.names; + else throw new Error(JSON.stringify(response)); + } catch (error) { + console.groupCollapsed("GitHub fetch tags error"); + console.log(error); + console.groupEnd(); + return []; + } + }; +} diff --git a/preview/pr-117/_scripts/search.js b/preview/pr-117/_scripts/search.js new file mode 100644 index 00000000..fa23ca4c --- /dev/null +++ b/preview/pr-117/_scripts/search.js @@ -0,0 +1,215 @@ +/* + filters elements on page based on url or search box. + syntax: term1 term2 "full phrase 1" "full phrase 2" "tag: tag 1" + match if: all terms AND at least one phrase AND at least one tag +*/ +{ + // elements to filter + const elementSelector = ".card, .citation, .post-excerpt"; + // search box element + const searchBoxSelector = ".search-box"; + // results info box element + const infoBoxSelector = ".search-info"; + // tags element + const tagSelector = ".tag"; + + // split search query into terms, phrases, and tags + const splitQuery = (query) => { + // split into parts, preserve quotes + const parts = query.match(/"[^"]*"|\S+/g) || []; + + // bins + const terms = []; + const phrases = []; + const tags = []; + + // put parts into bins + for (let part of parts) { + if (part.startsWith('"')) { + part = part.replaceAll('"', "").trim(); + if (part.startsWith("tag:")) + tags.push(normalizeTag(part.replace(/tag:\s*/, ""))); + else phrases.push(part.toLowerCase()); + } else terms.push(part.toLowerCase()); + } + + return { terms, phrases, tags }; + }; + + // normalize tag string for comparison + window.normalizeTag = (tag) => + tag.trim().toLowerCase().replaceAll(/-|\s+/g, " "); + + // get data attribute contents of element and children + const getAttr = (element, attr) => + [element, ...element.querySelectorAll(`[data-${attr}]`)] + .map((element) => element.dataset[attr]) + .join(" "); + + // determine if element should show up in results based on query + const elementMatches = (element, { terms, phrases, tags }) => { + // tag elements within element + const tagElements = [...element.querySelectorAll(".tag")]; + + // check if text content exists in element + const hasText = (string) => + ( + element.innerText + + getAttr(element, "tooltip") + + getAttr(element, "search") + ) + .toLowerCase() + .includes(string); + // check if text matches a tag in element + const hasTag = (string) => + tagElements.some((tag) => normalizeTag(tag.innerText) === string); + + // match logic + return ( + (terms.every(hasText) || !terms.length) && + (phrases.some(hasText) || !phrases.length) && + (tags.some(hasTag) || !tags.length) + ); + }; + + // loop through elements, hide/show based on query, and return results info + const filterElements = (parts) => { + let elements = document.querySelectorAll(elementSelector); + + // results info + let x = 0; + let n = elements.length; + let tags = parts.tags; + + // filter elements + for (const element of elements) { + if (elementMatches(element, parts)) { + element.style.display = ""; + x++; + } else element.style.display = "none"; + } + + return [x, n, tags]; + }; + + // highlight search terms + const highlightMatches = async ({ terms, phrases }) => { + // make sure Mark library available + if (typeof Mark === "undefined") return; + + // reset + new Mark(document.body).unmark(); + + // limit number of highlights to avoid slowdown + let counter = 0; + const filter = () => counter++ < 100; + + // highlight terms and phrases + new Mark(elementSelector) + .mark(terms, { separateWordSearch: true, filter }) + .mark(phrases, { separateWordSearch: false, filter }); + }; + + // update search box based on query + const updateSearchBox = (query = "") => { + const boxes = document.querySelectorAll(searchBoxSelector); + + for (const box of boxes) { + const input = box.querySelector("input"); + const button = box.querySelector("button"); + const icon = box.querySelector("button i"); + input.value = query; + icon.className = input.value.length + ? "icon fa-solid fa-xmark" + : "icon fa-solid fa-magnifying-glass"; + button.disabled = input.value.length ? false : true; + } + }; + + // update info box based on query and results + const updateInfoBox = (query, x, n) => { + const boxes = document.querySelectorAll(infoBoxSelector); + + if (query.trim()) { + // show all info boxes + boxes.forEach((info) => (info.style.display = "")); + + // info template + let info = ""; + info += `Showing ${x.toLocaleString()} of ${n.toLocaleString()} results
`; + info += "Clear search"; + + // set info HTML string + boxes.forEach((el) => (el.innerHTML = info)); + } + // if nothing searched + else { + // hide all info boxes + boxes.forEach((info) => (info.style.display = "none")); + } + }; + + // update tags based on query + const updateTags = (query) => { + const { tags } = splitQuery(query); + document.querySelectorAll(tagSelector).forEach((tag) => { + // set active if tag is in query + if (tags.includes(normalizeTag(tag.innerText))) + tag.setAttribute("data-active", ""); + else tag.removeAttribute("data-active"); + }); + }; + + // run search with query + const runSearch = (query = "") => { + const parts = splitQuery(query); + const [x, n] = filterElements(parts); + updateSearchBox(query); + updateInfoBox(query, x, n); + updateTags(query); + highlightMatches(parts); + }; + + // update url based on query + const updateUrl = (query = "") => { + const url = new URL(window.location); + let params = new URLSearchParams(url.search); + params.set("search", query); + url.search = params.toString(); + window.history.replaceState(null, null, url); + }; + + // search based on url param + const searchFromUrl = () => { + const query = + new URLSearchParams(window.location.search).get("search") || ""; + runSearch(query); + }; + + // return func that runs after delay + const debounce = (callback, delay = 250) => { + let timeout; + return (...args) => { + window.clearTimeout(timeout); + timeout = window.setTimeout(() => callback(...args), delay); + }; + }; + + // when user types into search box + const debouncedRunSearch = debounce(runSearch, 1000); + window.onSearchInput = (target) => { + debouncedRunSearch(target.value); + updateUrl(target.value); + }; + + // when user clears search box with button + window.onSearchClear = () => { + runSearch(); + updateUrl(); + }; + + // after page loads + window.addEventListener("load", searchFromUrl); + // after tags load + window.addEventListener("tagsfetched", searchFromUrl); +} diff --git a/preview/pr-117/_scripts/site-search.js b/preview/pr-117/_scripts/site-search.js new file mode 100644 index 00000000..caff0a61 --- /dev/null +++ b/preview/pr-117/_scripts/site-search.js @@ -0,0 +1,14 @@ +/* + for site search component. searches site/domain via google. +*/ + +{ + // when user submits site search form/box + window.onSiteSearchSubmit = (event) => { + event.preventDefault(); + const google = "https://www.google.com/search?q=site:"; + const site = window.location.origin; + const query = event.target.elements.query.value; + window.location = google + site + " " + query; + }; +} diff --git a/preview/pr-117/_scripts/tooltip.js b/preview/pr-117/_scripts/tooltip.js new file mode 100644 index 00000000..49eccfc5 --- /dev/null +++ b/preview/pr-117/_scripts/tooltip.js @@ -0,0 +1,41 @@ +/* + shows a popup of text on hover/focus of any element with the data-tooltip + attribute. +*/ + +{ + const onLoad = () => { + // make sure Tippy library available + if (typeof tippy === "undefined") return; + + // get elements with non-empty tooltips + const elements = [...document.querySelectorAll("[data-tooltip]")].filter( + (element) => element.dataset.tooltip.trim() && !element._tippy + ); + + // add tooltip to elements + tippy(elements, { + content: (element) => element.dataset.tooltip.trim(), + delay: [200, 0], + offset: [0, 20], + allowHTML: true, + interactive: true, + appendTo: () => document.body, + aria: { + content: "describedby", + expanded: null, + }, + onShow: ({ reference, popper }) => { + const dark = reference.closest("[data-dark]")?.dataset.dark; + if (dark === "false") popper.dataset.dark = true; + if (dark === "true") popper.dataset.dark = false; + }, + // onHide: () => false, // debug + }); + }; + + // after page loads + window.addEventListener("load", onLoad); + // after tags load + window.addEventListener("tagsfetched", onLoad); +} diff --git a/preview/pr-117/_styles/-theme.css b/preview/pr-117/_styles/-theme.css new file mode 100644 index 00000000..7e6d3f79 --- /dev/null +++ b/preview/pr-117/_styles/-theme.css @@ -0,0 +1,41 @@ +[data-dark=false] { + --primary: #14b8a6; + --secondary: #5eead4; + --text: #000000; + --background: #ffffff; + --background-alt: #fafafa; + --light-gray: #e0e0e0; + --gray: #808080; + --overlay: #00000020; +} + +[data-dark=true] { + --primary: #14b8a6; + --secondary: #0f766e; + --text: #ffffff; + --background: #181818; + --background-alt: #1c1c1c; + --light-gray: #404040; + --gray: #808080; + --overlay: #ffffff10; +} + +:root { + --title: "Barlow", sans-serif; + --heading: "Barlow", sans-serif; + --body: "Barlow", sans-serif; + --code: "Roboto Mono", monospace; + --medium: 1rem; + --large: 1.2rem; + --xl: 1.4rem; + --xxl: 1.6rem; + --thin: 200; + --regular: 400; + --semi-bold: 500; + --bold: 600; + --spacing: 2; + --rounded: 3px; + --shadow: 0 0 10px 0 var(--overlay); +} + +/*# sourceMappingURL=-theme.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/-theme.css.map b/preview/pr-117/_styles/-theme.css.map new file mode 100644 index 00000000..d77d2663 --- /dev/null +++ b/preview/pr-117/_styles/-theme.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["-theme.scss"],"names":[],"mappings":"AACA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAEF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EAEE;EACA;EACA;EACA;EAGA;EACA;EACA;EACA;EAGA;EACA;EACA;EACA;EAGA;EAGA;EACA","sourcesContent":["// colors\n[data-dark=\"false\"] {\n --primary: #14b8a6;\n --secondary: #5eead4;\n --text: #000000;\n --background: #ffffff;\n --background-alt: #fafafa;\n --light-gray: #e0e0e0;\n --gray: #808080;\n --overlay: #00000020;\n}\n[data-dark=\"true\"] {\n --primary: #14b8a6;\n --secondary: #0f766e;\n --text: #ffffff;\n --background: #181818;\n --background-alt: #1c1c1c;\n --light-gray: #404040;\n --gray: #808080;\n --overlay: #ffffff10;\n}\n\n:root {\n // font families\n --title: \"Barlow\", sans-serif;\n --heading: \"Barlow\", sans-serif;\n --body: \"Barlow\", sans-serif;\n --code: \"Roboto Mono\", monospace;\n\n // font sizes\n --medium: 1rem;\n --large: 1.2rem;\n --xl: 1.4rem;\n --xxl: 1.6rem;\n\n // font weights\n --thin: 200;\n --regular: 400;\n --semi-bold: 500;\n --bold: 600;\n\n // text line spacing\n --spacing: 2;\n\n // effects\n --rounded: 3px;\n --shadow: 0 0 10px 0 var(--overlay);\n}\n"],"file":"-theme.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/alert.css b/preview/pr-117/_styles/alert.css new file mode 100644 index 00000000..a270c6f4 --- /dev/null +++ b/preview/pr-117/_styles/alert.css @@ -0,0 +1,36 @@ +.alert { + position: relative; 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+} + +.anchor:hover { + color: var(--text) !important; +} + +/*# sourceMappingURL=anchor.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/anchor.css.map b/preview/pr-117/_styles/anchor.css.map new file mode 100644 index 00000000..060a4538 --- /dev/null +++ b/preview/pr-117/_styles/anchor.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["anchor.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;AAAA;EAEE;;;AAGF;EACE","sourcesContent":[".anchor {\n display: inline-block;\n position: relative;\n width: 0;\n margin: 0;\n left: 0.5em;\n color: var(--primary) !important;\n opacity: 0;\n font-size: 0.75em;\n text-decoration: none;\n transition-property: opacity, color;\n}\n\n*:hover > .anchor,\n.anchor:focus {\n opacity: 1;\n}\n\n.anchor:hover {\n color: var(--text) !important;\n}\n"],"file":"anchor.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/background.css b/preview/pr-117/_styles/background.css new file mode 100644 index 00000000..025e56ad --- /dev/null +++ b/preview/pr-117/_styles/background.css @@ -0,0 +1,20 @@ +.background { + position: relative; + background: var(--background); + color: var(--text); + z-index: 1; +} + +.background:before { + content: ""; + position: absolute; + inset: 0; + background-image: var(--image); + background-size: cover; + background-repeat: no-repeat; + background-position: 50% 50%; + opacity: 0.25; + z-index: -1; +} + +/*# sourceMappingURL=background.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/background.css.map b/preview/pr-117/_styles/background.css.map new file mode 100644 index 00000000..b655d9e5 --- /dev/null +++ b/preview/pr-117/_styles/background.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["background.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA","sourcesContent":[".background {\n position: relative;\n background: var(--background);\n color: var(--text);\n z-index: 1;\n}\n\n.background:before {\n content: \"\";\n position: absolute;\n inset: 0;\n background-image: var(--image);\n background-size: cover;\n background-repeat: no-repeat;\n background-position: 50% 50%;\n opacity: 0.25;\n z-index: -1;\n}\n"],"file":"background.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/body.css b/preview/pr-117/_styles/body.css new file mode 100644 index 00000000..72872612 --- /dev/null +++ b/preview/pr-117/_styles/body.css @@ -0,0 +1,17 @@ +html, +body { + margin: 0; + padding: 0; + min-height: 100vh; + background: var(--background); + color: var(--text); + font-family: var(--body); +} + +body { + display: flex; + flex-direction: column; + text-align: center; +} + +/*# sourceMappingURL=body.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/body.css.map b/preview/pr-117/_styles/body.css.map new file mode 100644 index 00000000..5fc55860 --- /dev/null +++ b/preview/pr-117/_styles/body.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["body.scss"],"names":[],"mappings":"AAAA;AAAA;EAEE;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA","sourcesContent":["html,\nbody {\n margin: 0;\n padding: 0;\n min-height: 100vh;\n background: var(--background);\n color: var(--text);\n font-family: var(--body);\n}\n\nbody {\n display: flex;\n flex-direction: column;\n text-align: center;\n}\n"],"file":"body.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/bold.css b/preview/pr-117/_styles/bold.css new file mode 100644 index 00000000..94a711f1 --- /dev/null +++ b/preview/pr-117/_styles/bold.css @@ -0,0 +1,6 @@ +b, +strong { + font-weight: var(--bold); +} + +/*# sourceMappingURL=bold.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/bold.css.map b/preview/pr-117/_styles/bold.css.map new file mode 100644 index 00000000..57012fd4 --- /dev/null +++ b/preview/pr-117/_styles/bold.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["bold.scss"],"names":[],"mappings":"AAAA;AAAA;EAEE","sourcesContent":["b,\nstrong {\n font-weight: var(--bold);\n}\n"],"file":"bold.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/button.css b/preview/pr-117/_styles/button.css new file mode 100644 index 00000000..505da8bd --- /dev/null +++ b/preview/pr-117/_styles/button.css @@ -0,0 +1,50 @@ +button { + cursor: pointer; +} + +.button-wrapper { + display: contents; +} + +.button { + display: inline-flex; + justify-content: center; + align-items: center; + gap: 10px; + max-width: calc(100% - 5px - 5px); + margin: 5px; + padding: 10px 15px; + border: none; + border-radius: var(--rounded); + background: var(--primary); + color: var(--background); + text-align: center; + font-family: var(--heading); + font-weight: var(--semi-bold); + line-height: 1; + text-decoration: none; + vertical-align: middle; + -webkit-appearance: none; + appearance: none; + transition-property: background, color; +} + +.button:hover { + background: var(--text); + color: var(--background); +} + +.button[data-style=bare] { + padding: 5px; + background: none; + color: var(--primary); +} +.button[data-style=bare]:hover { + color: var(--text); +} + +.button[data-flip] { + flex-direction: row-reverse; +} + +/*# sourceMappingURL=button.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/button.css.map b/preview/pr-117/_styles/button.css.map new file mode 100644 index 00000000..351a5ae8 --- /dev/null +++ b/preview/pr-117/_styles/button.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["button.scss"],"names":[],"mappings":"AAAA;EACE;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;;;AAGF;EACE;EACA;EACA;;AAEA;EACE;;;AAIJ;EACE","sourcesContent":["button {\n cursor: pointer;\n}\n\n.button-wrapper {\n display: contents;\n}\n\n.button {\n display: inline-flex;\n justify-content: center;\n align-items: center;\n gap: 10px;\n max-width: calc(100% - 5px - 5px);\n margin: 5px;\n padding: 10px 15px;\n border: none;\n border-radius: var(--rounded);\n background: var(--primary);\n color: var(--background);\n text-align: center;\n font-family: var(--heading);\n font-weight: var(--semi-bold);\n line-height: 1;\n text-decoration: none;\n vertical-align: middle;\n -webkit-appearance: none;\n appearance: none;\n transition-property: background, color;\n}\n\n.button:hover {\n background: var(--text);\n color: var(--background);\n}\n\n.button[data-style=\"bare\"] {\n padding: 5px;\n background: none;\n color: var(--primary);\n\n &:hover {\n color: var(--text);\n }\n}\n\n.button[data-flip] {\n flex-direction: row-reverse;\n}\n"],"file":"button.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/card.css b/preview/pr-117/_styles/card.css new file mode 100644 index 00000000..49e24a5a --- /dev/null +++ b/preview/pr-117/_styles/card.css @@ -0,0 +1,51 @@ +.card { + display: inline-flex; + justify-content: stretch; + align-items: center; + flex-direction: column; + width: 350px; + max-width: calc(100% - 20px - 20px); + margin: 20px; + background: var(--background); + border-radius: var(--rounded); + overflow: hidden; + box-shadow: var(--shadow); + vertical-align: top; +} + +.card[data-style=small] { + width: 250px; +} + +.card-image img { + aspect-ratio: 3/2; + object-fit: cover; + width: 100%; +} + +.card-text { + display: inline-flex; + justify-content: flex-start; + align-items: center; + flex-direction: column; + gap: 20px; + max-width: 100%; + padding: 20px; +} + +.card-text > *, +.card-text > .tags { + margin: 0; +} + +.card-title { + font-family: var(--heading); + font-weight: var(--semi-bold); +} + +.card-subtitle { + margin-top: -15px; + font-style: italic; +} + +/*# sourceMappingURL=card.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/card.css.map b/preview/pr-117/_styles/card.css.map new file mode 100644 index 00000000..da57e994 --- /dev/null +++ b/preview/pr-117/_styles/card.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["card.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;;;AAIF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;AAAA;EAEE;;;AAGF;EACE;EACA;;;AAGF;EACE;EACA","sourcesContent":[".card {\n display: inline-flex;\n justify-content: stretch;\n align-items: center;\n flex-direction: column;\n width: 350px;\n max-width: calc(100% - 20px - 20px);\n margin: 20px;\n background: var(--background);\n border-radius: var(--rounded);\n overflow: hidden;\n box-shadow: var(--shadow);\n vertical-align: top;\n}\n\n.card[data-style=\"small\"] {\n width: 250px;\n}\n\n.card-image img {\n aspect-ratio: 3 / 2;\n object-fit: cover;\n width: 100%;\n // box-shadow: var(--shadow);\n}\n\n.card-text {\n display: inline-flex;\n justify-content: flex-start;\n align-items: center;\n flex-direction: column;\n gap: 20px;\n max-width: 100%;\n padding: 20px;\n}\n\n.card-text > *,\n.card-text > .tags {\n margin: 0;\n}\n\n.card-title {\n font-family: var(--heading);\n font-weight: var(--semi-bold);\n}\n\n.card-subtitle {\n margin-top: -15px;\n font-style: italic;\n}\n"],"file":"card.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/checkbox.css b/preview/pr-117/_styles/checkbox.css new file mode 100644 index 00000000..8c77dc53 --- /dev/null +++ b/preview/pr-117/_styles/checkbox.css @@ -0,0 +1,5 @@ +input[type=checkbox] { + cursor: pointer; +} + +/*# sourceMappingURL=checkbox.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/checkbox.css.map b/preview/pr-117/_styles/checkbox.css.map new file mode 100644 index 00000000..90fb4932 --- /dev/null +++ b/preview/pr-117/_styles/checkbox.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["checkbox.scss"],"names":[],"mappings":"AAAA;EACE","sourcesContent":["input[type=\"checkbox\"] {\n cursor: pointer;\n}\n"],"file":"checkbox.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/citation.css b/preview/pr-117/_styles/citation.css new file mode 100644 index 00000000..0defd0a1 --- /dev/null +++ b/preview/pr-117/_styles/citation.css @@ -0,0 +1,90 @@ +.citation { + display: flex; + margin: 15px 0; + border-radius: var(--rounded); + background: var(--background); + overflow: hidden; + box-shadow: var(--shadow); +} + +.citation-image { + position: relative; + width: 180px; + flex-shrink: 0; +} + +.citation-image img { + position: absolute; + inset: 0; + width: 100%; + height: 100%; + object-fit: cover; +} + +.citation-text { + position: relative; + display: inline-flex; + flex-wrap: wrap; + gap: 15px; + max-width: 100%; + height: min-content; + padding: 20px; + padding-left: 30px; + text-align: left; + overflow-wrap: break-word; + z-index: 0; +} + +.citation-title, +.citation-authors, +.citation-details, +.citation-description { + width: 100%; + line-height: calc(var(--spacing) - 0.4); +} + +.citation-title { + font-weight: var(--semi-bold); +} + +.citation-text > .icon { + position: absolute; + top: 20px; + right: 20px; + color: var(--light-gray); + opacity: 0.5; + font-size: 30px; + z-index: -1; +} + +.citation-description { + color: var(--gray); +} + +.citation-buttons { + display: flex; + flex-wrap: wrap; + gap: 10px; +} + +.citation-buttons .button { + margin: 0; +} + +.citation-text > .tags { + display: inline-flex; + justify-content: flex-start; + margin: 0; +} + +@media (max-width: 800px) { + .citation { + flex-direction: column; + } + .citation-image { + width: unset; + height: 180px; + } +} + +/*# sourceMappingURL=citation.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/citation.css.map b/preview/pr-117/_styles/citation.css.map new file mode 100644 index 00000000..ecf90b12 --- /dev/null +++ b/preview/pr-117/_styles/citation.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["citation.scss"],"names":[],"mappings":"AAGA;EACE;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA,OAdW;EAeX;;;AAIF;EACE;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;AAAA;AAAA;AAAA;EAIE;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;;;AAGF;EACE;IACE;;EAGF;IACE;IACA,QA1FS","sourcesContent":["$thumb-size: 180px;\n$wrap: 800px;\n\n.citation {\n display: flex;\n margin: 15px 0;\n border-radius: var(--rounded);\n background: var(--background);\n overflow: hidden;\n box-shadow: var(--shadow);\n}\n\n.citation-image {\n position: relative;\n width: $thumb-size;\n flex-shrink: 0;\n // box-shadow: var(--shadow);\n}\n\n.citation-image img {\n position: absolute;\n inset: 0;\n width: 100%;\n height: 100%;\n object-fit: cover;\n}\n\n.citation-text {\n position: relative;\n display: inline-flex;\n flex-wrap: wrap;\n gap: 15px;\n max-width: 100%;\n height: min-content;\n padding: 20px;\n padding-left: 30px;\n text-align: left;\n overflow-wrap: break-word;\n z-index: 0;\n}\n\n.citation-title,\n.citation-authors,\n.citation-details,\n.citation-description {\n width: 100%;\n line-height: calc(var(--spacing) - 0.4);\n}\n\n.citation-title {\n font-weight: var(--semi-bold);\n}\n\n.citation-text > .icon {\n position: absolute;\n top: 20px;\n right: 20px;\n color: var(--light-gray);\n opacity: 0.5;\n font-size: 30px;\n z-index: -1;\n}\n\n.citation-description {\n color: var(--gray);\n}\n\n.citation-buttons {\n display: flex;\n flex-wrap: wrap;\n gap: 10px;\n}\n\n.citation-buttons .button {\n margin: 0;\n}\n\n.citation-text > .tags {\n display: inline-flex;\n justify-content: flex-start;\n margin: 0;\n}\n\n@media (max-width: $wrap) {\n .citation {\n flex-direction: column;\n }\n\n .citation-image {\n width: unset;\n height: $thumb-size;\n }\n}\n"],"file":"citation.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/code.css b/preview/pr-117/_styles/code.css new file mode 100644 index 00000000..a8077f4c --- /dev/null +++ b/preview/pr-117/_styles/code.css @@ -0,0 +1,35 @@ +pre, +code, +pre *, +code * { + font-family: var(--code); +} + +code.highlighter-rouge { + padding: 2px 6px; + background: var(--light-gray); + border-radius: var(--rounded); + line-height: calc(var(--spacing) - 0.2); +} + +div.highlighter-rouge { + width: 100%; + margin: 40px 0; + border-radius: var(--rounded); + overflow-x: auto; + overflow-y: auto; + text-align: left; + line-height: calc(var(--spacing) - 0.4); +} +div.highlighter-rouge div.highlight { + display: contents; +} +div.highlighter-rouge div.highlight pre.highlight { + width: fit-content; + min-width: 100%; + margin: 0; + padding: 20px; + color: var(--white); +} + +/*# sourceMappingURL=code.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/code.css.map b/preview/pr-117/_styles/code.css.map new file mode 100644 index 00000000..048eb764 --- /dev/null +++ b/preview/pr-117/_styles/code.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["code.scss"],"names":[],"mappings":"AAAA;AAAA;AAAA;AAAA;EAIE;;;AAIF;EACE;EACA;EACA;EACA;;;AAIF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;AAEA;EACE;;AAEA;EACE;EACA;EACA;EACA;EACA","sourcesContent":["pre,\ncode,\npre *,\ncode * {\n font-family: var(--code);\n}\n\n// inline code\ncode.highlighter-rouge {\n padding: 2px 6px;\n background: var(--light-gray);\n border-radius: var(--rounded);\n line-height: calc(var(--spacing) - 0.2);\n}\n\n// code block\ndiv.highlighter-rouge {\n width: 100%;\n margin: 40px 0;\n border-radius: var(--rounded);\n overflow-x: auto;\n overflow-y: auto;\n text-align: left;\n line-height: calc(var(--spacing) - 0.4);\n\n div.highlight {\n display: contents;\n\n pre.highlight {\n width: fit-content;\n min-width: 100%;\n margin: 0;\n padding: 20px;\n color: var(--white);\n }\n }\n}\n"],"file":"code.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/cols.css b/preview/pr-117/_styles/cols.css new file mode 100644 index 00000000..13dfb6e8 --- /dev/null +++ b/preview/pr-117/_styles/cols.css @@ -0,0 +1,34 @@ +.cols { + display: grid; + --repeat: min(3, var(--cols)); + grid-template-columns: repeat(var(--repeat), 1fr); + align-items: flex-start; + gap: 40px; + margin: 40px 0; +} + +.cols > * { + min-width: 0; + min-height: 0; +} + +.cols > div > *:first-child { + margin-top: 0 !important; +} + +.cols > div > *:last-child { + margin-bottom: 0 !important; +} + +@media (max-width: 750px) { + .cols { + --repeat: min(2, var(--cols)); + } +} +@media (max-width: 500px) { + .cols { + --repeat: min(1, var(--cols)); + } +} + +/*# sourceMappingURL=cols.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/cols.css.map b/preview/pr-117/_styles/cols.css.map new file mode 100644 index 00000000..488b8272 --- /dev/null +++ b/preview/pr-117/_styles/cols.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["cols.scss"],"names":[],"mappings":"AAGA;EACE;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;IACE;;;AAIJ;EACE;IACE","sourcesContent":["$two: 750px;\n$one: 500px;\n\n.cols {\n display: grid;\n --repeat: min(3, var(--cols));\n grid-template-columns: repeat(var(--repeat), 1fr);\n align-items: flex-start;\n gap: 40px;\n margin: 40px 0;\n}\n\n.cols > * {\n min-width: 0;\n min-height: 0;\n}\n\n.cols > div > *:first-child {\n margin-top: 0 !important;\n}\n\n.cols > div > *:last-child {\n margin-bottom: 0 !important;\n}\n\n@media (max-width: $two) {\n .cols {\n --repeat: min(2, var(--cols));\n }\n}\n\n@media (max-width: $one) {\n .cols {\n --repeat: min(1, var(--cols));\n }\n}\n"],"file":"cols.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/dark-toggle.css b/preview/pr-117/_styles/dark-toggle.css new file mode 100644 index 00000000..daedc5db --- /dev/null +++ b/preview/pr-117/_styles/dark-toggle.css @@ -0,0 +1,31 @@ +.dark-toggle { + position: relative; + width: 40px; + height: 25px; + margin: 0; + border-radius: 999px; + background: var(--primary); + -webkit-appearance: none; + appearance: none; + transition-property: background; +} + +.dark-toggle:after { + content: "\f185"; + position: absolute; + left: 12px; + top: 50%; + color: var(--text); + font-size: 15px; + font-family: "Font Awesome 6 Free"; + font-weight: 900; + transform: translate(-50%, -50%); + transition: left 0.2s; +} + +.dark-toggle:checked:after { + content: "\f186"; + left: calc(100% - 12px); +} + +/*# sourceMappingURL=dark-toggle.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/dark-toggle.css.map b/preview/pr-117/_styles/dark-toggle.css.map new file mode 100644 index 00000000..88294f04 --- /dev/null +++ b/preview/pr-117/_styles/dark-toggle.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["dark-toggle.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA","sourcesContent":[".dark-toggle {\n position: relative;\n width: 40px;\n height: 25px;\n margin: 0;\n border-radius: 999px;\n background: var(--primary);\n -webkit-appearance: none;\n appearance: none;\n transition-property: background;\n}\n\n.dark-toggle:after {\n content: \"\\f185\";\n position: absolute;\n left: 12px;\n top: 50%;\n color: var(--text);\n font-size: 15px;\n font-family: \"Font Awesome 6 Free\";\n font-weight: 900;\n transform: translate(-50%, -50%);\n transition: left 0.2s;\n}\n\n.dark-toggle:checked:after {\n content: \"\\f186\";\n left: calc(100% - 12px);\n}\n"],"file":"dark-toggle.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/feature.css b/preview/pr-117/_styles/feature.css new file mode 100644 index 00000000..a2d72f6b --- /dev/null +++ b/preview/pr-117/_styles/feature.css @@ -0,0 +1,49 @@ +.feature { + display: flex; + justify-content: center; + align-items: center; + gap: 40px; + margin: 40px 0; +} + +.feature-image { + flex-shrink: 0; + width: 40%; + aspect-ratio: 3/2; + border-radius: var(--rounded); + overflow: hidden; + box-shadow: var(--shadow); +} + +.feature-image img { + width: 100%; + height: 100%; + object-fit: cover; +} + +.feature-text { + flex-grow: 1; +} + +.feature-title { + font-size: var(--large); + text-align: center; + font-family: var(--heading); + font-weight: var(--semi-bold); +} + +.feature[data-flip] { + flex-direction: row-reverse; +} + +@media (max-width: 800px) { + .feature { + flex-direction: column !important; + } + .feature-image { + width: unset; + max-width: 400px; + } +} + +/*# sourceMappingURL=feature.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/feature.css.map b/preview/pr-117/_styles/feature.css.map new file mode 100644 index 00000000..60e3d532 --- /dev/null +++ b/preview/pr-117/_styles/feature.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["feature.scss"],"names":[],"mappings":"AAEA;EACE;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;IACE;;EAGF;IACE;IACA","sourcesContent":["$wrap: 800px;\n\n.feature {\n display: flex;\n justify-content: center;\n align-items: center;\n gap: 40px;\n margin: 40px 0;\n}\n\n.feature-image {\n flex-shrink: 0;\n width: 40%;\n aspect-ratio: 3 / 2;\n border-radius: var(--rounded);\n overflow: hidden;\n box-shadow: var(--shadow);\n}\n\n.feature-image img {\n width: 100%;\n height: 100%;\n object-fit: cover;\n}\n\n.feature-text {\n flex-grow: 1;\n}\n\n.feature-title {\n font-size: var(--large);\n text-align: center;\n font-family: var(--heading);\n font-weight: var(--semi-bold);\n}\n\n.feature[data-flip] {\n flex-direction: row-reverse;\n}\n\n@media (max-width: $wrap) {\n .feature {\n flex-direction: column !important;\n }\n\n .feature-image {\n width: unset;\n max-width: calc($wrap / 2);\n }\n}\n"],"file":"feature.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/figure.css b/preview/pr-117/_styles/figure.css new file mode 100644 index 00000000..95589387 --- /dev/null +++ b/preview/pr-117/_styles/figure.css @@ -0,0 +1,25 @@ +.figure { + display: flex; + justify-content: center; + align-items: center; + flex-direction: column; + gap: 10px; + margin: 40px 0; +} + +.figure-image { + display: contents; +} + +.figure-image img { + border-radius: var(--rounded); + overflow: hidden; + box-shadow: var(--shadow); +} + +.figure-caption { + font-style: italic; + text-align: center; +} + +/*# sourceMappingURL=figure.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/figure.css.map b/preview/pr-117/_styles/figure.css.map new file mode 100644 index 00000000..4d62fcf1 --- /dev/null +++ b/preview/pr-117/_styles/figure.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["figure.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;;;AAGF;EACE;EACA","sourcesContent":[".figure {\n display: flex;\n justify-content: center;\n align-items: center;\n flex-direction: column;\n gap: 10px;\n margin: 40px 0;\n}\n\n.figure-image {\n display: contents;\n}\n\n.figure-image img {\n border-radius: var(--rounded);\n overflow: hidden;\n box-shadow: var(--shadow);\n}\n\n.figure-caption {\n font-style: italic;\n text-align: center;\n}\n"],"file":"figure.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/float.css b/preview/pr-117/_styles/float.css new file mode 100644 index 00000000..c91b46eb --- /dev/null +++ b/preview/pr-117/_styles/float.css @@ -0,0 +1,35 @@ +.float { + margin-bottom: 20px; + max-width: 50%; +} + +.float > * { + margin: 0 !important; +} + +.float:not([data-flip]) { + float: left; + margin-right: 40px; +} + +.float[data-flip] { + float: right; + margin-left: 40px; +} + +.float[data-clear] { + float: unset; + clear: both; + margin: 0; +} + +@media (max-width: 600px) { + .float { + float: unset !important; + clear: both !important; + margin: auto !important; + max-width: unset; + } +} + +/*# sourceMappingURL=float.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/float.css.map b/preview/pr-117/_styles/float.css.map new file mode 100644 index 00000000..42c53e0b --- /dev/null +++ b/preview/pr-117/_styles/float.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["float.scss"],"names":[],"mappings":"AAEA;EACE;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;;;AAGF;EACE;EACA;;;AAGF;EACE;EACA;EACA;;;AAGF;EACE;IACE;IACA;IACA;IACA","sourcesContent":["$wrap: 600px;\n\n.float {\n margin-bottom: 20px;\n max-width: 50%;\n}\n\n.float > * {\n margin: 0 !important;\n}\n\n.float:not([data-flip]) {\n float: left;\n margin-right: 40px;\n}\n\n.float[data-flip] {\n float: right;\n margin-left: 40px;\n}\n\n.float[data-clear] {\n float: unset;\n clear: both;\n margin: 0;\n}\n\n@media (max-width: $wrap) {\n .float {\n float: unset !important;\n clear: both !important;\n margin: auto !important;\n max-width: unset;\n }\n}\n"],"file":"float.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/font.css b/preview/pr-117/_styles/font.css new file mode 100644 index 00000000..c40e1559 --- /dev/null +++ b/preview/pr-117/_styles/font.css @@ -0,0 +1,3 @@ +@font-face {} + +/*# sourceMappingURL=font.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/font.css.map b/preview/pr-117/_styles/font.css.map new file mode 100644 index 00000000..e1d56c04 --- /dev/null +++ b/preview/pr-117/_styles/font.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["font.scss"],"names":[],"mappings":"AAAA","sourcesContent":["@font-face {\n}\n"],"file":"font.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/footer.css b/preview/pr-117/_styles/footer.css new file mode 100644 index 00000000..a85b907f --- /dev/null +++ b/preview/pr-117/_styles/footer.css @@ -0,0 +1,24 @@ +footer { + display: flex; + justify-content: center; + align-items: center; + flex-direction: column; + gap: 20px; + padding: 40px; + line-height: var(--spacing); + box-shadow: var(--shadow); +} + +footer a { + color: var(--text) !important; +} + +footer a:hover { + color: var(--primary) !important; +} + +footer .icon { + font-size: var(--xl); +} + +/*# sourceMappingURL=footer.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/footer.css.map b/preview/pr-117/_styles/footer.css.map new file mode 100644 index 00000000..61ae1179 --- /dev/null +++ b/preview/pr-117/_styles/footer.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["footer.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE","sourcesContent":["footer {\n display: flex;\n justify-content: center;\n align-items: center;\n flex-direction: column;\n gap: 20px;\n padding: 40px;\n line-height: var(--spacing);\n box-shadow: var(--shadow);\n}\n\nfooter a {\n color: var(--text) !important;\n}\n\nfooter a:hover {\n color: var(--primary) !important;\n}\n\nfooter .icon {\n font-size: var(--xl);\n}\n"],"file":"footer.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/form.css b/preview/pr-117/_styles/form.css new file mode 100644 index 00000000..76114595 --- /dev/null +++ b/preview/pr-117/_styles/form.css @@ -0,0 +1,8 @@ +form { + display: flex; + justify-content: center; + align-items: center; + gap: 10px; +} + +/*# sourceMappingURL=form.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/form.css.map b/preview/pr-117/_styles/form.css.map new file mode 100644 index 00000000..65939cb6 --- /dev/null +++ b/preview/pr-117/_styles/form.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["form.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA","sourcesContent":["form {\n display: flex;\n justify-content: center;\n align-items: center;\n gap: 10px;\n}\n"],"file":"form.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/grid.css b/preview/pr-117/_styles/grid.css new file mode 100644 index 00000000..3931eb21 --- /dev/null +++ b/preview/pr-117/_styles/grid.css @@ -0,0 +1,45 @@ +.grid { + display: grid; + --repeat: 3; + grid-template-columns: repeat(var(--repeat), 1fr); + justify-content: center; + align-items: flex-start; + gap: 40px; + margin: 40px 0; +} + +.grid > * { + min-width: 0; + min-height: 0; + width: 100%; + margin: 0 !important; +} + +@media (max-width: 750px) { + .grid { + --repeat: 2; + } +} +@media (max-width: 500px) { + .grid { + --repeat: 1; + } +} +.grid[data-style=square] { + align-items: center; +} +.grid[data-style=square] > * { + aspect-ratio: 1/1; +} +.grid[data-style=square] img { + aspect-ratio: 1/1; + object-fit: cover; + max-width: unset; + max-height: unset; +} + +.grid > *:where(h1, h2, h3, h4) { + display: none; +} + +/*# sourceMappingURL=grid.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/grid.css.map b/preview/pr-117/_styles/grid.css.map new file mode 100644 index 00000000..7baeedc0 --- /dev/null +++ b/preview/pr-117/_styles/grid.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["grid.scss"],"names":[],"mappings":"AAGA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EAEA;;;AAGF;EACE;IACE;;;AAIJ;EACE;IACE;;;AAIJ;EACE;;AAEA;EACE;;AAGF;EACE;EACA;EACA;EACA;;;AAIJ;EACE","sourcesContent":["$two: 750px;\n$one: 500px;\n\n.grid {\n display: grid;\n --repeat: 3;\n grid-template-columns: repeat(var(--repeat), 1fr);\n justify-content: center;\n align-items: flex-start;\n gap: 40px;\n margin: 40px 0;\n}\n\n.grid > * {\n min-width: 0;\n min-height: 0;\n width: 100%;\n // max-height: 50vh;\n margin: 0 !important;\n}\n\n@media (max-width: $two) {\n .grid {\n --repeat: 2;\n }\n}\n\n@media (max-width: $one) {\n .grid {\n --repeat: 1;\n }\n}\n\n.grid[data-style=\"square\"] {\n align-items: center;\n\n & > * {\n aspect-ratio: 1 / 1;\n }\n\n & img {\n aspect-ratio: 1 / 1;\n object-fit: cover;\n max-width: unset;\n max-height: unset;\n }\n}\n\n.grid > *:where(h1, h2, h3, h4) {\n display: none;\n}\n"],"file":"grid.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/header.css b/preview/pr-117/_styles/header.css new file mode 100644 index 00000000..22c98416 --- /dev/null +++ b/preview/pr-117/_styles/header.css @@ -0,0 +1,146 @@ +header { + display: flex; + justify-content: space-between; + align-items: center; + flex-wrap: wrap; + gap: 20px; + padding: 20px; + box-shadow: var(--shadow); + position: sticky !important; + top: 0; + z-index: 10 !important; +} + +header a { + color: var(--text); + text-decoration: none; +} + +.home { + display: flex; + justify-content: flex-start; + align-items: center; + gap: 10px; + flex-basis: 0; + flex-grow: 1; + max-width: 100%; +} + +.logo { + height: 80px; +} + +.logo > * { + height: 100%; +} + +.title { + display: flex; + justify-content: flex-start; + align-items: baseline; + flex-wrap: wrap; + gap: 5px; + min-width: 0; + font-family: var(--title); + text-align: left; +} + +.title > *:first-child { + font-size: var(--large); +} + +.title > *:last-child { + opacity: 0.65; + font-weight: var(--thin); +} + +.nav-toggle { + display: none; + position: relative; + width: 30px; + height: 30px; + margin: 0; + color: var(--text); + -webkit-appearance: none; + appearance: none; + transition-property: background; +} + +.nav-toggle:after { + content: "\f0c9"; + position: absolute; + left: 50%; + top: 50%; + color: var(--text); + font-size: 15px; + font-family: "Font Awesome 6 Free"; + font-weight: 900; + transform: translate(-50%, -50%); +} + +.nav-toggle:checked:after { + content: "\f00d"; +} + +nav { + display: flex; + justify-content: center; + align-items: center; + flex-wrap: wrap; + gap: 10px; + font-family: var(--heading); + text-transform: uppercase; +} + +nav > a { + padding: 5px; +} + +nav > a:hover { + color: var(--primary); +} + +@media (max-width: 700px) { + header:not([data-big]) { + justify-content: flex-end; + } + header:not([data-big]) .nav-toggle { + display: flex; + } + header:not([data-big]) .nav-toggle:not(:checked) + nav { + display: none; + } + header:not([data-big]) nav { + align-items: flex-end; + flex-direction: column; + width: 100%; + } +} + +header[data-big] { + justify-content: center; + align-items: center; + flex-direction: column; + padding: 100px 20px; + top: unset; +} +header[data-big] .home { + flex-direction: column; + flex-grow: 0; +} +header[data-big] .logo { + height: 150px; +} +header[data-big] .title { + flex-direction: column; + align-items: center; + text-align: center; +} +header[data-big] .title > *:first-child { + font-size: var(--xxl); +} +header[data-big] .title > *:last-child { + font-size: var(--large); +} + +/*# sourceMappingURL=header.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/header.css.map b/preview/pr-117/_styles/header.css.map new file mode 100644 index 00000000..9430c51d --- /dev/null +++ b/preview/pr-117/_styles/header.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["header.scss"],"names":[],"mappings":"AAMA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EAGE;EACA;EACA;;;AAIJ;EACE;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE,QArCK;;;AAwCP;EACE;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAIF;EACE;;;AAIF;EACE;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;;;AAIA;EADF;IAEI;;EAEA;IACE;;EAGF;IACE;;EAGF;IACE;IACA;IACA;;;;AAKN;EACE;EACA;EACA;EACA;EAGE;;AAGF;EACE;EACA;;AAGF;EACE,QArJO;;AAwJT;EACE;EACA;EACA;;AAGF;EACE;;AAGF;EACE","sourcesContent":["$logo-big: 150px;\n$logo: 80px;\n$big-padding: 100px;\n$collapse: 700px;\n$sticky: true;\n\nheader {\n display: flex;\n justify-content: space-between;\n align-items: center;\n flex-wrap: wrap;\n gap: 20px;\n padding: 20px;\n box-shadow: var(--shadow);\n\n @if $sticky {\n position: sticky !important;\n top: 0;\n z-index: 10 !important;\n }\n}\n\nheader a {\n color: var(--text);\n text-decoration: none;\n}\n\n.home {\n display: flex;\n justify-content: flex-start;\n align-items: center;\n gap: 10px;\n flex-basis: 0;\n flex-grow: 1;\n max-width: 100%;\n}\n\n.logo {\n height: $logo;\n}\n\n.logo > * {\n height: 100%;\n}\n\n.title {\n display: flex;\n justify-content: flex-start;\n align-items: baseline;\n flex-wrap: wrap;\n gap: 5px;\n min-width: 0;\n font-family: var(--title);\n text-align: left;\n}\n\n// main title\n.title > *:first-child {\n font-size: var(--large);\n}\n\n// subtitle\n.title > *:last-child {\n opacity: 0.65;\n font-weight: var(--thin);\n}\n\n.nav-toggle {\n display: none;\n position: relative;\n width: 30px;\n height: 30px;\n margin: 0;\n color: var(--text);\n -webkit-appearance: none;\n appearance: none;\n transition-property: background;\n}\n\n.nav-toggle:after {\n content: \"\\f0c9\";\n position: absolute;\n left: 50%;\n top: 50%;\n color: var(--text);\n font-size: 15px;\n font-family: \"Font Awesome 6 Free\";\n font-weight: 900;\n transform: translate(-50%, -50%);\n}\n\n.nav-toggle:checked:after {\n content: \"\\f00d\";\n}\n\nnav {\n display: flex;\n justify-content: center;\n align-items: center;\n flex-wrap: wrap;\n gap: 10px;\n font-family: var(--heading);\n text-transform: uppercase;\n}\n\nnav > a {\n padding: 5px;\n}\n\nnav > a:hover {\n color: var(--primary);\n}\n\nheader:not([data-big]) {\n @media (max-width: $collapse) {\n justify-content: flex-end;\n\n .nav-toggle {\n display: flex;\n }\n\n .nav-toggle:not(:checked) + nav {\n display: none;\n }\n\n nav {\n align-items: flex-end;\n flex-direction: column;\n width: 100%;\n }\n }\n}\n\nheader[data-big] {\n justify-content: center;\n align-items: center;\n flex-direction: column;\n padding: $big-padding 20px;\n\n @if $sticky {\n top: unset;\n }\n\n .home {\n flex-direction: column;\n flex-grow: 0;\n }\n\n .logo {\n height: $logo-big;\n }\n\n .title {\n flex-direction: column;\n align-items: center;\n text-align: center;\n }\n\n .title > *:first-child {\n font-size: var(--xxl);\n }\n\n .title > *:last-child {\n font-size: var(--large);\n }\n}\n"],"file":"header.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/heading.css b/preview/pr-117/_styles/heading.css new file mode 100644 index 00000000..41ce7c16 --- /dev/null +++ b/preview/pr-117/_styles/heading.css @@ -0,0 +1,47 @@ +h1, +h2, +h3, +h4 { + font-family: var(--heading); + line-height: calc(var(--spacing) - 0.2); +} + +h1 { + margin: 40px 0 20px 0; + font-size: var(--xxl); + font-weight: var(--regular); + letter-spacing: 1px; + text-transform: uppercase; + text-align: left; +} + +h2 { + margin: 40px 0 20px 0; + padding-bottom: 5px; + border-bottom: solid 1px var(--light-gray); + font-size: var(--xl); + font-weight: var(--regular); + letter-spacing: 1px; + text-align: left; +} + +h3 { + margin: 40px 0 20px 0; + font-size: var(--large); + font-weight: var(--semi-bold); + text-align: left; +} + +h4 { + margin: 40px 0 20px 0; + font-size: var(--medium); + font-weight: var(--semi-bold); + text-align: left; +} + +:where(h1, h2, h3, h4) > .icon { + margin-right: 1em; + color: var(--light-gray); +} + +/*# sourceMappingURL=heading.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/heading.css.map b/preview/pr-117/_styles/heading.css.map new file mode 100644 index 00000000..95d4210c --- /dev/null +++ b/preview/pr-117/_styles/heading.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["heading.scss"],"names":[],"mappings":"AAAA;AAAA;AAAA;AAAA;EAIE;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;;;AAGF;EACE;EACA","sourcesContent":["h1,\nh2,\nh3,\nh4 {\n font-family: var(--heading);\n line-height: calc(var(--spacing) - 0.2);\n}\n\nh1 {\n margin: 40px 0 20px 0;\n font-size: var(--xxl);\n font-weight: var(--regular);\n letter-spacing: 1px;\n text-transform: uppercase;\n text-align: left;\n}\n\nh2 {\n margin: 40px 0 20px 0;\n padding-bottom: 5px;\n border-bottom: solid 1px var(--light-gray);\n font-size: var(--xl);\n font-weight: var(--regular);\n letter-spacing: 1px;\n text-align: left;\n}\n\nh3 {\n margin: 40px 0 20px 0;\n font-size: var(--large);\n font-weight: var(--semi-bold);\n text-align: left;\n}\n\nh4 {\n margin: 40px 0 20px 0;\n font-size: var(--medium);\n font-weight: var(--semi-bold);\n text-align: left;\n}\n\n:where(h1, h2, h3, h4) > .icon {\n margin-right: 1em;\n color: var(--light-gray);\n}\n"],"file":"heading.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/highlight.css b/preview/pr-117/_styles/highlight.css new file mode 100644 index 00000000..a8cf7d3c --- /dev/null +++ b/preview/pr-117/_styles/highlight.css @@ -0,0 +1,6 @@ +mark { + background: #fef08a; + color: #000000; +} + +/*# sourceMappingURL=highlight.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/highlight.css.map b/preview/pr-117/_styles/highlight.css.map new file mode 100644 index 00000000..957ceb13 --- /dev/null +++ b/preview/pr-117/_styles/highlight.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["highlight.scss"],"names":[],"mappings":"AAAA;EACE;EACA","sourcesContent":["mark {\n background: #fef08a;\n color: #000000;\n}\n"],"file":"highlight.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/icon.css b/preview/pr-117/_styles/icon.css new file mode 100644 index 00000000..ab61327d --- /dev/null +++ b/preview/pr-117/_styles/icon.css @@ -0,0 +1,15 @@ +.icon { + font-size: 1em; +} + +span.icon { + line-height: 1; +} + +span.icon > svg { + position: relative; + top: 0.1em; + height: 1em; +} + +/*# sourceMappingURL=icon.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/icon.css.map b/preview/pr-117/_styles/icon.css.map new file mode 100644 index 00000000..22298685 --- /dev/null +++ b/preview/pr-117/_styles/icon.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["icon.scss"],"names":[],"mappings":"AAAA;EACE;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA","sourcesContent":[".icon {\n font-size: 1em;\n}\n\nspan.icon {\n line-height: 1;\n}\n\nspan.icon > svg {\n position: relative;\n top: 0.1em;\n height: 1em;\n}\n"],"file":"icon.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/image.css b/preview/pr-117/_styles/image.css new file mode 100644 index 00000000..70340d33 --- /dev/null +++ b/preview/pr-117/_styles/image.css @@ -0,0 +1,6 @@ +img { + max-width: 100%; + max-height: 100%; +} + +/*# sourceMappingURL=image.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/image.css.map b/preview/pr-117/_styles/image.css.map new file mode 100644 index 00000000..e88ec450 --- /dev/null +++ b/preview/pr-117/_styles/image.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["image.scss"],"names":[],"mappings":"AAAA;EACE;EACA","sourcesContent":["img {\n max-width: 100%;\n max-height: 100%;\n}\n"],"file":"image.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/link.css b/preview/pr-117/_styles/link.css new file mode 100644 index 00000000..a20e40bc --- /dev/null +++ b/preview/pr-117/_styles/link.css @@ -0,0 +1,15 @@ +a { + color: var(--primary); + transition-property: color; + overflow-wrap: break-word; +} + +a:hover { + color: var(--text); +} + +a:not([href]) { + color: var(--text); +} + +/*# sourceMappingURL=link.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/link.css.map b/preview/pr-117/_styles/link.css.map new file mode 100644 index 00000000..976b37f2 --- /dev/null +++ b/preview/pr-117/_styles/link.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["link.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE","sourcesContent":["a {\n color: var(--primary);\n transition-property: color;\n overflow-wrap: break-word;\n}\n\na:hover {\n color: var(--text);\n}\n\na:not([href]) {\n color: var(--text);\n}\n"],"file":"link.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/list.css b/preview/pr-117/_styles/list.css new file mode 100644 index 00000000..02a7cf16 --- /dev/null +++ b/preview/pr-117/_styles/list.css @@ -0,0 +1,18 @@ +ul, +ol { + margin: 20px 0; + padding-left: 40px; +} + +ul { + list-style-type: square; +} + +li { + margin: 5px 0; + padding-left: 10px; + text-align: justify; + line-height: var(--spacing); +} + +/*# sourceMappingURL=list.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/list.css.map b/preview/pr-117/_styles/list.css.map new file mode 100644 index 00000000..38fb1e50 --- /dev/null +++ b/preview/pr-117/_styles/list.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["list.scss"],"names":[],"mappings":"AAAA;AAAA;EAEE;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;EACA","sourcesContent":["ul,\nol {\n margin: 20px 0;\n padding-left: 40px;\n}\n\nul {\n list-style-type: square;\n}\n\nli {\n margin: 5px 0;\n padding-left: 10px;\n text-align: justify;\n line-height: var(--spacing);\n}\n"],"file":"list.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/main.css b/preview/pr-117/_styles/main.css new file mode 100644 index 00000000..f72eb0d3 --- /dev/null +++ b/preview/pr-117/_styles/main.css @@ -0,0 +1,7 @@ +main { + display: flex; + flex-direction: column; + flex-grow: 1; +} + +/*# sourceMappingURL=main.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/main.css.map b/preview/pr-117/_styles/main.css.map new file mode 100644 index 00000000..a2a0fa8d --- /dev/null +++ b/preview/pr-117/_styles/main.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["main.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA","sourcesContent":["main {\n display: flex;\n flex-direction: column;\n flex-grow: 1;\n}\n"],"file":"main.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/paragraph.css b/preview/pr-117/_styles/paragraph.css new file mode 100644 index 00000000..7e46c391 --- /dev/null +++ b/preview/pr-117/_styles/paragraph.css @@ -0,0 +1,7 @@ +p { + margin: 20px 0; + text-align: justify; + line-height: var(--spacing); +} + +/*# sourceMappingURL=paragraph.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/paragraph.css.map b/preview/pr-117/_styles/paragraph.css.map new file mode 100644 index 00000000..7eb50a68 --- /dev/null +++ b/preview/pr-117/_styles/paragraph.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["paragraph.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA","sourcesContent":["p {\n margin: 20px 0;\n text-align: justify;\n line-height: var(--spacing);\n}\n"],"file":"paragraph.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/portrait.css b/preview/pr-117/_styles/portrait.css new file mode 100644 index 00000000..f9b31a1d --- /dev/null +++ b/preview/pr-117/_styles/portrait.css @@ -0,0 +1,76 @@ +.portrait-wrapper { + display: contents; +} + +.portrait { + position: relative; + display: inline-flex; + justify-content: center; + align-items: center; + flex-direction: column; + gap: 20px; + margin: 20px; + width: 175px; + max-width: calc(100% - 20px - 20px); + text-decoration: none; +} + +.portrait[data-style=small] { + width: 100px; +} + +.portrait[data-style=tiny] { + flex-direction: row; + gap: 15px; + width: unset; + text-align: left; +} + +.portrait-image { + width: 100%; + aspect-ratio: 1/1; + border-radius: 999px; + object-fit: cover; + box-shadow: var(--shadow); +} + +.portrait[data-style=tiny] .portrait-image { + width: 50px; +} + +.portrait[data-style=tiny] .portrait-role { + display: none; +} + +.portrait-text { + display: flex; + flex-direction: column; + line-height: calc(var(--spacing) - 0.4); +} + +.portrait-name { + font-family: var(--heading); + font-weight: var(--semi-bold); +} + +.portrait-role .icon { + position: absolute; + left: 0; + top: 0; + display: flex; + justify-content: center; + align-items: center; + width: 20%; + aspect-ratio: 1/1; + border-radius: 999px; + background: var(--background); + box-shadow: var(--shadow); + transform: translate(14%, 14%); +} + +.portrait[data-style=small] .portrait-role .icon { + left: -2px; + top: -2px; +} + +/*# sourceMappingURL=portrait.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/portrait.css.map b/preview/pr-117/_styles/portrait.css.map new file mode 100644 index 00000000..c3d5789d --- /dev/null +++ b/preview/pr-117/_styles/portrait.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["portrait.scss"],"names":[],"mappings":"AAAA;EACE;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;EACA;EACA;;;AAGF;EACE;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA","sourcesContent":[".portrait-wrapper {\n display: contents;\n}\n\n.portrait {\n position: relative;\n display: inline-flex;\n justify-content: center;\n align-items: center;\n flex-direction: column;\n gap: 20px;\n margin: 20px;\n width: 175px;\n max-width: calc(100% - 20px - 20px);\n text-decoration: none;\n}\n\n.portrait[data-style=\"small\"] {\n width: 100px;\n}\n\n.portrait[data-style=\"tiny\"] {\n flex-direction: row;\n gap: 15px;\n width: unset;\n text-align: left;\n}\n\n.portrait-image {\n width: 100%;\n aspect-ratio: 1 / 1;\n border-radius: 999px;\n object-fit: cover;\n box-shadow: var(--shadow);\n}\n\n.portrait[data-style=\"tiny\"] .portrait-image {\n width: 50px;\n}\n\n.portrait[data-style=\"tiny\"] .portrait-role {\n display: none;\n}\n\n.portrait-text {\n display: flex;\n flex-direction: column;\n line-height: calc(var(--spacing) - 0.4);\n}\n\n.portrait-name {\n font-family: var(--heading);\n font-weight: var(--semi-bold);\n}\n\n.portrait-role .icon {\n position: absolute;\n left: 0;\n top: 0;\n display: flex;\n justify-content: center;\n align-items: center;\n width: 20%;\n aspect-ratio: 1 / 1;\n border-radius: 999px;\n background: var(--background);\n box-shadow: var(--shadow);\n transform: translate(14%, 14%);\n}\n\n.portrait[data-style=\"small\"] .portrait-role .icon {\n left: -2px;\n top: -2px;\n}\n"],"file":"portrait.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/post-excerpt.css b/preview/pr-117/_styles/post-excerpt.css new file mode 100644 index 00000000..cfccd68b --- /dev/null +++ b/preview/pr-117/_styles/post-excerpt.css @@ -0,0 +1,30 @@ +.post-excerpt { + display: flex; + flex-wrap: wrap; + gap: 20px; + margin: 20px 0; + padding: 20px 30px; + border-radius: var(--rounded); + background: var(--background); + text-align: left; + box-shadow: var(--shadow); +} + +.post-excerpt > * { + margin: 0 !important; +} + +.post-excerpt > a:first-child { + width: 100%; + font-weight: var(--semi-bold); +} + +.post-excerpt > div { + justify-content: flex-start; +} + +.post-excerpt > p { + width: 100%; +} + +/*# sourceMappingURL=post-excerpt.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/post-excerpt.css.map b/preview/pr-117/_styles/post-excerpt.css.map new file mode 100644 index 00000000..e2041f2c --- /dev/null +++ b/preview/pr-117/_styles/post-excerpt.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["post-excerpt.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;EACA;;;AAGF;EACE;;;AAGF;EACE","sourcesContent":[".post-excerpt {\n display: flex;\n flex-wrap: wrap;\n gap: 20px;\n margin: 20px 0;\n padding: 20px 30px;\n border-radius: var(--rounded);\n background: var(--background);\n text-align: left;\n box-shadow: var(--shadow);\n}\n\n.post-excerpt > * {\n margin: 0 !important;\n}\n\n.post-excerpt > a:first-child {\n width: 100%;\n font-weight: var(--semi-bold);\n}\n\n.post-excerpt > div {\n justify-content: flex-start;\n}\n\n.post-excerpt > p {\n width: 100%;\n}\n"],"file":"post-excerpt.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/post-info.css b/preview/pr-117/_styles/post-info.css new file mode 100644 index 00000000..abb6b510 --- /dev/null +++ b/preview/pr-117/_styles/post-info.css @@ -0,0 +1,32 @@ +.post-info { + display: flex; + justify-content: center; + align-items: center; + flex-wrap: wrap; + gap: 20px; + margin: 20px 0; + color: var(--gray); +} + +.post-info .portrait { + margin: 0; +} + +.post-info .icon { + margin-right: 0.5em; +} + +.post-info a { + color: inherit; +} + +.post-info a:hover { + color: var(--primary); +} + +.post-info > span { + text-align: center; + white-space: nowrap; +} + +/*# sourceMappingURL=post-info.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/post-info.css.map b/preview/pr-117/_styles/post-info.css.map new file mode 100644 index 00000000..74c149ed --- /dev/null +++ b/preview/pr-117/_styles/post-info.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["post-info.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;EACA","sourcesContent":[".post-info {\n display: flex;\n justify-content: center;\n align-items: center;\n flex-wrap: wrap;\n gap: 20px;\n margin: 20px 0;\n color: var(--gray);\n}\n\n.post-info .portrait {\n margin: 0;\n}\n\n.post-info .icon {\n margin-right: 0.5em;\n}\n\n.post-info a {\n color: inherit;\n}\n\n.post-info a:hover {\n color: var(--primary);\n}\n\n.post-info > span {\n text-align: center;\n white-space: nowrap;\n}\n"],"file":"post-info.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/post-nav.css b/preview/pr-117/_styles/post-nav.css new file mode 100644 index 00000000..fe210bb5 --- /dev/null +++ b/preview/pr-117/_styles/post-nav.css @@ -0,0 +1,36 @@ +.post-nav { + display: flex; + justify-content: space-between; + align-items: flex-start; + gap: 10px; + color: var(--gray); + line-height: calc(var(--spacing) - 0.4); +} + +.post-nav > *:first-child { + text-align: left; +} + +.post-nav > *:last-child { + text-align: right; +} + +.post-nav > *:first-child .icon { + margin-right: 0.5em; +} + +.post-nav > *:last-child .icon { + margin-left: 0.5em; +} + +@media (max-width: 600px) { + .post-nav { + align-items: center; + flex-direction: column; + } + .post-nav > * { + text-align: center !important; + } +} + +/*# sourceMappingURL=post-nav.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/post-nav.css.map b/preview/pr-117/_styles/post-nav.css.map new file mode 100644 index 00000000..2ba6fba2 --- /dev/null +++ b/preview/pr-117/_styles/post-nav.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["post-nav.scss"],"names":[],"mappings":"AAEA;EACE;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;IACE;IACA;;EAGF;IACE","sourcesContent":["$wrap: 600px;\n\n.post-nav {\n display: flex;\n justify-content: space-between;\n align-items: flex-start;\n gap: 10px;\n color: var(--gray);\n line-height: calc(var(--spacing) - 0.4);\n}\n\n.post-nav > *:first-child {\n text-align: left;\n}\n\n.post-nav > *:last-child {\n text-align: right;\n}\n\n.post-nav > *:first-child .icon {\n margin-right: 0.5em;\n}\n\n.post-nav > *:last-child .icon {\n margin-left: 0.5em;\n}\n\n@media (max-width: $wrap) {\n .post-nav {\n align-items: center;\n flex-direction: column;\n }\n\n .post-nav > * {\n text-align: center !important;\n }\n}\n"],"file":"post-nav.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/quote.css b/preview/pr-117/_styles/quote.css new file mode 100644 index 00000000..456c767f --- /dev/null +++ b/preview/pr-117/_styles/quote.css @@ -0,0 +1,15 @@ +blockquote { + margin: 20px 0; + padding: 10px 20px; + border-left: solid 4px var(--light-gray); +} + +blockquote > *:first-child { + margin-top: 0; +} + +blockquote > *:last-child { + margin-bottom: 0; +} + +/*# sourceMappingURL=quote.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/quote.css.map b/preview/pr-117/_styles/quote.css.map new file mode 100644 index 00000000..2cc84a2b --- /dev/null +++ b/preview/pr-117/_styles/quote.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["quote.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE","sourcesContent":["blockquote {\n margin: 20px 0;\n padding: 10px 20px;\n border-left: solid 4px var(--light-gray);\n}\n\nblockquote > *:first-child {\n margin-top: 0;\n}\n\nblockquote > *:last-child {\n margin-bottom: 0;\n}\n"],"file":"quote.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/rule.css b/preview/pr-117/_styles/rule.css new file mode 100644 index 00000000..28ca0809 --- /dev/null +++ b/preview/pr-117/_styles/rule.css @@ -0,0 +1,8 @@ +hr { + margin: 40px 0; + background: var(--light-gray); + border: none; + height: 1px; +} + +/*# sourceMappingURL=rule.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/rule.css.map b/preview/pr-117/_styles/rule.css.map new file mode 100644 index 00000000..a955dd9f --- /dev/null +++ b/preview/pr-117/_styles/rule.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["rule.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA","sourcesContent":["hr {\n margin: 40px 0;\n background: var(--light-gray);\n border: none;\n height: 1px;\n}\n"],"file":"rule.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/search-box.css b/preview/pr-117/_styles/search-box.css new file mode 100644 index 00000000..9766e924 --- /dev/null +++ b/preview/pr-117/_styles/search-box.css @@ -0,0 +1,25 @@ +.search-box { + position: relative; + height: 40px; +} + +.search-box .search-input { + width: 100%; + height: 100%; + padding-right: 40px; +} + +.search-box button { + position: absolute; + inset: 0 0 0 auto; + display: flex; + justify-content: center; + align-items: center; + padding: 0; + aspect-ratio: 1/1; + background: none; + color: var(--black); + border: none; +} + +/*# sourceMappingURL=search-box.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/search-box.css.map b/preview/pr-117/_styles/search-box.css.map new file mode 100644 index 00000000..7d452743 --- /dev/null +++ b/preview/pr-117/_styles/search-box.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["search-box.scss"],"names":[],"mappings":"AAAA;EACE;EACA;;;AAGF;EACE;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA","sourcesContent":[".search-box {\n position: relative;\n height: 40px;\n}\n\n.search-box .search-input {\n width: 100%;\n height: 100%;\n padding-right: 40px;\n}\n\n.search-box button {\n position: absolute;\n inset: 0 0 0 auto;\n display: flex;\n justify-content: center;\n align-items: center;\n padding: 0;\n aspect-ratio: 1 / 1;\n background: none;\n color: var(--black);\n border: none;\n}\n"],"file":"search-box.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/search-info.css b/preview/pr-117/_styles/search-info.css new file mode 100644 index 00000000..e5c9a305 --- /dev/null +++ b/preview/pr-117/_styles/search-info.css @@ -0,0 +1,8 @@ +.search-info { + margin: 20px 0; + text-align: center; + font-style: italic; + line-height: var(--spacing); +} + +/*# sourceMappingURL=search-info.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/search-info.css.map b/preview/pr-117/_styles/search-info.css.map new file mode 100644 index 00000000..d825cee0 --- /dev/null +++ b/preview/pr-117/_styles/search-info.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["search-info.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA","sourcesContent":[".search-info {\n margin: 20px 0;\n text-align: center;\n font-style: italic;\n line-height: var(--spacing);\n}\n"],"file":"search-info.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/section.css b/preview/pr-117/_styles/section.css new file mode 100644 index 00000000..4b9c58bd --- /dev/null +++ b/preview/pr-117/_styles/section.css @@ -0,0 +1,35 @@ +section { + padding: 40px max(40px, (100% - 1000px) / 2); + transition-property: background, color; +} + +section[data-size=wide] { + padding: 40px; +} + +section[data-size=full] { + padding: 0; +} + +section[data-size=full] > * { + margin: 0; + border-radius: 0; +} + +section[data-size=full] img { + border-radius: 0; +} + +main > section:last-of-type { + flex-grow: 1; +} + +main > section:nth-of-type(odd) { + background: var(--background); +} + +main > section:nth-of-type(even) { + background: var(--background-alt); +} + +/*# sourceMappingURL=section.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/section.css.map b/preview/pr-117/_styles/section.css.map new file mode 100644 index 00000000..f6304679 --- /dev/null +++ b/preview/pr-117/_styles/section.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["section.scss"],"names":[],"mappings":"AAGA;EACE;EACA;;;AAGF;EACE,SARQ;;;AAWV;EACE;;;AAGF;EACE;EACA;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE;;;AAGF;EACE","sourcesContent":["$page: 1000px;\n$padding: 40px;\n\nsection {\n padding: $padding max($padding, calc((100% - $page) / 2));\n transition-property: background, color;\n}\n\nsection[data-size=\"wide\"] {\n padding: $padding;\n}\n\nsection[data-size=\"full\"] {\n padding: 0;\n}\n\nsection[data-size=\"full\"] > * {\n margin: 0;\n border-radius: 0;\n}\n\nsection[data-size=\"full\"] img {\n border-radius: 0;\n}\n\nmain > section:last-of-type {\n flex-grow: 1;\n}\n\nmain > section:nth-of-type(odd) {\n background: var(--background);\n}\n\nmain > section:nth-of-type(even) {\n background: var(--background-alt);\n}\n"],"file":"section.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/table.css b/preview/pr-117/_styles/table.css new file mode 100644 index 00000000..eb687ccb --- /dev/null +++ b/preview/pr-117/_styles/table.css @@ -0,0 +1,21 @@ +.table-wrapper { + margin: 40px 0; + overflow-x: auto; +} + +table { + margin: 0 auto; + border-collapse: collapse; +} + +th { + font-weight: var(--semi-bold); +} + +th, +td { + padding: 10px 15px; + border: solid 1px var(--light-gray); +} + +/*# sourceMappingURL=table.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/table.css.map b/preview/pr-117/_styles/table.css.map new file mode 100644 index 00000000..25e08df6 --- /dev/null +++ b/preview/pr-117/_styles/table.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["table.scss"],"names":[],"mappings":"AAAA;EACE;EACA;;;AAGF;EACE;EACA;;;AAGF;EACE;;;AAGF;AAAA;EAEE;EACA","sourcesContent":[".table-wrapper {\n margin: 40px 0;\n overflow-x: auto;\n}\n\ntable {\n margin: 0 auto;\n border-collapse: collapse;\n}\n\nth {\n font-weight: var(--semi-bold);\n}\n\nth,\ntd {\n padding: 10px 15px;\n border: solid 1px var(--light-gray);\n}\n"],"file":"table.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/tags.css b/preview/pr-117/_styles/tags.css new file mode 100644 index 00000000..1225ba41 --- /dev/null +++ b/preview/pr-117/_styles/tags.css @@ -0,0 +1,33 @@ +.tags { + display: inline-flex; + justify-content: center; + align-items: center; + flex-wrap: wrap; + gap: 10px; + max-width: 100%; + margin: 20px 0; +} + +.tag { + max-width: 100%; + margin: 0; + padding: 5px 10px; + border-radius: 999px; + background: var(--secondary); + color: var(--text); + text-decoration: none; + overflow: hidden; + text-overflow: ellipsis; + white-space: nowrap; + transition-property: background, color; +} + +.tag:hover { + background: var(--light-gray); +} + +.tag[data-active] { + background: var(--light-gray); +} + +/*# sourceMappingURL=tags.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/tags.css.map b/preview/pr-117/_styles/tags.css.map new file mode 100644 index 00000000..82c35319 --- /dev/null +++ b/preview/pr-117/_styles/tags.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["tags.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;;AAGF;EACE;;;AAGF;EACE","sourcesContent":[".tags {\n display: inline-flex;\n justify-content: center;\n align-items: center;\n flex-wrap: wrap;\n gap: 10px;\n max-width: 100%;\n margin: 20px 0;\n}\n\n.tag {\n max-width: 100%;\n margin: 0;\n padding: 5px 10px;\n border-radius: 999px;\n background: var(--secondary);\n color: var(--text);\n text-decoration: none;\n overflow: hidden;\n text-overflow: ellipsis;\n white-space: nowrap;\n transition-property: background, color;\n}\n\n.tag:hover {\n background: var(--light-gray);\n}\n\n.tag[data-active] {\n background: var(--light-gray);\n}\n"],"file":"tags.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/textbox.css b/preview/pr-117/_styles/textbox.css new file mode 100644 index 00000000..d35615b1 --- /dev/null +++ b/preview/pr-117/_styles/textbox.css @@ -0,0 +1,17 @@ +input[type=text] { + width: 100%; + height: 40px; + margin: 0; + padding: 5px 10px; + border: solid 1px var(--light-gray); + border-radius: var(--rounded); + background: var(--background); + color: var(--text); + font-family: inherit; + font-size: inherit; + -webkit-appearance: none; + appearance: none; + box-shadow: var(--shadow); +} + +/*# sourceMappingURL=textbox.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/textbox.css.map b/preview/pr-117/_styles/textbox.css.map new file mode 100644 index 00000000..9e46f918 --- /dev/null +++ b/preview/pr-117/_styles/textbox.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["textbox.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA","sourcesContent":["input[type=\"text\"] {\n width: 100%;\n height: 40px;\n margin: 0;\n padding: 5px 10px;\n border: solid 1px var(--light-gray);\n border-radius: var(--rounded);\n background: var(--background);\n color: var(--text);\n font-family: inherit;\n font-size: inherit;\n -webkit-appearance: none;\n appearance: none;\n box-shadow: var(--shadow);\n}\n"],"file":"textbox.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/tooltip.css b/preview/pr-117/_styles/tooltip.css new file mode 100644 index 00000000..28b590eb --- /dev/null +++ b/preview/pr-117/_styles/tooltip.css @@ -0,0 +1,72 @@ +.tippy-box { + background: var(--background); + color: var(--text); + padding: 7.5px; + text-align: left; + box-shadow: var(--shadow); +} + +.tippy-arrow { + width: 30px; + height: 30px; +} + +.tippy-arrow:before { + width: 10px; + height: 10px; + background: var(--background); + box-shadow: var(--shadow); +} + +.tippy-arrow { + overflow: hidden; + pointer-events: none; +} + +.tippy-box[data-placement=top] .tippy-arrow { + inset: unset; + top: 100%; +} + +.tippy-box[data-placement=bottom] .tippy-arrow { + inset: unset; + bottom: 100%; +} + +.tippy-box[data-placement=left] .tippy-arrow { + inset: unset; + left: 100%; +} + +.tippy-box[data-placement=right] .tippy-arrow { + inset: unset; + right: 100%; +} + +.tippy-arrow:before { + border: unset !important; + transform-origin: center !important; + transform: translate(-50%, -50%) rotate(45deg) !important; +} + +.tippy-box[data-placement=top] .tippy-arrow:before { + left: 50% !important; + top: 0 !important; +} + +.tippy-box[data-placement=bottom] .tippy-arrow:before { + left: 50% !important; + top: 100% !important; +} + +.tippy-box[data-placement=left] .tippy-arrow:before { + left: 0 !important; + top: 50% !important; +} + +.tippy-box[data-placement=right] .tippy-arrow:before { + left: 100% !important; + top: 50% !important; +} + +/*# sourceMappingURL=tooltip.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/tooltip.css.map b/preview/pr-117/_styles/tooltip.css.map new file mode 100644 index 00000000..6b52e915 --- /dev/null +++ b/preview/pr-117/_styles/tooltip.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["tooltip.scss"],"names":[],"mappings":"AAAA;EACE;EACA;EACA;EACA;EACA;;;AAGF;EACE;EACA;;;AAGF;EACE;EACA;EACA;EACA;;;AAIF;EACE;EACA;;;AAEF;EACE;EACA;;;AAEF;EACE;EACA;;;AAEF;EACE;EACA;;;AAEF;EACE;EACA;;;AAEF;EACE;EACA;EACA;;;AAEF;EACE;EACA;;;AAEF;EACE;EACA;;;AAEF;EACE;EACA;;;AAEF;EACE;EACA","sourcesContent":[".tippy-box {\n background: var(--background);\n color: var(--text);\n padding: 7.5px;\n text-align: left;\n box-shadow: var(--shadow);\n}\n\n.tippy-arrow {\n width: 30px;\n height: 30px;\n}\n\n.tippy-arrow:before {\n width: 10px;\n height: 10px;\n background: var(--background);\n box-shadow: var(--shadow);\n}\n\n// correct tippy arrow styles to support intuitive arrow styles above\n.tippy-arrow {\n overflow: hidden;\n pointer-events: none;\n}\n.tippy-box[data-placement=\"top\"] .tippy-arrow {\n inset: unset;\n top: 100%;\n}\n.tippy-box[data-placement=\"bottom\"] .tippy-arrow {\n inset: unset;\n bottom: 100%;\n}\n.tippy-box[data-placement=\"left\"] .tippy-arrow {\n inset: unset;\n left: 100%;\n}\n.tippy-box[data-placement=\"right\"] .tippy-arrow {\n inset: unset;\n right: 100%;\n}\n.tippy-arrow:before {\n border: unset !important;\n transform-origin: center !important;\n transform: translate(-50%, -50%) rotate(45deg) !important;\n}\n.tippy-box[data-placement=\"top\"] .tippy-arrow:before {\n left: 50% !important;\n top: 0 !important;\n}\n.tippy-box[data-placement=\"bottom\"] .tippy-arrow:before {\n left: 50% !important;\n top: 100% !important;\n}\n.tippy-box[data-placement=\"left\"] .tippy-arrow:before {\n left: 0 !important;\n top: 50% !important;\n}\n.tippy-box[data-placement=\"right\"] .tippy-arrow:before {\n left: 100% !important;\n top: 50% !important;\n}\n"],"file":"tooltip.css"} \ No newline at end of file diff --git a/preview/pr-117/_styles/util.css b/preview/pr-117/_styles/util.css new file mode 100644 index 00000000..995ea77c --- /dev/null +++ b/preview/pr-117/_styles/util.css @@ -0,0 +1,13 @@ +.left { + text-align: left; +} + +.center { + text-align: center; +} + +.right { + text-align: right; +} + +/*# sourceMappingURL=util.css.map */ \ No newline at end of file diff --git a/preview/pr-117/_styles/util.css.map b/preview/pr-117/_styles/util.css.map new file mode 100644 index 00000000..c21a68d3 --- /dev/null +++ b/preview/pr-117/_styles/util.css.map @@ -0,0 +1 @@ +{"version":3,"sourceRoot":"","sources":["util.scss"],"names":[],"mappings":"AAAA;EACE;;;AAGF;EACE;;;AAGF;EACE","sourcesContent":[".left {\n text-align: left;\n}\n\n.center {\n text-align: center;\n}\n\n.right {\n text-align: right;\n}\n"],"file":"util.css"} \ No newline at end of file diff --git a/preview/pr-117/alums.html b/preview/pr-117/alums.html new file mode 100644 index 00000000..a25ebdab --- /dev/null +++ b/preview/pr-117/alums.html @@ -0,0 +1,16 @@ + + + + + + Redirecting… + + + + + + +

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+ Click here if you are not redirected. + + diff --git a/preview/pr-117/blog/index.html b/preview/pr-117/blog/index.html new file mode 100644 index 00000000..806bee2b --- /dev/null +++ b/preview/pr-117/blog/index.html @@ -0,0 +1,1108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Blog | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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2020

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+ + + Deep Learning in Biology Workshop + + + + + + + + + + + + + + + +

+ Discovering the beauty of math and the fun of computer science + +

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2019

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+ + + Why do we have application fees? + + + + + + + + + + + + + +

+ Context + +

+
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+ + + The Harassment Tax + + + + + + + + + + + + + +

+ TL;DR: This twitter thread from Michael Hendricks is on the money. + +

+
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+ + + Infant in arms: Some thoughts from a father traveling solo with an infant + + + + + + + + + + + + + +

+ Brief Context + +

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+ +

Our lab is part of the University of Colorado School of Medicine’s Department of Biomedical Informatics and Center for Health AI. +We are a geographically distributed team that is headquartered on the 6th Floor of the Anschutz Health Sciences Building.

+ +
+ + figure image + + +
+ + + + + + + +
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+ + figure image + + +
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+ + + + + + + diff --git a/preview/pr-117/feed.xml b/preview/pr-117/feed.xml new file mode 100644 index 00000000..68e8c256 --- /dev/null +++ b/preview/pr-117/feed.xml @@ -0,0 +1,507 @@ +Jekyll2024-01-09T18:10:27+00:00/preview/pr-117/feed.xmlThe Greene LabWhere data and biology meetDeep Learning in Biology Workshop2020-10-19T00:00:00+00:002024-01-09T18:10:06+00:00/preview/pr-117/2020/10/19/DL-workshopDiscovering the beauty of math and the fun of computer science + +

My mother saw math in everything around us; in the geometry of a bridge we drove across, in the permutations of numbers that make up my birthday. +Growing up she would get excited as she explained the solution to a math problem. +She would tell me that math is beautiful. +As a high school student, I remember thinking that math was simply a graduation requirement. +However my understanding and appreciation for math soon changed. +After taking an applied mathematics course in college (Bryn Mawr College), I discovered how math paired with computer science could be used to model and solve real world problems such as predicting the spread of influenza virus through a population given different control measures such as antiviral drugs. +This course introduced me to mathematical concepts that allowed me to make quasi-discoveries within a simplified dynamical system. +I found the beauty in math was combining it with computer science to translate science and research to clinical applications – It was exciting that I could make discoveries about seal populations with a few lines of code and some math equations!

+ +

I started to actively pursue opportunities to continue applying computational methods to science problems. +This eventually lead to me to start a graduate degree program in Genomics and Computational Biology at the University of Pennsylvania in 2017. +In 2018, I joined Casey Greene’s lab, which has a lot of expertise in using deep learning methods to study biology. +Despite having a computational background, I had a lot to learn about what deep learning was. +Additionally, my educational background was purely computational and so I also needed to learn biology – in my first graduate course I remember my first question was “what is a gene?”

+ +

After a long journey, I have published a paper using a generative multi-layer neural network to simulate compendia of gene expression experiments from large-scale microbial and human datasets. +I have contributed to a community-written manuscript about tips for using deep learning in biology. +Overall, my dissertation research has focused on using deep learning methods to extract patterns from large-scale gene expression datasets. +I am currently applying these methods to understand mechanisms of P.aeruginosa infection. +My goal is to develop methods that help gain insight into the complexities of disease traits. +You can find my current research projects on my github page.

+ + + + +

Deep learning in biology workshop

+ +

To celebrate and pass on the knowledge, my lab mate, Ben Heil and I are hosting a “Deep Learning for Biologists Workshop”.

+ +

For biologists with no computational background, we hope that after this course:

+ +
    +
  1. You will have an idea of what deep learning is
  2. +
  3. You will be inspired to find applications of deep learning in your own research
  4. +
+ +

For those with some computational background, you will also gain an intuitive sense for how these methods work with a little bit of math (what else would you expect from a former math major).

+ +

We know the idea of deep learning feels very daunting, but we know that you can learn this too!

+ +

Come join us Thursday, October 29 at 11am - 2pm EST.

+ +

Registration can be found here

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alex-lee
Why do we have application fees?2019-05-01T00:00:00+00:002024-01-09T18:10:06+00:00/preview/pr-117/2019/05/01/why-do-we-have-application-feesContext + +

I’m considering this question in regards to PhD programs in the biological sciences. +For a brief bit of context, these are programs where trainees, once they join a program, have their tuition paid for and also receive a stipend. +The funds to offer the stipend and tuition coverage primarily come from an institution, from training grants (which are given to an individual or institution to support training in areas of need), and from research project grants (which are given to an institution for the purposes of carrying out a specific research project). +In short, the training program includes classwork, which is an investment that the institution makes in each student, as well as a research component, which involves the trainee carrying out a project that also benefits the institution.

+ +

What are the application fees?

+ +

When students want to apply to one of these programs, they are often required to pay a fee to have their application considered. +The fee to apply to our Genomics and Computational Biology (GCB) program for the 2019 class year was $80. +This means that we raise from applicants, at most (see the bit on fee waivers below), about $16000 per year if we assume roughly 200 applications. +A student applying to 10 PhD programs would spend roughly $800 with the hopes of matriculating into one.

+ +

What are the arguments in favor of application fees?

+ +

I’ve heard a few arguments for fees. +I can continue to add to this list if folks provide new reasons (mention @greenescientist on twitter or email greenescientist@gmail.com). +If you want to add a reason, please keep it to a few sentences or provide a link to a twitter thread / blog post / something else that I can link to.

+ +
    +
  • It signifies that the applicant is seriously considering the program. +By paying the fee the student is essentially anteing up and saying they would be interested in attending the program if invited.
  • +
  • It raises funds that can be used for purposes that would be otherwise difficult to cover on certain other sources of support (e.g., beer at interview weekends).
  • +
  • It does not create a barrier to anyone because domestic applicants can request fee waivers. +I am under the impression that the Penn Biomedical Graduate Studies (BGS) program policies are to grant waivers to any domestic applicant who requests one.
  • +
+ +

What are my concerns with application fees?

+ +

I worry that the fees present barriers for reasons that I’ll detail below. +I can also continue to add to this list if folks provide new reasons (mention @greenescientist on twitter or email greenescientist@gmail.com). +If you want to add a reason, please keep it to a few sentences or provide a link to a twitter thread / blog post / something else that I can link to.

+ +
    +
  • The barrier imposed by fees is unequally felt by students. +Students for whom $1000 is a negligible cost at the conclusion of their undergraduate careers may apply to many programs, increasing their likelihood of admission, while those for whom this is a major cost may apply to fewer programs. +Even with fee waivers (which seem to only apply to domestic students), students who face this hurdle and who do not realize they can ask for a fee waiver, who feel that asking for a fee waiver may reveal something that they do not wish to share, or who feel that asking for a fee waiver burdens a program may apply to fewer programs reducing their chances of admission.
  • +
  • The amount of money that a program gains is not that substantial relative to other program expenses. +For our example of the Penn GCB program, applicants’ fees provide about $16,000 in revenue per year. +However, the stipends alone for each entering class of roughly ten students run more than $300,000 per year. +Including the tuition, and the fact that the first two years are covered by institutional funds at Penn, each class of students for a ten-person program must cost at least $650,000 before students are transitioned onto research grant support. +A more accurate number is probably ~$960,000, but I wanted to provide the most conservative estimate.
  • +
  • Programs benefit from attracting the best possible set of matriculating students. +Students are engaged in both coursework and research. +Their research efforts directly benefit the institution. +Thus while it is true that students are competing for spots in each class, programs are also competing for students. +Admission to a PhD program can be quite difficult to predict and depends on certain factors related to the student (application strength as perceived by an admissions committee) but also factors beyond the control of the student (the composition of the rest of the applicant pool with respect to research interests and potential research advisors). +It seems unfair and inefficient to penalize students for applying to programs that may initially seem like a reach.
  • +
+ +

What could the next steps be?

+ +

I have been made aware that at Penn we looked into the effect of application fees and little evidence was found that our fees were a barrier. I did look through the peer-reviewed literature a bit, and I couldn’t find data on the results of a complete elimination of application fees. I did find results that suggested that granting fee waivers as a matter of routine could be helpful. It seems that perhaps there isn’t evidence simply because the experiment hasn’t been done.

+ +

I hope that one or more graduate programs at an institution will run an experiment with the complete elimination of application fees. It is probably best, from an experimental design point of view, to eliminate fees for randomly selected set of programs while leaving other programs at the institution’s application fee unchanged. Interesting outcomes to examine would include committee-assigned scores for applicants invited to interview; the number of first generation, low income, and underrepresented minority scientists invited to interview; and the yield from the interview process. I had hoped that we would be able to run such an evaluation at Penn, but this will not come to pass. +I am posting this to the blog in the hopes that another institution will find the question to be worth asking.

+ +

Update 5/1/19:

+ +

After posting, I was pointed to CMU’s Department of Philosophy’s elimination of application fees in 2017.

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casey-greene
The Harassment Tax2019-04-06T00:00:00+00:002024-01-09T18:10:06+00:00/preview/pr-117/2019/04/06/the-harassment-taxTL;DR: This twitter thread from Michael Hendricks is on the money.

+ +

In a recent article in Science about the National Academies developing a procedure to expel sexual harassers, Dr. Robert Weinberg (Member, Whitehead Institute; and Daniel K. Ludwig Professor for Cancer Research in the Department of Biology at MIT) was quoted as saying, “Before there is a mad rush to approve such an ejection procedure, it might be useful to ask whether sexual harassment by a member has anything whatsoever to do with their credibility as a scientist and the soundness of their research accomplishments—the criteria that were used to elect them in the first place.” +When scientists reach these milestones by imposing costs on others through falsification, harassment, or other means they are externalizing costs onto the rest of the field. +We shouldn’t honor that.

+ +

We might be tempted to buy into a lone genius model of science. +In popular media, scientists are sometimes presented as brilliant folks who toil in isolation and only emerge when they have some deep, self-evident insight that nobody can disagree with. +However, this model is a myth and nothing could be further from the truth. +Science is a messy, community-based process. +The scientist toiling long hours in the lab has based work on the findings of others. +That scientist has had ideas honed by a mentor, feedback from others in the research group, and directly or indirectly by external peers. +For the work to be convincing and impactful, the scientist will need to rule out additional models raised by the community by performing more experiments. +The ultimate trajectory of a research program and its influence is shaped by others.

+ +

As soon as one leaves the lone genius myth behind, it is obvious why harassers should not be admitted to the National Academies and should be expelled if they already have been admitted. +Unfortunately, harassment is all too common in academia, with fifty-eight percent of female faculty and staff in academia reporting behaviors that constitute harassment. +Scientists who are harassed have their time and attention unfairly taken from them. +They may leave one field and transition to another to escape their harasser(s) – requiring them to spend time gaining additional skills and knowledge – or even leave science entirely (see the NASEM report on Sexual Harassment of Women, Chapter 4). +Those who support such scientists (for example Dr. BethAnn McLaughlin, founder of #MeTooSTEM) are also taxed for their own time and attention. +Too often, these may be ghost mentors who receive little or no credit for their efforts.*

+ +

Harassment taxes the harassed scientist’s time, attention and resources, as well as those of other scientists. +It weakens the community: by promoting a homogeneity of experiences and backgrounds it reduces the effectiveness of scientific inquiry. +In short, it imposes the costs for the failings of the harasser on others. +Revisiting Dr. Weinberg’s question of whether or not sexual harassment has anything to do with a perpetrator’s credibility and research accomplishments, my answer is an emphatic “Yes!”

+ +

It’s clear that the National Academies can be a force for good: see, for example, their own report on the impact of Sexual Harassment. +If the National Academies fail to pass this policy during the vote on April 30th, then they will have failed the scientific community. +Other organizations, for example the Wellcome Trusts, are moving ahead with policies to reduce harassment in science. +Every time that the National Academies fail to expel harassers, they look more like relics of a bygone age. +This diminishes the relevance of the Academies to the future of science and the honor associated with membership.

+ +
+ +

* Take Dr. McLaughlin for example: her work is more widely cited than mine, she’s received more NIH funding than I have (in addition to other federal funding), and she’s clearly had a larger impact on the practice of science than I have (AAAS and NAS among many others). +It’s clear that she is far more qualified to be a tenured faculty member than I am. +In a seemingly absurd decision, Vanderbilt denied her tenure case after the dean of VUMC, Jeffrey Balser, had her case reconsidered by a committee that included a faculty member now on leave for sexual misconduct (David Sweatt). +The committee in question was overturning two initial favorable tenure decisions. +The Chancellor of Vanderbilt University, Nick Zeppos, has failed to support her tenure case, though he has published a blog post on the importance of women at Vanderbilt. +It conspicuously ignores Dr. McLaughlin, a winner of the MIT Disobedience Prize.

+ +

P.S. I gave a talk at UAB recently, where I included some slides (+ a new bonus slide with Dr. Weinberg’s quotation for a seminar I’m giving at NYU on Monday, April 8). +You are welcome to use them in your own talks (note the arrangement, which is my own, is CC0 licensed, but certain content is by others and not openly licensed and so uses of those portions must fall under fair use).

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casey-greene
Infant in arms: Some thoughts from a father traveling solo with an infant2019-01-29T00:00:00+00:002024-01-09T18:10:06+00:00/preview/pr-117/2019/01/29/infant-in-armsBrief Context + +

As a scientist, I often attend conferences/meetings/etc. +Making this work as a childless, married academic husband was reasonably straightforward for my wife and me. +However, things changed in April of 2018 when our daughter was born. +Finding a way to integrate our daughter into this schedule is important because academic life bleeds heavily into times that are normally reserved for family life (weekends, evenings). +Many academic conferences and events are scheduled over a weekend or involve weekend travel. +What works for us is that I will take the baby with me when I travel for trips where it makes sense for both of our schedules. +In our daughter’s first six months, I traveled roughly 25,000 miles with her via air, car, and Amtrak. +Here I’m compiling some observations from my travel that may be informative or helpful to others.

+ +
+ + Visiting the Broad Institute on the first solo trip I took with our daughter, which we did via Amtrak. + + +
+ Visiting the Broad Institute on the first solo trip I took with our daughter, which we did via Amtrak. + +
+ +
+ + + + +

Travel Supplies

+ +

A good backpack beats a diaper bag. +I received an Aer Travel Pack 2 as a gift and used it as a travel backpack for some time before our daughter was born. +It was fine for that, but it makes a great travel diaper bag. +The features that I have found most important are that 1) electronics get stored in a separate, padded compartment; 2) the separate “shoe compartment” can be used for soiled clothes (or diapers if you haven’t found a place to dispose of them) wrapped in a plastic bag; 3) it opens like a clamshell, so you can access different contents easily: I store diapers and wipes at the bottom, a couple changes of clothes above that, and then bottles, formula, and toys at the top; and 4) it fits under the seats of nearly all aircraft (there are a few aircraft types that have very narrow underseat storage for the aisle seat where it won’t fit).

+ +
+ + Napping on the Boppy pillow. + + +
+ Napping on the Boppy pillow. + +
+ +
+ +

Have a support for the baby on your lap. +I’ve had good success with a Boppy pillow. +These things look like a huge neck pillow for the waist. +I’ve found this helps with feeding, but it also gives our baby something to sleep on during the flight. +For me, it reduces the discomfort from having her on my lap for long stretches.

+ +
+ + Everything’s a toy! This cup was a big hit with me in Houston. + + +
+ Everything’s a toy! This cup was a big hit with me in Houston. + +
+ +
+ +

Bring a few toys, but find a bunch more. +Our baby’s philosophy seems to be that an object is just a toy she hasn’t figured out how to have fun with yet. +Travel leads to lots of new objects. +We’ve had fun with snack mix bags, plastic cups, spoons, and many other items. +I’ve had good luck bringing a few toys and planning to find more along the way.

+ +
+ + Car seat, stroller, Boppy in the walking-through-the-airport configuration. + + +
+ Car seat, stroller, Boppy in the walking-through-the-airport configuration. + +
+ +
+ +

My travel go-to items for baby moving are an Ergobaby carrier, travel stroller, and car seat. +I like a travel stroller that the car seat gets attached to via a strap that goes where the seat belt would be. +In general, I use these as one would expect. +The best way I’ve found to board a plane solo is to, a few minutes before boarding begins, put the baby into the ergobaby. +Wheel the stroller with the car seat inside down the ramp. +Fold the stroller and place both the stroller and the car seat at the end of the ramp for the ground crew. +For deplaning, I do this in reverse. +Finding a routine that works has helped me to keep everything together in some hectic situations. +The one caveat of going this route is to note that you need two gate-check tags - one for the stroller and a second one for the car seat.

+ + + + +

Feeding

+ +

Traveling with formula was the best option for me. +I traveled with a cooler of breastmilk for the first trip I took with our baby, which was via Amtrak. +It dramatically increased how much I needed to carry, the logistics involved with timing, and meant that I needed to make absolutely sure that the hotel would have a suitably cold fridge (and freezer) on arrival. +It is something that is possible to do via train. +I only did this for the first trip, though I looked at what it would take to pack for travel via air and decided against for subsequent trips. +Formula is easier for me since I can easily pack it or buy it upon arrival.

+ +

Feed when the baby is hungry, and stay consistent in the size of the bottle. +For the first trips I had planned out when our baby would be hungry based on her normal schedule, and so I knew where I would be for each one. +Unfortunately, travel seems to alter babies eating schedules in unpredictable ways. +I tried to compensate by feeding an “interim” bottle that was half-size to tide her over to the planned feeding time, but I have found this to be a path straight to a fussy baby and don’t recommend it.

+ +

Whenever I find the perfect size cups, I ask for a few. +When I travel with room-temperature formula and happen across paper cups for hot drinks that hold the bottle plus a roughly equal amount of water, I snag a few. +When I ask for water to heat up formula on a plane, I usually get near-boiling water (when I use this water to heat formula, I let the water cool just a little bit, and then swirl the formula pretty quickly while it’s warming - I didn’t do this the first time, cooked the formula, and had to throw it out and start over). +I’ve found that with the rate of heat loss from such cups, equal amounts of formula and water is about the right size to get a suitably warm bottle of formula for our baby. +If the volume of the cup is too large the formula ends up too hot and I increase the risk of cooking it. +If it’s too low, our baby won’t drink it.

+ + + + +

In Air and Airport

+ +

Flights with a connection are better for longer itineraries. +When I traveled alone, I preferred the direct flight. +I’ve found that when traveling with a baby, the opportunity to disembark, walk around a little bit, feed and change the baby in a less cramped space, and then continue to the destination is far more compatible with the happiness of me and our baby. +As a side benefit, these flights are often a bit cheaper than direct ones.

+ +
+ + Snack mix bags crinkle, and wow that is fun! + + +
+ Snack mix bags crinkle, and wow that is fun! + +
+ +
+ +

Airline club membership is helpful when traveling with an infant. +In 2017, I flew enough that I had complimentary access to Delta’s Sky Clubs in 2018. +The ability to take my stuff and baby in, set the stuff down, get a bite of food and some water, eat, feed the baby, change the baby, and get to the next flight made all of this far more pleasant.

+ +
+ + Skyclub membership was helpful. This one in SLC let us put our stuff down and recharge mid-itinerary. + + +
+ Skyclub membership was helpful. This one in SLC let us put our stuff down and recharge mid-itinerary. + +
+ +
+ +

Certain aircraft do not have changing tables in the restrooms. +Delta flies a number of older aircraft (MD-88s, MD-90s, and 717s) and they use them heavily for flights to Philadelphia. +The existence of changing tables on these aircraft has been hit or miss. +If they do have changing tables, they’re usually in one of the economy restrooms in the tail. +At least on Delta, you won’t know this when you book - only when you look. +You probably want to check all three restrooms unless you are comfortable changing an infant who you are holding vertically. +I’ve had to change three blowouts while holding our baby vertically in these aircraft without any tables. +It’s something you get ok at. +I highly recommend traveling with the baby in either kimono-style onesies or zippy jamz pajamas. +Anything that goes over the head is bad news for a standing blowout change.

+ +
+ + Even as our daughter has grown, the Boppy pillow remains a favorite in the air. + + +
+ Even as our daughter has grown, the Boppy pillow remains a favorite in the air. + +
+ +
+ +

Ask for more cabin comfort. +The time that this most comes to mind for me was an early morning flight out of Houston’s Hobby Airport. +We’d gotten up around 4AM to catch a 6AM flight, and the aircraft was inordinately warm when we boarded. +My daughter actually did ok during the boarding process, but the flight continued to warm up on ascent. +My daughter started crying and was very difficult to console. +I thought the heat might be an issue, but it also could have been the early wake-up or something else. +I waited until the drink service to ask if the cabin could be cooled down. +After service, the flight attendants must have asked the cockpit to reduce the temperature. +As soon as it started cooling down, she went to sleep and slept the rest of the flight. +If I’d used the call button before service, I could have saved everyone a half-hour of listening to a crying baby.

+ + + + +

Hotels

+ +

For our baby at least, the first night in each new hotel room was a rough one. +I usually had at least a few wake-ups at unusual times in addition to the usual ones. +I haven’t found a solution to this, but at least I’m now aware of what it’ll be like.

+ +

Don’t expect a crib in the room when you arrive. +I don’t care how many times you call the hotel. +I don’t care if it’s the AAA four-diamond rated Fairmont Orchid and you noted it on your reservation, confirmed again a week before, and confirmed at the desk when you checked in. +Do not expect it to be there. +Expect it to take at least an hour and three calls to the service desk after you arrive (at 10 PM Hawaii time after traveling from the east coast - I’m still glaring at you Fairmont Orchid). +We occasionally found the crib we had asked for (every time for our hotels in Japan, almost never anywhere else). +But this seems to be something hotels in the US are more or less terrible at, so I’d say just imagine it won’t be there. +We did purchase a travel crib, which we have used when my wife and I have traveled together. +My daughter sleeps better in this, but the weight and added item makes it too cumbersome for me to take when it’s just me.

+ + + + +

Other Venue Notes

+ +

Some places have been remarkably wonderful to work with. +In particular, the folks who scheduled the Annual Keck Center Research Conference for the Gulf Coast Consortia were incredible. +I was invited to speak at this event and initially declined because it was the day after a previously-scheduled return flight from Japan. +After some discussion with the organizers, I decided to skip my final Detroit to Philadelphia leg and fly to Houston for the event before returning home. +While in Japan, we found it hard to get liquid formula that we’d need for the Houston part of the trip. +When I asked for suggestions of a place to buy formula near the airport or hotel, the folks from the event put enough bottles of formula at the hotel check-in that we were able to make it through the first night. +Then I just had to walk to a store to buy formula before the meeting the next day. +I also want to give a shout out to the folks from Northwestern Mutual’s HQ in Milwaukee. +They hosted ALSF’s Young Investigator Summit and made traveling with the baby a breeze.

+ +
+ + Speaker dinner for the Keck Center Research Conference. + + +
+ Speaker dinner for the Keck Center Research Conference. + +
+ +
+ +

Traveling with an infant may cost you some opportunities. +I was invited to give talks both during a symposium and for the community in my area of expertise at the University of Oslo that would have involved weekend travel. +When I asked the organizers to ask the hotel to add a crib to the room during the reservation process, this led to some red flags that ultimately led to the decision to find another speaker for their event and seminar series. +The advice that I’ve gotten from folks on social media who traveled to work-related seminars where they needed to take their kids was to not give organizers a heads up and to deal directly with the hotel for a crib. +If it’s an opportunity you can’t afford to miss, it sounds like this is still the way to go in 2018. +However, if missing the event wouldn’t be hugely costly, I’ve found other places to be helpful and willing to ask the hotel for a crib when they make the reservation.

+ +
+ + Our daughter spending lunch with me at PSB. + + +
+ Our daughter spending lunch with me at PSB. + +
+ +
+ +

Certain conferences and meetings also have very restrictive policies on children, so before you go it’s probably good to see where your society falls. +I mentioned to a colleague that I would be at the American Association for Cancer Research (AACR) meeting with our daughter, and they mentioned that they had seen a scientist barred from the meeting because they were with a child. +It turns out that AACR bans children from exhibit halls, poster sessions, and scientific sessions at their annual meeting though it does provide a childcare option that might work for some. +The American Society for Clinical Oncology (ASCO) also bans children at their annual meeting and has not generally provided childcare for attendees. +In 2019 both of these meetings include a weekend, making the policies even more family-unfriendly. +On the other hand, the American Society for Cell Biology (ASCB) has clear, inclusive policies during the meeting. +The Pacific Symposium on Biocomputing (PSB), a computational biology conference, has been family friendly for as long as I can remember. +The American Society for Human Genetics (ASHG) and International Society for Computational Biology (ISCB) get special shoutouts for both providing childcare options and allowing children at the meeting itself providing parents with the flexibility they need.

+ + + + +

Closing thoughts

+ +

I’ve enjoyed traveling with our daughter during this time. +For fathers who are considering traveling with their infants to a conference or symposium, I’ve found that it is very practical to do so. +I would be remiss not to note that we give women traveling with a baby far less support than men. +There have been numerous situations throughout my time traveling that have made this clear to me. +On multiple flights, attendants have offered to hold my daughter if I needed to go to the restroom. +I haven’t seen the same level of support for women traveling alone with their babies. +In one case, a flight attendant walked my daughter up and down the aisle of the aircraft to calm her. +Even fellow passengers seemed less irritated by a fussy infant with me: in all of this travel I can only think of one dirty look that I got from a fellow passenger while I was traveling alone with my daughter. +When you travel, offer assistance and understanding to women who need it as well.

+ +
+ + figure image + + +
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casey-greene
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Where data and biology meet

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The Greene Lab is a team of researchers at the University of Colorado School of Medicine dedicated to answering important questions in biology and medicine with computation. +We focus on bringing together publicly available big data, developing new computational methods to analyze that data, and creating tools to put those resources into the hands of every biologist.

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+ + figure image + + +
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Highlights

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+ + Biology + AI → insight + +
+ +

Biology + AI → insight

+ + +

We use data science to answer important questions in biology and medicine. +In all of our research, we prioritize transparency, rigor, and reproducibility.

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+ + Open source, all the way + +
+ +

Open source, all the way

+ + +

We believe that anyone around the world should be able to use and extend our work. +We push to make software, tools, datasets, etc. that are freely available and openly licensed.

+ + + + +
+
+ +
+ + The next generation of data scientists + +
+ +

The next generation of data scientists

+ + +

We are a team of enthusiastic researchers that want to push the frontier of data science. +We strive to build an inclusive environment for research, and recognize the value of diversity in the process of discovery.

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+ + +
+ + + + + + + diff --git a/preview/pr-117/join/index.html b/preview/pr-117/join/index.html new file mode 100644 index 00000000..529449f0 --- /dev/null +++ b/preview/pr-117/join/index.html @@ -0,0 +1,829 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Join the Team | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

+Join the Team

+ +

You can learn a bit about working in the lab by reading our onboarding document. +Positions across our Department of Biomedical Informatics, including in our lab, for staff and postdocs are usually listed on the employment section of the DBMI website.

+ +

Postdoctoral Researchers

+ +

The Greene Lab welcomes applications for computational postdoctoral positions at the University of Colorado School of Medicine. +Learn about these opportunities through our recent Post-Doctoral Fellow posting, and applications can only be accepted through the CU Anschutz Taleo Portal.

+ +

Graduate Students

+ +

The University of Colorado has both an umbrella program and discipline-specific ones. +The umbrella program is the Biomedical Sciences Program. +Our primary program affiliation is the University of Colorado’s Computational Biosciences Program. +We are also excited to welcome students who want to pursue computational research from other graduate programs on a case-by-case basis.

+ +

Our goal is to help our students develop both a deep familiarity with the computational methods required for data-intensive science and a strong understanding of one or more biological application areas. +We provide training in all aspects through group meetings, individual meetings, and a supportive lab environment.

+ +

If you have not yet joined one of the PhD programs above, the first step to joining our group is to apply and be admitted to one of these programs. +If you are already a PhD student in one of the above programs and are interested in rotating in our lab, please contact Casey to set up a time to discuss your interest.

+ +

Programmers

+ +

We work with programmers at DBMI’s software engineering team to bring research products to practice. +Visit their website to learn about opportunities on the team.

+ + + +
+ + figure image + + +
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+ + + + + + + diff --git a/preview/pr-117/lab-members.html b/preview/pr-117/lab-members.html new file mode 100644 index 00000000..a25ebdab --- /dev/null +++ b/preview/pr-117/lab-members.html @@ -0,0 +1,16 @@ + + + + + + Redirecting… + + + + + + +

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+ Click here if you are not redirected. + + diff --git a/preview/pr-117/mascots.html b/preview/pr-117/mascots.html new file mode 100644 index 00000000..a25ebdab --- /dev/null +++ b/preview/pr-117/mascots.html @@ -0,0 +1,16 @@ + + + + + + Redirecting… + + + + + + +

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+ Click here if you are not redirected. + + diff --git a/preview/pr-117/members/ace.html b/preview/pr-117/members/ace.html new file mode 100644 index 00000000..9584441c --- /dev/null +++ b/preview/pr-117/members/ace.html @@ -0,0 +1,787 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Ace | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + +

Ace is the Nicholson family’s miniature schnauzer. +He lives in Pittsburgh, Pennsylvania and joined the team in summer of 2017. +His interests include network analysis and running around in dog parks.

+ + + + + + +

+ + Search for Ace's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/adriana-ivich.html b/preview/pr-117/members/adriana-ivich.html new file mode 100644 index 00000000..057373a7 --- /dev/null +++ b/preview/pr-117/members/adriana-ivich.html @@ -0,0 +1,856 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Adriana Ivich | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Adriana is a Ph.D. student in the Greene Lab through CU Anschutz’s Bioengineering (BIOE) Program. +She graduated from The University of Arizona with a B.S. in Neuroscience in 2019. +Before coming to CU, Adriana worked at The University of Arizona as a Research Assistant, and spent two years at Roche as an Associate Scientist. +Adriana is interested in developing machine learning models to improve gene-expression data in cancer.

+ + + + + + +

+ + Search for Adriana Ivich's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/alex-lee.html b/preview/pr-117/members/alex-lee.html new file mode 100644 index 00000000..76380f9c --- /dev/null +++ b/preview/pr-117/members/alex-lee.html @@ -0,0 +1,861 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Alex Lee | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Alexandra is a Ph.D. student in the Greene Lab through Penn’s Genomics and Computational Biology (GCB) PhD Program. +She graduated from Bryn Mawr College with a B.A. in Mathematics and a minor in Computer Science. +She also earned an M.S. in Applied Mathematics from the University of Washington. +Prior to coming to Penn, she worked as a bioinformatics analyst at the J. Craig Venter Institute, where she studied viral genomics. +Since joining the Greene lab in 2018, her research has focused on using deep learning methods to extract patterns from large-scale gene expression datasets. +She is currently applying these methods to understand mechanisms of P.aeruginosa infection. +Her goal is to develop methods that help gain insight into the complexities of disease traits. +She is currently a Sr. Community engagement/Bio data scientist at DNAnexus. +Check out her personal website to follow her recent work.

+ + + + + + +

+ + Search for Alex Lee's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/amy-campbell.html b/preview/pr-117/members/amy-campbell.html new file mode 100644 index 00000000..47992579 --- /dev/null +++ b/preview/pr-117/members/amy-campbell.html @@ -0,0 +1,821 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Amy Campbell | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + +

Amy worked as an analyst in the Greene Lab for a year between graduating from Oberlin College and beginning a PhD at Penn’s very own GCB Program. +In Dr. Elizabeth Grice’s lab, Amy now studies the genomics of Staphylococcus aureus in human wounds. +In her free time, she enjoys cooking, making pottery, and suing the state of Pennsylvania to protect mail-in & absentee ballots from being discarded unfairly.

+ + + + + + +

+ + Search for Amy Campbell's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/ariel-hippen.html b/preview/pr-117/members/ariel-hippen.html new file mode 100644 index 00000000..401740d9 --- /dev/null +++ b/preview/pr-117/members/ariel-hippen.html @@ -0,0 +1,856 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Ariel Hippen | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Ariel is a Ph.D. student through Penn’s Genomics and Computational Biology (GCB) PhD program. +She graduated from Brigham Young University in 2016 with a B.S. in Bioinformatics and a minor in Statistics. +She then worked as a a bioinformatics analyst at AncestryDNA, before coming to Penn in 2018 and joining the Greene lab in the summer of 2019. +Ariel’s research focuses on leveraging single-cell gene expression data to help define and ultimately treat subtypes of high-grade serous ovarian cancer.

+ + + + + + +

+ + Search for Ariel Hippen's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/ben-heil.html b/preview/pr-117/members/ben-heil.html new file mode 100644 index 00000000..8bb84b03 --- /dev/null +++ b/preview/pr-117/members/ben-heil.html @@ -0,0 +1,875 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Ben Heil | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Ben was a PhD student in the Genomics and Computational Biology program at Penn who defended his thesis in Dec. 2022. +Previously he graduated from Baylor University with a degree in bioinformatics in 2018, and joined the Greene lab in the summer of 2019. +Ben’s research focuses on using transfer learning to gain insight from large gene expression datasets. +Outside of school, Ben is a mostly retired swimmer, a bass singer, and a person who can talk for hours about the collected works of Patrick Rothfuss. +He also operates a blog, AutoBenCoding, that talks about machine learning, reproducible research, and other sciency things.

+ + + + + + + +

+ + Search for Ben Heil's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/brett-beaulieu-jones.html b/preview/pr-117/members/brett-beaulieu-jones.html new file mode 100644 index 00000000..cc7c8255 --- /dev/null +++ b/preview/pr-117/members/brett-beaulieu-jones.html @@ -0,0 +1,807 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Brett Beaulieu-Jones | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + +

Brett graduated in 2011 with a B.S. in Computer Science from Boston College. +After graduation he worked as a technology consultant doing information management and data science at large financial institutions. +He co-founded Wymsee, an entertainment technology company in 2012. +He is a Ph.D. student in Penn’s Genomics and Computational Biology program. +He is a member of both the Greene and Moore labs. +His research centers on using deep learning-based methods to more precisely define phenotypes from large-scale data repositories, e.g. those contained in clinical records.

+ + + + + + +

+ + Search for Brett Beaulieu-Jones's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/casey-greene.html b/preview/pr-117/members/casey-greene.html new file mode 100644 index 00000000..d4162a0b --- /dev/null +++ b/preview/pr-117/members/casey-greene.html @@ -0,0 +1,7641 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Casey Greene | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
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+ +
+ + +
+ + +

Casey is the Chair of and a Professor in the Department of Biomedical Informatics and the founding Director of the Center for Health AI. +His lab develops machine learning methods that integrate distinct large-scale datasets to extract the rich and intrinsic information embedded in such integrated data. +This approach reveals underlying principles of an organism’s genetics, its environment, and its response to that environment. +Extracting this key contextual information reveals where the data’s context doesn’t fit existing models and raises the questions that a complete collection of publicly available data indicates researchers should be asking. +In addition to developing deep learning methods for extracting context, a core mission of his lab is bringing these capabilities into every molecular biology lab through open, transparent science conducted by a diverse team of researchers. +Before starting the Integrative Genomics Lab in 2012, Casey earned his Ph.D. for his study of gene-gene interactions in the field of computational genetics from Dartmouth College in 2009 and moved to the Lewis-Sigler Institute for Integrative Genomics at Princeton University where he worked as a postdoctoral fellow from 2009-2012. +The overarching theme of his work has been the development and evaluation of methods that acknowledge the emergent complexity of biological systems.

+ +
+ + +
+ +

All papers under Casey’s ORCID:

+ +
+ +

2023

+ +
+ + +
+ + + + + Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors + + +
+ Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene +
+ +
+ Genome Biology +   ·   + 20 Oct 2023 +   ·   + doi:10.1186/s13059-023-03077-7 +
+ + +
+
+ +
+ + +
+ + + + + Integration of 168,000 samples reveals global patterns of the human gut microbiome + + +
+ Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 11 Oct 2023 +   ·   + doi:10.1101/2023.10.11.560955 +
+ + +
+
+ +
+ + +
+ + + + + Human Microbiome Compendium dataset + + +
+ Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman +
+ +
+ Zenodo +   ·   + 11 Oct 2023 +   ·   + doi:10.5281/zenodo.8186993 +
+ + +
+
+ +
+ + +
+ + + + + Analysis ofPseudomonas aeruginosatranscription in anex vivocystic fibrosis sputum model identifies metal restriction as a gene expression stimulus + + +
+ Samuel L. Neff, Georgia Doing, Taylor Reiter, Thomas H. Hampton, Casey S. Greene, Deborah A. Hogan +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 21 Aug 2023 +   ·   + doi:10.1101/2023.08.21.554169 +
+ + +
+
+ +
+ + +
+ + + + + MousiPLIER: A Mouse Pathway-Level Information Extractor Model + + +
+ Shuo Zhang, Benjamin J. Heil, Weiguang Mao, Maria Chikina, Casey S. Greene, Elizabeth A. Heller +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 02 Aug 2023 +   ·   + doi:10.1101/2023.07.31.551386 +
+ + +
+
+ +
+ + +
+ + + + + BuDDI:Bulk Deconvolution with Domain Invarianceto predict cell-type-specific perturbations from bulk + + +
+ Natalie R. Davidson, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 22 Jul 2023 +   ·   + doi:10.1101/2023.07.20.549951 +
+ + +
+
+ +
+ + +
+ + + + + Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry Estimates from Direct-to-Consumer Canine Genetic Tests + + +
+ Halie M. Rando, Kiley Graim, Greg Hampikian, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 29 Jun 2023 +   ·   + doi:10.1101/2023.06.28.546898 +
+ + +
+
+ +
+ + +
+ + + + + Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction + + +
+ Jake Crawford, Maria Chikina, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 26 Jun 2023 +   ·   + doi:10.1101/2023.06.26.546586 +
+ + +
+
+ +
+ + +
+ + + + + greenelab/phenoplier: a computational framework to integrate genetic studies with gene co-expression patterns + + +
+ Milton Pividori, Casey Greene +
+ +
+ Zenodo +   ·   + 22 Jun 2023 +   ·   + doi:10.5281/zenodo.8044955 +
+ + +
+
+ +
+ + +
+ + + + + Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes + + +
+ Ariel A. Hippen, Natalie R. Davidson, Mollie E. Barnard, Lukas M. Weber, Jason Gertz, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 15 Jun 2023 +   ·   + doi:10.1101/2023.06.14.544991 +
+ + +
+
+ +
+ + +
+ + + + + Machine learning in rare disease + + +
+ Jineta Banerjee, Jaclyn N. Taroni, Robert J. Allaway, Deepashree Venkatesh Prasad, Justin Guinney, Casey Greene +
+ +
+ Nature Methods +   ·   + 29 May 2023 +   ·   + doi:10.1038/s41592-023-01886-z +
+ + +
+
+ +
+ + +
+ + + + + Changing word meanings in biomedical literature reveal pandemics and new technologies + + +
+ David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti, Casey S. Greene +
+ +
+ BioData Mining +   ·   + 05 May 2023 +   ·   + doi:10.1186/s13040-023-00332-2 +
+ + +
+
+ +
+ + +
+ + + + + The Coming of Age of Nucleic Acid Vaccines during COVID-19 + + +
+ Halie M. Rando, Ronan Lordan, Likhitha Kolla, Elizabeth Sell, Alexandra J. Lee, ..., Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen +
+ +
+ mSystems +   ·   + 27 Apr 2023 +   ·   + doi:10.1128/msystems.00928-22 +
+ + +
+
+ +
+ + +
+ + + + + Application of Traditional Vaccine Development Strategies to SARS-CoV-2 + + +
+ Halie M. Rando, Ronan Lordan, Alexandra J. Lee, Amruta Naik, Nils Wellhausen, ..., Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen +
+ +
+ mSystems +   ·   + 27 Apr 2023 +   ·   + doi:10.1128/msystems.00927-22 +
+ + +
+
+ +
+ + +
+ + + + + MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes + + +
+ Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu +
+ +
+ Nucleic Acids Research +   ·   + 18 Apr 2023 +   ·   + doi:10.1093/nar/gkad289 +
+ + +
+
+ +
+ + +
+ + + + + Data underlying OpenPBTA Manuscript Figures and Molecular Alterations + + +
+ Joshua A. Shapiro, Krutika S. Gaonkar, Stephanie J. Spielman, Candace L. Savonen, Chante J. Bethell, ..., Miguel A. Brown, Adam C. Resnick, Casey S. Greene, Jo Lynne Rokita, Jaclyn N. Taroni +
+ +
+ Zenodo +   ·   + 06 Apr 2023 +   ·   + doi:10.5281/zenodo.7805407 +
+ + +
+
+ +
+ + +
+ + + + + The effect of non-linear signal in classification problems using gene expression + + +
+ Benjamin J. Heil, Jake Crawford, Casey S. Greene +
+ +
+ PLOS Computational Biology +   ·   + 27 Mar 2023 +   ·   + doi:10.1371/journal.pcbi.1010984 +
+ + +
+
+ +
+ + +
+ + + + + Biomonitoring and precision health in deep space supported by artificial intelligence + + +
+ Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-min Park, ..., Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes +
+ +
+ Nature Machine Intelligence +   ·   + 23 Mar 2023 +   ·   + doi:10.1038/s42256-023-00617-5 +
+ + +
+
+ +
+ + +
+ + + + + Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously + + +
+ Steven M. Foltz, Casey S. Greene, Jaclyn N. Taroni +
+ +
+ Communications Biology +   ·   + 25 Feb 2023 +   ·   + doi:10.1038/s42003-023-04588-6 +
+ + +
+
+ +
+ + +
+ + + + + Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia + + +
+ Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Taylor Reiter, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan +
+ +
+ mSystems +   ·   + 23 Feb 2023 +   ·   + doi:10.1128/msystems.00341-22 +
+ + +
+
+ +
+ + +
+ + + + + Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14 + + +
+ Alexandra J. Lee, Georgia Doing, Samuel L. Neff, Taylor Reiter, Deborah A. Hogan, Casey S. Greene +
+ +
+ mSystems +   ·   + 23 Feb 2023 +   ·   + doi:10.1128/msystems.00342-22 +
+ + +
+
+ +
+ + +
+ + + + + Analysis of science journalism reveals gender and regional disparities in coverage + + +
+ Natalie R. Davidson, Casey S. Greene +
+ +
+ eLife Sciences Publications, Ltd +   ·   + 09 Feb 2023 +   ·   + doi:10.7554/eLife.84855 +
+ + +
+
+ +
+ + +
+ + + + + Analysis of science journalism reveals gender and regional disparities in coverage + + +
+ Natalie R. Davidson, Casey S. Greene +
+ +
+ eLife Sciences Publications, Ltd +   ·   + 09 Feb 2023 +   ·   + doi:10.7554/eLife.84855.1 +
+ + +
+
+ +
+ + +
+ + + + + A publishing infrastructure for AI-assisted academic authoring + + +
+ Milton Pividori, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 23 Jan 2023 +   ·   + doi:10.1101/2023.01.21.525030 +
+ + +
+
+ +
+ + +
+ + + + + The probability of edge existence due to node degree: a baseline for network-based predictions + + +
+ Michael Zietz, Daniel S. Himmelstein, Kyle Kloster, Christopher Williams, Michael W. Nagle, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 06 Jan 2023 +   ·   + doi:10.1101/2023.01.05.522939 +
+ + +
+
+ +
+ + +
+ + + + + The Field-Dependent Nature of PageRank Values in Citation Networks + + +
+ Benjamin J. Heil, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 06 Jan 2023 +   ·   + doi:10.1101/2023.01.05.522943 +
+ + +
+
+ +
+ + +
+ + + + + Supporting data for "Hetnet connectivity search provides rapid insights into how two biomedical entities are related" + + +
+ Himmelstein S Daniel, Zietz Michael, Rubinetti Vincent, Kloster Kyle, Heil J Benjamin, ..., Nicholson N David, Hao Yun, Sullivan D Blair, Nagle W Michael, Greene S Casey +
+ +
+ GigaScience Database +   ·   + 01 Jan 2023 +   ·   + doi:10.5524/102389 +
+ + +
+
+ +

2022

+ +
+ + +
+ + + + + Hetnet connectivity search provides rapid insights into how biomedical entities are related + + +
+ Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, ..., David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene +
+ +
+ GigaScience +   ·   + 28 Dec 2022 +   ·   + doi:10.1093/gigascience/giad047 +
+ + +
+
+ +
+ + +
+ + + + + Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors + + +
+ Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 05 Dec 2022 +   ·   + doi:10.1101/2022.12.04.519045 +
+ + +
+
+ +
+ + +
+ + + + + Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts + + +
+ David N. Nicholson, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ BioData Mining +   ·   + 18 Oct 2022 +   ·   + doi:10.1186/s13040-022-00311-z +
+ + +
+
+ +
+ + +
+ + + + + wenda_gpu: fast domain adaptation for genomic data + + +
+ Ariel A Hippen, Jake Crawford, Jacob R Gardner, Casey S Greene +
+ +
+ Bioinformatics +   ·   + 04 Oct 2022 +   ·   + doi:10.1093/bioinformatics/btac663 +
+ + +
+
+ +
+ + +
+ + + + + SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses + + +
+ Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene +
+ +
+ Genomics, Proteomics & Bioinformatics +   ·   + 01 Oct 2022 +   ·   + doi:10.1016/j.gpb.2022.09.011 +
+ + +
+
+ +
+ + +
+ + + + + Changing word meanings in biomedical literature reveal pandemics and new technologies + + +
+ David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 28 Jun 2022 +   ·   + doi:10.1101/2022.06.27.497742 +
+ + +
+
+ +
+ + +
+ + + + + GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases + + +
+ Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent J. Carey, Casey S. Greene, Levi Waldron, Sean Davis +
+ +
+ Nature Communications +   ·   + 27 Jun 2022 +   ·   + doi:10.1038/s41467-022-31411-3 +
+ + +
+
+ +
+ + +
+ + + + + Widespread redundancy in -omics profiles of cancer mutation states + + +
+ Jake Crawford, Brock C. Christensen, Maria Chikina, Casey S. Greene +
+ +
+ Genome Biology +   ·   + 27 Jun 2022 +   ·   + doi:10.1186/s13059-022-02705-y +
+ + +
+
+ +
+ + +
+ + + + + The Effects of Nonlinear Signal on Expression-Based Prediction Performance + + +
+ Benjamin J. Heil, Jake Crawford, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 26 Jun 2022 +   ·   + doi:10.1101/2022.06.22.497194 +
+ + +
+
+ +
+ + +
+ + + + + An efficient not-only-linear correlation coefficient based on machine learning + + +
+ Milton Pividori, Marylyn D. Ritchie, Diego H. Milone, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 17 Jun 2022 +   ·   + doi:10.1101/2022.06.15.496326 +
+ + +
+
+ +
+ + +
+ + + + + An expert knowledge-guided mutation operator for genome-wide genetic analysis using genetic programming + + +
+ [no author info] +
+ +
+ Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) +   ·   + 26 May 2022 +   ·   + source-work-id:0417180825475-141 +
+ + +
+
+ +
+ + +
+ + + + + Using expert knowledge in initialization for genome-wide analysis of epistasis using genetic programming + + +
+ [no author info] +
+ +
+ GECCO’08: Proceedings of the 10th Annual Conference on Genetic and Evolutionary Computation 2008 +   ·   + 26 May 2022 +   ·   + source-work-id:0417180825475-140 +
+ + +
+
+ +
+ + +
+ + + + + Enabling personal genomics with an explicit test of epistasis + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing 2010, PSB 2010 +   ·   + 26 May 2022 +   ·   + wosuid:WOS:000411479100034 +
+ + +
+
+ +
+ + +
+ + + + + Text and data mining for biomedical discovery + + +
+ [no author info] +
+ +
+ 18th Pacific Symposium on Biocomputing, PSB 2013 +   ·   + 26 May 2022 +   ·   + source-work-id:0417180825987-112 +
+ + +
+
+ +
+ + +
+ + + + + Text and data mining for biomedical discovery + + +
+ [no author info] +
+ +
+ 19th Pacific Symposium on Biocomputing, PSB 2014 +   ·   + 26 May 2022 +   ·   + source-work-id:0417180825987-109 +
+ + +
+
+ +
+ + +
+ + + + + Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing + + +
+ [no author info] +
+ +
+ 19th Pacific Symposium on Biocomputing, PSB 2014 +   ·   + 26 May 2022 +   ·   + source-work-id:0417180825986-104 +
+ + +
+
+ +
+ + +
+ + + + + Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders + + +
+ [no author info] +
+ +
+ 20th Pacific Symposium on Biocomputing, PSB 2015 +   ·   + 26 May 2022 +   ·   + source-work-id:0417180825986-103 +
+ + +
+
+ +
+ + +
+ + + + + Nothing but a hound dog + + +
+ [no author info] +
+ +
+ Science Translational Medicine +   ·   + 26 May 2022 +   ·   + source-work-id:0417180825983-88 +
+ + +
+
+ +
+ + +
+ + + + + NO-BOUNDARY THINKING IN BIOINFORMATICS + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 26 May 2022 +   ·   + source-work-id:0417180825983-87 +
+ + +
+
+ +
+ + +
+ + + + + NO-BOUNDARY THINKING IN BIOINFORMATICS + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 26 May 2022 +   ·   + eid:2-s2.0-85015595524 +
+ + +
+
+ +
+ + +
+ + + + + Computational approaches to study microbes and microbiomes + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing 2016, PSB 2016 +   ·   + 26 May 2022 +   ·   + wosuid:WOS:000386326200051 +
+ + +
+
+ +
+ + +
+ + + + + Computational approaches to study microbes and microbiomes + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing 2016, PSB 2016 +   ·   + 26 May 2022 +   ·   + eid:2-s2.0-85012144154 +
+ + +
+
+ +
+ + +
+ + + + + Text and data mining for biomedical discovery + + +
+ [no author info] +
+ +
+ 18th Pacific Symposium on Biocomputing, PSB 2013 +   ·   + 25 May 2022 +   ·   + eid:2-s2.0-84961190214 +
+ + +
+
+ +
+ + +
+ + + + + Text and data mining for biomedical discovery + + +
+ [no author info] +
+ +
+ 19th Pacific Symposium on Biocomputing, PSB 2014 +   ·   + 25 May 2022 +   ·   + eid:2-s2.0-84960944853 +
+ + +
+
+ +
+ + +
+ + + + + Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders + + +
+ [no author info] +
+ +
+ 20th Pacific Symposium on Biocomputing, PSB 2015 +   ·   + 25 May 2022 +   ·   + eid:2-s2.0-84971231452 +
+ + +
+
+ +
+ + +
+ + + + + Nothing but a hound dog + + +
+ [no author info] +
+ +
+ Science Translational Medicine +   ·   + 25 May 2022 +   ·   + eid:2-s2.0-84971009612 +
+ + +
+
+ +
+ + +
+ + + + + An expert knowledge-guided mutation operator for genome-wide genetic analysis using genetic programming + + +
+ [no author info] +
+ +
+ Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) +   ·   + 24 May 2022 +   ·   + eid:2-s2.0-38349045395 +
+ + +
+
+ +
+ + +
+ + + + + Using expert knowledge in initialization for genome-wide analysis of epistasis using genetic programming + + +
+ [no author info] +
+ +
+ GECCO'08: Proceedings of the 10th Annual Conference on Genetic and Evolutionary Computation 2008 +   ·   + 24 May 2022 +   ·   + eid:2-s2.0-57349142365 +
+ + +
+
+ +
+ + +
+ + + + + Multifactor Dimensionality Reduction 2.0 + + +
+ [no author info] +
+ +
+ Genetic Epidemiology +   ·   + 24 May 2022 +   ·   + wosuid:WOS:000260871600142 +
+ + +
+
+ +
+ + +
+ + + + + Computationally Efficient Relief-based Algorithms for Detecting Epistasis in Genome-wide Association Studies + + +
+ [no author info] +
+ +
+ Genetic Epidemiology +   ·   + 24 May 2022 +   ·   + wosuid:WOS:000272540600064 +
+ + +
+
+ +
+ + +
+ + + + + A Computational Evolution System for Open-Ended Automated Learning of Complex Genetic Relationships + + +
+ [no author info] +
+ +
+ Genetic Epidemiology +   ·   + 24 May 2022 +   ·   + wosuid:WOS:000272540600026 +
+ + +
+
+ +
+ + +
+ + + + + Enabling personal genomics with an explicit test of epistasis. + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 24 May 2022 +   ·   + wosuid:MEDLINE:19908385 +
+ + +
+
+ +
+ + +
+ + + + + Enabling personal genomics with an explicit test of epistasis + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing 2010, PSB 2010 +   ·   + 24 May 2022 +   ·   + eid:2-s2.0-77949497409 +
+ + +
+
+ +
+ + +
+ + + + + Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing. + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 24 May 2022 +   ·   + wosuid:MEDLINE:24297566 +
+ + +
+
+ +
+ + +
+ + + + + Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing + + +
+ [no author info] +
+ +
+ 19th Pacific Symposium on Biocomputing, PSB 2014 +   ·   + 24 May 2022 +   ·   + eid:2-s2.0-84905885881 +
+ + +
+
+ +
+ + +
+ + + + + Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. + + +
+ [no author info] +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 24 May 2022 +   ·   + wosuid:MEDLINE:25592575 +
+ + +
+
+ +
+ + +
+ + + + + Compendium-wide analysis of P. aeruginosa core and accessory genes reveal more nuanced transcriptional patterns + + +
+ Alexandra J. Lee, Georgia Doing, Samuel L. Neff, Taylor Reiter, Deborah A. Hogan, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 15 Apr 2022 +   ·   + doi:10.1101/2022.04.14.488429 +
+ + +
+
+ +
+ + +
+ + + + + wenda_gpu: fast domain adaptation for genomic data + + +
+ Ariel A. Hippen, Jake Crawford, Jacob R. Gardner, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 11 Apr 2022 +   ·   + doi:10.1101/2022.04.09.487671 +
+ + +
+
+ +
+ + +
+ + + + + Ten quick tips for deep learning in biology + + +
+ Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, ..., Alexandr A. Kalinin, Brandon Signal, Benjamin J. Lengerich, Timothy J. Triche, Simina M. Boca +
+ +
+ PLOS Computational Biology +   ·   + 24 Mar 2022 +   ·   + doi:10.1371/journal.pcbi.1009803 +
+ + +
+
+ +
+ + +
+ + + + + Ten simple rules for large-scale data processing + + +
+ Arkarachai Fungtammasan, Alexandra Lee, Jaclyn Taroni, Kurt Wheeler, Chen-Shan Chin, Sean Davis, Casey Greene +
+ +
+ PLOS Computational Biology +   ·   + 10 Feb 2022 +   ·   + doi:10.1371/journal.pcbi.1009757 +
+ + +
+
+ +
+ + +
+ + + + + Examining linguistic shifts between preprints and publications + + +
+ David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene +
+ +
+ PLOS Biology +   ·   + 01 Feb 2022 +   ·   + doi:10.1371/journal.pbio.3001470 +
+ + +
+
+ +
+ + +
+ + + + + Computationally efficient assembly of a Pseudomonas aeruginosa gene expression compendium + + +
+ Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 25 Jan 2022 +   ·   + doi:10.1101/2022.01.24.477642 +
+ + +
+
+ +
+ + +
+ + + + + Computational audits combat disparities in recognition + + +
+ Ariel A. Hippen, Natalie R. Davidson, Casey S. Greene +
+ +
+ Nature Human Behaviour +   ·   + 17 Jan 2022 +   ·   + doi:10.1038/s41562-021-01279-2 +
+ + +
+
+ +

2021

+ +
+ + +
+ + + + + Widespread redundancy in -omics profiles of cancer mutation states + + +
+ Jake Crawford, Brock C. Christensen, Maria Chikina, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 28 Oct 2021 +   ·   + doi:10.1101/2021.10.27.466140 +
+ + +
+
+ +
+ + +
+ + + + + A field guide to cultivating computational biology + + +
+ Gregory P. Way, Casey S. Greene, Piero Carninci, Benilton S. Carvalho, Michiel de Hoon, ..., Suzanne S. Sindi, Fabian J. Theis, Jean Y. H. Yang, Anne E. Carpenter, Elana J. Fertig +
+ +
+ PLOS Biology +   ·   + 07 Oct 2021 +   ·   + doi:10.1371/journal.pbio.3001419 +
+ + +
+
+ +
+ + +
+ + + + + Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design + + +
+ Lukas M Weber, Ariel A Hippen, Peter F Hickey, Kristofer C Berrett, Jason Gertz, Jennifer Anne Doherty, Casey S Greene, Stephanie C Hicks +
+ +
+ GigaScience +   ·   + 01 Sep 2021 +   ·   + doi:10.1093/gigascience/giab062 +
+ + +
+
+ +
+ + +
+ + + + + miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data + + +
+ Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks +
+ +
+ PLOS Computational Biology +   ·   + 24 Aug 2021 +   ·   + doi:10.1371/journal.pcbi.1009290 +
+ + +
+
+ +
+ + +
+ + + + + Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment + + +
+ Ronan Lordan, Halie M. Rando, Casey S. Greene +
+ +
+ mSystems +   ·   + 29 Jun 2021 +   ·   + doi:10.1128/mSystems.00122-21 +
+ + +
+
+ +
+ + +
+ + + + + Characterizing Long COVID: Deep Phenotype of a Complex Condition + + +
+ Rachel R Deer, Madeline A Rock, Nicole Vasilevsky, Leigh Carmody, Halie Rando, ..., Marc D Basson, Umit Topaloglu, Liwei Wang, Melissa A Haendel, Peter N Robinson +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 29 Jun 2021 +   ·   + doi:10.1101/2021.06.23.21259416 +
+ + +
+
+ +
+ + +
+ + + + + Analysis of science journalism reveals gender and regional disparities in coverage + + +
+ Natalie R. Davidson, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 22 Jun 2021 +   ·   + doi:10.1101/2021.06.21.449261 +
+ + +
+
+ +
+ + +
+ + + + + GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases + + +
+ Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent Carey, Casey Greene, Levi Waldron, Sean Davis +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 27 May 2021 +   ·   + doi:10.1101/2021.05.26.445900 +
+ + +
+
+ +
+ + +
+ + + + + Generative neural networks separate common and specific transcriptional responses + + +
+ Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 24 May 2021 +   ·   + doi:10.1101/2021.05.24.445440 +
+ + +
+
+ +
+ + +
+ + + + + Response to NOT-OD-21-066 - Racial EDI in Biomedical Research Workforce + + +
+ Monica Munoz-Torres, Melissa Haendel, Sean Davis, Lawrence Hunter, Andrew Neumann, ..., Mary Ann Tuli, Deepak Unni, Halie Rando, Shawn T. O'Neil, Matthew H. Brush +
+ +
+ Zenodo +   ·   + 09 Apr 2021 +   ·   + doi:10.5281/zenodo.4677668 +
+ + +
+
+ +
+ + +
+ + + + + Response to NOT-OD-21-066 - Racial EDI in Biomedical Research Workforce + + +
+ Monica Munoz-Torres, Melissa Haendel, Sean Davis, Lawrence Hunter, Andrew Neumann, ..., Mary Ann Tuli, Deepak Unni, Halie Rando, Shawn T. O'Neil, Matthew H. Brush +
+ +
+ Zenodo +   ·   + 09 Apr 2021 +   ·   + doi:10.5281/zenodo.4677667 +
+ + +
+
+ +
+ + +
+ + + + + Expanding and Remixing the Metadata Landscape + + +
+ Ariel A. Hippen, Casey S. Greene +
+ +
+ Trends in Cancer +   ·   + 01 Apr 2021 +   ·   + doi:10.1016/j.trecan.2020.10.011 +
+ + +
+
+ +
+ + +
+ + + + + Linguistic Analysis of the bioRxiv Preprint Landscape + + +
+ David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 04 Mar 2021 +   ·   + doi:10.1101/2021.03.04.433874 +
+ + +
+
+ +
+ + +
+ + + + + miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data + + +
+ Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 03 Mar 2021 +   ·   + doi:10.1101/2021.03.03.433798 +
+ + +
+
+ +

2020

+ +
+ + +
+ + + + + Open collaborative writing with Manubot + + +
+ Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter +
+ +
+ PLOS Computational Biology +   ·   + 04 Dec 2020 +   ·   + doi:10.1371/journal.pcbi.1007128 +
+ + +
+
+ +
+ + +
+ + + + + Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design + + +
+ Lukas M. Weber, Ariel A. Hippen, Peter F. Hickey, Kristofer C. Berrett, Jason Gertz, Jennifer Anne Doherty, Casey S. Greene, Stephanie C. Hicks +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 07 Nov 2020 +   ·   + doi:10.1101/2020.11.06.371963 +
+ + +
+
+ +
+ + +
+ + + + + Correcting for experiment-specific variability in expression compendia can remove underlying signals + + +
+ Alexandra J Lee, YoSon Park, Georgia Doing, Deborah A Hogan, Casey S Greene +
+ +
+ GigaScience +   ·   + 01 Nov 2020 +   ·   + doi:10.1093/gigascience/giaa117 +
+ + +
+
+ +
+ + +
+ + + + + Transparency and reproducibility in artificial intelligence + + +
+ Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, Thakkar Shraddha, ..., Robert Tibshirani, Trevor Hastie, John P. A. Ioannidis, John Quackenbush, Hugo J. W. L. Aerts +
+ +
+ Nature +   ·   + 14 Oct 2020 +   ·   + doi:10.1038/s41586-020-2766-y +
+ + +
+
+ +
+ + +
+ + + + + Responsible, practical genomic data sharing that accelerates research + + +
+ James Brian Byrd, Anna C. Greene, Deepashree Venkatesh Prasad, Xiaoqian Jiang, Casey S. Greene +
+ +
+ Nature Reviews Genetics +   ·   + 21 Jul 2020 +   ·   + doi:10.1038/s41576-020-0257-5 +
+ + +
+
+ +
+ + +
+ + + + + Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE). + + +
+ Aline Talhouk, Joshy George, Chen Wang, Timothy Budden, Tuan Zea Tan, ..., Ellen L Goode, Susan J Ramus, Jennifer A Doherty, David D Bowtell, Michael S Anglesio +
+ +
+ American Association for Cancer Research (AACR) +   ·   + 04 Jun 2020 +   ·   + doi:10.17863/cam.53202 +
+ + +
+
+ +
+ + +
+ + + + + Incorporating biological structure into machine learning models in biomedicine + + +
+ Jake Crawford, Casey S Greene +
+ +
+ Current Opinion in Biotechnology +   ·   + 01 Jun 2020 +   ·   + doi:10.1016/j.copbio.2019.12.021 +
+ + +
+
+ +
+ + +
+ + + + + Recommendations to enhance rigor and reproducibility in biomedical research + + +
+ Jaqueline J Brito, Jun Li, Jason H Moore, Casey S Greene, Nicole A Nogoy, Lana X Garmire, Serghei Mangul +
+ +
+ GigaScience +   ·   + 01 Jun 2020 +   ·   + doi:10.1093/gigascience/giaa056 +
+ + +
+
+ +
+ + +
+ + + + + Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ Genome Biology +   ·   + 11 May 2020 +   ·   + doi:10.1186/s13059-020-02021-3 +
+ + +
+
+ +
+ + +
+ + + + + Correcting for experiment-specific variability in expression compendia can remove underlying signals + + +
+ Alexandra J. Lee, YoSon Park, Georgia Doing, Deborah A. Hogan, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 03 May 2020 +   ·   + doi:10.1101/2020.05.03.066597 +
+ + +
+
+ +
+ + +
+ + + + + Analysis of ISCB honorees and keynotes reveals disparities + + +
+ Trang T. Le, Daniel S. Himmelstein, Ariel A. Hippen Anderson, Matthew R. Gazzara, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 14 Apr 2020 +   ·   + doi:10.1101/2020.04.14.927251 +
+ + +
+
+ +
+ + +
+ + + + + greenelab/BioBombe: Accepted Manuscript - Genome Biology + + +
+ Gregory Way, Michael Zietz, Vincent Rubinetti, Daniel Himmelstein, Casey Greene +
+ +
+ Zenodo +   ·   + 08 Apr 2020 +   ·   + doi:10.5281/zenodo.2550266 +
+ + +
+
+ +
+ + +
+ + + + + greenelab/BioBombe: Accepted Manuscript - Genome Biology + + +
+ Gregory Way, Michael Zietz, Vincent Rubinetti, Daniel Himmelstein, Casey Greene +
+ +
+ Zenodo +   ·   + 08 Apr 2020 +   ·   + doi:10.5281/zenodo.3744941 +
+ + +
+
+ +
+ + +
+ + + + + Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1 + + +
+ Jineta Banerjee, Robert J Allaway, Jaclyn N Taroni, Aaron Baker, Xiaochun Zhang, ..., Jaishri O Blakeley, Justin Guinney, Angela Hirbe, Casey S Greene, Sara JC Gosline +
+ +
+ Genes +   ·   + 21 Feb 2020 +   ·   + doi:10.3390/genes11020226 +
+ + +
+
+ +
+ + +
+ + + + + Pseudomonas aeruginosa lasR + mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin + + +
+ Michelle E. Clay, John H. Hammond, Fangfang Zhong, Xiaolei Chen, Caitlin H. Kowalski, ..., Monique S. Porter, Thomas H. Hampton, Casey S. Greene, Ekaterina V. Pletneva, Deborah A. Hogan +
+ +
+ Proceedings of the National Academy of Sciences +   ·   + 24 Jan 2020 +   ·   + doi:10.1073/pnas.1917576117 +
+ + +
+
+ +
+ + +
+ + + + + Graph biased feature selection of genes is better than random for many genes + + +
+ Jake Crawford, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 21 Jan 2020 +   ·   + doi:10.1101/2020.01.17.910703 +
+ + +
+
+ +
+ + +
+ + + + + Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1 + + +
+ Jineta Banerjee, Robert J Allaway, Jaclyn N Taroni, Aaron Baker, Xiaochun Zhang, ..., Jaishri O Blakeley, Justin Guinney, Angela Hirbe, Casey S Greene, Sara JC Gosline +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 14 Jan 2020 +   ·   + doi:10.1101/2020.01.13.904771 +
+ + +
+
+ +
+ + +
+ + + + + Supporting data for "Correcting for experiment-specific variability in expression compendia can remove underlying signals" + + +
+ Lee J Alexandra, Park YoSon, Doing Georgia, Hogan A Deborah, Greene S Casey +
+ +
+ GigaScience Database +   ·   + 01 Jan 2020 +   ·   + doi:10.5524/100796 +
+ + +
+
+ +
+ + +
+ + + + + Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.c.4972634.v1 +
+ + +
+
+ +
+ + +
+ + + + + Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.c.4972634 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 7 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285521.v1 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 7 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285521 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 6 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285518 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 6 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285518.v1 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 5 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285515.v1 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 5 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285515 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 4 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285512 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 4 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285512.v1 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 3 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285506.v1 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 3 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285506 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 2 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285500.v1 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 2 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285500 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 1 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285494.v1 +
+ + +
+
+ +
+ + +
+ + + + + Additional file 1 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ figshare +   ·   + 01 Jan 2020 +   ·   + doi:10.6084/m9.figshare.12285494 +
+ + +
+
+ +

2019

+ +
+ + +
+ + + + + Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma + + +
+ Yu-Hsiu T. Lin, Gregory P. Way, Benjamin G. Barwick, Margarette C. Mariano, Makeba Marcoulis, Ian D. Ferguson, Christoph Driessen, Lawrence H. Boise, Casey S. Greene, Arun P. Wiita +
+ +
+ Blood Advances +   ·   + 29 Oct 2019 +   ·   + doi:10.1182/bloodadvances.2019000303 +
+ + +
+
+ +
+ + +
+ + + + + Pseudomonas aeruginosa lasRmutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin + + +
+ Michelle E. Clay, John H. Hammond, Fangfang Zhong, Xiaolei Chen, Caitlin H. Kowalski, Alexandra J. Lee, Monique S. Porter, Casey S. Greene, Ekaterina V. Pletneva, Deborah A. Hogan +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 13 Oct 2019 +   ·   + doi:10.1101/802934 +
+ + +
+
+ +
+ + +
+ + + + + Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts + + +
+ David N. Nicholson, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 08 Aug 2019 +   ·   + doi:10.1101/730085 +
+ + +
+
+ +
+ + +
+ + + + + Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 11 Mar 2019 +   ·   + doi:10.1101/573782 +
+ + +
+
+ +
+ + +
+ + + + + Integrated Phosphoproteomics and Transcriptional Classifiers Reveal Hidden RAS Signaling Dynamics in Multiple Myeloma + + +
+ Yu-Hsiu T. Lin, Gregory P. Way, Benjamin G. Barwick, Margarette C. Mariano, Makeba Marcoulis, Ian D. Ferguson, Christoph Driessen, Lawrence H. Boise, Casey S. Greene, Arun P. Wiita +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 28 Feb 2019 +   ·   + doi:10.1101/563312 +
+ + +
+
+ +
+ + +
+ + + + + MultiPLIER Fileset + + +
+ Jaclyn Taroni, Casey Greene +
+ +
+ figshare +   ·   + 01 Jan 2019 +   ·   + doi:10.6084/M9.FIGSHARE.6982919 +
+ + +
+
+ +
+ + +
+ + + + + MultiPLIER Fileset + + +
+ Jaclyn Taroni, Casey Greene +
+ +
+ figshare +   ·   + 01 Jan 2019 +   ·   + doi:10.6084/m9.figshare.6982919.v2 +
+ + +
+
+ +
+ + +
+ + + + + NewDrosophilaLong-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods + + +
+ Balint Z Kacsoh, Stephen Barton, Yuxiang Jiang, Naihui Zhou, Sean D Mooney, Iddo Friedberg, Predrag Radivojac, Casey S Greene, Giovanni Bosco +
+ +
+ G3 Genes|Genomes|Genetics +   ·   + 01 Jan 2019 +   ·   + doi:10.1534/g3.118.200867 +
+ + +
+
+ +

2018

+ +
+ + +
+ + + + + Bayesian deep learning for single-cell analysis + + +
+ Gregory P. Way, Casey S. Greene +
+ +
+ Nature Methods +   ·   + 30 Nov 2018 +   ·   + doi:10.1038/s41592-018-0230-9 +
+ + +
+
+ +
+ + +
+ + + + + Node connectivity measurements for Hetionet v1.0 metapaths + + +
+ Daniel Himmelstein, Michael Zietz, Kyle Kloster, Michael Nagle, Blair Sullivan, Casey Greene +
+ +
+ Zenodo +   ·   + 06 Nov 2018 +   ·   + doi:10.5281/zenodo.1435833 +
+ + +
+
+ +
+ + +
+ + + + + Node connectivity measurements for Hetionet v1.0 metapaths + + +
+ Daniel Himmelstein, Michael Zietz, Kyle Kloster, Michael Nagle, Blair Sullivan, Casey Greene +
+ +
+ Zenodo +   ·   + 06 Nov 2018 +   ·   + doi:10.5281/zenodo.1435834 +
+ + +
+
+ +
+ + +
+ + + + + A parasite's perspective on data sharing + + +
+ YoSon Park, Casey S Greene +
+ +
+ GigaScience +   ·   + 01 Nov 2018 +   ·   + doi:10.1093/gigascience/giy129 +
+ + +
+
+ +
+ + +
+ + + + + Learning and Imputation for Mass-spec Bias Reduction (LIMBR) + + +
+ Alexander M Crowell, Casey S Greene, Jennifer J Loros, Jay C Dunlap +
+ +
+ Bioinformatics +   ·   + 24 Sep 2018 +   ·   + doi:10.1093/bioinformatics/bty828 +
+ + +
+
+ +
+ + +
+ + + + + Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning + + +
+ Gregory P Way, Casey S Greene +
+ +
+ PeerJ +   ·   + 20 Sep 2018 +   ·   + doi:10.7287/peerj.preprints.27229 +
+ + +
+
+ +
+ + +
+ + + + + Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning + + +
+ Gregory P Way, Casey S Greene +
+ +
+ PeerJ +   ·   + 20 Sep 2018 +   ·   + doi:10.7287/peerj.preprints.27229v1 +
+ + +
+
+ +
+ + +
+ + + + + New Drosophila long-term memory genes revealed by assessing computational function prediction methods + + +
+ Balint Z. Kacsoh, Stephen Barton, Yuxiang Jiang, Naihui Zhou, Sean D. Mooney, Iddo Friedberg, Predrag Radivojac, Casey S. Greene, Giovanni Bosco +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 11 Sep 2018 +   ·   + doi:10.1101/414565 +
+ + +
+
+ +
+ + +
+ + + + + MultiPLIER: a transfer learning framework for transcriptomics reveals systemic features of rare disease + + +
+ Jaclyn N. Taroni, Peter C. Grayson, Qiwen Hu, Sean Eddy, Matthias Kretzler, Peter A. Merkel, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 20 Aug 2018 +   ·   + doi:10.1101/395947 +
+ + +
+
+ +
+ + +
+ + + + + Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics + + +
+ Qiwen Hu, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 05 Aug 2018 +   ·   + doi:10.1101/385534 +
+ + +
+
+ +
+ + +
+ + + + + Specific histone modifications associate with alternative exon selection during mammalian development + + +
+ Q Hu, CS Greene, EA Heller +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 04 Jul 2018 +   ·   + doi:10.1101/361816 +
+ + +
+
+ +
+ + +
+ + + + + PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia + + +
+ Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene +
+ +
+ BioData Mining +   ·   + 03 Jul 2018 +   ·   + doi:10.1186/s13040-018-0175-7 +
+ + +
+
+ +
+ + +
+ + + + + A Multimodal Strategy Used by a Large c-di-GMP Network + + +
+ Kurt M. Dahlstrom, Alan J. Collins, Georgia Doing, Jaclyn N. Taroni, Timothy J. Gauvin, Casey S. Greene, Deborah A. Hogan, George A. O'Toole +
+ +
+ Journal of Bacteriology +   ·   + 15 Apr 2018 +   ·   + doi:10.1128/JB.00703-17 +
+ + +
+
+ +
+ + +
+ + + + + Learning and Imputation for Mass-spec Bias Reduction (LIMBR) + + +
+ Alexander M Crowell, Casey S Greene, Jennifer J. Loros, Jay C Dunlap +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 14 Apr 2018 +   ·   + doi:10.1101/301242 +
+ + +
+
+ +
+ + +
+ + + + + Oncogenic Signaling Pathways in The Cancer Genome Atlas + + +
+ Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze +
+ +
+ Cell +   ·   + 01 Apr 2018 +   ·   + doi:10.1016/j.cell.2018.03.035 +
+ + +
+
+ +
+ + +
+ + + + + Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas + + +
+ Gregory P. Way, Francisco Sanchez-Vega, Konnor La, Joshua Armenia, Walid K. Chatila, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze +
+ +
+ Cell Reports +   ·   + 01 Apr 2018 +   ·   + doi:10.1016/j.celrep.2018.03.046 +
+ + +
+
+ +
+ + +
+ + + + + Sci-Hub provides access to nearly all scholarly literature + + +
+ Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene +
+ +
+ eLife +   ·   + 01 Mar 2018 +   ·   + doi:10.7554/eLife.32822 +
+ + +
+
+ +
+ + +
+ + + + + Sci-Hub provides access to nearly all scholarly literature + + +
+ Daniel S Himmelstein, Ariel R Romero, Jacob G Levernier, Thomas A Munro, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene +
+ +
+ PeerJ +   ·   + 02 Feb 2018 +   ·   + doi:10.7287/peerj.preprints.3100 +
+ + +
+
+ +
+ + +
+ + + + + Sci-Hub provides access to nearly all scholarly literature + + +
+ Daniel S Himmelstein, Ariel R Romero, Jacob G Levernier, Thomas A Munro, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene +
+ +
+ PeerJ +   ·   + 02 Feb 2018 +   ·   + doi:10.7287/peerj.preprints.3100v3 +
+ + +
+
+ +
+ + +
+ + + + + MultiPLIER Fileset + + +
+ Jaclyn Taroni, Casey Greene +
+ +
+ figshare +   ·   + 01 Jan 2018 +   ·   + doi:10.6084/m9.figshare.6982919.v1 +
+ + +
+
+ +

2017

+ +
+ + +
+ + + + + A Pilot Characterization of the Human Chronobiome + + +
+ Carsten Skarke, Nicholas F. Lahens, Seth D. Rhoades, Amy Campbell, Kyle Bittinger, ..., Frederic D. Bushman, Casey S. Greene, Gregory R. Grant, Aalim M. Weljie, Garret A. FitzGerald +
+ +
+ Scientific Reports +   ·   + 07 Dec 2017 +   ·   + doi:10.1038/s41598-017-17362-6 +
+ + +
+
+ +
+ + +
+ + + + + ADAGE signature analysis: differential expression analysis with data-defined gene sets + + +
+ Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene +
+ +
+ BMC Bioinformatics +   ·   + 22 Nov 2017 +   ·   + doi:10.1186/s12859-017-1905-4 +
+ + +
+
+ +
+ + +
+ + + + + Machine Learning Analysis IdentifiesDrosophila Grunge/Atrophinas an Important Learning and Memory Gene Required for Memory Retention and Social Learning + + +
+ Balint Z Kacsoh, Casey S Greene, Giovanni Bosco +
+ +
+ G3 Genes|Genomes|Genetics +   ·   + 01 Nov 2017 +   ·   + doi:10.1534/g3.117.300172 +
+ + +
+
+ +
+ + +
+ + + + + Sci-Hub provides access to nearly all scholarly literature + + +
+ Daniel S Himmelstein, Ariel R Romero, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene +
+ +
+ PeerJ +   ·   + 12 Oct 2017 +   ·   + doi:10.7287/peerj.preprints.3100v2 +
+ + +
+
+ +
+ + +
+ + + + + Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations + + +
+ Genevieve L. Stein-O’Brien, Raman Arora, Aedin C. Culhane, Alexander V. Favorov, Lana X. Garmire, ..., Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 02 Oct 2017 +   ·   + doi:10.1101/196915 +
+ + +
+
+ +
+ + +
+ + + + + Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders + + +
+ Gregory P. Way, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 11 Aug 2017 +   ·   + doi:10.1101/174474 +
+ + +
+
+ +
+ + +
+ + + + + Implicating candidate genes at GWAS signals by leveraging topologically associating domains + + +
+ Gregory P Way, Daniel W Youngstrom, Kurt D Hankenson, Casey S Greene, Struan FA Grant +
+ +
+ European Journal of Human Genetics +   ·   + 09 Aug 2017 +   ·   + doi:10.1038/ejhg.2017.108 +
+ + +
+
+ +
+ + +
+ + + + + Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules + + +
+ Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Casey S. Greene, Jason H. Moore, Andrew J. Saykin, Li Shen +
+ +
+ Bioinformatics +   ·   + 20 Jul 2017 +   ·   + doi:10.1093/bioinformatics/btx344 +
+ + +
+
+ +
+ + +
+ + + + + Sci-Hub provides access to nearly all scholarly literature + + +
+ Daniel S Himmelstein, Ariel R Romero, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene +
+ +
+ PeerJ +   ·   + 20 Jul 2017 +   ·   + doi:10.7287/peerj.preprints.3100v1 +
+ + +
+
+ +
+ + +
+ + + + + Functional Network Community Detection Can Disaggregate and Filter Multiple Underlying Pathways in Enrichment Analyses + + +
+ Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 20 Jul 2017 +   ·   + doi:10.1101/166207 +
+ + +
+
+ +
+ + +
+ + + + + Privacy-preserving generative deep neural networks support clinical data sharing + + +
+ Brett K. Beaulieu-Jones, Zhiwei Steven Wu, Chris Williams, Ran Lee, Sanjeev P. Bhavnani, James Brian Byrd, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 05 Jul 2017 +   ·   + doi:10.1101/159756 +
+ + +
+
+ +
+ + +
+ + + + + Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks + + +
+ Jie Tan, Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady, Barret Perchuk, Michael T. Laub, Deborah A. Hogan, Casey S. Greene +
+ +
+ Cell Systems +   ·   + 01 Jul 2017 +   ·   + doi:10.1016/j.cels.2017.06.003 +
+ + +
+
+ +
+ + +
+ + + + + Machine learning analysis identifies Drosophila Grunge/Atrophin as an important learning and memory gene required for memory retention and social learning + + +
+ Balint Z Kacsoh, Casey S. Greene, Giovanni Bosco +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 29 Jun 2017 +   ·   + doi:10.1101/157610 +
+ + +
+
+ +
+ + +
+ + + + + ADAGE signature analysis: differential expression analysis with data-defined gene sets + + +
+ Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 27 Jun 2017 +   ·   + doi:10.1101/156620 +
+ + +
+
+ +
+ + +
+ + + + + Data-Sharing Models + + +
+ [no author info] +
+ +
+ New England Journal of Medicine +   ·   + 08 Jun 2017 +   ·   + doi:10.1056/NEJMc1705477 +
+ + +
+
+ +
+ + +
+ + + + + PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia + + +
+ Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 08 Jun 2017 +   ·   + doi:10.1101/147645 +
+ + +
+
+ +
+ + +
+ + + + + Opportunities and obstacles for deep learning in biology and medicine + + +
+ Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, ..., Simina M. Boca, S. Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 28 May 2017 +   ·   + doi:10.1101/142760 +
+ + +
+
+ +
+ + +
+ + + + + Celebrating parasites + + +
+ Casey S Greene, Lana X Garmire, Jack A Gilbert, Marylyn D Ritchie, Lawrence E Hunter +
+ +
+ Nature Genetics +   ·   + 01 Apr 2017 +   ·   + doi:10.1038/ng.3830 +
+ + +
+
+ +
+ + +
+ + + + + A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis + + +
+ Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood, Romy B. Christmann, ..., Christopher P. Denton, Monique E. Hinchcliff, Patricia A. Pioli, J. Matthew Mahoney, Michael L. Whitfield +
+ +
+ Genome Medicine +   ·   + 23 Mar 2017 +   ·   + doi:10.1186/s13073-017-0417-1 +
+ + +
+
+ +
+ + +
+ + + + + Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously + + +
+ Jaclyn N Taroni, Casey S Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 20 Mar 2017 +   ·   + doi:10.1101/118349 +
+ + +
+
+ +
+ + +
+ + + + + Reproducibility of computational workflows is automated using continuous analysis + + +
+ Brett K Beaulieu-Jones, Casey S Greene +
+ +
+ Nature Biotechnology +   ·   + 13 Mar 2017 +   ·   + doi:10.1038/nbt.3780 +
+ + +
+
+ +
+ + +
+ + + + + Tell me your neighbors, and I will tell you what you are + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 08 Feb 2017 +   ·   + doi:10.1126/scitranslmed.aam6058 +
+ + +
+
+ +
+ + +
+ + + + + A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma + + +
+ Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene +
+ +
+ BMC Genomics +   ·   + 06 Feb 2017 +   ·   + doi:10.1186/s12864-017-3519-7 +
+ + +
+
+ +
+ + +
+ + + + + "Cross-platform normalization enables analysis of microarray and RNA-seq data simultaneously" - Fileset + + +
+ Jaclyn Taroni, Casey Greene +
+ +
+ figshare +   ·   + 01 Jan 2017 +   ·   + doi:10.6084/m9.figshare.5035997.v1 +
+ + +
+
+ +
+ + +
+ + + + + "Cross-platform normalization enables analysis of microarray and RNA-seq data simultaneously" - Fileset + + +
+ Jaclyn Taroni, Casey Greene +
+ +
+ figshare +   ·   + 01 Jan 2017 +   ·   + doi:10.6084/m9.figshare.5035997.v2 +
+ + +
+
+ +
+ + +
+ + + + + "Cross-platform normalization enables analysis of microarray and RNA-seq data simultaneously" - Fileset + + +
+ Jaclyn Taroni, Casey Greene +
+ +
+ figshare +   ·   + 01 Jan 2017 +   ·   + doi:10.6084/M9.FIGSHARE.5035997 +
+ + +
+
+ +

2016

+ +
+ + +
+ + + + + Cheap-seq + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 21 Dec 2016 +   ·   + doi:10.1126/scitranslmed.aal3701 +
+ + +
+
+ +
+ + +
+ + + + + Semi-supervised learning of the electronic health record for phenotype stratification + + +
+ Brett K. Beaulieu-Jones, Casey S. Greene +
+ +
+ Journal of Biomedical Informatics +   ·   + 01 Dec 2016 +   ·   + doi:10.1016/j.jbi.2016.10.007 +
+ + +
+
+ +
+ + +
+ + + + + Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes + + +
+ Gregory P Way, James Rudd, Chen Wang, Habib Hamidi, Brooke L Fridley, Gottfried E Konecny, Ellen L Goode, Casey S Greene, Jennifer A Doherty +
+ +
+ G3 Genes|Genomes|Genetics +   ·   + 01 Dec 2016 +   ·   + doi:10.1534/g3.116.033514 +
+ + +
+
+ +
+ + +
+ + + + + Implicating candidate genes at GWAS signals by leveraging topologically associating domains + + +
+ Gregory P. Way, Daniel W. Youngstrom, Kurt D. Hankenson, Casey S. Greene, Struan F. A. Grant +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 15 Nov 2016 +   ·   + doi:10.1101/087718 +
+ + +
+
+ +
+ + +
+ + + + + How to know what we don’t + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 09 Nov 2016 +   ·   + doi:10.1126/scitranslmed.aal0067 +
+ + +
+
+ +
+ + +
+ + + + + Unsupervised extraction of stable expression signatures from public compendia with eADAGE + + +
+ Jie Tan, Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady, Barret Perchuk, Michael T. Laub, Deborah A. Hogan, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 03 Oct 2016 +   ·   + doi:10.1101/078659 +
+ + +
+
+ +
+ + +
+ + + + + A stromal focus reveals tumor immune signatures + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 28 Sep 2016 +   ·   + doi:10.1126/scitranslmed.aai8224 +
+ + +
+
+ +
+ + +
+ + + + + A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma + + +
+ Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 15 Sep 2016 +   ·   + doi:10.1101/075382 +
+ + +
+
+ +
+ + +
+ + + + + An expanded evaluation of protein function prediction methods shows an improvement in accuracy + + +
+ Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur, Daniel D’Andrea, ..., Burkhard Rost, Casey S. Greene, Sean D. Mooney, Iddo Friedberg, Predrag Radivojac +
+ +
+ Genome Biology +   ·   + 07 Sep 2016 +   ·   + doi:10.1186/s13059-016-1037-6 +
+ + +
+
+ +
+ + +
+ + + + + Integrative networks illuminate biological factors underlying gene-disease associations + + +
+ Arjun Krishnan, Jaclyn N. Taroni, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 28 Aug 2016 +   ·   + doi:10.1101/062695 +
+ + +
+
+ +
+ + +
+ + + + + Gut check + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 17 Aug 2016 +   ·   + doi:10.1126/scitranslmed.aah5494 +
+ + +
+
+ +
+ + +
+ + + + + Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes + + +
+ Gregory P. Way, James Rudd, Chen Wang, Habib Hamidi, Brooke L. Fridley, Gottfried Konecny, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 12 Jul 2016 +   ·   + doi:10.1101/030239 +
+ + +
+
+ +
+ + +
+ + + + + The future is unsupervised + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 06 Jul 2016 +   ·   + doi:10.1126/scitranslmed.aag3101 +
+ + +
+
+ +
+ + +
+ + + + + Pathway and network-based strategies to translate genetic discoveries into effective therapies + + +
+ Casey S. Greene, Benjamin F. Voight +
+ +
+ Human Molecular Genetics +   ·   + 23 Jun 2016 +   ·   + doi:10.1093/hmg/ddw160 +
+ + +
+
+ +
+ + +
+ + + + + Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression + + +
+ Adam J. Book, Gina R. Lewin, Bradon R. McDonald, Taichi E. Takasuka, Evelyn Wendt-Pienkowski, Drew T. Doering, Steven Suh, Kenneth F. Raffa, Brian G. Fox, Cameron R. Currie +
+ +
+ PLOS Biology +   ·   + 08 Jun 2016 +   ·   + doi:10.1371/journal.pbio.1002475 +
+ + +
+
+ +
+ + +
+ + + + + Reproducible Computational Workflows with Continuous Analysis + + +
+ Brett K. Beaulieu-Jones, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 01 Jun 2016 +   ·   + doi:10.1101/056473 +
+ + +
+
+ +
+ + +
+ + + + + Tribe: The collaborative platform for reproducible web-based analysis of gene sets + + +
+ René A. Zelaya, Aaron K. Wong, Alex T. Frase, Marylyn D. Ritchie, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 27 May 2016 +   ·   + doi:10.1101/055913 +
+ + +
+
+ +
+ + +
+ + + + + Nothing but a hound dog + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 25 May 2016 +   ·   + doi:10.1126/scitranslmed.aaf9196 +
+ + +
+
+ +
+ + +
+ + + + + Pathway and network-based strategies to translate genetic discoveries into effective therapies + + +
+ Casey S. Greene, Benjamin F. Voight +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 03 May 2016 +   ·   + doi:10.1101/051524 +
+ + +
+
+ +
+ + +
+ + + + + CoINcIDE: All together now + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 13 Apr 2016 +   ·   + doi:10.1126/scitranslmed.aaf6940 +
+ + +
+
+ +
+ + +
+ + + + + Genetic Association–Guided Analysis of Gene Networks for the Study of Complex Traits + + +
+ Casey S. Greene, Daniel S. Himmelstein +
+ +
+ Circulation: Cardiovascular Genetics +   ·   + 01 Apr 2016 +   ·   + doi:10.1161/CIRCGENETICS.115.001181 +
+ + +
+
+ +
+ + +
+ + + + + Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites + + +
+ Robert J. Allaway, Dawn A. Fischer, Francine B. de Abreu, Timothy B. Gardner, Stuart R. Gordon, ..., Gregory J. Tsongalis, Arief A. Suriawinata, Casey S. Greene, Yolanda Sanchez, Kerrington D. Smith +
+ +
+ Oncotarget +   ·   + 25 Feb 2016 +   ·   + doi:10.18632/oncotarget.7718 +
+ + +
+
+ +
+ + +
+ + + + + ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions + + +
+ Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene +
+ +
+ mSystems +   ·   + 23 Feb 2016 +   ·   + doi:10.1128/mSystems.00025-15 +
+ + +
+
+ +
+ + +
+ + + + + Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification + + +
+ Brett K. Beaulieu-Jones, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 18 Feb 2016 +   ·   + doi:10.1101/039800 +
+ + +
+
+ +
+ + +
+ + + + + A Novel Multi-network Approach Reveals Tissue-specific Cellular Modulators of Fibrosis in Systemic Sclerosis, Pulmonary Fibrosis and Pulmonary Arterial Hypertension + + +
+ Jaclyn N Taroni, Casey S Greene, Viktor Martyanov, Tammara A Wood, Romy Christmann, ..., Christopher P Denton, Monique E Hinchcliff, Patricia A Pioli, J. Matthew Mahoney, Michael L Whitfield +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 06 Feb 2016 +   ·   + doi:10.1101/038950 +
+ + +
+
+ +
+ + +
+ + + + + Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology + + +
+ Daniel S. Himmelstein, Casey S. Greene, Jason H. Moore +
+ +
+ BioData Mining +   ·   + 03 Feb 2016 +   ·   + doi:10.1186/s13040-016-0085-5 +
+ + +
+
+ +
+ + +
+ + + + + Cross-platform normalization of microarray and RNA-seq data for machine learning applications + + +
+ Jeffrey A. Thompson, Jie Tan, Casey S. Greene +
+ +
+ PeerJ +   ·   + 21 Jan 2016 +   ·   + doi:10.7717/peerj.1621 +
+ + +
+
+ +
+ + +
+ + + + + Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer’s disease: a study of ADNI cohorts + + +
+ Ailin Song, Jingwen Yan, Sungeun Kim, Shannon Leigh Risacher, Aaron K. Wong, Andrew J. Saykin, Li Shen, Casey S. Greene +
+ +
+ BioData Mining +   ·   + 19 Jan 2016 +   ·   + doi:10.1186/s13040-016-0082-8 +
+ + +
+
+ +

2015

+ +
+ + +
+ + + + + Leveraging global gene expression patterns to predict expression of unmeasured genes + + +
+ James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty +
+ +
+ BMC Genomics +   ·   + 01 Dec 2015 +   ·   + doi:10.1186/s12864-015-2250-5 +
+ + +
+
+ +
+ + +
+ + + + + ADAGE analysis of publicly available gene expression data collections illuminates Pseudomonas aeruginosa-host interactions + + +
+ Jie Tan, John H Hammond, Deborah A Hogan, Casey S Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 05 Nov 2015 +   ·   + doi:10.1101/030650 +
+ + +
+
+ +
+ + +
+ + + + + Cross-platform normalization of microarray and RNA-seq data for machine learning applications + + +
+ Jeffrey A Thompson, Jie Tan, Casey S Greene +
+ +
+ PeerJ +   ·   + 30 Oct 2015 +   ·   + doi:10.7287/PEERJ.PREPRINTS.1460 +
+ + +
+
+ +
+ + +
+ + + + + Cross-platform normalization of microarray and RNA-seq data for machine learning applications + + +
+ Jeffrey A Thompson, Jie Tan, Casey S Greene +
+ +
+ PeerJ +   ·   + 30 Oct 2015 +   ·   + doi:10.7287/PEERJ.PREPRINTS.1460V1 +
+ + +
+
+ +
+ + +
+ + + + + Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions + + +
+ David C. Qian, Jinyoung Byun, Younghun Han, Casey S. Greene, John K. Field, ..., Fredrick R. Schumacher, Rosalind A. Eeles, Douglas F. Easton, Daniela Seminara, Christopher I. Amos +
+ +
+ Human Molecular Genetics +   ·   + 19 Oct 2015 +   ·   + doi:10.1093/hmg/ddv440 +
+ + +
+
+ +
+ + +
+ + + + + Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery + + +
+ Graciela H. Gonzalez, Tasnia Tahsin, Britton C. Goodale, Anna C. Greene, Casey S. Greene +
+ +
+ Briefings in Bioinformatics +   ·   + 29 Sep 2015 +   ·   + doi:10.1093/bib/bbv087 +
+ + +
+
+ +
+ + +
+ + + + + International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways + + +
+ Heather J. Cordell, Younghun Han, George F. Mells, Yafang Li, Gideon M. Hirschfield, ..., Pietro Invernizzi, Michael F. Seldin, Richard N. Sandford, Christopher I. Amos, Katherine A. Siminovitch +
+ +
+ Nature Communications +   ·   + 22 Sep 2015 +   ·   + doi:10.1038/ncomms9019 +
+ + +
+
+ +
+ + +
+ + + + + Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study + + +
+ Jiang Gui, Casey S. Greene, Con Sullivan, Walter Taylor, Jason H. Moore, Carol Kim +
+ +
+ BioData Mining +   ·   + 01 Jun 2015 +   ·   + doi:10.1186/s13040-015-0050-8 +
+ + +
+
+ +
+ + +
+ + + + + Understanding multicellular function and disease with human tissue-specific networks + + +
+ Casey S Greene, Arjun Krishnan, Aaron K Wong, Emanuela Ricciotti, Rene A Zelaya, ..., Daniel I Chasman, Garret A FitzGerald, Kara Dolinski, Tilo Grosser, Olga G Troyanskaya +
+ +
+ Nature Genetics +   ·   + 27 Apr 2015 +   ·   + doi:10.1038/ng.3259 +
+ + +
+
+ +
+ + +
+ + + + + Adapting bioinformatics curricula for big data + + +
+ Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore +
+ +
+ Briefings in Bioinformatics +   ·   + 30 Mar 2015 +   ·   + doi:10.1093/bib/bbv018 +
+ + +
+
+ +
+ + +
+ + + + + Targeted exploration and analysis of large cross-platform human transcriptomic compendia + + +
+ Qian Zhu, Aaron K Wong, Arjun Krishnan, Miriam R Aure, Alicja Tadych, ..., Lars A Bongo, Vessela N Kristensen, Moses Charikar, Kai Li, Olga G Troyanskaya +
+ +
+ Nature Methods +   ·   + 12 Jan 2015 +   ·   + doi:10.1038/NMETH.3249 +
+ + +
+
+ +
+ + +
+ + + + + Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms + + +
+ J. Matthew Mahoney, Jaclyn Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield +
+ +
+ PLoS Computational Biology +   ·   + 08 Jan 2015 +   ·   + doi:10.1371/journal.pcbi.1004005 +
+ + +
+
+ +

2014

+ +
+ + +
+ + + + + Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study + + +
+ Jiang Gui, Walter Taylor, Jason H. Moore, Con Sullivan, Carol H. Kim, Casey S. Greene +
+ +
+ 2014 8th International Conference on Systems Biology (ISB) +   ·   + 01 Oct 2014 +   ·   + doi:10.1109/ISB.2014.6990733 +
+ + +
+
+ +
+ + +
+ + + + + Big Data Bioinformatics + + +
+ Casey S. Greene, Jie Tan, Matthew Ung, Jason H. Moore, Chao Cheng +
+ +
+ Journal of Cellular Physiology +   ·   + 27 Aug 2014 +   ·   + doi:10.1002/jcp.24662 +
+ + +
+
+ +
+ + +
+ + + + + Computational genetics analysis of grey matter density in Alzheimer’s disease + + +
+ Amanda L Zieselman, Jonathan M Fisher, Ting Hu, Peter C Andrews, Casey S Greene, Li Shen, Andrew J Saykin, Jason H Moore +
+ +
+ BioData Mining +   ·   + 22 Aug 2014 +   ·   + doi:10.1186/1756-0381-7-17 +
+ + +
+
+ +
+ + +
+ + + + + Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity + + +
+ Nadia M Penrod, Casey S Greene, Jason H Moore +
+ +
+ Genome Medicine +   ·   + 01 Jan 2014 +   ·   + doi:10.1186/gm550 +
+ + +
+
+ +

2013

+ +
+ + +
+ + + + + Defining cell-type specificity at the transcriptional level in human disease + + +
+ Wenjun Ju, Casey S. Greene, Felix Eichinger, Viji Nair, Jeffrey B. Hodgin, ..., Song Jiang, Maria Pia Rastaldi, Clemens D. Cohen, Olga G. Troyanskaya, Matthias Kretzler +
+ +
+ Genome Research +   ·   + 15 Aug 2013 +   ·   + doi:10.1101/gr.155697.113 +
+ + +
+
+ +
+ + +
+ + + + + LT-IIb(T13I), a Non-Toxic Type II Heat-Labile Enterotoxin, Augments the Capacity of a Ricin Toxin Subunit Vaccine to Evoke Neutralizing Antibodies and Protective Immunity + + +
+ Christopher J. Greene, Chrystal M. Chadwick, Lorrie M. Mandell, John C. Hu, Joanne M. O’Hara, Robert N. Brey, Nicholas J. Mantis, Terry D. Connell +
+ +
+ PLoS ONE +   ·   + 02 Aug 2013 +   ·   + doi:10.1371/journal.pone.0069678 +
+ + +
+
+ +
+ + +
+ + + + + Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes + + +
+ Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars A. Bongo, Rebecca D. Burdine, Olga G. Troyanskaya +
+ +
+ PLoS Computational Biology +   ·   + 14 Mar 2013 +   ·   + doi:10.1371/journal.pcbi.1002957 +
+ + +
+
+ +
+ + +
+ + + + + Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments + + +
+ Jie Tan, Gavin D. Grant, Michael L. Whitfield, Casey S. Greene +
+ +
+ Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics +   ·   + 01 Jan 2013 +   ·   + doi:10.1007/978-3-642-37189-9_2 +
+ + +
+
+ +

2012

+ +
+ + +
+ + + + + Chapter 2: Data-Driven View of Disease Biology + + +
+ Casey S. Greene, Olga G. Troyanskaya +
+ +
+ PLoS Computational Biology +   ·   + 27 Dec 2012 +   ·   + doi:10.1371/journal.pcbi.1002816 +
+ + +
+
+ +
+ + +
+ + + + + IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks + + +
+ Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars A. Bongo, Yuanfang Guan, Olga G. Troyanskaya +
+ +
+ Nucleic Acids Research +   ·   + 07 Jun 2012 +   ·   + doi:10.1093/nar/gks458 +
+ + +
+
+ +
+ + +
+ + + + + Accurate evaluation and analysis of functional genomics data and methods + + +
+ Casey S. Greene, Olga G. Troyanskaya +
+ +
+ Annals of the New York Academy of Sciences +   ·   + 23 Jan 2012 +   ·   + doi:10.1111/j.1749-6632.2011.06383.x +
+ + +
+
+ +

2011

+ +
+ + +
+ + + + + Evolving hard problems: Generating human genetics datasets with a complex etiology + + +
+ Daniel S Himmelstein, Casey S Greene, Jason H Moore +
+ +
+ BioData Mining +   ·   + 07 Jul 2011 +   ·   + doi:10.1186/1756-0381-4-21 +
+ + +
+
+ +
+ + +
+ + + + + PILGRM: an interactive data-driven discovery platform for expert biologists + + +
+ C. S. Greene, O. G. Troyanskaya +
+ +
+ Nucleic Acids Research +   ·   + 07 Jun 2011 +   ·   + doi:10.1093/nar/gkr440 +
+ + +
+
+ +
+ + +
+ + + + + An Open-Ended Computational Evolution Strategy for Evolving Parsimonious Solutions to Human Genetics Problems + + +
+ Casey S. Greene, Douglas P. Hill, Jason H. Moore +
+ +
+ Advances in Artificial Life. Darwin Meets von Neumann +   ·   + 01 Jan 2011 +   ·   + doi:10.1007/978-3-642-21283-3_39 +
+ + +
+
+ +
+ + +
+ + + + + An Analysis of New Expert Knowledge Scaling Methods for Biologically Inspired Computing + + +
+ Jason M. Gilmore, Casey S. Greene, Peter C. Andrews, Jeff Kiralis, Jason H. Moore +
+ +
+ Advances in Artificial Life. Darwin Meets von Neumann +   ·   + 01 Jan 2011 +   ·   + doi:10.1007/978-3-642-21314-4_36 +
+ + +
+
+ +

2010

+ +
+ + +
+ + + + + Integrative Systems Biology for Data-Driven Knowledge Discovery + + +
+ Casey S. Greene, Olga G. Troyanskaya +
+ +
+ Seminars in Nephrology +   ·   + 01 Sep 2010 +   ·   + doi:10.1016/j.semnephrol.2010.07.002 +
+ + +
+
+ +
+ + +
+ + + + + Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units + + +
+ Nicholas A. Sinnott-Armstrong, Casey S. Greene, Jason H. Moore +
+ +
+ Proceedings of the 12th annual conference on Genetic and evolutionary computation +   ·   + 07 Jul 2010 +   ·   + doi:10.1145/1830483.1830523 +
+ + +
+
+ +
+ + +
+ + + + + Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS + + +
+ Casey S. Greene, Nicholas A. Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, Brent T. Harris +
+ +
+ Bioinformatics +   ·   + 16 Jan 2010 +   ·   + doi:10.1093/bioinformatics/btq009 +
+ + +
+
+ +

2009

+ +
+ + +
+ + + + + Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions + + +
+ Casey S Greene, Nadia M Penrod, Jeff Kiralis, Jason H Moore +
+ +
+ BioData Mining +   ·   + 22 Sep 2009 +   ·   + doi:10.1186/1756-0381-2-5 +
+ + +
+
+ +
+ + +
+ + + + + Accelerating epistasis analysis in human genetics with consumer graphics hardware + + +
+ Nicholas A Sinnott-Armstrong, Casey S Greene, Fabio Cancare, Jason H Moore +
+ +
+ BMC Research Notes +   ·   + 24 Jul 2009 +   ·   + doi:10.1186/1756-0500-2-149 +
+ + +
+
+ +
+ + +
+ + + + + Environmental noise improves epistasis models of genetic data discovered using a computational evolution system + + +
+ Casey S. Greene, Douglas P. Hill, Jason H. Moore +
+ +
+ Proceedings of the 11th Annual conference on Genetic and evolutionary computation +   ·   + 08 Jul 2009 +   ·   + doi:10.1145/1569901.1570160 +
+ + +
+
+ +
+ + +
+ + + + + Failure to Replicate a Genetic Association May Provide Important Clues About Genetic Architecture + + +
+ Casey S. Greene, Nadia M. Penrod, Scott M. Williams, Jason H. Moore +
+ +
+ PLoS ONE +   ·   + 02 Jun 2009 +   ·   + doi:10.1371/journal.pone.0005639 +
+ + +
+
+ +
+ + +
+ + + + + Sensible initialization using expert knowledge for genome-wide analysis of epistasis using genetic programming + + +
+ Casey S. Greene, Bill C. White, Jason H. Moore +
+ +
+ 2009 IEEE Congress on Evolutionary Computation +   ·   + 01 May 2009 +   ·   + doi:10.1109/CEC.2009.4983093 +
+ + +
+
+ +
+ + +
+ + + + + Nature-inspired algorithms for the genetic analysis of epistasis in common human diseases: Theoretical assessment of wrapper vs. filter approaches + + +
+ Casey S. Greene, Jeff Kiralis, Jason H. Moore +
+ +
+ 2009 IEEE Congress on Evolutionary Computation +   ·   + 01 May 2009 +   ·   + doi:10.1109/CEC.2009.4983027 +
+ + +
+
+ +
+ + +
+ + + + + Development and evaluation of an open-ended computational evolution system for the creation of digital organisms with complex genetic architecture + + +
+ Anna L. Tyler, Bill C. White, Casey S. Greene, Peter C. Andrews, Richard Cowper-Sa, Jason H. Moore +
+ +
+ 2009 IEEE Congress on Evolutionary Computation +   ·   + 01 May 2009 +   ·   + doi:10.1109/CEC.2009.4983308 +
+ + +
+
+ +
+ + +
+ + + + + Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease + + +
+ Casey S. Greene, Jason M. Gilmore, Jeff Kiralis, Peter C. Andrews, Jason H. Moore +
+ +
+ Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics +   ·   + 01 Jan 2009 +   ·   + doi:10.1007/978-3-642-01184-9_9 +
+ + +
+
+ +

2008

+ +
+ + +
+ + + + + Ability of epistatic interactions of cytokine single‐nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patients + + +
+ Lorenzo Beretta, Francesca Cappiello, Jason H. Moore, Morena Barili, Casey S. Greene, Raffaella Scorza +
+ +
+ Arthritis & Rheumatism +   ·   + 15 Jul 2008 +   ·   + doi:10.1002/art.23836 +
+ + +
+
+ +
+ + +
+ + + + + Solving complex problems in human genetics using GP + + +
+ Casey S. Greene, Jason H. Moore +
+ +
+ ACM SIGEVOlution +   ·   + 01 Jul 2008 +   ·   + doi:10.1145/1527063.1527064 +
+ + +
+
+ +

2006

+ +
+ + +
+ + + + + LTR Retrotransposon-Gene Associations in Drosophila melanogaster + + +
+ Eric W. Ganko, Casey S. Greene, Judson A. Lewis, Vikram Bhattacharjee, John F. McDonald +
+ +
+ Journal of Molecular Evolution +   ·   + 01 Jan 2006 +   ·   + doi:10.1007/s00239-004-0312-4 +
+ + +
+
+ +

+ +
+ + +
+ + + + + Relief-based bioinformatics methods for the analysis of epistasis in genetic association studies. + + +
+ Casey Stephen. Greene +
+ +
+ Dartmouth College Library Press +   ·   + [no date info] +   ·   + doi:10.1349/ddlp.303 +
+ + +
+
+ +
+ + +
+ + + + + Ant Colony Optimization for Genome-Wide Genetic Analysis + + +
+ Casey S. Greene, Bill C. White, Jason H. Moore +
+ +
+ Ant Colony Optimization and Swarm Intelligence +   ·   + [no date info] +   ·   + doi:10.1007/978-3-540-87527-7_4 +
+ + +
+
+ +
+ + +
+ + + + + Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms Requires Strategies which Exploit Domain-Specific Knowledge + + +
+ Casey S. Greene, Jason H. Moore +
+ +
+ Nature-Inspired Informatics for Intelligent Applications and Knowledge Discovery +   ·   + [no date info] +   ·   + doi:10.4018/978-1-60566-705-8.ch007 +
+ + +
+
+ +
+ + +
+ + + + + pendingpublications + + +
+ [no author info] +
+ +
+ [no publisher info] +   ·   + [no date info] +   ·   + doi:10.1093/gigascience/giae001 +
+ + +
+
+ +

+ +
+ + +
+ + + + + [no title info] + + +
+ [no author info] +
+ +
+ [no publisher info] +   ·   + [no date info] +   ·   + doi:10.1007/978-3-642-12211-8-16 +
+ + +
+
+ +
+ + +
+ + + + + [no title info] + + +
+ [no author info] +
+ +
+ [no publisher info] +   ·   + [no date info] +   ·   + doi:10.1007/978-3-642-12211-8-17 +
+ + +
+
+ +
+ + +
+ + + + + [no title info] + + +
+ [no author info] +
+ +
+ [no publisher info] +   ·   + [no date info] +   ·   + doi:10.1007/978-3-642-12211-8-7 +
+ + +
+
+ + +
+ + + + + + + +

+ + Search for Casey Greene's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/daniel-himmelstein.html b/preview/pr-117/members/daniel-himmelstein.html new file mode 100644 index 00000000..3576df91 --- /dev/null +++ b/preview/pr-117/members/daniel-himmelstein.html @@ -0,0 +1,891 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Daniel Himmelstein | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
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+ + + +
+ + + + + + + + + +
+ + + + + + + + + +
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+ +
+ + +
+ + +

Daniel joined the Greene Lab as a Postdoctoral Researcher in June 2016, after receiving his PhD in Biological & Medical Informatics at UCSF. +He uses hetnets — networks with multiple types of nodes and relationship — to integrate and learn from the past several decades of biomedical research. +All of Daniel’s research is entirely open: openly licensed and immediately available. +Check out his GitHub to follow his recent work. +Daniel also performs many data science projects designed to make science more open and hence productive.

+ + + + + + +

+ + Search for Daniel Himmelstein's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/david-nicholson.html b/preview/pr-117/members/david-nicholson.html new file mode 100644 index 00000000..733dfc57 --- /dev/null +++ b/preview/pr-117/members/david-nicholson.html @@ -0,0 +1,877 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +David Nicholson | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
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+ + + +
+ + + + + + + + + +
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+ +
+ + +
+ + +

David is a rising 6th year Ph.D. candidate at the Unversity of Pennsylvania (Penn) in the Genomics and Computational Biology program. +He utilizes Deep Learning and Natural Language Processing techniques to analyze biomedical text. +At Penn, he joined the Greenelab in 2017 and was appointed as a trainee on the T32 Computational Genomics training grant from the National Human Genome Research Institute (NHGRI). +He has presented at the International Society for Computational Biology (ISCB) Rocky Mountain Bioinformatics conference, Cold Spring Harbor’s Biological Data Science Symposium, and was invited to speak at Elsevier’s Labs Online Lecture series. +He graduated from the University of Maryland Baltimore County (UMBC) with a B.S. degree in Computer Science and a minor in Bioinformatics. +During his time at UMBC, he was a part of the Meyerhoff Scholars program (M23) and was appointed as a Marc U*Star Scholar. +While he is not working in the lab, he spends his time investing in the stock/crypto market and playing on his PS4 or Nintendo Switch Lite. +As he advances towards the end of his Ph.D. journey, he seeks to become a data scientist where he can continue to improve and use his analytical skills.

+ + + + + + +

+ + Search for David Nicholson's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/dongbo-hu.html b/preview/pr-117/members/dongbo-hu.html new file mode 100644 index 00000000..87a483dd --- /dev/null +++ b/preview/pr-117/members/dongbo-hu.html @@ -0,0 +1,821 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Dongbo Hu | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
+ +
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+ + + +
+ + + + + + + + + +
+ + + + + + + + + +
+ +
+ + +
+ + +

Dongbo used to be a chemist but was eventually attracted into computer science because of its elegance. +Before taking this position, he worked in the Neurology Department of Penn’s hospital, Penn’s Genetics Department and at a local financial firm. +In the Greene lab, he is working on the ADAGE web server.

+ + + + + + +

+ + Search for Dongbo Hu's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/doodle.html b/preview/pr-117/members/doodle.html new file mode 100644 index 00000000..331b7397 --- /dev/null +++ b/preview/pr-117/members/doodle.html @@ -0,0 +1,786 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Doodle | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+ + + +

Doodle is Jie’s toy poodle. Despite weighting less than 10lbs, he is an accomplished high jumper and routinely reaches altitudes of three feet while leaping. +As of Jie’s thesis defense and graduation (Spring, 2017) he has become a lab alum.

+ + + + + + +

+ + Search for Doodle's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/greg-way.html b/preview/pr-117/members/greg-way.html new file mode 100644 index 00000000..799a56c2 --- /dev/null +++ b/preview/pr-117/members/greg-way.html @@ -0,0 +1,824 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Greg Way | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ +
+ + + + + + + + + + + + + +
+ + + +

Greg was a Ph.D. candidate in the Greene Lab through Penn’s Genomics and Computational Biology (GCB) PhD program. +Greg graduated from The College of New Jersey in 2011 with a B.S. in Biology and from Saint Joseph’s University in 2014 with an M.S. in Biology. +He joined the lab in 2015 at Dartmouth and transferred with Casey to Penn. +At Penn, he was awarded a T32 Training Grant. +He has published papers on supervised methods to detect glioblastoma tumors with NF1 inactivation, and unsupervised deep learning methods to aggregate pan-cancer gene expression features. +His goal is to improve outcomes for cancer patients through the development of methods that help unravel the complexity of cancer.

+ + + + + + +

+ + Search for Greg Way's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/halie-rando.html b/preview/pr-117/members/halie-rando.html new file mode 100644 index 00000000..54ebaf31 --- /dev/null +++ b/preview/pr-117/members/halie-rando.html @@ -0,0 +1,857 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Halie Rando | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+
+ + + +
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+ + + + + + + + + +
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+ +
+ + +
+ + +

Halie was a postdoctoral researcher in the Greene Lab from 2020 to 2023. +Her work focused on expanding Manubot for the synthesis of information related to the COVID-19 pandemic. +Prior to joining the Greene Lab, she received her PhD in 2019 from the Illinois Informatics Institute at the University of Illinois - Urbana-Champaign, where she studied the genome structure of canids and the evolutionary genomics of behavior in the Russian Farm Fox Experiment. +Since July 2023, Halie has been an assistant professor in the Department of Computer Science at Smith College conducting research in veterinary and biological informatics. +Her lab’s current work can be found on GitHub.

+ + + + + + +

+ + Search for Halie Rando's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/irene-song.html b/preview/pr-117/members/irene-song.html new file mode 100644 index 00000000..c7da4e56 --- /dev/null +++ b/preview/pr-117/members/irene-song.html @@ -0,0 +1,787 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Irene Song | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + +

Irene is a Biomedical Engineering major and Statistics minor at Dartmouth College. +As a member of the Greene lab, she performed a network-based analysis of genetic variants associated with Alzheimer’s disease endophenotypes. +Her long-term goal is to apply her STEM background to improving people’s health and well-being.

+ + + + + + +

+ + Search for Irene Song's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/jaclyn-taroni.html b/preview/pr-117/members/jaclyn-taroni.html new file mode 100644 index 00000000..a7f62281 --- /dev/null +++ b/preview/pr-117/members/jaclyn-taroni.html @@ -0,0 +1,839 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Jaclyn Taroni | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
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Jaclyn joined the Greene Lab as a Postdoctoral Researcher in May 2016. +She is currently interested in integrating large amounts of publicly available data and utilizing unsupervised machine learning to answer big outstanding in the fields of rheumatology, autoimmunity, and in rare diseases in particular. +She works in close collaboration with clinicians and biologists who are experts in these disorders and she is currently appointed to Penn Rheumatology’s T32. +Before coming to Penn, Jaclyn received her PhD from the Molecular and Cellular Biology program at Dartmouth where she studied the rare autoimmune disease systemic sclerosis with Michael Whitfield and where she was awarded the John H. Copenhaver, Jr. and William H. Thomas, MD 1952 Fellowship.

+ + + + + + +

+ + Search for Jaclyn Taroni's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/jake-crawford.html b/preview/pr-117/members/jake-crawford.html new file mode 100644 index 00000000..5f455efb --- /dev/null +++ b/preview/pr-117/members/jake-crawford.html @@ -0,0 +1,873 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Jake Crawford | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Jake is a Ph.D. student in the Greene Lab through Penn’s Genomics and Computational Biology (GCB) program. +He graduated from Tufts University with a B.S. in Biology in 2012, and received an M.S. in Computer Science from Tufts in 2017. +Before coming to Penn, he spent a year at Microsoft Research New England as a research assistant in computational biology and machine learning. +Jake is interested in using machine learning models of gene expression data to better understand cancer signaling pathways.

+ + + + + + +

+ + Search for Jake Crawford's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/jie-tan.html b/preview/pr-117/members/jie-tan.html new file mode 100644 index 00000000..5521a315 --- /dev/null +++ b/preview/pr-117/members/jie-tan.html @@ -0,0 +1,807 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Jie Tan | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Jie was a Ph.D. student in Dartmouth’s Molecular and Cellular Biology program. +She is originally from Qingdao, China and graduated from Zhejiang University with a B.A in Biotechnology in 2012. +She joined the Integrative Genomics Lab in the summer of 2013. +She has published papers on the analysis of time-series data for functional network construction, rule compaction for learning classifier systems, and unsupervised feature construction methods for genomic data. +Jie has also been awarded a Neukom Graduate Fellowship. +She is currently a data scientist at Kaleido Biosciences in Cambridge, MA.

+ + + + + + +

+ + Search for Jie Tan's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/kathy-chen.html b/preview/pr-117/members/kathy-chen.html new file mode 100644 index 00000000..2c2d08b8 --- /dev/null +++ b/preview/pr-117/members/kathy-chen.html @@ -0,0 +1,790 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Kathy Chen | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Kathy was an undergraduate at the University of Pennsylvania studying Biochemistry and Computer Science. +She joined the Greene lab to learn more about the intersection of her two majors. +Kathy’s project involved the identification of pathway-pathway relationships from genomic “big data” using patterns extracted by deep learning techniques. +She was a co-author on a manuscript in Cell Systems describing the eADAGE method and the primary author of a manuscript describing the PathCORE software that she developed. +Currently, she is a data scientist at the Simons Foundation. +She plans to continue developing and applying computational algorithms to address key challenges in the life sciences.

+ + + + + + +

+ + Search for Kathy Chen's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/kurt-wheeler.html b/preview/pr-117/members/kurt-wheeler.html new file mode 100644 index 00000000..38b72f41 --- /dev/null +++ b/preview/pr-117/members/kurt-wheeler.html @@ -0,0 +1,805 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Kurt Wheeler | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Kurt graduated from Drexel University in 2014 with a B.S. in Computer Science. +After working at a tech startup on a Business Intelligence tool for a couple years he decided to try and make a greater impact with his software skills. +He found the Greene Lab and has been happily creating software for researchers since. +Kurt values clean maintainable code, scalable engineering, and ultimately making software that is useful to researchers answering important questions.

+ + + + + + +

+ + Search for Kurt Wheeler's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/lamonica-shinholster.html b/preview/pr-117/members/lamonica-shinholster.html new file mode 100644 index 00000000..326918ce --- /dev/null +++ b/preview/pr-117/members/lamonica-shinholster.html @@ -0,0 +1,789 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Lamonica Shinholster | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Lamonica is a senior majoring in biology with a minor in chemistry at Mercer University. +Her research interests include antibiotic resistance, drug design, and public health. +Her previous research projects included synthesizing and testing novel biofilm inhibitors. +In the Greene lab she summarized literature related to infection and immunity for a broad review of the COVID-19 literature. +Her long-term goals include attending medical school to become a physician.

+ + + + + + +

+ + Search for Lamonica Shinholster's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/magnus.html b/preview/pr-117/members/magnus.html new file mode 100644 index 00000000..5f2f0370 --- /dev/null +++ b/preview/pr-117/members/magnus.html @@ -0,0 +1,786 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Magnus | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Magnus joined the team of mascots in 2014. +He holds world records for both number and scale of pillows crushed.

+ + + + + + +

+ + Search for Magnus's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/matt-hyuck.html b/preview/pr-117/members/matt-hyuck.html new file mode 100644 index 00000000..31ce9b73 --- /dev/null +++ b/preview/pr-117/members/matt-hyuck.html @@ -0,0 +1,808 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Matt Hyuck | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Matt has been translating questions posed by biologists and businesses into software that computers can contemplate for over 20 years. +He earned his Bachelor’s Degree in Applied and Engineering Physics at Cornell University at the same time the Human Genome Project was getting underway. +He has a broad and deep background in using and developing complex computer software. +As a Project Manager for diverse consulting clients, he developed a specialty for systems integration. +He also has worked as a programmer and data analyst in an array of academic settings, including the MIRAGE Alzheimer Disease project at Boston University Medical Center and as a member of the Harvard Computational Biology Initiative, where he played an integral role in creating innovative visual displays of gene networks that became Autworks. +His research interests include visualization of information and human-computer interaction as applied to complex data sets. +At the Greene Lab, he enjoys the challenge of making novel research methods available and useful to a broader audience of biologists

+ + + + + + +

+ + Search for Matt Hyuck's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/michael-zietz.html b/preview/pr-117/members/michael-zietz.html new file mode 100644 index 00000000..fc300978 --- /dev/null +++ b/preview/pr-117/members/michael-zietz.html @@ -0,0 +1,806 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Michael Zietz | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Michael was an undergraduate at Penn who worked in the Greene Lab. +He graduated in May 2019 with bachelor’s and master’s degrees in Physics through the Vagelos Scholars Program in Molecular Life Science, an intensive research-focused undergraduate program in the Chemistry Department. +He began a Ph.D. in Biomedical Informatics at Columbia University in the fall of 2019. +Michael started working in the Greene Lab with Daniel in 2017. +He developed tools for graph traversal within hetnets and completed a network permutation project.

+ + + + + + +

+ + Search for Michael Zietz's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/milton-pividori.html b/preview/pr-117/members/milton-pividori.html new file mode 100644 index 00000000..41b9b098 --- /dev/null +++ b/preview/pr-117/members/milton-pividori.html @@ -0,0 +1,874 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Milton Pividori | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Milton joined the GreeneLab in 2020 as a postdoctoral researcher. +He received his Ph.D. in Information Systems Engineering in 2016 from Universidad Tecnológica Nacional (Argentina) and the Research Institute for Signals, Systems, and Computational Intelligence. +Milton’s research focuses on machine learning and its application to bioinformatics and genetic medicine. +He is currently an Assistant Professor in the Department of Biomedical Informatics at the University of Colorado Anschutz Medical Campus. +His research and work can be found in the Pividori Lab website and GitHub.

+ + + + + + +

+ + Search for Milton Pividori's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/mulin-xiong.html b/preview/pr-117/members/mulin-xiong.html new file mode 100644 index 00000000..9b957787 --- /dev/null +++ b/preview/pr-117/members/mulin-xiong.html @@ -0,0 +1,790 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Mulin Xiong | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Mulin was a Biology major and AMES minor on the premed track at Dartmouth College. +Mulin’s senior project sat at the intersection of computational and wet-bench techniques, which she used to study Pseudomonas aeruginosa. +This opportunistic human pathogen readily forms biofilms and is difficult to treat. +In the Greene lab, Mulin developed and applied new computational approaches to analyze the antibiotic response of Pseduomonas aeruginosa, and, in the Hogan lab, she measured this response to test her computational approach. +Mulin is currently working in clinical research lab in Rochester, New York. +In this lab she is focused on bringing specialized care to patients with movement disorders (such as Parkinson’s and Huntington’s) using telemedicine.

+ + + + + + +

+ + Search for Mulin Xiong's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/myshkin.html b/preview/pr-117/members/myshkin.html new file mode 100644 index 00000000..9d4a7e70 --- /dev/null +++ b/preview/pr-117/members/myshkin.html @@ -0,0 +1,787 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Myshkin | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Myshkin is Greg’s cat. +He has a fiery personality and a zest for life. +When he’s not computing neural network gradients, you can find him napping in the sun.

+ + + + + + +

+ + Search for Myshkin's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/natalie-davidson.html b/preview/pr-117/members/natalie-davidson.html new file mode 100644 index 00000000..c76a82e4 --- /dev/null +++ b/preview/pr-117/members/natalie-davidson.html @@ -0,0 +1,874 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Natalie Davidson | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Natalie is a postdoctoral researcher who joined the GreeneLab in 2020. +She received her PhD in Computational Biology and Medicine in 2019 from the Tri-Institutional Program for Computational Biology and Medicine in New York while conducting research at ETH Zürich’s Biomedical Informatics Lab. +During her PhD, she participated in the International Cancer Genome Consortium where she performed integrative analyses across multiple transcriptional aberrations to identify cancer relevant genes and alteration patterns.

+ +

Building upon her previous experience in analyzing large cancer cohorts, she aims to leverage freely availble datasets and integrate them with single-patient -omic data to help guide precision oncology.

+ + + + + + +

+ + Search for Natalie Davidson's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/olivia-cheng.html b/preview/pr-117/members/olivia-cheng.html new file mode 100644 index 00000000..1ec0381e --- /dev/null +++ b/preview/pr-117/members/olivia-cheng.html @@ -0,0 +1,822 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Olivia Cheng | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Olivia is a junior at Penn majoring in Mathematics and minoring in Computer Science. +She works on mining large datasets for associations between gene patterns and diseases. +She hopes to use math and code to contribute to discoveries that will improve people’s lives. +Apart from school and the lab, Olivia is an amateur speedcuber and a crossword enthusiast.

+ + + + + + +

+ + Search for Olivia Cheng's papers on the Research page + +

+ + + + +
+ + +
+ + + + + + + diff --git a/preview/pr-117/members/qiwen-hu.html b/preview/pr-117/members/qiwen-hu.html new file mode 100644 index 00000000..5a2d23a4 --- /dev/null +++ b/preview/pr-117/members/qiwen-hu.html @@ -0,0 +1,822 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Qiwen Hu | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Qiwen was Postdoctoral Researcher at the University of Pennsylvania Perelman School of Medicine. +She received her PhD in Bioinformatics from North Carolina State University in 2016, where she studied translational regulation in plant genomes. +She developed machine learning and statistical approaches based on high-throughput sequencing datasets to identify regulatory elements that affect transcription and translation. +Qiwen joined the Greene Lab in 2017. Her research interests focus on integration of different types of high-throughput sequencing data to identify meaningful biological patterns, key transcriptional regulators related to drug addiction and chromatin-regulated alternative splicing using computational approaches. She is currently working at Bristol Myers Squibb, department of informatics & predictive sciences, developing computational methods for cell responses through single-cell and bulk measurements.

+ + + + + + +

+ + Search for Qiwen Hu's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/rene-zelaya.html b/preview/pr-117/members/rene-zelaya.html new file mode 100644 index 00000000..53d3b63a --- /dev/null +++ b/preview/pr-117/members/rene-zelaya.html @@ -0,0 +1,790 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +René Zelaya | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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René graduated in 2012 with a B.A. in Engineering Sciences from Dartmouth College. +He started working as a programmer in the Integrative Genomics Lab during the spring of 2013. +His primary mission is to put our research advances into the hands of biologists. +He works with users to understand how we can make their lives easier through accessible computation. +He translates these conversations, in the context of our machine learning advances, into functionality embedded in webservers such as GIANT and Tribe that address key biological challenges. +René also managed the code review process in the lab, to keep the group thinking about both design and documentation principles.

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+ + Search for René Zelaya's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/roshan-ravishankar.html b/preview/pr-117/members/roshan-ravishankar.html new file mode 100644 index 00000000..61e02d92 --- /dev/null +++ b/preview/pr-117/members/roshan-ravishankar.html @@ -0,0 +1,787 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Roshan Ravishankar | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Roshan was a senior in the Life Sciences and Management program at Penn studying mathematical biology and statistics. +He is especially interested in studying the interactions between biology, mathematics, statistics, and other related areas. +His project involved building an ADAGE model to analyze gene expression in kidney biopsies.

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+ + Search for Roshan Ravishankar's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/sophie.html b/preview/pr-117/members/sophie.html new file mode 100644 index 00000000..ba704867 --- /dev/null +++ b/preview/pr-117/members/sophie.html @@ -0,0 +1,787 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Sophie | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Sophie is a bichon-poodle-shih tzu mix. +Her research focus is on machine learning for dog breed identification. +Sophie joined the team in 2013.

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+ + Search for Sophie's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/steven-foltz.html b/preview/pr-117/members/steven-foltz.html new file mode 100644 index 00000000..bacd1312 --- /dev/null +++ b/preview/pr-117/members/steven-foltz.html @@ -0,0 +1,837 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Steven Foltz | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Steven was a postdoctoral researcher who worked with the Childhood Cancer Data Lab and the Greene Lab from 2020-2023. +He received his PhD in 2020 after studying computational cancer genomics with Li Ding at Washington University in St. Louis.

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+ + Search for Steven Foltz's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/taylor-reiter.html b/preview/pr-117/members/taylor-reiter.html new file mode 100644 index 00000000..2567b96f --- /dev/null +++ b/preview/pr-117/members/taylor-reiter.html @@ -0,0 +1,874 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Taylor Reiter | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Taylor joined the GreeneLab in 2022. +Her work was supported by the Computational Bioscience Program’s T15 through the NIH NLM. +She received her PhD in Food Science in 2020 from UC Davis under the mentorship of Drs. C. Titus Brown and Ben Montpetit where she developed new methods to find hidden patterns in microbial sequencing data. +She used publicly availble RNA-seq data to improve functional inference from metatranscriptomes. +After leaving the GreeneLab, she became a Data Scientist at Arcadia Science.

+ + + + + + +

+ + Search for Taylor Reiter's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/tesla.html b/preview/pr-117/members/tesla.html new file mode 100644 index 00000000..a6bb2589 --- /dev/null +++ b/preview/pr-117/members/tesla.html @@ -0,0 +1,786 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Tesla | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Tesla is Jaclyn’s pineapple green-cheeked conure. +His interests include genome-scale gene expression data and papaya.

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+ + Search for Tesla's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/timothy-chang.html b/preview/pr-117/members/timothy-chang.html new file mode 100644 index 00000000..abae4d4c --- /dev/null +++ b/preview/pr-117/members/timothy-chang.html @@ -0,0 +1,787 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Timothy Chang | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Timothy was an undergraduate at the University of Pennsylvania who studied Biochemistry, Finance, and Operations and Information Management. +He found the Greene Lab through the intersection of his majors and interests: biological systems, information systems, and computer science. +Timothy worked on integrating genomic data and computational methods towards strengthening our understanding on cancer and other diseases.

+ + + + + + +

+ + Search for Timothy Chang's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/vincent-rubinetti.html b/preview/pr-117/members/vincent-rubinetti.html new file mode 100644 index 00000000..fe7aaf40 --- /dev/null +++ b/preview/pr-117/members/vincent-rubinetti.html @@ -0,0 +1,873 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Vincent Rubinetti | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Vince is a staff frontend developer in the Greene Lab. +His job is to take the studies, projects, and ideas of his colleagues and turn them into beautiful, dynamic, fully-realized web applications. +His work includes app development, website development, UI/UX design, logo design, and anything else visual or creative. +Outside of the lab, Vince is a freelance music composer for indie video games and the YouTube channel 3Blue1Brown.

+ + + + + + +

+ + Search for Vincent Rubinetti's papers on the Research page + +

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+ + + + + + + diff --git a/preview/pr-117/members/yoson.park.html b/preview/pr-117/members/yoson.park.html new file mode 100644 index 00000000..66b5cded --- /dev/null +++ b/preview/pr-117/members/yoson.park.html @@ -0,0 +1,804 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Yoson Park | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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YoSon joined the Greene Lab as a Postdoctoral Researcher in 2018. +She graduated from University of Miami with a PhD in Human Genetics and Genomics with a focus on statistical and computational methods development for large scale genomic data analyses. +She works on building a platform for the community-driven causal inference using publicly available summary statistics and developing a tool to study biologically meaningful network graphs.

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+ + Search for Yoson Park's papers on the Research page + +

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New technologies allow researchers to extensively profile biological systems, and researchers have embraced these technologies. Anyone can download more than 1.9 million genome-wide assays from Array Express, a repository of such data. Now the challenge is to understand what these data reveal about underlying biology. We develop and apply methods that extract biological principles from these data, and we train the next generation of biological data scientists.

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Lab Highlights

Keep up with our latest papers, grants, and webservers.

Recent News →

Meet our group

We're a team of enthusiastic scientists who aim to bring big data to every biology lab.

Meet Us →


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+ + /collaborators + Collaborators + Sun, 09 Aug 2015 14:01:59 +0000 + Many aspects of our research are made possible through ongoing strong collaborations with outstanding research groups around the world.

Personalized Medicine

Yoli Sanchez

Kerry Smith

Camilo Fadul

Greg Tsongalis

Ovarian Cancer

Uganda Cancer Institute

Jen Doherty

Laura Tafe

Evelyn Flemming

Deep Learning of Microbial Regulatory Programs

Deb Hogan

Aging and Memory

Gio Bosco

Gene Function Prediction

Iddo Friedberg

Pedja Radivojac

Sean Mooney

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+ + /news + News + Sun, 09 Aug 2015 14:10:00 +0000 + Keep up with our lab news by following @GreeneLab on Twitter.

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+ news + page + 2 + publish +
+ + /research + Research + Wed, 28 Sep 2016 18:45:07 +0000 + tl;dr: There's a lot of public data about biological systems under various perturbations. But they are also noisy. Our lab develops algorithms that integrate that data to model complex biological systems. We do this because we want to understand how biological systems work. This way when we need to intervene to improve health we aren't taking a shot in the dark. We recognize that our lab won't have all the answers, or even all of the questions, so we develop systems that any biologist can use.

Overview

Right now anyone can download genome-wide measurements from more than 2 million assays of diverse physiological conditions. We develop and apply computational methods that analyze these large and heterogeneous data compendia to provide a data-driven lens into pathways, cell-lineages, diseases, and other biological systems of interest.

Our projects are grouped into three major areas:

  • new algorithms for noisy data,
  • improving the accessibility of data and methods,
  • and applications that span from basic biology to precision treatments for human diseases.

Members of our lab work on specific research questions related to these topics, and frequently find that their research eventually touches on more than one of these core areas. We have a strong commitment to open and reproducible science: our webservers are freely available and our code is released under open source licenses on github and bitbucket.

Our work is funded by grants from the National Science Foundation (NSF), the Gordon and Betty Moore Foundation, and the Cystic Fibrosis Foundation. In the past we have received funding from the Norris Cotton Cancer Center and the American Cancer Society.

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+ Our recent research, compressed into sketch form by  YoSon Park &nbsp;during the 2016  #PennGenRetreat . +
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Our recent research, compressed into sketch form by YoSon Park during the 2016 #PennGenRetreat.

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Algorithms for noisy public data

The goal of this aim is to develop algorithms that can integrate data across multiple experiments and platforms to capture useful biological patterns. We develop both supervised and unsupervised approaches. We focus on supervised methods when we know precisely what question we’d like to answer and unsupervised methods for discovery-oriented projects

We’ve developed supervised methods that address key biological challenges related to genes’ developmental roles, tissue-specific expression, and tissue-specific function. We’ve developed unsupervised methods to identify the key biological patterns in cancer and microbial genomics data.

Many of our methods are based on “deep learning” approaches. These techniques are trendy right now. However, we adapt them because the denoising autoencoder framing works well on the types of data that we deal with, i.e. noisy data. We were the first to apply these methods to genomic data integration, and we have found them to be particularly robust to cross-dataset noise. Our recent work has also demonstrated that these methods can be broadly applied, e.g. to electronic health records.

In summary, we develop robust machine learning based approaches. Our methods perform well in many contexts, and we continue to devise new strategies to tackle pressing biomedical challenges.

Reproducible "big data" analysis for everyone

We don’t feel that it’s enough to develop an algorithm and publish a one-off paper demonstrating “good” performance. We want to see these methods used by the wettest molecular biologists and the driest bioinformaticians.

Our driving principle is that “big data” analysis should be as routinely used in biological labs as common wet-bench techniques such as PCR. But we’re not willing to wait the many years required for molecular biology training programs to refocus on providing their students with these capabilities. Instead, we develop robust webservers that provide molecular labs with these analytical capabilities.

For primarily computational researchers, we make our source code available and develop techniques that make such research routinely reproducible. For example, we have repurposed continuous integration systems for scientific analysis. We use these in our own work and we have described how others can employ them. These methods ensure that analyses can be reproduced from start to finish in a new computing environment with little effort on the part of the researcher.

APPLICATIONs from basic biology to human disease

The methods that we develop are grounded in biology. We focus relatively little effort on improving traditional performance metrics such as cross-validated AUC and accuracy. Our own work and the work of many others has demonstrated the limits of such evaluations. In short: the biases present in how scientific discovery proceeds render these analyses fraught with peril at best. Instead, we aim to validate findings where the scientific rubber meets the road: in new experiments designed to perturb the system.

We’ve worked on zebrafish development, bacterial responses to the environment, cancer genomics data, hypertension, Alzheimer’s disease, nephrotic syndromes, and many other areas. We choose to focus where can partner with biologists who will engage in the process of discovery and, when the time comes, test predictions from our methods.

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+ + /publications + Publications + Fri, 10 Jul 2020 17:26:33 +0000 + Recent Preprints

Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Correcting for experiment-specific variability in expression compendia can remove underlying signals. bioRxiv. [GitHub]

Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, et al. The importance of transparency and reproducibility in artificial intelligence research. arXiv.

Cousminer DL, Wagley Y, Pippin J, Elhakeem A, Way GP, et al. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping. bioRxiv.

Le TT, Himmelstein DS, Hippen Anderson AA, Gazzara MR, Greene CS. Analysis of ISCB honorees and keynotes reveals disparities. [GitHub: iscb-diversity, wiki-nationality-estimate, pubmedpy]

Dang MT, Gonzalez M, Gaonkar KS, Rathi KS, Young P, et al. Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment. bioRxiv. 10.1101/2020.02.12.945642

Gay NR, Gloudemans M, Antonio MLL, Balliu B, Park Y, et al. Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx. bioRxiv. 10.1101/836825

Pividori M, Rajagopal PS, Barbeira A, Liang Y, Melia O, Bastarache L, Park Y et al. PhenomeXcan: Mapping the genome to the phenome through the transcriptome. bioRxiv. 10.1101/833210

de Goede OM et al. Long non-coding RNA gene regulation and trait associations across human tissues. bioRxiv. 10.1101/793091

Ferraro et al. Diverse transcriptomic signatures across human tissues identify functional rare genetic variation. bioRxiv. 10.1101/786053

(* Equal contributions, alphabetically ordered co-first authors) Barbeira AN*, Bonazzola R*, Gamazon ER*, Liang Y*, Park Y* et al. Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits. bioRxiv. 10.1101/814350

Aguet F et al. The GTEx Consortium atlas of genetic regulatory effects across human tissues. bioRxiv. 10.1101/787903

Nicholson DN, Himmelstein DS, Greene CS. Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts. bioRxiv. [Manubot Manuscript, GitHub Source]

Taroni JN, Greene CS. Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously. bioRxiv. doi:10.1101/118349. [GitHub]

Zelaya RA, Wong AK, Frase AT, Ritchie MD, Greene CS. Tribe: The collaborative platform for reproducible web-based analysis of gene setsbioRxiv. doi:10.1101/055913 [Bitbucket: Tribe Server; Tribe Client]

Recent Publications

Talhouk A, George J, Wang C, Budden T. et al., Development and validation of the gene-expression Predictor of high-grade-serous Ovarian carcinoma molecular subTYPE (PrOTYPE). Clinical Cancer Research.

Nicholson DN, Greene CS. Constructing knowledge graphs and their biomedical applications. Computational and Structural Biotechnology Journal. [manubot instance]

Millstein J, Budden T, Goode EL, Anglesio MS. et al., Prognostic gene expression signature for high-grade serous ovarian cancer. Annals of Oncology.

Segal E, Zhang F, Lin X, King G, et al. Building an International Consortium for Tracking Coronavirus Health Status. Nature Medicine. [Preprint]

Brito JJ, Li J, Moore JH, Greene CS, Nogoy NA, Garmire LX, Mangul S. Recommendations to enhance rigor and reproducibility in biomedical research. GigaScience. [manubot, arXiv]

Way GP, Zietz M, Rubinetti V, Himmelstein DS, Greene CS. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations. Genome Biology. [GitHub, Preprint]

Hu Q, Greene CS, Heller E. Specific histone modifications associate with alternative exon selection during mammalian development. Nucleic Acids Research. [GitHub, Preprint]

Rokita JL, et al., Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Reports. [preprint, intermediate data, classifier, processed data, source code for: PDX mouse subtraction, ethnicity inference, oncoprint generation, gene classification, RNA clustering, RNA fusion, copy number / structural variant analysis, correlation analysis, mutational signatures]

Banerjee J, Allawawy RJ, Taroni JN, Baker A, Zhang X, Moon CI, Blakeley JO, Guinney J, Hirbe A, Greene CS, Gosline SJC. Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1. Genes. [GitHub, Preprint]

Clay ME, Hammond JH, Zhong F, Chen X, Kowalski CH, Lee AJ, Porter MS, Greene CS, Pletneva EV, Hogan DA. Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin. PNAS. [Preprint]

Crawford J, Greene CS. Graph biased feature selection of genes is better than random for many genes. bioRxiv [contradictory results, no peer reviewed submission currently planned]. [GitHub]

Crawford J, Greene CS. Incorporating biological structure into machine learning models in biomedicine. Current Opinion in Biotechnology. [arXiv, manubot].

2019

Martinez-Lage M, Lynch TM, Bi Y, Cocito C, Way GP, et al. Immune landscapes associated with different glioblastoma molecular subtypes. Acta Neuropathologica Communications. [GitHub, DockerHub, Zenodo]

Anikeeva P, Boyden E, et al. Voices in method development. Nature Methods.

Liu Y, Huang J, Urbanowicz RJ, Chen K, Manduchi E, Greene CS, Moore JH, Scheet P, Chen Y. Embracing study heterogeneity for finding genetic interactions in large‐scale research consortia. Genetic Epidemiology. [YETI2 Software]

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, The Critical Assessment of Function Annotation, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco GD, Hogan DA, Martin MJ, O’Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. [Preprint]

Yu-Hsiu TL, Way GP, Barwick BG, Mariano MC, Marcoulis M, Ferguson ID, Driessen C, Boise LH, Greene CS, Wiita AP. Integrated Phosphoproteomics and Transcriptional Classifiers Reveal Hidden RAS Signaling Dynamics in Multiple Myeloma. Blood Advances. [classifier code, preprint]

Way GP, Greene CS. Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning. Annual Review of Biomedical Data Science.

Beaulieu-Jones BK, Wu ZS, Williams C, Lee R, Bhavnani SP, Byrd JB, Greene CS. Privacy-preserving generative deep neural networks support clinical data sharing. Circulation: Cardiovascular Quality and Outcomes. [GitHub source code, preprint]

Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, Greene CS, Gitter A. Open collaborative writing with Manubot. PLOS Computational Biology. [Manubot, Manubot-formatted Document, Source Repository]

Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A., …, White PC. The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolution. Developmental Cell.

Teichmann S, Kim J, Zhuang X, Zeng H, Boeke J, Ramakrishnan V, Greene CS. Technologies to Watch in 2019. Nature.

Taroni JN, Grayson PC, Hu Q, Eddy S, Kretzler M, Merkel PA, Greene CS. MultiPLIER: a transfer learning framework for transcriptomics reveals systemic features of rare disease. Cell Systems. [GitHub]

Greene CS. Show me the models. Nature Biotech.

Hu Q, Greene CS. Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. Pac Symp Biocomput. [GitHub]

2018

Way GP, Greene CS. Bayesian deep learning for single-cell analysis. Nature Methods.

Park Y, Greene CS. Parasite’s perspective on data sharing. GigaScience.

Kacsoh B, Barton S, Jiang Y, Zhou N, Mooney S, Friedberg I, Radivojac P, Greene CS, Bosco G. New Drosophila long-term memory genes revealed by assessing computational function prediction methods. G3: Genes | Genomes | Genetics. [Preprint]

Crowell AM, Greene CS, Loros JJ, Dunlap JC. Learning and Imputation for Mass-spec Bias Reduction (LIMBR). Bioinformatics. [GitHub, Preprint]

Stein-O'Brien GL, Arora R, Culhane AC, Favorov A, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Enter the matrix: interpreting unsupervised feature learning with matrix decomposition to discover hidden knowledge in high-throughput omics data. Trends in Genetics. [Preprint]

Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS. PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. BioData Mining. [GitHub to reproduce results, GitHub PathCORE Software, GitHub PathCORE demo server, GitHub crosstalk correction package, Preprint]

Grayson PC, Eddy S, Taroni JN, Lightfoot YL, Mariani L, Parikh H, Lindenmeyer MT, Ju W, Greene CS, Godfrey B, Cohen CD, Krischer J, Kretzler M, Merkel PA; Vasculitis Clinical Research Consortium, the European Renal cDNA Bank cohort, and the Nephrotic Syndrome Study Network. Metabolic pathways and immunometabolism in rare kidney diseases. Ann Rheum Dis. 2018. Epub ahead of print.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferro E, Agapow P, Zietz M, Hoffman MM, Xie W, Rosen GL, Legenrich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Gitter A+, Greene CS+. Opportunities and Obstacles for Deep Learning in Biology and Medicine. J R Soc Interface. 15:20170387. [PreprintGitHub]

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang W, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Devershi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormic F, Meyerson M, Cancer Genome Analysis Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018. 173(2):321-337.e10.

Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I; Cancer Genome Atlas Research Network, Monnat RJ Jr., Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):239-254.e6. PMID: 29617664 [GitHub for ML portion]

Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N; Cancer Genome Atlas Research Network, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):172-180.e3. PMID: 29617658 [GitHub]

Weissman GE, Hubbard RA, Ungar LH, Harhay MO, Greene CS, Himes BE, Halpern SD. Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU StayCrit Care Med.

Himmelstein DS, Romero AR, McLaughlin SR, Greshake B, Greene CS. Sci-Hub provides access to nearly all scholarly literature. eLife. [GitHub for Analyses, GitHub for Manuscript, Current build of manuscript, Preprint]

Dahlstrom, KM, Collins AJ, Doing G, Taroni JN, Gauvin TJ, Greene CS, Hogan DA, O'Toole GA. A Multimodal Strategy Used By A Large c-di-GMP NetworkJ Bacteriol. [Preprint]

Gonzalez-Hernandez G, Sarker A, O'Connor K, Greene C, Liu H. Advances in Text Mining and Visualization for Precision Medicine. Pac Symp Biocomput. 2018;23:559-565.

Way GP, Greene CS. Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders. Pac Symp Biocomput. 2018;23:80-91. [GitHub, Preprint]

Harrington LX, Way GP, Doherty JA, Greene CS. Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analysesPac Symp Biocomput. 2018;23:157-167. [GitHub source code, Preprint]

2017

Doherty JA, Peres LC, Wang C, Way GP, Greene CS, Schildkraut JM. Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes. Curr Epidemiol Rep. 2017 Sep;4(3):211-220.

Skarke C, Lahens NF, Rhoades SD, Campbell A, Bittinger K, Bailey A, Hoffmann C, Olson RS, Chen L, Yang G, Price TS, Moore JH, Bushman FD, Greene CS, Grant GR, Weljie AM, FitzGerald GA. A pilot characterization of the human chronobiomeScientific Reports.

Tan J, Huyck M, Hu D, Zelaya RA, Hogan DA, Greene CS. ADAGE signature analysis: differential expression analysis with data-defined gene sets. BMC Bioinformatics. [Preprint][GitHub R Package][GitHub Webserver][Running Webserver]

Kacsoh BZ, Greene CS, Bosco G. Machine learning analysis identifies Drosophila Grunge/Atrophin as an important learning and memory gene required for memory retention and social learning. G3: Genes | Genomes | Genetics. [Preprint]

Way GP, Youngstrom DW, Hankenson KD, Greene CS*, Grant SFA*. Implicating candidate genes at GWAS signals by leveraging topologically associating domains. European Journal of Human Genetics. [preprintGitHub - Zenodo, Docker - Zenodo]

Byrd JB, Greene CS. Data-Sharing ModelsNEJM. 376:2305-2306.

Tan J, Doing G, Lewis KA, Price CE, Chen KM, Cady KC, Perchuk B, Laub MT, Hogan DA, Greene CS. Unsupervised extraction of stable expression signatures from public compendia with an ensemble of neural networks. Cell Systems. [preprint][Bitbucket]

Yao X, Yan J, Liu K, Kim S, Nho K, Risacher SL, Greene CS, Moore JH, Saykin AJ, Shen L. Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinformatics. In Press.

Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating ParasitesNature Genetics. 2017;49:483-484.

Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann R, Farber HW, Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML. A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis. Genome Medicine. 2017;9:27. [preprint]

Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysisNature Biotechnology. [preprint][Github]

Greene CS. Tell me your neighbors, and I will tell you who you areScience Translational Medicine. 8:370ec203. [Editor's Choice Summary of Khurana et al.]

2016

Way GP, Allaway RA, Bouley SJ, Fadul CE, Sanchez Y, Greene CS. A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. BMC Genomics. 2016;18:127. [GitHub, Docker, Preprint]

Greene CS. Cheap-Seq. Science Translational Medicine. 8:370ec203. [Editor's Choice Summary of Tatlow et al.]

Moore JH, Jennings SF, Greene CS, Hunter LE, Perkins AD, Williams-Devane C, Wunsch DC, Zhao Z, Huang X. No-boundary Thinking in Bioinformatics. Pac Symp Biocomput. 2016;22:646-648.

Greene CS. How to know what we don't. Science Translational Medicine. 8:364ec179. [Editor's Choice Summary of Zhou et al.]

Beaulieu-Jones BK, Greene CS. Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification. Journal of Biomedical Informatics. 2016;64:168-178. [preprint][Github - results built via continuous analysis]

Greene CS. A stromal focus reveals tumor immune signatures. Science Translational Medicine. 2016;8:358ec155. [Editor's Choice Summary]

Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny G, Goode EL, Greene CS*, Doherty JA*. Comprehensive cross-population analysis of high-grade serous ovarian cancer supports no more than three subtypesG3: Genes | Genomes | Genetics. 6(12) 4097-4103. [preprint][source & data][Docker image

Krishnan A, Taroni JN, Greene CS. Integrative networks illuminate biological factors underlying gene-disease associations. Curr Genet Med Rep. 2016. [preprint]

Greene CS. Gut Check. Science Translational Medicine. 8:352ec131. [Editor's Choice Summary]

Greene CS. The future is unsupervisedScience Translational Medicine. 8:346ec108. [Editor's Choice Summary]

Jiang Y, Oron TR, Clark WT, Bankapur A, ... [>100 authors]. An expanded evaluation of protein function prediction methods shows an improvement in accuracyGenome Biology. 2016. 17:184. [preprint]

Greene CS. Nothing but a hound dogScience Translational Medicine. 8:340ec83. [Editor's Choice Summary]

Greene CS, Voight BF. Pathway and network-based strategies to translate genetic discoveries into effective therapies. Human Molecular Genetics. doi:10.1093/hmg/ddw160. [preprint]

Greene CS. CoINcIDE: All together now. Science Translational Medicine. 8:334ec61. [Editor's Choice Summary]

Greene CS, Himmelstein DS. Genetic Association Guided Analysis of Gene Networks for the Study of Complex Traits. Circulation: Cardiovascular Genetics. 2016 9:179-184. [source & data][free full text]

Song A, Yan J, Kim S, Risacher SL, Wong AK, Saykin AD, Shen L, Greene CS. Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. BioData Mining. 2016 9:3. doi:10.1186/s13040-016-0082-8. [source & data]

Tan J, Hammond JH, Hogan DA, Greene CS. ADAGE-based integration of publicly available pseudomonas aeruginosa gene expression data with denoising autoencoders illuminates microbe-host interactionsmSystems. 2016 1(1):e00025-15. doi: 10.1128/mSystems.00025-15. [preprint][source & data]

Thompson JA, Tan J, Greene CS. Cross-platform normalization of microarray and RNA-seq data for machine learning applications. PeerJ. 2016 4:e1621. [preprint][R package][source & data]

Allaway RJ*, Fischer DA*, de Abreu FB, Gardner TB, Gordon SR, Barth RJ, Colacchio TA, Wood M, Kacsoh BZ, Bouley SJ, Cui J, Hamilton J, Choi JA, Lange JT, Peterson JD, Padmanabhan V, Tomlinson CR, Tsongalis GJ, Suriawinata A, Greene CS*, Sanchez Y*, Smith KD. Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites. Oncotarget. Feb 25. doi: 10.18632/oncotarget.7718. [Epub ahead of print]. [source & data]

Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y. Computational approaches to study microbes and microbiomesPac Sym Biocomput. 2016 21:557-67. [pdf]

2015 and Older

Rudd J, Zelaya RA, Demidenko E, Goode EL, Greene CS, Doherty JA. Leveraging global gene expression patterns to predict expression of unmeasured genesBMC Genomics. 2015 16:1065. doi:10.1186/s12864-015-2250-5. [source & data]

Qian DC, Byun J, Han Y, Greene CS, Field JK, Hung RJ, Brhane Y, Mclaughlin JR, Fehringer G, Landi MT, Rosenberger A, Bickeböller H, Malhotra J, Risch A, Heinrich J, Hunter DJ, Henderson BE, Haiman CA, Schumacher FR, Eeles RA, Easton DF, Seminara D, Amos CI. Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. Hum Mol Genet. 2015 Dec 20;24(25):7406-20. doi: 10.1093/hmg/ddv440.

Gonzalez GH, Tahsin T, Goodale BC, Greene AC, Greene CS. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Brief Bioinform. 2015 Sep 29. pii: bbv087. [Epub ahead of print]

Cordell HJ, Han Y, Mells GF, Li Y, Hirschfield GM, Greene CS et al. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways. Nat Commun. 2015; PMID:26394269

Gui J, Greene CS, Sullivan C, Taylor W, Moore JH, Kim C. Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study. BioData Min. 2015; PMID:26097506

Greene CS, Krishnan A, Wong AK,  Riccioti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. Understanding multicellular function and disease with human tissue-specific networks. Nat Genetics. 2015; PMID:25915600 [processed networks][raw networks][webserver]

Zhu Q, Wong AK, Krishnan A, Aure MR, Tadych A, Zhang R, Corney DC, Greene CS, Bongo LA, Kristensen VN, Charikar M, Li K, Troyanskaya OG. Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nat Methods. 2015; PMID:25581801 [webserver]

Greene AC, Giffin KA, Greene CS, Moore JH. Adapting bioinformatics curricula for big data. Brief Bioinform. 2015; PMID:25829469

Tan J, Ung M, Cheng C, and Greene, CS. Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Pac Symp Biocomput. 2015; 20:132-43. PMID:25592575 [data & results]

Mahoney JM, Taroni J, Martyanov V, Wood TA, Greene CS, Pioli PA, Hinchcliff ME, Whitfield ML. Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms. PLoS Comput Biol. 2015; 11(1):e1004005. PMID:25569146

Zieselman AL, Fisher JM, Hu T, Andrews PC, Greene CS, Shen L, Saykin AJ, Moore JH. Computational genetics analysis of grey matter density in Alzheimer's disease. BioData Min. 2014; 7:17. PMID: 25165488

Penrod NM, Greene CS, Moore JH. Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity. Genome Med 2014; 6(4):33. PMID: 24944582

Greene CS, Tan J, Ung M, Moore JH, Cheng C. Big Data Bioinformatics. J Cell Physiol 2014 May 6. PMID: 24799088

Tan J, Grant GD, Whitfield ML, Greene, CS. Time-Point specific weighting improves coexpression networks from time-course experiments. Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO) 2013. 11-22.

Ju W, Greene CS, Eichinger F, Nair V, Hodgin JB, Bitzer M, Lee YS, Zhu Q, Kehata M, Li M, Jiang S, Rastaldi MP, Cohen CD, Troyanskaya OG, Kretzler M. Defining cell-type specificity at the transcriptional level in human disease. Genome Res 2013 Nov; 23(11):1862-73. PMID: 23950145 [Highlighted by Nature Reviews Genetics]

Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol 2013; 9(3):e1002957. PMID: 23516347

Greene CS, Troyanskaya OG. Chapter 2: Data-driven view of disease biology. PLoS Comput Biol 2012; 8(12):e1002816. PMID: 23300408

Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res 2012 Jul; 40(Web Server issue):W484-90. PMID: 22684505

Greene CS, Troyanskaya OG. Accurate evaluation and analysis of functional genomics data and methods. Ann N Y Acad Sci 2012 Jul; 1260:95-100. PMID: 22268703

See more publications at PubMed or Google Scholar

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+ + /join-the-team + Join the Team + Thu, 11 Jun 2020 19:16:52 +0000 + Our lab is made up of a highly engaged and collaborative team of scientists in the Perelman School of Medicine at the University of Pennsylvania dedicated to: 1) developing methods that analyze big data to understand complex biological systems and 2) putting these methods and big data into the hands of every biologist. Read through the appropriate heading below for information about joining the lab.

Programmer & Software Engineer Positions

Our programmers and software engineers are expected to contribute most of the code that goes into our production ready webservers and analytical pipelines. These professionals are expected to maintain high standards for code documentation, clarity, efficiency and maintainability. In addition to maintaining these standards in their own code, these members of the lab set high expectations for other lab members and share their expertise to improve the code that all members of the lab are writing. For the machine learning aspects of our work, we currently use a technology stack consisting of C/C++ (limited and decreasing), Python + numpy/scipy/scikit-learn/theano, and R with assorted packages. For the web development side of the lab, we currently use a technology stack of Postgres, Python (Django), and JavaScript (Angular.js and d3). Our data processing framework and webservers run on cloud instances, so experience with optimizing workloads for this type of environment is a plus. Feel free to contact Casey to be notified when job postings are available.

Postdoctoral Researchers

The Greene lab welcomes applications for computational postdoctoral positions at the University of Pennsylvania Perelman School of Medicine. The Greene lab's overarching goal is to transform how we understand complex biological systems by developing and applying computational algorithms that effectively model processes by integrating multiple types of big data from diverse experiments. Our goal is to then put these algorithms into the hands of biologists, through the development of usable webservers, the dissemination of successful applications, and the distribution of open source software.

Objectives:

Postdocs in our lab contribute to the development of new analytical methods and/or the application of these methods to new datasets. Postdocs will have the opportunity to work with large collections of genomic data, both publicly available and from collaborative projects, and to extract testable biological hypotheses from these large collections. Research projects center around new computational methods to integrate genomic data as well as to incorporate additional environmental and phenotypic information with these genomic data. Postdocs are expected to contribute to the lab's culture of open scientific discovery and to share methodological advances and biological discoveries at both national and international venues.

Qualifications:

  1. Candidates are expected to have an MD, PhD, or equivalent, with a strong background in computer science, machine learning, statistics, genetics, bioinformatics, or closely related field and programming experience with attributable contributions to source code.

  2. The ideal candidate will have a track record of scientific productivity and leadership and will strive for robust and reproducible analytical workflows.

  3. The ideal candidate will have experience handling large datasets in a UNIX/LINUX environment, experience with high performance cluster or cloud computing, and a knowledge of existing software packages used for machine learning.

Pay and Benefits:

Postdoc positions in our lab start at a non-negotiable starting salary, which is currently $70,000 per year. These positions are considered Postdoctoral Trainee Appointments at Penn, which makes the postdoc eligible for an insurance plan and other benefits including a New Child Leave Policy. Additional information about Biomedical Postdoc Positions at Penn is available on the program website.

Applying:

To apply, provide a CV, a one to two page statement of research interests, and the names and contact information for three references through our application portal.

Graduate STudents

We welcome graduate students in Penn’s Genomics and Computational Biology (GCB) program. Our goal is to help our students to develop both a deep familiarity with the computational methods required for data-intensive science and a strong understanding of one or more biological application areas. We provide training in all aspects through group meetings, individual meetings, and a supportive lab environment. If you are interested in rotating in our lab, please e-mail Casey to set up a time to discuss your interest.

Undergraduate Students

We welcome undergraduate students into our lab, and undergraduate researchers have become first authors on papers submitted on research that they performed as part of our group. We are happy to train undergraduates in many aspects of data-intensive biology, and we have high expectations for their level of commitment to research. As an undergraduate, if you are interested in discussing research opportunities please e-mail Casey.

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+ + /webservers + Software + Thu, 25 Jun 2020 17:58:51 +0000 + ADAGE

Hetnet Connectivity Search

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+ Adage helps you explore gene expression data and discover new insights from machine learning models.  See how genes relate to each other, other genes, and how they are represented in machine learning signatures. View the activities of samples as a colored heatmap, and cluster them on the fly. Explore the genes that contribute to signatures, the experiments in which they vary the most, and the pathways they significantly overlap with. +
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Adage helps you explore gene expression data and discover new insights from machine learning models. See how genes relate to each other, other genes, and how they are represented in machine learning signatures. View the activities of samples as a colored heatmap, and cluster them on the fly. Explore the genes that contribute to signatures, the experiments in which they vary the most, and the pathways they significantly overlap with.

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+ Connectivity search allows you to find the most important paths connecting any two nodes in Hetionet , even when they are different types or not known to be related. If you want to investigate how the  eye and breast cancer  may be related, you can. Filter nodes by type, see computed significance data about paths, create graph visualizations with highlighted paths, and more. +
+ + + + + + +
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Connectivity search allows you to find the most important paths connecting any two nodes in Hetionet, even when they are different types or not known to be related. If you want to investigate how the eye and breast cancer may be related, you can. Filter nodes by type, see computed significance data about paths, create graph visualizations with highlighted paths, and more.

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Tribe

Manubot

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+ Manubot is a workflow and set of tools for the next generation of scholarly publishing.  Write your manuscript in  markdown , track it with  git , automatically convert it to .html, .pdf, or .docx, and deploy it to your  destination  of choice. +
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Manubot is a workflow and set of tools for the next generation of scholarly publishing. Write your manuscript in markdown, track it with git, automatically convert it to .html, .pdf, or .docx, and deploy it to your destination of choice.

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PILGRM

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+ + + + + + + +
+ PILGRM uses a data-driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets.  Users, primarily biologists, translate their literature search results into gold standards for machine learning and mine PILGRM's data compendia. The PILGRM webserver was retired after five years of service when the hardware it was running on was retired. +
+ +
+ + + + +
+

PILGRM uses a data-driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets. Users, primarily biologists, translate their literature search results into gold standards for machine learning and mine PILGRM's data compendia. The PILGRM webserver was retired after five years of service when the hardware it was running on was retired.

+
+ + +
+ + +
+ + + + + + +

GIANT

+ + + + + + + + + + + + +
+ + + + +
+ + + + + + + +
+ GIANT provides functional relationship networks for 144 human tissues.  GIANT helps researchers identify which genes are working together in specific tissues. This tissue-specific lens into human biology helps researchers study complex human diseases. +
+ +
+ + + + +
+

GIANT provides functional relationship networks for 144 human tissues. GIANT helps researchers identify which genes are working together in specific tissues. This tissue-specific lens into human biology helps researchers study complex human diseases.

+
+ + +
+ + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + + + +
+ Tribe connects webservers together.  For biologists, Tribe puts literature search and experimental results to work mining large data compendia without re-entering information at each server. For computational biologists, Tribe allows biologists to use your webservers seamlessly as part of an analytical pipeline. +
+ +
+ + + + +
+

Tribe connects webservers together. For biologists, Tribe puts literature search and experimental results to work mining large data compendia without re-entering information at each server. For computational biologists, Tribe allows biologists to use your webservers seamlessly as part of an analytical pipeline.

+
+ + +
+ + +
+ + + + + + +

IMP

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+ + + + +
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+ IMP provides functional relationship networks and biological process predictions for seven commonly studied organisms.  IMP helps researchers identify new gene-gene and gene-process associations that are supported by existing data but currently unannotated. +
+ +
+ + + + +
+

IMP provides functional relationship networks and biological process predictions for seven commonly studied organisms. IMP helps researchers identify new gene-gene and gene-process associations that are supported by existing data but currently unannotated.

+
+ + +
+ + +
+ + + + + + +

Nano-dissection


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+ + + + +
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+ The nano-dissection webserver implements the in silico nano-dissection method from    Ju et al.     Nano-dissection allows researchers to identify genes expressed in specific tissues and cell lineages from microarray data that are not resolved to the level of the cell lineage of interest. +
+ +
+ + + + +
+

The nano-dissection webserver implements the in silico nano-dissection method from Ju et al. Nano-dissection allows researchers to identify genes expressed in specific tissues and cell lineages from microarray data that are not resolved to the level of the cell lineage of interest.

+
+ + +
+ + +
]]>
+ webservers + page + 6 + publish +
+ + /contact + Contact + Mon, 18 Sep 2017 14:21:07 +0000 + Write or Visit 

Affiliations:

Our lab is part of the Department of Systems Pharmacology and Translational Therapeutics at the Perelman School of Medicine at the University of Pennsylvania.

Join our team →

Lab Location:

10th Floor of the Smilow Center for Translational Research, Department of Systems Pharmacology and Translational Therapeutics 

Mailing Address:

3400 Civic Center Blvd.
10-131 SCTR
Philadelphia, PA 19104-5158

Email: greenescientist@gmail.com

Twitter: GreeneScientist

Phone: (215) 573-2991

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+ contact + page + 7 + publish +
+ + /lab-members + Our Team + Thu, 10 Nov 2016 20:45:17 +0000 + Our Team

The lab is made up of a highly engaged and collaborative team of scientists in the Perelman School of Medicine at the University of Pennsylvania dedicated to: 1) developing methods that analyze big data to understand complex biological systems and 2) putting these methods and big data into the hands of every biologist. We recognize the value of diversity in the process of discovery, and we foster an environment where team members are treated equally and we respect and admire our differences. The team includes postdocs, students at all levels, staff, and our lab mascots. Click on anyone below for more info about them.

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In addition to members of our lab, our collaborators are key contributors to our work.

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+ lab-members + page + 8 + publish +
+ + /parasite-award + The 2017 PSB Research Parasite Awards + Sun, 10 Jul 2016 13:03:30 +0000 + PSB Awards for rigorous secondary data analysis (The “Parasites”)

The act of generating new hypotheses from existing data is a major component in the process of science. Dr. Albert Szent-Györgyi has been quoted as saying "discovery consists of seeing what everybody has seen, and thinking what nobody has thought." Recent advances in data sharing, combined with the expectation that publicly funded research will be shared, have led to projects that consist largely of secondary analysis of data. The practitioners of this craft may analyze or combine these data in ways that answer scientific questions that the initial investigators did not consider. In a recent editorial, the New England Journal of Medicine termed these people "research parasites."

The Parasite awards, given annually, recognize outstanding contributions to the rigorous secondary analysis of data. This practice of secondary analysis plays a key role in scientific ecosystem: conclusions that persist through substantial reanalysis are expected to be more credible; and analyses that extract more knowledge from underutilized data make the practice of science more efficient.

Or, put slightly differently:

+ + + + + + + +

The Parasites currently consist of two awards: the first recognizes an outstanding contribution from a junior parasite (postdoctoral, graduate, or undergraduate trainee), and the second recognizes an individual for a sustained period of exemplary research parasitism.

Application Process

For either award, submit an application by October 14, 2016 at 5PM HST (Hawaii Standard Time) to parasite.award@gmail.com. An application requires:

  • A nomination letter describing how each selected paper meets the criteria for the award. Self nominations are encouraged, and all nominees must be aware that they have been nominated.
  • Junior Parasite (aka the sporozoite): a PDF of one paper published after peer review on which the application will be judged.
  • Sustained Parasitism (aka the merozoite): PDFs of three papers published after peer review on which the application will be judged.

The award winners will be recognized at the Pacific Symposium on Biocomputing each year, and listed on the PSB website, along with links to the winning papers.  

Selection criteria (both awards) for the work in question:

  • The awardee must not have been involved the design of the experiments that generated the data. 
  • The awardee published independently of the original investigators, and the original investigators are not authors of the secondary analyses but are appropriately credited in the manuscripts.
  • The awardee may have extended, replicated or disproved what the original investigators had posited.
  • The awardee has provided source code and intermediate or final results in a manner that enhances reproducibility.

Additional selection criteria for the Junior Parasite award:

  • The awardee must have published the work at the training stage of their career (postdoctoral, graduate, or undergraduate). If the awardee has assumed a position as an independent investigator she or he should not have been in that position for more than 2 years.
  • The award will be based on work described in a single manuscript (submitted alongside the nomination letter).

Additional selection criteria for the Sustained Parasitism award:

  • The awardee must be in an independent investigator position in academia, industry or public sector.
  • The awardee must be a last or corresponding author on the three manuscripts submitted alongside the nomination letter.
  • At least a five-year period must have elapsed between the publication of the first manuscript and the final manuscript.

Prizes & Supporters

The winners of each award will receive:

Financial support for the award has been provided by: Nature Genetics, The Arnold Foundation, The Gordon and Betty Moore Foundation (via GBMF 4552 to CSG), and Casey Greene. If you'd like to contribute, please send an e-mail to Casey Greene at csgreene@upenn.edu. We'd like to be able to provide travel support to award winners.


Committee

  + + + + + + + + + + + +
+ + + + +
+ + + + + + + +
+ Casey Greene - Chair. Award Cycles 2017-2020. +
+ + + + + + +
+

Casey Greene - Chair. Award Cycles 2017-2020.

+
+ + +
+ + +
+ + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + + + +
+ Lana Garmire - Award Cycles 2017-2019 +
+ + + + + + +
+

Lana Garmire - Award Cycles 2017-2019

+
+ + +
+ + +
+ + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + + + +
+ Jack Gilbert - Award Cycle 2017 +
+ + + + + + +
+

Jack Gilbert - Award Cycle 2017

+
+ + +
+ + +
+ + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + + + +
+ Marylyn Ritchie - Award Cycles 2017 - 2018 +
+ + + + + + +
+

Marylyn Ritchie - Award Cycles 2017 - 2018

+
+ + +
+ + +
+ + + + + + + + + + + + + + + + +
+ + + + +
+ + + + + + + +
+ Larry Hunter - Award Cycle 2017 +
+ + + + + + +
+

Larry Hunter - Award Cycle 2017

+
+ + +
+ + +
+ + + + + 

Selection of new committee members: For the three four-year term positions, the award committee will have the right to nominate new members, and the PSB organizers will have the right to confirm selected nominees. For the two two-year terms positions, recipients of the Sustained Parasitism award will rotate on to the committee.


Conflict of Interest Rules

  1. PSB conference co-chairs do not serve as nominator or endorser for any nomination submitted for this award.
  2. Members of this award committee do not serve as a nominator for any nomination for this award. If you have nominated a candidate, inform the committee chair immediately so that one of two actions may be taken: (a) the nomination will be set aside for the year, or (b) you will step down from the committee for the year.
  3. Members of this committee should not be directly involved in nominations prior to their submittal. You can answer general questions about what a nomination should include, but you may not pre-review or comment on draft nominations.
  4. You must maintain confidentiality about the internal discussions of the committee.  Information about committee deliberations should not be shared with anyone outside the committee, nor should the winner be discussed until PSB has issued a formal statement.
  5. Members of this committee do not provide feedback to unsuccessful candidates. If a member is asked for feedback, this policy should be cited.
  6. Members of this committee must self-identify any relationships/affiliations that might be perceived as a source of potential bias, and inform the committee chair of the COIs before any candidates have been discussed.  Identify any candidates with whom you: have had close personal or working relationships within the past 5 years or the period covered by the award, whichever is longer; anyone for whom you were thesis advisor/advisee; anyone for whom you were a postdoctoral advisor/advisee; anyone form whom you were a faculty mentor/mentee; or any other case where your judgment could be affected.  Also identify any candidates from your current institution or one where you worked within the past 5 years.

When COIs are identified, the normal practice is for conflicted committee members to recuse themselves from discussions related to the corresponding nominations. In this sense, recusal means that the committee member will refrain from any commentary/input before or during the decision-making process, and will absent him/herself during committee discussions of the nomination. In the case of tie votes arising during a recusal, a PSB conference co-chair will cast the tiebreaking vote.

In any of the cases above, if you are to notify the committee chair but the committee chair has the conflict of interest, notification should instead be sent to the co-chairs of PSB. Potential conflicts involving the chair must be identified in advance and the chair should contact the PSB co-chairs immediately to determine whether the nomination might be deferred a year (in consultation with the nominator) or whether the chair should be replaced. For most potential situations involving a conflicted chair, it will be sufficient for a PSB conference co-chair to, in the case of ties, vote.

At any time where a PSB conference co-chair is brought in for discussions and voting, they will be expected to also identify potential conflicts, report them to the committee, and recuse themselves in accordance with the rules applied to committee members.

 

]]>
+ parasite-award + page + 9 + publish +
+ + /princeton-server-shutdown + Princeton Server Shutdown + Fri, 19 Jul 2019 13:40:11 +0000 + PILGRM and DFP Servers

The webserver hosting PILGRM and the data free prediction (DFP) server has reached the end of life after more than five years of availability. These servers were developed to use cluster infrastructure at Princeton, which my lab no longer has access to.

 

 

]]>
+ princeton-server-shutdown + page + 10 + publish +
+ + Our Team + /our-team + Thu, 06 Aug 2020 17:33:09 +0000 + ]]> + our-team + page + 11 + publish + + + http://static1.squarespace.com/static/53ce848ce4b029ce6cd25fe3/5772707d15d5db5378ebfeb8/577270a059cc685163c42561/1565795662308/greg_square.png + http://static1.squarespace.com/static/53ce848ce4b029ce6cd25fe3/5772707d15d5db5378ebfeb8/577270a059cc685163c42561/1565795662308/greg_square.png + attachment-577270a059cc685163c42561 + greg-square-png + attachment + 12 + 11 + inherit + + + Tue, 28 Jun 2016 12:42:08 +0000 + 2016-06-28 12:42:08 + 2016-06-28 12:42:08 + csgreene@upenn.edu + + + http://static1.squarespace.com/static/53ce848ce4b029ce6cd25fe3/5772707d15d5db5378ebfeb8/577270a959cc685163c4258c/1467138441981/irene-song.jpg + http://static1.squarespace.com/static/53ce848ce4b029ce6cd25fe3/5772707d15d5db5378ebfeb8/577270a959cc685163c4258c/1467138441981/irene-song.jpg + attachment-577270a959cc685163c4258c + irene-song-jpg + attachment + 13 + 11 + inherit + + + Tue, 28 Jun 2016 12:42:17 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17:37:47 +0000 + Alums

These former members of the Greene lab have moved to new positions outside the lab. We are grateful to everyone who has been part of our efforts, and we wish them all well on their future endeavors!

Jaclyn Taroni (Postdoc Alum)

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Jaclyn joined the Greene Lab as a Postdoctoral Researcher in May 2016. She is currently interested in integrating large amounts of publicly available data and utilizing unsupervised machine learning to answer big outstanding in the fields of rheumatology, autoimmunity, and in rare diseases in particular. She works in close collaboration with clinicians and biologists who are experts in these disorders and she is currently appointed to Penn Rheumatology’s T32. Before coming to Penn, Jaclyn received her PhD from the Molecular and Cellular Biology program at Dartmouth where she studied the rare autoimmune disease systemic sclerosis with Michael Whitfield and where she was awarded the John H. Copenhaver, Jr. and William H. Thomas, MD 1952 Fellowship. [EmailWebsite]

 

QIWEN HU (POSTDOC ALUM)

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Qiwen is Postdoctoral Researcher at the University of Pennsylvania Perelman School of Medicine. She received her PhD in Bioinformatics from North Carolina State University in 2016, where she studied translational regulation in plant genomes. She developed machine learning and statistical approaches based on high-throughput sequencing datasets to identify regulatory elements that affect transcription and translation. Qiwen joined the Greene Lab in 2017. Currently, her research interests focus on integration of different types of high-throughput sequencing data to identify meaningful biological patterns, key transcriptional regulators related to drug addiction and chromatin-regulated alternative splicing using computational approaches.

 

Jie Tan, PhD (PHD Student Alum)

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Jie was a Ph.D. student in Dartmouth's Molecular and Cellular Biology program. She is originally from Qingdao, China and graduated from Zhejiang University with a B.A in Biotechnology in 2012. She joined the Integrative Genomics Lab in the summer of 2013. She has published papers on the analysis of time-series data for functional network constructionrule compaction for learning classifier systems, and unsupervised feature construction methods for genomic data. Jie has also been awarded a Neukom Graduate Fellowship. She is currently a data scientist at Kaleido Biosciences in Cambridge, MA. [E-mail]

 

Brett Beaulieu-Jones (PHD Student Alum)

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Brett graduated in 2011 with a B.S. in Computer Science from Boston College. After graduation he worked as a technology consultant doing information management and data science at large financial institutions. He co-founded Wymsee, an entertainment technology company in 2012. He is a Ph.D. student in Penn's Genomics and Computational Biology program. He is a member of both the Greene and Moore labs. His research centers on using deep learning-based methods to more precisely define phenotypes from large-scale data repositories, e.g. those contained in clinical records.

 

Greg Way (PHD Student Alum)

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Greg is a Ph.D. candidate in the Greene Lab through Penn's Genomics and Computational Biology (GCB) PhD program. Greg graduated from The College of New Jersey in 2011 with a B.S. in Biology and from Saint Joseph's University in 2014 with an M.S. in Biology. He joined the lab in 2015 at Dartmouth and transferred with Casey to Penn. At Penn, he was awarded a T32 Training Grant. He has published papers on supervised methods to detect glioblastoma tumors with NF1 inactivation, and unsupervised deep learning methods to aggregate pan-cancer gene expression features. His goal is to improve outcomes for cancer patients through the development of methods that help unravel the complexity of cancer.

[Website]

 

Amy Campbell (Analyst Alum)

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Amy was an awesome analyst who worked for us for a year between graduation and starting a PhD program. She owes me more of a bio, but I can summarize her current position by saying that she's a PhD student in the GCB program at Penn!

 

Kathy Chen (Undergrad ALum)

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Kathy is an undergraduate at the University of Pennsylvania studying Biochemistry and Computer Science. She joined the Greene lab to learn more about the intersection of her two majors. Kathy's project involved the identification of pathway-pathway relationships from genomic "big data" using patterns extracted by deep learning techniques. She was a co-author on a manuscript in Cell Systems describing the eADAGE method and the primary author of a manuscript describing the PathCORE software that she developed. Currently, she is a data scientist at the Simons Foundation. She plans to continue developing and applying computational algorithms to address key challenges in the life sciences.

 

Timothy Chang (Undergrad ALum)

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Timothy was an undergraduate at the University of Pennsylvania who studied Biochemistry, Finance, and Operations and Information Management. He found the Greene Lab through the intersection of his majors and interests: biological systems, information systems, and computer science. Timothy worked on integrating genomic data and computational methods towards strengthening our understanding on cancer and other diseases.

 

Roshan Ravishankar (Undergrad ALum)

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Roshan is a senior in the Life Sciences and Management program at Penn studying mathematical biology and statistics. He is especially interested in studying the interactions between biology, mathematics, statistics, and other related areas. His project involved building an ADAGE model to analyze gene expression in kidney biopsies. 

 

IRENE SONG (Undergrad Alum)

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Irene is a Biomedical Engineering major and Statistics minor at Dartmouth College. As a member of the Greene lab, she performed a network-based analysis of genetic variants associated with Alzheimer’s disease endophenotypes. Her long-term goal is to apply her STEM background to improving people’s health and well-being.

 

MULIN XIONG (Undergrad ALum)

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Mulin was a Biology major and AMES minor on the premed track at Dartmouth College. Mulin's senior project sat at the intersection of computational and wet-bench techniques, which she used to study Pseudomonas aeruginosa. This opportunistic human pathogen readily forms biofilms and is difficult to treat. In the Greene lab, Mulin developed and applied new computational approaches to analyze the antibiotic response of Pseduomonas aeruginosa, and, in the Hogan lab, she measured this response to test her computational approach. Mulin is currently working in clinical research lab in Rochester, New York. In this lab she is focused on bringing specialized care to patients with movement disorders (such as Parkinson's and Huntington's) using telemedicine.

 

Michael Zietz (Undergrad Alum)

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Michael was an undergraduate at Penn who worked in the Greene Lab. He graduated in May 2019 with bachelor's and master's degrees in Physics through the Vagelos Scholars Program in Molecular Life Science, an intensive research-focused undergraduate program in the Chemistry Department. He began a Ph.D. in Biomedical Informatics at Columbia University in the fall of 2019. Michael started working in the Greene Lab with Daniel in 2017. He developed tools for graph traversal within hetnets and completed a network permutation project.

 

Lamonica Shinholster (Undergrad Alum)

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Lamonica is a senior majoring in biology with a minor in chemistry at Mercer University. Her research interests include antibiotic resistance, drug design, and public health. Her previous research projects included synthesizing and testing novel biofilm inhibitors. In the Greene lab she summarized literature related to infection and immunity for a broad review of the COVID-19 literature. Her long-term goals include attending medical school to become a physician.

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+ alums + page + 46 + publish +
+ + /casey + Casey + Mon, 25 Mar 2019 21:00:17 +0000 + Casey Greene + + + + + + + + + + + +
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Casey is an Associate Professor of Systems Pharmacology and Translational Therapeutics in the Perelman School of Medicine at the University of Pennsylvania. His lab develops deep learning methods that integrate distinct large-scale datasets to extract the rich and intrinsic information embedded in such integrated data. This approach reveals underlying principles of an organism’s genetics, its environment, and its response to that environment. Extracting this key contextual information reveals where the data’s context doesn’t fit existing models and raises the questions that a complete collection of publicly available data indicates researchers should be asking. In addition to developing deep learning methods for extracting context, a core mission of his lab is bringing these capabilities into every molecular biology lab. Before starting the Integrative Genomics Lab in 2012, Casey earned his Ph.D. for his study of gene-gene interactions in the field of computational genetics from Dartmouth College in 2009 and moved to the Lewis-Sigler Institute for Integrative Genomics at Princeton University where he worked as a postdoctoral fellow from 2009-2012. The overarching theme of his work has been the development and evaluation of methods that acknowledge the emergent complexity of biological systems.

[Google Scholar] [Twitter]

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+ + /mascots + Mascots + Fri, 16 Aug 2019 13:45:25 +0000 + Lab Mascots

The lab mascots bring their own unique qualities to the team. We appreciate them for their guidance and commitment to our mission.

 

Doodle

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Doodle is Jie's toy poodle. Despite weighting less than 10lbs, he is an accomplished high jumper and routinely reaches altitudes of three feet while leaping. As of Jie's thesis defense and graduation (Spring, 2017) he has become a lab alum.

 

Magnus

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Magnus joined the team of mascots in 2014. He holds world records for both number and scale of pillows crushed.

 

Miso

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Miso spent the early part of her life under a curse that began with her no-good-dirty-rotten-pig-stealing-great-great-grandfather. She wound up wrongfully convicted of stealing an orphanage donation and had to choose between prison or Camp Green Lake. She decided to go the camp, which ends up being a terrible place where she and her campmates were forced to dig holes in the desert all day on the orders of the warden, who was actually using the efforts of the campers to look for buried treasure. But with the help of a few new friends, Miso plotted a daring escape from the camp to solve the mystery and is now finally free of the family curse. 

 

Myshkin

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Myshkin is Greg's cat. He has a fiery personality and a zest for life. When he's not computing neural network gradients, you can find him napping in the sun.

 

SOPHIE

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Sophie is a bichon-poodle-shih tzu mix. Her research focus is on machine learning for dog breed identification. Sophie joined the team in 2013.

 

Tesla

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Tesla is Jaclyn’s pineapple green-cheeked conure. His interests include genome-scale gene expression data and papaya.

 

aCE

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Ace is the Nicholson family’s miniature schnauzer. He lives in Pittsburgh, Pennsylvania and joined the team in summer of 2017. His interests include network analysis and running around in dog parks.

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+ mascots + page + 48 + publish +
+ + /trainees + Trainees + Fri, 23 Aug 2019 08:56:30 +0000 + Postdocs

Daniel Himmelstein

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Daniel joined the Greene Lab as a Postdoctoral Researcher in June 2016, after receiving his PhD in _Biological & Medical Informatics_ at UCSF. He uses hetnets — networks with muliple types of nodes and relationship — to integrate and learn from the past several decades of biomedical research. All of Daniel's research is entirely open: openly licensed and immediately available.
Check out his GitHub to follow his recent work. Daniel also performs many data science projects designed to make science more open and hence productive. [Website, Email (for support questions or feedback on Daniel's research, please first consider public venues — such as GitHub Issues — before email)]

 

YoSon Park

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YoSon joined the Greene Lab as a Postdoctoral Researcher in 2018. She graduated from University of Miami with a PhD in Human Genetics and Genomics with a focus on statistical and computational methods development for large scale genomic data analyses. She works on building a platform for the community-driven causal inference using publicly available summary statistics and developing a tool to study biologically meaningful network graphs.

 

PhD Students

David NicholsoN

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David is a Ph.D. student in the Greene Lab through Penn’s Genomics and Computational Biology (GCB) PhD Program. David graduated from University of Maryland Baltimore County in 2015 with a B.S. in Computer Science and minor in Bioinformatics. He joined the lab in summer 2017. He was awarded a T32 Training Grant. His research interests include machine learning with a focus on deep learning methods, natural language processing (NLP) and network analysis. Currently, his work focuses on using a publicly available resource called Hetionet, which is a heterogeneous network that contains pharmacological and biological information. He recently submitted a manuscript that involved evaluating a text mining framework that to quickly scale up Hetionet.

 

Alex Lee

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Alexandra is a Ph.D. student in the Greene Lab through Penn’s Genomics and Computational Biology (GCB) PhD Program.  She graduated from Bryn Mawr College with a B.A. in Mathematics and a minor in Computer Science and an M.S. in Applied Mathematics from the University of Washington.  Prior to coming to Penn, she worked as a bioinformatics analyst at the J. Craig Venter Institute.  Since joining the Greene lab in 2018, she has been exploring the use of deep learning methods to model gene response to different environmental perturbations.     

 

Ariel Hippen Anderson

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Ariel is a Ph.D. student through Penn’s Genomics and Computational Biology (GCB) PhD program. She graduated from Brigham Young University in 2016 with a B.S. in Bioinformatics and a minor in Statistics. She then worked as a a bioinformatics analyst at AncestryDNA, before coming to Penn in 2018 and joining the Greene lab in the summer of 2019. Ariel’s research focuses on leveraging single-cell gene expression data to help define and ultimately treat subtypes of high-grade serous ovarian cancer.

 

Jake Crawford

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Jake is a Ph.D. student in the Greene Lab through Penn's Genomics and Computational Biology (GCB) program. He graduated from Tufts University with a B.S. in Biology from Tufts University in 2012, and received an M.S. in Computer Science from Tufts in 2017. Before coming to Penn, he spent a year at Microsoft Research New England as a research assistant in computational biology and machine learning. Jake is interested in combining machine learning models of gene expression data with structured biological priors, such as gene interaction networks and pathway databases.

[Website, Github]

 

Ben HEil

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Ben is a PhD student in the Genomics and Computational Biology program at Penn. He graduated from Baylor University with a degree in bioinformatics in 2018, and joined the Greene lab in the summer of 2019. Ben's research focuses on using transfer learning to gain insight from large gene expression datasets. Outside of school, Ben is a mostly retired swimmer, a bass singer, and a person who can talk for hours about the collected works of Patrick Rothfuss.

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+ + /staff + Staff + Fri, 16 Aug 2019 13:51:17 +0000 + Staff

Our programmers and software engineers are expected to contribute most of the code that goes into our production ready webservers and analytical pipelines. These professionals are expected to maintain high standards for code documentation, clarity, efficiency and maintainability. In addition to maintaining these standards in their own code, these members of the lab set high expectations for other lab members and share their expertise to improve the code that all members of the lab are writing. For the machine learning aspects of our work, we currently use a technology stack consisting of C/C++ (limited and decreasing), Python + numpy/scipy/scikit-learn/theano/keras/tensor flow, and R with assorted packages. For the web development side of the lab, we currently use a technology stack of Postgres, Python (Django), and JavaScript (Angular.js and d3).

 

Dongbo Hu

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Dongbo used to be a chemist but was eventually attracted into computer science because of its elegance. Before taking this position, he worked in the Neurology Department of Penn's hospital, Penn's Genetics Department and at a local financial firm. In the Greene lab, he is working on the ADAGE web server. 

 

Matt Huyck

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Matt has been translating questions posed by biologists and businesses into software that computers can contemplate for over 20 years. He earned his Bachelor’s Degree in Applied and Engineering Physics at Cornell University at the same time the Human Genome Project was getting underway. He has a broad and deep background in using and developing complex computer software. As a Project Manager for diverse consulting clients, he developed a specialty for systems integration. He also has worked as a programmer and data analyst in an array of academic settings, including the MIRAGE Alzheimer Disease project at Boston University Medical Center and as a member of the Harvard Computational Biology Initiative, where he played an integral role in creating innovative visual displays of gene networks that became Autworks. His research interests include visualization of information and human-computer interaction as applied to complex data sets. At the Greene Lab, he enjoys the challenge of making novel research methods available and useful to a broader audience of biologists. [E-mail]

 

Kurt Wheeler

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Kurt graduated from Drexel University in 2014 with a B.S. in Computer Science. After working at a tech startup on a Business Intelligence tool for a couple years he decided to try and make a greater impact with his software skills. He found the Greene Lab and has been happily creating software for researchers since. Kurt values clean maintainable code, scalable engineering, and ultimately making software that is useful to researchers answering important questions.

 

RENÉ Zelaya

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René graduated in 2012 with a B.A. in Engineering Sciences from Dartmouth College. He started working as a programmer in the Integrative Genomics Lab during the spring of 2013. His primary mission is to put our research advances into the hands of biologists. He works with users to understand how we can make their lives easier through accessible computation. He translates these conversations, in the context of our machine learning advances, into functionality embedded inwebservers such as GIANT and Tribe that address key biological challenges. René also manages the code review process in the lab, which keeps our group thinking about both design and documentation principles.

 

Vincent Rubinetti

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Vince is a staff frontend developer in the Greene Lab. His job is to take the studies, projects, and ideas of his colleagues and turn them into beautiful, dynamic, fully-realized web applications. His work includes app development, website development, UI/UX design, logo design, and anything else visual or creative. Outside of the lab, Vince is a freelance music composer for indie video games and YouTube channels.

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+ + /new-pi-slack-code-of-conduct + New PI Slack Code of Conduct + Fri, 05 May 2017 11:16:51 +0000 + New PI Slack Code of Conduct

All members of the New PI Slack are expected to abide by this code of conduct. We expect cooperation from all members to help ensure a safe environment for everybody. We are dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, or religion (or lack thereof). We do not tolerate harassment of team members in any form.

Harassment includes offensive verbal comments related to gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, religion, sexual images in public spaces or direct messages, deliberate intimidation, stalking, following, inappropriate physical contact, and unwelcome sexual attention. Sexual language and imagery are generally not appropriate. However, we work on biological matters so work-related discussions can be appropriate.

New PI Slack is designed to be a supportive environment. We value divergent viewpoints and solicited, constructive feedback of scientific ideas, projects, and outputs, but please refrain from personal criticism. Also, #humblebrag is a criticism-free zone.

Members asked to stop any harassing or other undesired behavior are expected to comply immediately. If a participant engages in harassing behavior, team administrators may take any action they deem appropriate, including removal from the Slack team.

If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact Prachee Avasthi, Elana Fertig, Michael Hoffman, or Maitreyi Das.

The code of conduct section is licensed under a Creative Commons Attribution 3.0 Unported License adapted from the Biomedical Postdoc Slack Group code of conductthe Greene Lab code of conducthttp://2012.jsconf.us/#/about & The Ada Initiative. Please help by translating or improving: http://github.com/leftlogic/confcodeofconduct.com.

 

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+ + /computational-microbiology-postdoc + Computational Microbiology Postdoc + Thu, 26 Apr 2018 19:56:27 +0000 + POSTDOCTORAL RESEARCHER POSITION:

Position

The Greene lab welcomes applications for a computational postdoctoral position at the University of Pennsylvania’s Perelman School of Medicine. The Greene lab's overarching goal is to transform how we understand complex biological systems by developing and applying computational algorithms that effectively model processes by integrating multiple types of big data from diverse experiments. The successful candidate will have the opportunity to work with large collections of microbial transcriptomic data, both publicly available and from collaborative projects.


Objectives

This position will focus on the development and rigorous evaluation of new models for microbial transcriptomes and the development of methods to predict the genome-wide outcome of microbial responses to perturbations. We will extract testable biological hypotheses from these large collections and test these hypotheses in collaboration with the Hogan Lab at The Geisel School of Medicine at Dartmouth. Postdocs are expected to contribute to the lab's culture of open scientific discovery and to share methodological advances and biological discoveries at both national and international venues.


Qualifications

  1. Candidates are expected to have an MD, PhD, or equivalent, with programming experience and a strong background in microbiology, genetics, machine learning, statistics, bioinformatics, or closely related field.
  2. Candidates are expected to strive for robust and reproducible analytical workflows.

  3. The ideal candidate will also have attributable contributions to publicly available source code.

  4. The ideal candidate will have experience handling large datasets in a UNIX/LINUX environment, experience with high performance cluster or cloud computing, and a knowledge of existing software packages used for machine learning.


The Greene Lab focuses on open, reproducible science. Software and analytical workflows produced by the lab are available primarily via GitHub (https://github.com/greenelab). A listing of recent publications is available on the lab website (http://www.greenelab.com/publications/). We aim for a diverse group of lab members with complementary expertise and experience (http://www.greenelab.com/lab-members/). Our lab procedures are available on GitHub (https://github.com/greenelab/onboarding/blob/master/onboarding.md).

About the lab


Applying

To apply, send a cover letter that includes the names and contact information for three references, a short statement of research interests, and a current CV to Casey Greene (greenescientist@gmail.com).

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+ computational-microbiology-postdoc + page + 52 + publish +
+ + Infant in arms: some thoughts from a father traveling solo with an infant + /musings/2019/1/29/infant-in-arms-some-thoughts-from-a-father-traveling-solo-with-an-infant + Brief Context

As a scientist, I often attend conferences/meetings/etc. Making this work as a childless, married academic husband was reasonably straightforward for my wife and me. However, things changed in April of 2018 when our daughter was born. Finding a way to integrate our daughter into this schedule is important because academic life bleeds heavily into times that are normally reserved for family life (weekends, evenings). Many academic conferences and events are scheduled over a weekend or involve weekend travel. What works for us is that I will take the baby with me when I travel for trips where it makes sense for both of our schedules. In our daughter’s first six months, I traveled roughly 25,000 miles with her via air, car, and Amtrak. Here I’m compiling some observations from my travel that may be informative or helpful to others.

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Visiting the Broad Institute on the first solo trip I took with our daughter, which we did via Amtrak.

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Travel Supplies

  • A good backpack beats a diaper bag. I received an Aer Travel Pack 2 as a gift and used it as a travel backpack for some time before our daughter was born. It was fine for that, but it makes a great travel diaper bag. The features that I have found most important are that 1) electronics get stored in a separate, padded compartment; 2) the separate “shoe compartment” can be used for soiled clothes (or diapers if you haven’t found a place to dispose of them) wrapped in a plastic bag; 3) it opens like a clamshell, so you can access different contents easily: I store diapers and wipes at the bottom, a couple changes of clothes above that, and then bottles, formula, and toys at the top; and 4) it fits under the seats of nearly all aircraft (there are a few aircraft types that have very narrow underseat storage for the aisle seat where it won’t fit).

  • Have a support for the baby on your lap. I’ve had good success with a Boppy pillow. These things look like a huge neck pillow for the waist. I’ve found this helps with feeding, but it also gives our baby something to sleep on during the flight. For me, it reduces the discomfort from having her on my lap for long stretches.

  • Bring a few toys, but find a bunch more. Our baby’s philosophy seems to be that an object is just a toy she hasn’t figured out how to have fun with yet. Travel leads to lots of new objects. We’ve had fun with snack mix bags, plastic cups, spoons, and many other items. I’ve had good luck bringing a few toys and planning to find more along the way.

  • My travel go-to items for baby moving are an Ergobaby carrier, travel stroller, and car seat. I like a travel stroller that the car seat gets attached to via a strap that goes where the seat belt would be. In general, I use these as one would expect. The best way I’ve found to board a plane solo is to, a few minutes before boarding begins, put the baby into the ergobaby. Wheel the stroller with the car seat inside down the ramp. Fold the stroller and place both the stroller and the car seat at the end of the ramp for the ground crew. For deplaning, I do this in reverse. Finding a routine that works has helped me to keep everything together in some hectic situations. The one caveat of going this route is to note that you need two gate-check tags - one for the stroller and a second one for the car seat.

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Napping on the Boppy pillow.

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Everything’s a toy! This cup was a big hit with me in Houston.

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Car seat, stroller, Boppy in the walking-through-the-airport configuration.

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Feeding

  • Traveling with formula was the best option for me. I traveled with a cooler of breastmilk for the first trip I took with our baby, which was via Amtrak. It dramatically increased how much I needed to carry, the logistics involved with timing, and meant that I needed to make absolutely sure that the hotel would have a suitably cold fridge (and freezer) on arrival. It is something that is possible to do via train. I only did this for the first trip, though I looked at what it would take to pack for travel via air and decided against for subsequent trips. Formula is easier for me since I can easily pack it or buy it upon arrival.

  • Feed when the baby is hungry, and stay consistent in the size of the bottle. For the first trips I had planned out when our baby would be hungry based on her normal schedule, and so I knew where I would be for each one. Unfortunately, travel seems to alter babies eating schedules in unpredictable ways. I tried to compensate by feeding an “interim” bottle that was half-size to tide her over to the planned feeding time, but I have found this to be a path straight to a fussy baby and don’t recommend it.

  • Whenever I find the perfect size cups, I ask for a few. When I travel with room-temperature formula and happen across paper cups for hot drinks that hold the bottle plus a roughly equal amount of water, I snag a few. When I ask for water to heat up formula on a plane, I usually get near-boiling water (when I use this water to heat formula, I let the water cool just a little bit, and then swirl the formula pretty quickly while it’s warming - I didn’t do this the first time, cooked the formula, and had to throw it out and start over). I’ve found that with the rate of heat loss from such cups, equal amounts of formula and water is about the right size to get a suitably warm bottle of formula for our baby. If the volume of the cup is too large the formula ends up too hot and I increase the risk of cooking it. If it’s too low, our baby won’t drink it.

In Air and Airport

  • Flights with a connection are better for longer itineraries. When I traveled alone, I preferred the direct flight. I’ve found that when traveling with a baby, the opportunity to disembark, walk around a little bit, feed and change the baby in a less cramped space, and then continue to the destination is far more compatible with the happiness of me and our baby. As a side benefit, these flights are often a bit cheaper than direct ones.

  • Airline club membership is helpful when traveling with an infant. In 2017, I flew enough that I had complimentary access to Delta’s Sky Clubs in 2018. The ability to take my stuff and baby in, set the stuff down, get a bite of food and some water, eat, feed the baby, change the baby, and get to the next flight made all of this far more pleasant.

  • Certain aircraft do not have changing tables in the restrooms. Delta flies a number of older aircraft (MD-88s, MD-90s, and 717s) and they use them heavily for flights to Philadelphia. The existence of changing tables on these aircraft has been hit or miss. If they do have changing tables, they’re usually in one of the economy restrooms in the tail. At least on Delta, you won’t know this when you book - only when you look. You probably want to check all three restrooms unless you are comfortable changing an infant who you are holding vertically. I’ve had to change three blowouts while holding our baby vertically in these aircraft without any tables. It’s something you get ok at. I highly recommend traveling with the baby in either kimono-style onesies or zippy jamz pajamas. Anything that goes over the head is bad news for a standing blowout change.

  • Ask for more cabin comfort. The time that this most comes to mind for me was an early morning flight out of Houston’s Hobby Airport. We’d gotten up around 4AM to catch a 6AM flight, and the aircraft was inordinately warm when we boarded. My daughter actually did ok during the boarding process, but the flight continued to warm up on ascent. My daughter started crying and was very difficult to console. I thought the heat might be an issue, but it also could have been the early wake-up or something else. I waited until the drink service to ask if the cabin could be cooled down. After service, the flight attendants must have asked the cockpit to reduce the temperature. As soon as it started cooling down, she went to sleep and slept the rest of the flight. If I’d used the call button before service, I could have saved everyone a half-hour of listening to a crying baby.

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Snack mix bags crinkle, and wow that is fun!

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Skyclub membership was helpful. This one in SLC let us put our stuff down and recharge mid-itinerary.

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Even as our daughter has grown, the Boppy pillow remains a favorite in the air.

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Hotels

  • For our baby at least, the first night in each new hotel room was a rough one. I usually had at least a few wake-ups at unusual times in addition to the usual ones. I haven’t found a solution to this, but at least I’m now aware of what it’ll be like.

  • Don’t expect a crib in the room when you arrive. I don’t care how many times you call the hotel. I don’t care if it’s the AAA four-diamond rated Fairmont Orchid and you noted it on your reservation, confirmed again a week before, and confirmed at the desk when you checked in. Do not expect it to be there. Expect it to take at least an hour and three calls to the service desk after you arrive (at 10 PM Hawaii time after traveling from the east coast - I’m still glaring at you Fairmont Orchid). We occasionally found the crib we had asked for (every time for our hotels in Japan, almost never anywhere else). But this seems to be something hotels in the US are more or less terrible at, so I’d say just imagine it won’t be there. We did purchase a travel crib, which we have used when my wife and I have traveled together. My daughter sleeps better in this, but the weight and added item makes it too cumbersome for me to take when it’s just me.

Other Venue Notes

  • Some places have been remarkably wonderful to work with. In particular, the folks who scheduled the Annual Keck Center Research Conference for the Gulf Coast Consortia were incredible. I was invited to speak at this event and initially declined because it was the day after a previously-scheduled return flight from Japan. After some discussion with the organizers, I decided to skip my final Detroit to Philadelphia leg and fly to Houston for the event before returning home. While in Japan, we found it hard to get liquid formula that we’d need for the Houston part of the trip. When I asked for suggestions of a place to buy formula near the airport or hotel, the folks from the event put enough bottles of formula at the hotel check-in that we were able to make it through the first night. Then I just had to walk to a store to buy formula before the meeting the next day. I also want to give a shout out to the folks from Northwestern Mutual’s HQ in Milwaukee. They hosted ALSF’s Young Investigator Summit and made traveling with the baby a breeze.

  • Traveling with an infant may cost you some opportunities. I was invited to give talks both during a symposium and for the community in my area of expertise at the University of Oslo that would have involved weekend travel. When I asked the organizers to ask the hotel to add a crib to the room during the reservation process, this led to some red flags that ultimately led to the decision to find another speaker for their event and seminar series. The advice that I’ve gotten from folks on social media who traveled to work-related seminars where they needed to take their kids was to not give organizers a heads up and to deal directly with the hotel for a crib. If it’s an opportunity you can’t afford to miss, it sounds like this is still the way to go in 2018. However, if missing the event wouldn’t be hugely costly, I’ve found other places to be helpful and willing to ask the hotel for a crib when they make the reservation.

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Speaker dinner for the Keck Center Research Conference.

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Our daughter spending lunch with me at PSB.

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Closing thoughts

I’ve enjoyed traveling with our daughter during this time. For fathers who are considering traveling with their infants to a conference or symposium, I’ve found that it is very practical to do so. I would be remiss not to note that we give women traveling with a baby far less support than men. There have been numerous situations throughout my time traveling that have made this clear to me. On multiple flights, attendants have offered to hold my daughter if I needed to go to the restroom. I haven’t seen the same level of support for women traveling alone with their babies. In one case, a flight attendant walked my daughter up and down the aisle of the aircraft to calm her. Even fellow passengers seemed less irritated by a fussy infant with me: in all of this travel I can only think of one dirty look that I got from a fellow passenger while I was traveling alone with my daughter. When you travel, offer assistance and understanding to women who need it as well.

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+ In our daughter’s first six months, I traveled roughly 25,000 miles with her via air, car, and Amtrak. Here I’m compiling some observations from my travel that may be informative or helpful to others.

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+ 2019/1/29/infant-in-arms-some-thoughts-from-a-father-traveling-solo-with-an-infant + post + 53 + publish + Tue, 29 Jan 2019 12:00:00 +0000 + 2019-01-29 12:00:00 + 2019-01-29 12:00:00 + csgreene@upenn.edu + closed + + _thumbnail_id + + +
+ + http://static1.squarespace.com/static/53ce848ce4b029ce6cd25fe3/5c50269f4ae237b6d9c78736/5c5027388a922deab94d542b/1554549238666/Dx2CN1WW0AAwpqn.jpg + http://static1.squarespace.com/static/53ce848ce4b029ce6cd25fe3/5c50269f4ae237b6d9c78736/5c5027388a922deab94d542b/1554549238666/Dx2CN1WW0AAwpqn.jpg + attachment-5c5027388a922deab94d542b + Dx2CN1WW0AAwpqn-jpg + attachment + 54 + inherit + + + Tue, 29 Jan 2019 12:00:00 +0000 + 2019-01-29 12:00:00 + 2019-01-29 12:00:00 + csgreene@upenn.edu + + + The Harassment Tax. + /musings/2019/4/6/the-harassment-tax + The Harassment Tax

TL;DR: This twitter thread from Michael Hendricks is on the money.

In a recent article in Science about the National Academies developing a procedure to expel sexual harassers, Dr. Robert Weinberg (Member, Whitehead Institute; and Daniel K. Ludwig Professor for Cancer Research in the Department of Biology at MIT) was quoted as saying, “Before there is a mad rush to approve such an ejection procedure, it might be useful to ask whether sexual harassment by a member has anything whatsoever to do with their credibility as a scientist and the soundness of their research accomplishments—the criteria that were used to elect them in the first place.” When scientists reach these milestones by imposing costs on others through falsification, harassment, or other means they are externalizing costs onto the rest of the field. We shouldn’t honor that.

We might be tempted to buy into a lone genius model of science. In popular media, scientists are sometimes presented as brilliant folks who toil in isolation and only emerge when they have some deep, self-evident insight that nobody can disagree with. However, this model is a myth and nothing could be further from the truth. Science is a messy, community-based process. The scientist toiling long hours in the lab has based work on the findings of others. That scientist has had ideas honed by a mentor, feedback from others in the research group, and directly or indirectly by external peers. For the work to be convincing and impactful, the scientist will need to rule out additional models raised by the community by performing more experiments. The ultimate trajectory of a research program and its influence is shaped by others.

As soon as one leaves the lone genius myth behind, it is obvious why harassers should not be admitted to the National Academies and should be expelled if they already have been admitted. Unfortunately, harassment is all too common in academia, with fifty-eight percent of female faculty and staff in academia reporting behaviors that constitute harassment. Scientists who are harassed have their time and attention unfairly taken from them. They may leave one field and transition to another to escape their harasser(s) – requiring them to spend time gaining additional skills and knowledge – or even leave science entirely (see the NASEM report on Sexual Harassment of Women, Chapter 4). Those who support such scientists (for example Dr. BethAnn McLaughlin, founder of #MeTooSTEM) are also taxed for their own time and attention. Too often, these may be ghost mentors who receive little or no credit for their efforts.*

Harassment taxes the harassed scientist’s time, attention and resources, as well as those of other scientists. It weakens the community: by promoting a homogeneity of experiences and backgrounds it reduces the effectiveness of scientific inquiry. In short, it imposes the costs for the failings of the harasser on others. Revisiting Dr. Weinberg’s question of whether or not sexual harassment has anything to do with a perpetrator’s credibility and research accomplishments, my answer is an emphatic “Yes!”

It’s clear that the National Academies can be a force for good: see, for example, their own report on the impact of Sexual Harassment. If the National Academies fail to pass this policy during the vote on April 30th, then they will have failed the scientific community. Other organizations, for example the Wellcome Trusts, are moving ahead with policies to reduce harassment in science. Every time that the National Academies fail to expel harassers, they look more like relics of a bygone age. This diminishes the relevance of the Academies to the future of science and the honor associated with membership.


* Take Dr. McLaughlin for example: her work is more widely cited than mine, she’s received more NIH funding than I have (in addition to other federal funding), and she’s clearly had a larger impact on the practice of science than I have (AAAS and NAS among many others). It’s clear that she is far more qualified to be a tenured faculty member than I am. In a seemingly absurd decision, Vanderbilt denied her tenure case after the dean of VUMC, Jeffrey Balser, had her case reconsidered by a committee that included a faculty member now on leave for sexual misconduct (David Sweatt). The committee in question was overturning two initial favorable tenure decisions. The Chancellor of Vanderbilt University, Nick Zeppos, has failed to support her tenure case, though he has published a blog post on the importance of women at Vanderbilt. It conspicuously ignores Dr. McLaughlin, a winner of the MIT Disobedience Prize.

P.S. I gave a talk at UAB recently, where I included some slides (+ a new bonus slide with Dr. Weinberg’s quotation for a seminar I’m giving at NYU on Monday, April 8). You are welcome to use them in your own talks (note the arrangement, which is my own, is CC0 licensed, but certain content is by others and not openly licensed and so uses of those portions must fall under fair use).

Header image licensed CC-BY-SA by Another Believer.

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+ In a recent article in Science about the National Academies developing a procedure to expel sexual harassers, Dr. Robert Weinberg was quoted as saying, “Before there is a mad rush to approve such an ejection procedure, it might be useful to ask whether sexual harassment by a member has anything whatsoever to do with their credibility as a scientist and the soundness of their research accomplishments—the criteria that were used to elect them in the first place.” When scientists reach these milestones by imposing costs on others through falsification, harassment, or other means they are externalizing costs onto the rest of the field. We shouldn’t honor that.

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+ 2019/4/6/the-harassment-tax + post + 55 + publish + Sat, 06 Apr 2019 11:15:00 +0000 + 2019-04-06 11:15:00 + 2019-04-06 11:15:00 + csgreene@upenn.edu + closed + + _thumbnail_id + + +
+ + http://static1.squarespace.com/static/53ce848ce4b029ce6cd25fe3/5c50269f4ae237b6d9c78736/5ca88202e79c701af1e96c10/1554549290788/1280px-National_Academy_of_Sciences%2C_Washington%2C_D.C._01_-_2012.JPG + http://static1.squarespace.com/static/53ce848ce4b029ce6cd25fe3/5c50269f4ae237b6d9c78736/5ca88202e79c701af1e96c10/1554549290788/1280px-National_Academy_of_Sciences%2C_Washington%2C_D.C._01_-_2012.JPG + attachment-5ca88202e79c701af1e96c10 + 1280px-National-Academy-of-Sciences-Washington-D-C-01-2012-JPG + attachment + 56 + inherit + + + Sat, 06 Apr 2019 11:15:00 +0000 + 2019-04-06 11:15:00 + 2019-04-06 11:15:00 + csgreene@upenn.edu + + + Why do we have application fees? + /musings/2019/5/1/why-do-we-have-application-fees + Context

I’m considering this question in regards to PhD programs in the biological sciences. For a brief bit of context, these are programs where trainees, once they join a program, have their tuition paid for and also receive a stipend. The funds to offer the stipend and tuition coverage primarily come from an institution, from training grants (which are given to an individual or institution to support training in areas of need), and from research project grants (which are given to an institution for the purposes of carrying out a specific research project). In short, the training program includes classwork, which is an investment that the institution makes in each student, as well as a research component, which involves the trainee carrying out a project that also benefits the institution.

What are the application fees?

When students want to apply to one of these programs, they are often required to pay a fee to have their application considered. The fee to apply to our Genomics and Computational Biology (GCB) program for the 2019 class year was $80. This means that we raise from applicants, at most (see the bit on fee waivers below), about $16000 per year if we assume roughly 200 applications. A student applying to 10 PhD programs would spend roughly $800 with the hopes of matriculating into one.

What are the arguments in favor of application fees?

I’ve heard a few arguments for fees. I can continue to add to this list if folks provide new reasons (mention @greenescientist on twitter or email greenescientist@gmail.com). If you want to add a reason, please keep it to a few sentences or provide a link to a twitter thread / blog post / something else that I can link to.

  • It signifies that the applicant is seriously considering the program. By paying the fee the student is essentially anteing up and saying they would be interested in attending the program if invited.

  • It raises funds that can be used for purposes that would be otherwise difficult to cover on certain other sources of support (e.g., beer at interview weekends).

  • It does not create a barrier to anyone because domestic applicants can request fee waivers. I am under the impression that the Penn Biomedical Graduate Studies (BGS) program policies are to grant waivers to any domestic applicant who requests one.

What are my concerns with application fees?

I worry that the fees present barriers for reasons that I’ll detail below. I can also continue to add to this list if folks provide new reasons (mention @greenescientist on twitter or email greenescientist@gmail.com). If you want to add a reason, please keep it to a few sentences or provide a link to a twitter thread / blog post / something else that I can link to.

  • The barrier imposed by fees is unequally felt by students. Students for whom $1000 is a negligible cost at the conclusion of their undergraduate careers may apply to many programs, increasing their likelihood of admission, while those for whom this is a major cost may apply to fewer programs. Even with fee waivers (which seem to only apply to domestic students), students who face this hurdle and who do not realize they can ask for a fee waiver, who feel that asking for a fee waiver may reveal something that they do not wish to share, or who feel that asking for a fee waiver burdens a program may apply to fewer programs reducing their chances of admission.

  • The amount of money that a program gains is not that substantial relative to other program expenses. For our example of the Penn GCB program, applicants’ fees provide about $16,000 in revenue per year. However, the stipends alone for each entering class of roughly ten students run more than $300,000 per year. Including the tuition, and the fact that the first two years are covered by institutional funds at Penn, each class of students for a ten-person program must cost at least $650,000 before students are transitioned onto research grant support. A more accurate number is probably ~$960,000, but I wanted to provide the most conservative estimate.

  • Programs benefit from attracting the best possible set of matriculating students. Students are engaged in both coursework and research. Their research efforts directly benefit the institution. Thus while it is true that students are competing for spots in each class, programs are also competing for students. Admission to a PhD program can be quite difficult to predict and depends on certain factors related to the student (application strength as perceived by an admissions committee) but also factors beyond the control of the student (the composition of the rest of the applicant pool with respect to research interests and potential research advisors). It seems unfair and inefficient to penalize students for applying to programs that may initially seem like a reach.

What could the next steps be?

I have been made aware that at Penn we looked into the effect of application fees and little evidence was found that our fees were a barrier. I did look through the peer-reviewed literature a bit, and I couldn’t find data on the results of a complete elimination of application fees. I did find results that suggested that granting fee waivers as a matter of routine could be helpful. It seems that perhaps there isn’t evidence simply because the experiment hasn’t been done.

I hope that one or more graduate programs at an institution will run an experiment with the complete elimination of application fees. It is probably best, from an experimental design point of view, to eliminate fees for randomly selected set of programs while leaving other programs at the institution’s application fee unchanged. Interesting outcomes to examine would include committee-assigned scores for applicants invited to interview; the number of first generation, low income, and underrepresented minority scientists invited to interview; and the yield from the interview process. I had hoped that we would be able to run such an evaluation at Penn, but this will not come to pass. I am posting this to the blog in the hopes that another institution will find the question to be worth asking.

Update 5/1/19: After posting, I was pointed to CMU’s Department of Philosophy’s elimination of application fees in 2017.

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+ + 2019/5/1/why-do-we-have-application-fees + post + 57 + publish + Wed, 01 May 2019 14:35:51 +0000 + 2019-05-01 14:35:51 + 2019-05-01 14:35:51 + csgreene@upenn.edu + open +
+
+
+ diff --git a/preview/pr-117/publications.html b/preview/pr-117/publications.html new file mode 100644 index 00000000..828b69d8 --- /dev/null +++ b/preview/pr-117/publications.html @@ -0,0 +1,16 @@ + + + + + + Redirecting… + + + + + + +

Redirecting…

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+ + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+

+Research

+ +

There is an abundance of publicly available data about various biological systems, but it can be difficult to draw insight from individual datasets. +Our lab develops algorithms that integrate these data to help model and understand complex biological systems. +Doing this allows us to investigate many different biological conditions, including those with limited data, such as rare diseases. +We recognize that our lab won’t have all the answers, or even all of the questions, so we aim to develop tools and processes that any biologist can reuse. +Our approach to research prioritizes transparency, rigor, and reproducibility.

+
+ + + + + +
+ + + + + + +

The citations on this page were generated automatically from just identifiers using the Manubot cite utility developed right here in the Greene Lab!

+ + + +
+ +

2024

+ +
+ + + Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine + + + +
+ + + + + Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine + + +
+ Laura K. Wiley, Jonathan A. Shortt, Emily R. Roberts, Jan Lowery, Elizabeth Kudron, ..., Nicholas Rafaels, Kristy R. Crooks, Steve Hess, Kathleen C. Barnes, Christopher R. Gignoux +
+ +
+ The American Journal of Human Genetics +   ·   + 01 Jan 2024 +   ·   + doi:10.1016/j.ajhg.2023.12.001 +
+ + + + + + + + +
+
+ +

2023

+ +
+ + + Molecular subtypes of high grade serous ovarian cancer across racial groups and gene expression platforms + + + +
+ + + + + Molecular subtypes of high grade serous ovarian cancer across racial groups and gene expression platforms + + +
+ Natalie R. Davidson, Mollie E. Barnard, Ariel A. Hippen, Amy Campbell, Courtney Johnson, ..., Lauren C. Peres, Jeffrey R. Marks, Joellen M. Schildkraut, Casey S. Greene, Jennifer A. Doherty +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 04 Nov 2023 +   ·   + doi:10.1101/2023.11.01.565179 +
+ + + + + + + + +
+
+ +
+ + + Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors + + + +
+ + + + + Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors + + +
+ Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene +
+ +
+ Genome Biology +   ·   + 20 Oct 2023 +   ·   + doi:10.1186/s13059-023-03077-7 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Integration of 168,000 samples reveals global patterns of the human gut microbiome + + + +
+ + + + + Integration of 168,000 samples reveals global patterns of the human gut microbiome + + +
+ Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 11 Oct 2023 +   ·   + doi:10.1101/2023.10.11.560955 +
+ + + + + + + + +
+
+ +
+ + + Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms + + + +
+ + + + + Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms + + +
+ Milton Pividori, Sumei Lu, Binglan Li, Chun Su, Matthew E. Johnson, ..., Benjamin F. Voight, Carsten Skarke, Marylyn D. Ritchie, Struan F. A. Grant, Casey S. Greene +
+ +
+ Nature Communications +   ·   + 09 Sep 2023 +   ·   + doi:10.1038/s41467-023-41057-4 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Analysis of<i>Pseudomonas aeruginosa</i>transcription in an<i>ex vivo</i>cystic fibrosis sputum model identifies metal restriction as a gene expression stimulus + + + +
+ + + + + Analysis ofPseudomonas aeruginosatranscription in anex vivocystic fibrosis sputum model identifies metal restriction as a gene expression stimulus + + +
+ Samuel L. Neff, Georgia Doing, Taylor Reiter, Thomas H. Hampton, Casey S. Greene, Deborah A. Hogan +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 21 Aug 2023 +   ·   + doi:10.1101/2023.08.21.554169 +
+ + + + + + + + +
+
+ +
+ + + MousiPLIER: A Mouse Pathway-Level Information Extractor Model + + + +
+ + + + + MousiPLIER: A Mouse Pathway-Level Information Extractor Model + + +
+ Shuo Zhang, Benjamin J. Heil, Weiguang Mao, Maria Chikina, Casey S. Greene, Elizabeth A. Heller +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 02 Aug 2023 +   ·   + doi:10.1101/2023.07.31.551386 +
+ + + + + + + + +
+
+ +
+ + + SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics + + + +
+ + + + + SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics + + +
+ Halie M. Rando, Casey S. Greene, Michael P. Robson, Simina M. Boca, Nils Wellhausen, ..., Yusha Sun, Daniel S. Himmelstein, Jeremy P. Kamil, Jesse G. Meyer, Ariel I. Mundo +
+ +
+ Manubot +   ·   + 30 Jul 2023 +   ·   + url:https://greenelab.github.io/covid19-review/ +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + BuDDI:<i>Bulk Deconvolution with Domain Invariance</i>to predict cell-type-specific perturbations from bulk + + + +
+ + + + + BuDDI:Bulk Deconvolution with Domain Invarianceto predict cell-type-specific perturbations from bulk + + +
+ Natalie R. Davidson, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 22 Jul 2023 +   ·   + doi:10.1101/2023.07.20.549951 +
+ + + + + + + + +
+
+ +
+ + + Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry Estimates from Direct-to-Consumer Canine Genetic Tests + + + +
+ + + + + Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry Estimates from Direct-to-Consumer Canine Genetic Tests + + +
+ Halie M. Rando, Kiley Graim, Greg Hampikian, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 29 Jun 2023 +   ·   + doi:10.1101/2023.06.28.546898 +
+ + + + + + + + +
+
+ +
+ + + Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction + + + +
+ + + + + Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction + + +
+ Jake Crawford, Maria Chikina, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 26 Jun 2023 +   ·   + doi:10.1101/2023.06.26.546586 +
+ + + + + + + + +
+
+ +
+ + + Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes + + + +
+ + + + + Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes + + +
+ Ariel A. Hippen, Natalie R. Davidson, Mollie E. Barnard, Lukas M. Weber, Jason Gertz, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 15 Jun 2023 +   ·   + doi:10.1101/2023.06.14.544991 +
+ + + + + + + + +
+
+ +
+ + + Machine learning in rare disease + + + +
+ + + + + Machine learning in rare disease + + +
+ Jineta Banerjee, Jaclyn N. Taroni, Robert J. Allaway, Deepashree Venkatesh Prasad, Justin Guinney, Casey Greene +
+ +
+ Nature Methods +   ·   + 29 May 2023 +   ·   + doi:10.1038/s41592-023-01886-z +
+ + + + + + + + +
+
+ +
+ + + Changing word meanings in biomedical literature reveal pandemics and new technologies + + + +
+ + + + + Changing word meanings in biomedical literature reveal pandemics and new technologies + + +
+ David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti, Casey S. Greene +
+ +
+ BioData Mining +   ·   + 05 May 2023 +   ·   + doi:10.1186/s13040-023-00332-2 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + The Coming of Age of Nucleic Acid Vaccines during COVID-19 + + + +
+ + + + + The Coming of Age of Nucleic Acid Vaccines during COVID-19 + + +
+ Halie M. Rando, Ronan Lordan, Likhitha Kolla, Elizabeth Sell, Alexandra J. Lee, ..., Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen +
+ +
+ mSystems +   ·   + 27 Apr 2023 +   ·   + doi:10.1128/msystems.00928-22 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Application of Traditional Vaccine Development Strategies to SARS-CoV-2 + + + +
+ + + + + Application of Traditional Vaccine Development Strategies to SARS-CoV-2 + + +
+ Halie M. Rando, Ronan Lordan, Alexandra J. Lee, Amruta Naik, Nils Wellhausen, ..., Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen +
+ +
+ mSystems +   ·   + 27 Apr 2023 +   ·   + doi:10.1128/msystems.00927-22 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes + + + +
+ + + + + MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes + + +
+ Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu +
+ +
+ Nucleic Acids Research +   ·   + 18 Apr 2023 +   ·   + doi:10.1093/nar/gkad289 +
+ + + + + + + + +
+
+ +
+ + + The effect of non-linear signal in classification problems using gene expression + + + +
+ + + + + The effect of non-linear signal in classification problems using gene expression + + +
+ Benjamin J. Heil, Jake Crawford, Casey S. Greene +
+ +
+ PLOS Computational Biology +   ·   + 27 Mar 2023 +   ·   + doi:10.1371/journal.pcbi.1010984 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Biological research and self-driving labs in deep space supported by artificial intelligence + + + +
+ + + + + Biological research and self-driving labs in deep space supported by artificial intelligence + + +
+ Lauren M. Sanders, Ryan T. Scott, Jason H. Yang, Amina Ann Qutub, Hector Garcia Martin, ..., Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes +
+ +
+ Nature Machine Intelligence +   ·   + 23 Mar 2023 +   ·   + doi:10.1038/s42256-023-00618-4 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Biomonitoring and precision health in deep space supported by artificial intelligence + + + +
+ + + + + Biomonitoring and precision health in deep space supported by artificial intelligence + + +
+ Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-min Park, ..., Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes +
+ +
+ Nature Machine Intelligence +   ·   + 23 Mar 2023 +   ·   + doi:10.1038/s42256-023-00617-5 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously + + + +
+ + + + + Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously + + +
+ Steven M. Foltz, Casey S. Greene, Jaclyn N. Taroni +
+ +
+ Communications Biology +   ·   + 25 Feb 2023 +   ·   + doi:10.1038/s42003-023-04588-6 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia + + + +
+ + + + + Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia + + +
+ Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Taylor Reiter, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan +
+ +
+ mSystems +   ·   + 23 Feb 2023 +   ·   + doi:10.1128/msystems.00341-22 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14 + + + +
+ + + + + Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14 + + +
+ Alexandra J. Lee, Georgia Doing, Samuel L. Neff, Taylor Reiter, Deborah A. Hogan, Casey S. Greene +
+ +
+ mSystems +   ·   + 23 Feb 2023 +   ·   + doi:10.1128/msystems.00342-22 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Hetnet connectivity search provides rapid insights into how two biomedical entities are related + + + +
+ + + + + Hetnet connectivity search provides rapid insights into how two biomedical entities are related + + +
+ Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, ..., David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 07 Jan 2023 +   ·   + doi:10.1101/2023.01.05.522941 +
+ + + + + + + + +
+
+ +
+ + + The probability of edge existence due to node degree: a baseline for network-based predictions + + + +
+ + + + + The probability of edge existence due to node degree: a baseline for network-based predictions + + +
+ Michael Zietz, Daniel S. Himmelstein, Kyle Kloster, Christopher Williams, Michael W. Nagle, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 06 Jan 2023 +   ·   + doi:10.1101/2023.01.05.522939 +
+ + + + + + + + +
+
+ +
+ + + The Field-Dependent Nature of PageRank Values in Citation Networks + + + +
+ + + + + The Field-Dependent Nature of PageRank Values in Citation Networks + + +
+ Benjamin J. Heil, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 06 Jan 2023 +   ·   + doi:10.1101/2023.01.05.522943 +
+ + + + + + + + +
+
+ +

2022

+ +
+ + + A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC + + + +
+ + + + + A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC + + +
+ Laurel B. Darragh, Michael M. Knitz, Junxiao Hu, Eric T. Clambey, Jennifer Backus, ..., Antonio Jimeno, Angelo D’Alessandro, David Raben, Jessica D. McDermott, Sana D. Karam +
+ +
+ Nature Cancer +   ·   + 25 Nov 2022 +   ·   + doi:10.1038/s43018-022-00450-6 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Discerning asthma endotypes through comorbidity mapping + + + +
+ + + + + Discerning asthma endotypes through comorbidity mapping + + +
+ Gengjie Jia, Xue Zhong, Hae Kyung Im, Nathan Schoettler, Milton Pividori, ..., Michiaki Kubo, Nancy J. Cox, Carole Ober, Andrey Rzhetsky, Julian Solway +
+ +
+ Nature Communications +   ·   + 07 Nov 2022 +   ·   + doi:10.1038/s41467-022-33628-8 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts + + + +
+ + + + + Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts + + +
+ David N. Nicholson, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ BioData Mining +   ·   + 18 Oct 2022 +   ·   + doi:10.1186/s13040-022-00311-z +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + wenda_gpu: fast domain adaptation for genomic data + + + +
+ + + + + wenda_gpu: fast domain adaptation for genomic data + + +
+ Ariel A Hippen, Jake Crawford, Jacob R Gardner, Casey S Greene +
+ +
+ Bioinformatics +   ·   + 04 Oct 2022 +   ·   + doi:10.1093/bioinformatics/btac663 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses + + + +
+ + + + + SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses + + +
+ Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene +
+ +
+ Genomics, Proteomics & Bioinformatics +   ·   + 01 Oct 2022 +   ·   + doi:10.1016/j.gpb.2022.09.011 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + OpenPBTA: An Open Pediatric Brain Tumor Atlas + + + +
+ + + + + OpenPBTA: An Open Pediatric Brain Tumor Atlas + + +
+ Joshua A. Shapiro, Krutika S. Gaonkar, Candace L. Savonen, Stephanie J. Spielman, Chante J. Bethell, ..., Sabine Mueller, Adam C. Resnick, Casey S. Greene, Jo Lynne Rokita, Jaclyn N. Taroni +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 16 Sep 2022 +   ·   + doi:10.1101/2022.09.13.507832 +
+ + + + + + + + +
+
+ +
+ + + GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases + + + +
+ + + + + GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases + + +
+ Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent J. Carey, Casey S. Greene, Levi Waldron, Sean Davis +
+ +
+ Nature Communications +   ·   + 27 Jun 2022 +   ·   + doi:10.1038/s41467-022-31411-3 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Widespread redundancy in -omics profiles of cancer mutation states + + + +
+ + + + + Widespread redundancy in -omics profiles of cancer mutation states + + +
+ Jake Crawford, Brock C. Christensen, Maria Chikina, Casey S. Greene +
+ +
+ Genome Biology +   ·   + 27 Jun 2022 +   ·   + doi:10.1186/s13059-022-02705-y +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + An efficient not-only-linear correlation coefficient based on machine learning + + + +
+ + + + + An efficient not-only-linear correlation coefficient based on machine learning + + +
+ Milton Pividori, Marylyn D. Ritchie, Diego H. Milone, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 17 Jun 2022 +   ·   + doi:10.1101/2022.06.15.496326 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Ten Quick Tips for Deep Learning in Biology + + + +
+ + + + + Ten Quick Tips for Deep Learning in Biology + + +
+ Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, ..., Alexandr A. Kalinin, Beth Signal, Benjamin J. Lengerich, Timothy J. Triche, Simina M. Boca +
+ +
+ arXiv +   ·   + 04 May 2022 +   ·   + arxiv:2105.14372 +
+ + + + + + + + +
+
+ +
+ + + Molecular and Serologic Diagnostic Technologies for SARS-CoV-2 + + + +
+ + + + + Molecular and Serologic Diagnostic Technologies for SARS-CoV-2 + + +
+ Halie M. Rando, Christian Brueffer, Ronan Lordan, Anna Ada Dattoli, David Manheim, ..., David Mai, Nils Wellhausen, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene +
+ +
+ arXiv +   ·   + 29 Apr 2022 +   ·   + arxiv:2204.12598 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Ten simple rules for large-scale data processing + + + +
+ + + + + Ten simple rules for large-scale data processing + + +
+ Arkarachai Fungtammasan, Alexandra Lee, Jaclyn Taroni, Kurt Wheeler, Chen-Shan Chin, Sean Davis, Casey Greene +
+ +
+ PLOS Computational Biology +   ·   + 10 Feb 2022 +   ·   + doi:10.1371/journal.pcbi.1009757 +
+ + + + + + + + +
+
+ +
+ + + Examining linguistic shifts between preprints and publications + + + +
+ + + + + Examining linguistic shifts between preprints and publications + + +
+ David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene +
+ +
+ PLOS Biology +   ·   + 01 Feb 2022 +   ·   + doi:10.1371/journal.pbio.3001470 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Computational audits combat disparities in recognition + + + +
+ + + + + Computational audits combat disparities in recognition + + +
+ Ariel A. Hippen, Natalie R. Davidson, Casey S. Greene +
+ +
+ Nature Human Behaviour +   ·   + 17 Jan 2022 +   ·   + doi:10.1038/s41562-021-01279-2 +
+ + + + + + + + +
+
+ +
+ + + Using genome-wide expression compendia to study microorganisms + + + +
+ + + + + Using genome-wide expression compendia to study microorganisms + + +
+ Alexandra J. Lee, Taylor Reiter, Georgia Doing, Julia Oh, Deborah A. Hogan, Casey S. Greene +
+ +
+ Computational and Structural Biotechnology Journal +   ·   + 01 Jan 2022 +   ·   + doi:10.1016/j.csbj.2022.08.012 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +

2021

+ +
+ + + Identification and Development of Therapeutics for COVID-19 + + + +
+ + + + + Identification and Development of Therapeutics for COVID-19 + + +
+ Halie M. Rando, Nils Wellhausen, Soumita Ghosh, Alexandra J. Lee, Anna Ada Dattoli, ..., Rishi Raj Goel, YoSon Park, Simina M. Boca, Anthony Gitter, Casey S. Greene +
+ +
+ mSystems +   ·   + 21 Dec 2021 +   ·   + doi:10.1128/mSystems.00233-21 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Characterizing Long COVID: Deep Phenotype of a Complex Condition + + + +
+ + + + + Characterizing Long COVID: Deep Phenotype of a Complex Condition + + +
+ Rachel R Deer, Madeline A Rock, Nicole Vasilevsky, Leigh Carmody, Halie Rando, ..., Umit Topaloglu, George D. Vavougios, Liwei Wang, Melissa A Haendel, Peter N Robinson +
+ +
+ eBioMedicine +   ·   + 01 Dec 2021 +   ·   + doi:10.1016/j.ebiom.2021.103722 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer + + + +
+ + + + + Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer + + +
+ Anthony R. Kerlavage, Anne C. Kirchhoff, Jaime M. Guidry Auvil, Norman E. Sharpless, Kara L. Davis, ..., Jack DiGiovanna, Adam C. Resnick, Eve R. Shalley, Sorena Nadaf, Warren A. Kibbe +
+ +
+ JCO Clinical Cancer Informatics +   ·   + 01 Dec 2021 +   ·   + doi:10.1200/CCI.21.00040 +
+ + + + + + + + +
+
+ +
+ + + Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure + + + +
+ + + + + Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure + + +
+ Halie M. Rando, Adam L. MacLean, Alexandra J. Lee, Ronan Lordan, Sandipan Ray, ..., Rishi Raj Goel, Serghei Mangul, Tiago Lubiana, Anthony Gitter, Casey S. Greene +
+ +
+ mSystems +   ·   + 26 Oct 2021 +   ·   + doi:10.1128/mSystems.00095-21 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data + + + +
+ + + + + Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data + + +
+ Binglan Li, Yogasudha Veturi, Anastasia Lucas, Yuki Bradford, Shefali S. Verma, ..., Yuan Luo, Milton Pividori, Hae Kyung Im, Casey S. Greene, Marylyn D. Ritchie +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 26 Oct 2021 +   ·   + 10.1101/2021.10.21.21265225 +
+ + + + + + + + +
+
+ +
+ + + A field guide to cultivating computational biology + + + +
+ + + + + A field guide to cultivating computational biology + + +
+ Gregory P. Way, Casey S. Greene, Piero Carninci, Benilton S. Carvalho, Michiel de Hoon, ..., Suzanne S. Sindi, Fabian J. Theis, Jean Y. H. Yang, Anne E. Carpenter, Elana J. Fertig +
+ +
+ PLOS Biology +   ·   + 07 Oct 2021 +   ·   + doi:10.1371/journal.pbio.3001419 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + An Open-Publishing Response to the COVID-19 Infodemic + + + +
+ + + + + An Open-Publishing Response to the COVID-19 Infodemic + + +
+ Halie M. Rando, Simina M. Boca, Lucy D'Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, Anthony Gitter +
+ +
+ Digital Infrastructures for Scholarly Content Objects 2021 +   ·   + 30 Sep 2021 +   ·   + url:http://ceur-ws.org/Vol-2976/paper-2.pdf +
+ + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition + + + +
+ + + + + Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition + + +
+ Madison Cooley, Casey S. Greene, Davis Issac, Milton Pividori, Blair D. Sullivan +
+ +
+ arXiv +   ·   + 08 Sep 2021 +   ·   + arxiv:2106.00657 +
+ + + + + + + + +
+
+ +
+ + + Analysis of scientific society honors reveals disparities + + + +
+ + + + + Analysis of scientific society honors reveals disparities + + +
+ Trang T. Le, Daniel S. Himmelstein, Ariel A. Hippen, Matthew R. Gazzara, Casey S. Greene +
+ +
+ Cell Systems +   ·   + 01 Sep 2021 +   ·   + doi:10.1016/j.cels.2021.07.007 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design + + + +
+ + + + + Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design + + +
+ Lukas M Weber, Ariel A Hippen, Peter F Hickey, Kristofer C Berrett, Jason Gertz, Jennifer Anne Doherty, Casey S Greene, Stephanie C Hicks +
+ +
+ GigaScience +   ·   + 01 Sep 2021 +   ·   + doi:10.1093/gigascience/giab062 +
+ + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Reproducibility standards for machine learning in the life sciences + + + +
+ + + + + Reproducibility standards for machine learning in the life sciences + + +
+ Benjamin J. Heil, Michael M. Hoffman, Florian Markowetz, Su-In Lee, Casey S. Greene, Stephanie C. Hicks +
+ +
+ Nature Methods +   ·   + 30 Aug 2021 +   ·   + doi:10.1038/s41592-021-01256-7 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data + + + +
+ + + + + miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data + + +
+ Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks +
+ +
+ PLOS Computational Biology +   ·   + 24 Aug 2021 +   ·   + doi:10.1371/journal.pcbi.1009290 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Community-wide hackathons to identify central themes in single-cell multi-omics + + + +
+ + + + + Community-wide hackathons to identify central themes in single-cell multi-omics + + +
+ Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, ..., Michael I. Love, Matthew E. Ritchie, Guo-Cheng Yuan, Aedin C. Culhane, Elana Fertig +
+ +
+ Genome Biology +   ·   + 05 Aug 2021 +   ·   + doi:10.1186/s13059-021-02433-9 +
+ + + + + + + + +
+
+ +
+ + + Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment + + + +
+ + + + + Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment + + +
+ Ronan Lordan, Halie M. Rando, Casey S. Greene +
+ +
+ mSystems +   ·   + 29 Jun 2021 +   ·   + doi:10.1128/mSystems.00122-21 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Analysis of science journalism reveals gender and regional disparities in coverage + + + +
+ + + + + Analysis of science journalism reveals gender and regional disparities in coverage + + +
+ Natalie R. Davidson, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 22 Jun 2021 +   ·   + doi:10.1101/2021.06.21.449261 +
+ + + + + + + + +
+
+ +
+ + + Expanding and Remixing the Metadata Landscape + + + +
+ + + + + Expanding and Remixing the Metadata Landscape + + +
+ Ariel A. Hippen, Casey S. Greene +
+ +
+ Trends in Cancer +   ·   + 01 Apr 2021 +   ·   + doi:10.1016/j.trecan.2020.10.011 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information + + + +
+ + + + + Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information + + +
+ Halie M. Rando, Tellen D. Bennett, James Brian Byrd, Carolyn Bramante, Tiffany J. Callahan, ..., Joel H. Saltz, Anthony Solomonides, Anupam Sule, Umit Topaloglu, Melissa A. Haendel +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 26 Mar 2021 +   ·   + doi:10.1101/2021.03.20.21253896 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality + + + +
+ + + + + Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality + + +
+ Mai T. Dang, Michael V. Gonzalez, Krutika S. Gaonkar, Komal S. Rathi, Patricia Young, ..., Candace Savonen, Fernanda Mafra, Hakon Hakonarson, Tom Curran, Malay Haldar +
+ +
+ Cell Reports +   ·   + 01 Mar 2021 +   ·   + doi:10.1016/j.celrep.2021.108917 +
+ + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer + + + +
+ + + + + Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer + + +
+ Adam C. Mueller, Miles Piper, Andrew Goodspeed, Shiv Bhuvane, Jason S. Williams, ..., Antonio Galveo Neto, David Lagares, Kirk C. Hansen, Adrie Van Bokhoven, Sana D. Karam +
+ +
+ Cancer Research +   ·   + 01 Feb 2021 +   ·   + doi:10.1158/0008-5472.CAN-20-3892 +
+ + + + + + + + + + +
+ + + cancer + + +
+ + + + +
+
+ +
+ + + Exploiting the GTEx resources to decipher the mechanisms at GWAS loci + + + +
+ + + + + Exploiting the GTEx resources to decipher the mechanisms at GWAS loci + + +
+ Alvaro N. Barbeira, Rodrigo Bonazzola, Eric R. Gamazon, Yanyu Liang, YoSon Park, ..., Ayellet V. Segrè, Christopher D. Brown, Tuuli Lappalainen, Xiaoquan Wen, Hae Kyung Im +
+ +
+ Genome Biology +   ·   + 26 Jan 2021 +   ·   + doi:10.1186/s13059-020-02252-4 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual + + + +
+ + + + + Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual + + +
+ Diana L. Cousminer, Yadav Wagley, James A. Pippin, Ahmed Elhakeem, Gregory P. Way, ..., Benjamin F. Voight, Andrew D. Wells, Babette S. Zemel, Kurt D. Hankenson, Struan F. A. Grant +
+ +
+ Genome Biology +   ·   + 04 Jan 2021 +   ·   + doi:10.1186/s13059-020-02207-9 +
+ + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + +
+
+ +

2020

+ +
+ + + Open collaborative writing with Manubot + + + +
+ + + + + Open collaborative writing with Manubot + + +
+ Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter +
+ +
+ PLOS Computational Biology +   ·   + 04 Dec 2020 +   ·   + doi:10.1371/journal.pcbi.1007128 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Biologically Informed Neural Networks Predict Drug Responses + + + +
+ + + + + Biologically Informed Neural Networks Predict Drug Responses + + +
+ Casey S. Greene, James C. Costello +
+ +
+ Cancer Cell +   ·   + 01 Nov 2020 +   ·   + doi:10.1016/j.ccell.2020.10.014 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Correcting for experiment-specific variability in expression compendia can remove underlying signals + + + +
+ + + + + Correcting for experiment-specific variability in expression compendia can remove underlying signals + + +
+ Alexandra J Lee, YoSon Park, Georgia Doing, Deborah A Hogan, Casey S Greene +
+ +
+ GigaScience +   ·   + 01 Nov 2020 +   ·   + doi:10.1093/gigascience/giaa117 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE) + + + +
+ + + + + Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE) + + +
+ Aline Talhouk, Joshy George, Chen Wang, Timothy Budden, Tuan Zea Tan, ..., Ellen L. Goode, Susan J. Ramus, Jennifer A. Doherty, David D. Bowtell, Michael S. Anglesio +
+ +
+ Clinical Cancer Research +   ·   + 15 Oct 2020 +   ·   + doi:10.1158/1078-0432.CCR-20-0103 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Transparency and reproducibility in artificial intelligence + + + +
+ + + + + Transparency and reproducibility in artificial intelligence + + +
+ Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, Thakkar Shraddha, ..., Robert Tibshirani, Trevor Hastie, John P. A. Ioannidis, John Quackenbush, Hugo J. W. L. Aerts +
+ +
+ Nature +   ·   + 14 Oct 2020 +   ·   + doi:10.1038/s41586-020-2766-y +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Transcriptomic signatures across human tissues identify functional rare genetic variation + + + +
+ + + + + Transcriptomic signatures across human tissues identify functional rare genetic variation + + +
+ Nicole M. Ferraro, Benjamin J. Strober, Jonah Einson, Nathan S. Abell, Francois Aguet, ..., Helen M. Moore, Concepcion R. Nierras, Abhi K. Rao, Jimmie B. Vaught, Simona Volpi +
+ +
+ Science +   ·   + 11 Sep 2020 +   ·   + doi:10.1126/science.aaz5900 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + PhenomeXcan: Mapping the genome to the phenome through the transcriptome + + + +
+ + + + + PhenomeXcan: Mapping the genome to the phenome through the transcriptome + + +
+ Milton Pividori, Padma S. Rajagopal, Alvaro Barbeira, Yanyu Liang, Owen Melia, Lisa Bastarache, YoSon Park, GTEx Consortium, Xiaoquan Wen, Hae K. Im +
+ +
+ Science Advances +   ·   + 11 Sep 2020 +   ·   + doi:10.1126/sciadv.aba2083 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx + + + +
+ + + + + Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx + + +
+ Nicole R. Gay, Michael Gloudemans, Margaret L. Antonio, Nathan S. Abell, Brunilda Balliu, ..., Christopher D. Brown, Hae Kyung Im, Tuuli Lappalainen, Xiaoquan Wen, Stephen B. Montgomery +
+ +
+ Genome Biology +   ·   + 11 Sep 2020 +   ·   + doi:10.1186/s13059-020-02113-0 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Prognostic gene expression signature for high-grade serous ovarian cancer + + + +
+ + + + + Prognostic gene expression signature for high-grade serous ovarian cancer + + +
+ J. Millstein, T. Budden, E.L. Goode, M.S. Anglesio, A. Talhouk, ..., M. Buck, I. Haviv, D. Purdie, D. Whiteman, N. Zeps +
+ +
+ Annals of Oncology +   ·   + 01 Sep 2020 +   ·   + doi:10.1016/j.annonc.2020.05.019 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing + + + +
+ + + + + Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing + + +
+ William E. Allen, Han Altae-Tran, James Briggs, Xin Jin, Glen McGee, ..., Ryan Probasco, David R. Cheng, Ben Silbermann, Feng Zhang, Xihong Lin +
+ +
+ Nature Human Behaviour +   ·   + 26 Aug 2020 +   ·   + doi:10.1038/s41562-020-00944-2 +
+ + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment + + + +
+ + + + + The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment + + +
+ Melissa A Haendel, Christopher G Chute, Tellen D Bennett, David A Eichmann, Justin Guinney, ..., Sam G Michael, Lili M Portilla, Joni L Rutter, Christopher P Austin, Ken R Gersing +
+ +
+ Journal of the American Medical Informatics Association +   ·   + 17 Aug 2020 +   ·   + doi:10.1093/jamia/ocaa196 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Responsible, practical genomic data sharing that accelerates research + + + +
+ + + + + Responsible, practical genomic data sharing that accelerates research + + +
+ James Brian Byrd, Anna C. Greene, Deepashree Venkatesh Prasad, Xiaoqian Jiang, Casey S. Greene +
+ +
+ Nature Reviews Genetics +   ·   + 21 Jul 2020 +   ·   + doi:10.1038/s41576-020-0257-5 +
+ + + + + + + + + + + + + + + +
+
+ +
+ + + Constructing knowledge graphs and their biomedical applications + + + +
+ + + + + Constructing knowledge graphs and their biomedical applications + + +
+ David N. Nicholson, Casey S. Greene +
+ +
+ Computational and Structural Biotechnology Journal +   ·   + 02 Jun 2020 +   ·   + doi:10.1016/j.csbj.2020.05.017 +
+ + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Building an international consortium for tracking coronavirus health status + + + +
+ + + + + Building an international consortium for tracking coronavirus health status + + +
+ Eran Segal, Feng Zhang, Xihong Lin, Gary King, Ophir Shalem, ..., Tim Spector, Ron Steinherz, Irene Stevens, Jaak Vilo, Paul Wilmes +
+ +
+ Nature Medicine +   ·   + 02 Jun 2020 +   ·   + doi:10.1038/s41591-020-0929-x +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Incorporating biological structure into machine learning models in biomedicine + + + +
+ + + + + Incorporating biological structure into machine learning models in biomedicine + + +
+ Jake Crawford, Casey S Greene +
+ +
+ Current Opinion in Biotechnology +   ·   + 01 Jun 2020 +   ·   + doi:10.1016/j.copbio.2019.12.021 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Recommendations to enhance rigor and reproducibility in biomedical research + + + +
+ + + + + Recommendations to enhance rigor and reproducibility in biomedical research + + +
+ Jaqueline J Brito, Jun Li, Jason H Moore, Casey S Greene, Nicole A Nogoy, Lana X Garmire, Serghei Mangul +
+ +
+ GigaScience +   ·   + 01 Jun 2020 +   ·   + doi:10.1093/gigascience/giaa056 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + + +
+ + + + + Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations + + +
+ Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene +
+ +
+ Genome Biology +   ·   + 11 May 2020 +   ·   + doi:10.1186/s13059-020-02021-3 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Specific histone modifications associate with alternative exon selection during mammalian development + + + +
+ + + + + Specific histone modifications associate with alternative exon selection during mammalian development + + +
+ Qiwen Hu, Casey S Greene, Elizabeth A Heller +
+ +
+ Nucleic Acids Research +   ·   + 22 Apr 2020 +   ·   + doi:10.1093/nar/gkaa248 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1 + + + +
+ + + + + Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1 + + +
+ Jineta Banerjee, Robert J Allaway, Jaclyn N Taroni, Aaron Baker, Xiaochun Zhang, ..., Jaishri O Blakeley, Justin Guinney, Angela Hirbe, Casey S Greene, Sara JC Gosline +
+ +
+ Genes +   ·   + 21 Feb 2020 +   ·   + doi:10.3390/genes11020226 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+
+ +
+ + + <i>Pseudomonas aeruginosa lasR</i>
+            mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin + + + +
+ + + + + Pseudomonas aeruginosa lasR + mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin + + +
+ Michelle E. Clay, John H. Hammond, Fangfang Zhong, Xiaolei Chen, Caitlin H. Kowalski, ..., Monique S. Porter, Thomas H. Hampton, Casey S. Greene, Ekaterina V. Pletneva, Deborah A. Hogan +
+ +
+ Proceedings of the National Academy of Sciences +   ·   + 24 Jan 2020 +   ·   + doi:10.1073/pnas.1917576117 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Graph biased feature selection of genes is better than random for many genes + + + +
+ + + + + Graph biased feature selection of genes is better than random for many genes + + +
+ Jake Crawford, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 21 Jan 2020 +   ·   + doi:10.1101/2020.01.17.910703 +
+ + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + +
+
+ +

2019

+ +
+ + + Immune landscapes associated with different glioblastoma molecular subtypes + + + +
+ + + + + Immune landscapes associated with different glioblastoma molecular subtypes + + +
+ Maria Martinez-Lage, Timothy M. Lynch, Yingtao Bi, Carolina Cocito, Gregory P. Way, ..., Donald M. O’Rourke, Jeffrey P. Greenfield, Casey S. Greene, Ramana V. Davuluri, Nadia Dahmane +
+ +
+ Acta Neuropathologica Communications +   ·   + 29 Nov 2019 +   ·   + doi:10.1186/s40478-019-0803-6 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens + + + +
+ + + + + The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens + + +
+ Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, ..., Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg +
+ +
+ Genome Biology +   ·   + 19 Nov 2019 +   ·   + doi:10.1186/s13059-019-1835-8 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design + + + +
+ + + + + Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design + + +
+ Jo Lynne Rokita, Komal S. Rathi, Maria F. Cardenas, Kristen A. Upton, Joy Jayaseelan, ..., Malcolm A. Smith, Richard B. Lock, Pichai Raman, David A. Wheeler, John M. Maris +
+ +
+ Cell Reports +   ·   + 01 Nov 2019 +   ·   + doi:10.1016/j.celrep.2019.09.071 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma + + + +
+ + + + + Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma + + +
+ Yu-Hsiu T. Lin, Gregory P. Way, Benjamin G. Barwick, Margarette C. Mariano, Makeba Marcoulis, Ian D. Ferguson, Christoph Driessen, Lawrence H. Boise, Casey S. Greene, Arun P. Wiita +
+ +
+ Blood Advances +   ·   + 29 Oct 2019 +   ·   + doi:10.1182/bloodadvances.2019000303 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Long non-coding RNA gene regulation and trait associations across human tissues + + + +
+ + + + + Long non-coding RNA gene regulation and trait associations across human tissues + + +
+ O. M. de Goede, N. M. Ferraro, D. C. Nachun, A. S. Rao, F. Aguet, ..., H. K. Im, K. G. Ardlie, T. Quertermous, K. Kirkegaard, S. B. Montgomery +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 04 Oct 2019 +   ·   + doi:10.1101/793091 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Embracing study heterogeneity for finding genetic interactions in large‐scale research consortia + + + +
+ + + + + Embracing study heterogeneity for finding genetic interactions in large‐scale research consortia + + +
+ Yulun Liu, Jing Huang, Ryan J. Urbanowicz, Kun Chen, Elisabetta Manduchi, Casey S. Greene, Jason H. Moore, Paul Scheet, Yong Chen +
+ +
+ Genetic Epidemiology +   ·   + 04 Oct 2019 +   ·   + doi:10.1002/gepi.22262 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + The GTEx Consortium atlas of genetic regulatory effects across human tissues + + + +
+ + + + + The GTEx Consortium atlas of genetic regulatory effects across human tissues + + +
+ François Aguet, Alvaro N Barbeira, Rodrigo Bonazzola, Andrew Brown, Stephane E Castel, ..., Barbara E Stranger, Hae Kyung Im, Alexis Battle, Kristin G Ardlie, Tuuli Lappalainen +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 03 Oct 2019 +   ·   + doi:10.1101/787903 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Voices in methods development + + + +
+ + + + + Voices in methods development + + +
+ Polina Anikeeva, Edward Boyden, Clifford Brangwynne, Ibrahim I. Cissé, Oliver Fiehn, ..., Hong-Wei Wang, Chengqi Yi, Peng Yin, Magdalena Zernicka-Goetz, Xiaowei Zhuang +
+ +
+ Nature Methods +   ·   + 27 Sep 2019 +   ·   + doi:10.1038/s41592-019-0585-6 +
+ + + + + + + + +
+
+ +
+ + + Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning + + + +
+ + + + + Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning + + +
+ Gregory P. Way, Casey S. Greene +
+ +
+ Annual Review of Biomedical Data Science +   ·   + 20 Jul 2019 +   ·   + doi:10.1146/annurev-biodatasci-072018-021348 +
+ + + + + + + + +
+
+ +
+ + + Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing + + + +
+ + + + + Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing + + +
+ Brett K. Beaulieu-Jones, Zhiwei Steven Wu, Chris Williams, Ran Lee, Sanjeev P. Bhavnani, James Brian Byrd, Casey S. Greene +
+ +
+ Circulation: Cardiovascular Quality and Outcomes +   ·   + 01 Jul 2019 +   ·   + doi:10.1161/CIRCOUTCOMES.118.005122 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Show me the models + + + +
+ + + + + Show me the models + + +
+ Casey S. Greene +
+ +
+ Nature Biotechnology +   ·   + 28 May 2019 +   ·   + doi:10.1038/s41587-019-0143-x +
+ + + + + + + + +
+
+ +
+ + + MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease + + + +
+ + + + + MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease + + +
+ Jaclyn N. Taroni, Peter C. Grayson, Qiwen Hu, Sean Eddy, Matthias Kretzler, Peter A. Merkel, Casey S. Greene +
+ +
+ Cell Systems +   ·   + 01 May 2019 +   ·   + doi:10.1016/j.cels.2019.04.003 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution + + + +
+ + + + + The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution + + +
+ Deanne M. Taylor, Bruce J. Aronow, Kai Tan, Kathrin Bernt, Nathan Salomonis, ..., Yi Xing, Sek Won Kong, Carsten G. Bönnemann, Kenneth D. Mandl, Peter S. White +
+ +
+ Developmental Cell +   ·   + 01 Apr 2019 +   ·   + doi:10.1016/j.devcel.2019.03.001 +
+ + + + + + + + +
+
+ +
+ + + Technologies to watch in 2019 + + + +
+ + + + + Technologies to watch in 2019 + + +
+ Marissa Fessenden +
+ +
+ Nature +   ·   + 01 Jan 2019 +   ·   + doi:10.1038/d41586-019-00218-6 +
+ + + + + + + + +
+
+ +
+ + + New<i>Drosophila</i>Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods + + + +
+ + + + + NewDrosophilaLong-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods + + +
+ Balint Z Kacsoh, Stephen Barton, Yuxiang Jiang, Naihui Zhou, Sean D Mooney, Iddo Friedberg, Predrag Radivojac, Casey S Greene, Giovanni Bosco +
+ +
+ G3 Genes|Genomes|Genetics +   ·   + 01 Jan 2019 +   ·   + doi:10.1534/g3.118.200867 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +

2018

+ +
+ + + Bayesian deep learning for single-cell analysis + + + +
+ + + + + Bayesian deep learning for single-cell analysis + + +
+ Gregory P. Way, Casey S. Greene +
+ +
+ Nature Methods +   ·   + 30 Nov 2018 +   ·   + doi:10.1038/s41592-018-0230-9 +
+ + + + + + + + +
+
+ +
+ + + Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics + + + +
+ + + + + Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics + + +
+ Qiwen Hu, Casey S. Greene +
+ +
+ Biocomputing 2019 +   ·   + 01 Nov 2018 +   ·   + doi:10.1142/9789813279827_0033 +
+ + + + + + + + +
+
+ +
+ + + A parasite's perspective on data sharing + + + +
+ + + + + A parasite's perspective on data sharing + + +
+ YoSon Park, Casey S Greene +
+ +
+ GigaScience +   ·   + 01 Nov 2018 +   ·   + doi:10.1093/gigascience/giy129 +
+ + + + + + + + +
+
+ +
+ + + Enter the Matrix: Factorization Uncovers Knowledge from Omics + + + +
+ + + + + Enter the Matrix: Factorization Uncovers Knowledge from Omics + + +
+ Genevieve L. Stein-O’Brien, Raman Arora, Aedin C. Culhane, Alexander V. Favorov, Lana X. Garmire, ..., Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig +
+ +
+ Trends in Genetics +   ·   + 01 Oct 2018 +   ·   + doi:10.1016/j.tig.2018.07.003 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Learning and Imputation for Mass-spec Bias Reduction (LIMBR) + + + +
+ + + + + Learning and Imputation for Mass-spec Bias Reduction (LIMBR) + + +
+ Alexander M Crowell, Casey S Greene, Jennifer J Loros, Jay C Dunlap +
+ +
+ Bioinformatics +   ·   + 24 Sep 2018 +   ·   + doi:10.1093/bioinformatics/bty828 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia + + + +
+ + + + + PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia + + +
+ Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene +
+ +
+ BioData Mining +   ·   + 03 Jul 2018 +   ·   + doi:10.1186/s13040-018-0175-7 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay* + + + +
+ + + + + Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay* + + +
+ Gary E. Weissman, Rebecca A. Hubbard, Lyle H. Ungar, Michael O. Harhay, Casey S. Greene, Blanca E. Himes, Scott D. Halpern +
+ +
+ Critical Care Medicine +   ·   + 01 Jul 2018 +   ·   + doi:10.1097/CCM.0000000000003148 +
+ + + + + + + + +
+
+ +
+ + + Metabolic pathways and immunometabolism in rare kidney diseases + + + +
+ + + + + Metabolic pathways and immunometabolism in rare kidney diseases + + +
+ Peter C Grayson, Sean Eddy, Jaclyn N Taroni, Yaíma L Lightfoot, Laura Mariani, ..., Brad Godfrey, Clemens D Cohen, Jeffrey Krischer, Matthias Kretzler, Peter A Merkel +
+ +
+ Annals of the Rheumatic Diseases +   ·   + 03 May 2018 +   ·   + doi:10.1136/annrheumdis-2017-212935 +
+ + + + + + + + +
+
+ +
+ + + A Multimodal Strategy Used by a Large c-di-GMP Network + + + +
+ + + + + A Multimodal Strategy Used by a Large c-di-GMP Network + + +
+ Kurt M. Dahlstrom, Alan J. Collins, Georgia Doing, Jaclyn N. Taroni, Timothy J. Gauvin, Casey S. Greene, Deborah A. Hogan, George A. O'Toole +
+ +
+ Journal of Bacteriology +   ·   + 15 Apr 2018 +   ·   + doi:10.1128/JB.00703-17 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas + + + +
+ + + + + Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas + + +
+ Theo A. Knijnenburg, Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze +
+ +
+ Cell Reports +   ·   + 01 Apr 2018 +   ·   + doi:10.1016/j.celrep.2018.03.076 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Opportunities and obstacles for deep learning in biology and medicine + + + +
+ + + + + Opportunities and obstacles for deep learning in biology and medicine + + +
+ Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, ..., Simina M. Boca, S. Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S. Greene +
+ +
+ Journal of The Royal Society Interface +   ·   + 01 Apr 2018 +   ·   + doi:10.1098/rsif.2017.0387 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Oncogenic Signaling Pathways in The Cancer Genome Atlas + + + +
+ + + + + Oncogenic Signaling Pathways in The Cancer Genome Atlas + + +
+ Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze +
+ +
+ Cell +   ·   + 01 Apr 2018 +   ·   + doi:10.1016/j.cell.2018.03.035 +
+ + + + + + + + +
+
+ +
+ + + Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas + + + +
+ + + + + Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas + + +
+ Gregory P. Way, Francisco Sanchez-Vega, Konnor La, Joshua Armenia, Walid K. Chatila, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze +
+ +
+ Cell Reports +   ·   + 01 Apr 2018 +   ·   + doi:10.1016/j.celrep.2018.03.046 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Sci-Hub provides access to nearly all scholarly literature + + + +
+ + + + + Sci-Hub provides access to nearly all scholarly literature + + +
+ Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene +
+ +
+ eLife +   ·   + 01 Mar 2018 +   ·   + doi:10.7554/eLife.32822 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses + + + +
+ + + + + Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses + + +
+ Lia X Harrington, Gregory P Way, Jennifer A Doherty, Casey S Greene +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 01 Jan 2018 +   ·   + pmc:PMC5760988 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Advances in Text Mining and Visualization for Precision Medicine. + + + +
+ + + + + Advances in Text Mining and Visualization for Precision Medicine. + + +
+ Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O'Connor, Casey Greene, Hongfang Liu +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 01 Jan 2018 +   ·   + pubmed:29218914 +
+ + + + + + + + +
+
+ +

2017

+ +
+ + + A Pilot Characterization of the Human Chronobiome + + + +
+ + + + + A Pilot Characterization of the Human Chronobiome + + +
+ Carsten Skarke, Nicholas F. Lahens, Seth D. Rhoades, Amy Campbell, Kyle Bittinger, ..., Frederic D. Bushman, Casey S. Greene, Gregory R. Grant, Aalim M. Weljie, Garret A. FitzGerald +
+ +
+ Scientific Reports +   ·   + 07 Dec 2017 +   ·   + doi:10.1038/s41598-017-17362-6 +
+ + + + + + + + +
+
+ +
+ + + ADAGE signature analysis: differential expression analysis with data-defined gene sets + + + +
+ + + + + ADAGE signature analysis: differential expression analysis with data-defined gene sets + + +
+ Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene +
+ +
+ BMC Bioinformatics +   ·   + 22 Nov 2017 +   ·   + doi:10.1186/s12859-017-1905-4 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders + + + +
+ + + + + Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders + + +
+ Gregory P. Way, Casey S. Greene +
+ +
+ Biocomputing 2018 +   ·   + 17 Nov 2017 +   ·   + doi:10.1142/9789813235533_0008 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Machine Learning Analysis Identifies<i>Drosophila Grunge/Atrophin</i>as an Important Learning and Memory Gene Required for Memory Retention and Social Learning + + + +
+ + + + + Machine Learning Analysis IdentifiesDrosophila Grunge/Atrophinas an Important Learning and Memory Gene Required for Memory Retention and Social Learning + + +
+ Balint Z Kacsoh, Casey S Greene, Giovanni Bosco +
+ +
+ G3 Genes|Genomes|Genetics +   ·   + 01 Nov 2017 +   ·   + doi:10.1534/g3.117.300172 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Implicating candidate genes at GWAS signals by leveraging topologically associating domains + + + +
+ + + + + Implicating candidate genes at GWAS signals by leveraging topologically associating domains + + +
+ Gregory P Way, Daniel W Youngstrom, Kurt D Hankenson, Casey S Greene, Struan FA Grant +
+ +
+ European Journal of Human Genetics +   ·   + 09 Aug 2017 +   ·   + doi:10.1038/ejhg.2017.108 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules + + + +
+ + + + + Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules + + +
+ Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Casey S. Greene, Jason H. Moore, Andrew J. Saykin, Li Shen +
+ +
+ Bioinformatics +   ·   + 20 Jul 2017 +   ·   + doi:10.1093/bioinformatics/btx344 +
+ + + + + + + + +
+
+ +
+ + + Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes + + + +
+ + + + + Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes + + +
+ Jennifer Anne Doherty, Lauren Cole Peres, Chen Wang, Gregory P. Way, Casey S. Greene, Joellen M. Schildkraut +
+ +
+ Current Epidemiology Reports +   ·   + 10 Jul 2017 +   ·   + doi:10.1007/s40471-017-0115-y +
+ + + + + + + + +
+
+ +
+ + + Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks + + + +
+ + + + + Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks + + +
+ Jie Tan, Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady, Barret Perchuk, Michael T. Laub, Deborah A. Hogan, Casey S. Greene +
+ +
+ Cell Systems +   ·   + 01 Jul 2017 +   ·   + doi:10.1016/j.cels.2017.06.003 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Data-Sharing Models + + + +
+ + + + + Data-Sharing Models + + +
+ [no author info] +
+ +
+ New England Journal of Medicine +   ·   + 08 Jun 2017 +   ·   + doi:10.1056/NEJMc1705477 +
+ + + + + + + + +
+
+ +
+ + + Celebrating parasites + + + +
+ + + + + Celebrating parasites + + +
+ Casey S Greene, Lana X Garmire, Jack A Gilbert, Marylyn D Ritchie, Lawrence E Hunter +
+ +
+ Nature Genetics +   ·   + 01 Apr 2017 +   ·   + doi:10.1038/ng.3830 +
+ + + + + + + + +
+
+ +
+ + + A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis + + + +
+ + + + + A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis + + +
+ Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood, Romy B. Christmann, ..., Christopher P. Denton, Monique E. Hinchcliff, Patricia A. Pioli, J. Matthew Mahoney, Michael L. Whitfield +
+ +
+ Genome Medicine +   ·   + 23 Mar 2017 +   ·   + doi:10.1186/s13073-017-0417-1 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Reproducibility of computational workflows is automated using continuous analysis + + + +
+ + + + + Reproducibility of computational workflows is automated using continuous analysis + + +
+ Brett K Beaulieu-Jones, Casey S Greene +
+ +
+ Nature Biotechnology +   ·   + 13 Mar 2017 +   ·   + doi:10.1038/nbt.3780 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Tell me your neighbors, and I will tell you what you are + + + +
+ + + + + Tell me your neighbors, and I will tell you what you are + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 08 Feb 2017 +   ·   + doi:10.1126/scitranslmed.aam6058 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma + + + +
+ + + + + A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma + + +
+ Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene +
+ +
+ BMC Genomics +   ·   + 06 Feb 2017 +   ·   + doi:10.1186/s12864-017-3519-7 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +

2016

+ +
+ + + Cheap-seq + + + +
+ + + + + Cheap-seq + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 21 Dec 2016 +   ·   + doi:10.1126/scitranslmed.aal3701 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Semi-supervised learning of the electronic health record for phenotype stratification + + + +
+ + + + + Semi-supervised learning of the electronic health record for phenotype stratification + + +
+ Brett K. Beaulieu-Jones, Casey S. Greene +
+ +
+ Journal of Biomedical Informatics +   ·   + 01 Dec 2016 +   ·   + doi:10.1016/j.jbi.2016.10.007 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes + + + +
+ + + + + Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes + + +
+ Gregory P Way, James Rudd, Chen Wang, Habib Hamidi, Brooke L Fridley, Gottfried E Konecny, Ellen L Goode, Casey S Greene, Jennifer A Doherty +
+ +
+ G3 Genes|Genomes|Genetics +   ·   + 01 Dec 2016 +   ·   + doi:10.1534/g3.116.033514 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + NO-BOUNDARY THINKING IN BIOINFORMATICS + + + +
+ + + + + NO-BOUNDARY THINKING IN BIOINFORMATICS + + +
+ JASON H. MOORE, STEVEN F. JENNINGS, CASEY S. GREENE, LAWRENCE E. HUNTER, ANDY D. PERKINS, CLARLYNDA WILLIAMS-DEVANE, DONALD C. WUNSCH, ZHONGMING ZHAO, XIUZHEN HUANG +
+ +
+ Biocomputing 2017 +   ·   + 22 Nov 2016 +   ·   + doi:10.1142/9789813207813_0060 +
+ + + + + + + + +
+
+ +
+ + + How to know what we don’t + + + +
+ + + + + How to know what we don’t + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 09 Nov 2016 +   ·   + doi:10.1126/scitranslmed.aal0067 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + A stromal focus reveals tumor immune signatures + + + +
+ + + + + A stromal focus reveals tumor immune signatures + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 28 Sep 2016 +   ·   + doi:10.1126/scitranslmed.aai8224 +
+ + + + + + + + +
+
+ +
+ + + Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations + + + +
+ + + + + Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations + + +
+ Arjun Krishnan, Jaclyn N. Taroni, Casey S. Greene +
+ +
+ Current Genetic Medicine Reports +   ·   + 09 Sep 2016 +   ·   + doi:10.1007/s40142-016-0102-5 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + An expanded evaluation of protein function prediction methods shows an improvement in accuracy + + + +
+ + + + + An expanded evaluation of protein function prediction methods shows an improvement in accuracy + + +
+ Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur, Daniel D’Andrea, ..., Burkhard Rost, Casey S. Greene, Sean D. Mooney, Iddo Friedberg, Predrag Radivojac +
+ +
+ Genome Biology +   ·   + 07 Sep 2016 +   ·   + doi:10.1186/s13059-016-1037-6 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Gut check + + + +
+ + + + + Gut check + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 17 Aug 2016 +   ·   + doi:10.1126/scitranslmed.aah5494 +
+ + + + + + + + +
+
+ +
+ + + The future is unsupervised + + + +
+ + + + + The future is unsupervised + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 06 Jul 2016 +   ·   + doi:10.1126/scitranslmed.aag3101 +
+ + + + + + + + +
+
+ +
+ + + Pathway and network-based strategies to translate genetic discoveries into effective therapies + + + +
+ + + + + Pathway and network-based strategies to translate genetic discoveries into effective therapies + + +
+ Casey S. Greene, Benjamin F. Voight +
+ +
+ Human Molecular Genetics +   ·   + 23 Jun 2016 +   ·   + doi:10.1093/hmg/ddw160 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Tribe: The collaborative platform for reproducible web-based analysis of gene sets + + + +
+ + + + + Tribe: The collaborative platform for reproducible web-based analysis of gene sets + + +
+ René A. Zelaya, Aaron K. Wong, Alex T. Frase, Marylyn D. Ritchie, Casey S. Greene +
+ +
+ Cold Spring Harbor Laboratory +   ·   + 27 May 2016 +   ·   + doi:10.1101/055913 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Nothing but a hound dog + + + +
+ + + + + Nothing but a hound dog + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 25 May 2016 +   ·   + doi:10.1126/scitranslmed.aaf9196 +
+ + + + + + + + +
+
+ +
+ + + CoINcIDE: All together now + + + +
+ + + + + CoINcIDE: All together now + + +
+ Casey S. Greene +
+ +
+ Science Translational Medicine +   ·   + 13 Apr 2016 +   ·   + doi:10.1126/scitranslmed.aaf6940 +
+ + + + + + + + +
+
+ +
+ + + Genetic Association–Guided Analysis of Gene Networks for the Study of Complex Traits + + + +
+ + + + + Genetic Association–Guided Analysis of Gene Networks for the Study of Complex Traits + + +
+ Casey S. Greene, Daniel S. Himmelstein +
+ +
+ Circulation: Cardiovascular Genetics +   ·   + 01 Apr 2016 +   ·   + doi:10.1161/CIRCGENETICS.115.001181 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites + + + +
+ + + + + Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites + + +
+ Robert J. Allaway, Dawn A. Fischer, Francine B. de Abreu, Timothy B. Gardner, Stuart R. Gordon, ..., Gregory J. Tsongalis, Arief A. Suriawinata, Casey S. Greene, Yolanda Sanchez, Kerrington D. Smith +
+ +
+ Oncotarget +   ·   + 25 Feb 2016 +   ·   + doi:10.18632/oncotarget.7718 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions + + + +
+ + + + + ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions + + +
+ Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene +
+ +
+ mSystems +   ·   + 23 Feb 2016 +   ·   + doi:10.1128/mSystems.00025-15 +
+ + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Cross-platform normalization of microarray and RNA-seq data for machine learning applications + + + +
+ + + + + Cross-platform normalization of microarray and RNA-seq data for machine learning applications + + +
+ Jeffrey A. Thompson, Jie Tan, Casey S. Greene +
+ +
+ PeerJ +   ·   + 21 Jan 2016 +   ·   + doi:10.7717/peerj.1621 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer’s disease: a study of ADNI cohorts + + + +
+ + + + + Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer’s disease: a study of ADNI cohorts + + +
+ Ailin Song, Jingwen Yan, Sungeun Kim, Shannon Leigh Risacher, Aaron K. Wong, Andrew J. Saykin, Li Shen, Casey S. Greene +
+ +
+ BioData Mining +   ·   + 19 Jan 2016 +   ·   + doi:10.1186/s13040-016-0082-8 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES + + + +
+ + + + + COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES + + +
+ Casey S Greene, James A Foster, Bruce A Stanton, Deborah A Hogan, Yana Bromberg +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 01 Jan 2016 +   ·   + pmc:PMC4832978 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +

2015

+ +
+ + + Leveraging global gene expression patterns to predict expression of unmeasured genes + + + +
+ + + + + Leveraging global gene expression patterns to predict expression of unmeasured genes + + +
+ James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty +
+ +
+ BMC Genomics +   ·   + 01 Dec 2015 +   ·   + doi:10.1186/s12864-015-2250-5 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions + + + +
+ + + + + Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions + + +
+ David C. Qian, Jinyoung Byun, Younghun Han, Casey S. Greene, John K. Field, ..., Fredrick R. Schumacher, Rosalind A. Eeles, Douglas F. Easton, Daniela Seminara, Christopher I. Amos +
+ +
+ Human Molecular Genetics +   ·   + 19 Oct 2015 +   ·   + doi:10.1093/hmg/ddv440 +
+ + + + + + + + +
+
+ +
+ + + Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery + + + +
+ + + + + Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery + + +
+ Graciela H. Gonzalez, Tasnia Tahsin, Britton C. Goodale, Anna C. Greene, Casey S. Greene +
+ +
+ Briefings in Bioinformatics +   ·   + 29 Sep 2015 +   ·   + doi:10.1093/bib/bbv087 +
+ + + + + + + + +
+
+ +
+ + + International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways + + + +
+ + + + + International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways + + +
+ Heather J. Cordell, Younghun Han, George F. Mells, Yafang Li, Gideon M. Hirschfield, ..., Pietro Invernizzi, Michael F. Seldin, Richard N. Sandford, Christopher I. Amos, Katherine A. Siminovitch +
+ +
+ Nature Communications +   ·   + 22 Sep 2015 +   ·   + doi:10.1038/ncomms9019 +
+ + + + + + + + +
+
+ +
+ + + Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study + + + +
+ + + + + Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study + + +
+ Jiang Gui, Casey S. Greene, Con Sullivan, Walter Taylor, Jason H. Moore, Carol Kim +
+ +
+ BioData Mining +   ·   + 01 Jun 2015 +   ·   + doi:10.1186/s13040-015-0050-8 +
+ + + + + + + + +
+
+ +
+ + + Understanding multicellular function and disease with human tissue-specific networks + + + +
+ + + + + Understanding multicellular function and disease with human tissue-specific networks + + +
+ Casey S Greene, Arjun Krishnan, Aaron K Wong, Emanuela Ricciotti, Rene A Zelaya, ..., Daniel I Chasman, Garret A FitzGerald, Kara Dolinski, Tilo Grosser, Olga G Troyanskaya +
+ +
+ Nature Genetics +   ·   + 27 Apr 2015 +   ·   + doi:10.1038/ng.3259 +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ +
+ + + Adapting bioinformatics curricula for big data + + + +
+ + + + + Adapting bioinformatics curricula for big data + + +
+ Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore +
+ +
+ Briefings in Bioinformatics +   ·   + 30 Mar 2015 +   ·   + doi:10.1093/bib/bbv018 +
+ + + + + + + + +
+
+ +
+ + + Targeted exploration and analysis of large cross-platform human transcriptomic compendia + + + +
+ + + + + Targeted exploration and analysis of large cross-platform human transcriptomic compendia + + +
+ Qian Zhu, Aaron K Wong, Arjun Krishnan, Miriam R Aure, Alicja Tadych, ..., Lars A Bongo, Vessela N Kristensen, Moses Charikar, Kai Li, Olga G Troyanskaya +
+ +
+ Nature Methods +   ·   + 12 Jan 2015 +   ·   + doi:10.1038/nmeth.3249 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +
+ + + Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms + + + +
+ + + + + Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms + + +
+ J. Matthew Mahoney, Jaclyn Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield +
+ +
+ PLoS Computational Biology +   ·   + 08 Jan 2015 +   ·   + doi:10.1371/journal.pcbi.1004005 +
+ + + + + + + + +
+
+ +
+ + + Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders + + + +
+ + + + + Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders + + +
+ Jie Tan, Matthew Ung, Chao Cheng, Casey S Greene +
+ +
+ Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing +   ·   + 01 Jan 2015 +   ·   + pmc:PMC4299935 +
+ + + + + +
+ + + + + + + + + +
+ + + + +
+
+ +

2014

+ +
+ + + Big Data Bioinformatics + + + +
+ + + + + Big Data Bioinformatics + + +
+ Casey S. Greene, Jie Tan, Matthew Ung, Jason H. Moore, Chao Cheng +
+ +
+ Journal of Cellular Physiology +   ·   + 27 Aug 2014 +   ·   + doi:10.1002/jcp.24662 +
+ + + + + + + + +
+
+ +
+ + + Computational genetics analysis of grey matter density in Alzheimer’s disease + + + +
+ + + + + Computational genetics analysis of grey matter density in Alzheimer’s disease + + +
+ Amanda L Zieselman, Jonathan M Fisher, Ting Hu, Peter C Andrews, Casey S Greene, Li Shen, Andrew J Saykin, Jason H Moore +
+ +
+ BioData Mining +   ·   + 22 Aug 2014 +   ·   + doi:10.1186/1756-0381-7-17 +
+ + + + + + + + +
+
+ +
+ + + Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity + + + +
+ + + + + Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity + + +
+ Nadia M Penrod, Casey S Greene, Jason H Moore +
+ +
+ Genome Medicine +   ·   + 01 Jan 2014 +   ·   + doi:10.1186/gm550 +
+ + + + + + + + +
+
+ +

2013

+ +
+ + + Defining cell-type specificity at the transcriptional level in human disease + + + +
+ + + + + Defining cell-type specificity at the transcriptional level in human disease + + +
+ Wenjun Ju, Casey S. Greene, Felix Eichinger, Viji Nair, Jeffrey B. Hodgin, ..., Song Jiang, Maria Pia Rastaldi, Clemens D. Cohen, Olga G. Troyanskaya, Matthias Kretzler +
+ +
+ Genome Research +   ·   + 15 Aug 2013 +   ·   + doi:10.1101/gr.155697.113 +
+ + + + + + + + + + +
+
+ +
+ + + Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes + + + +
+ + + + + Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes + + +
+ Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars A. Bongo, Rebecca D. Burdine, Olga G. Troyanskaya +
+ +
+ PLoS Computational Biology +   ·   + 14 Mar 2013 +   ·   + doi:10.1371/journal.pcbi.1002957 +
+ + + + + + + + +
+
+ +
+ + + Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments + + + +
+ + + + + Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments + + +
+ Jie Tan, Gavin D. Grant, Michael L. Whitfield, Casey S. Greene +
+ +
+ Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics +   ·   + 01 Jan 2013 +   ·   + doi:10.1007/978-3-642-37189-9_2 +
+ + + + + + + + +
+
+ +

2012

+ +
+ + + Chapter 2: Data-Driven View of Disease Biology + + + +
+ + + + + Chapter 2: Data-Driven View of Disease Biology + + +
+ Casey S. Greene, Olga G. Troyanskaya +
+ +
+ PLoS Computational Biology +   ·   + 27 Dec 2012 +   ·   + doi:10.1371/journal.pcbi.1002816 +
+ + + + + + + + +
+
+ +
+ + + IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks + + + +
+ + + + + IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks + + +
+ Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars A. Bongo, Yuanfang Guan, Olga G. Troyanskaya +
+ +
+ Nucleic Acids Research +   ·   + 07 Jun 2012 +   ·   + doi:10.1093/nar/gks458 +
+ + + + + + + + +
+
+ +
+ + + Accurate evaluation and analysis of functional genomics data and methods + + + +
+ + + + + Accurate evaluation and analysis of functional genomics data and methods + + +
+ Casey S. Greene, Olga G. Troyanskaya +
+ +
+ Annals of the New York Academy of Sciences +   ·   + 23 Jan 2012 +   ·   + doi:10.1111/j.1749-6632.2011.06383.x +
+ + + + + + + + +
+
+
+ + +
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+ Click here if you are not redirected. + + diff --git a/preview/pr-117/team/index.html b/preview/pr-117/team/index.html new file mode 100644 index 00000000..74e87b43 --- /dev/null +++ b/preview/pr-117/team/index.html @@ -0,0 +1,1830 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Team | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + + + + + +
+

+Team

+ +

Our lab is made up of a highly engaged and collaborative team of researchers. +We recognize that diverse teams do better research. +We foster an environment where team members are treated equally, and where we respect and admire our differences. +The team includes postdocs, students at all levels, staff, and our lab mascots.

+ + + + + + + + + + + + +
+ + + + + +
+ + +

We work with a wide range of outstanding groups from around the world, and we’re always on the lookout for new and unique perspectives. +We want to push the frontier of data science and train the next generation of data scientists.

+ + +
+ + + + + +
+ + +

Alumni

+ +

Gone but never forgotten. +These are past lab members who have moved on to the Childhood Cancer Data Lab, other school programs, new jobs, or elsewhere. +They have all made lasting contributions to science and to our hearts. ❤️

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + +

Funding

+ +
+ +

Gordon and Betty Moore Foundation

+ +

National Cancer Institute

+ +

Alex's Lemonade Stand Foundation for Childhood Cancer

+ +

Chan Zuckerberg Initiative

+ +

Cystic Fibrosis Foundation

+ +

Alfred P. Sloan Foundation

+ +

National Human Genome Research Institute

+ +

National Heart, Lung, and Blood Institute

+ +

National Institute of Neurological Disorders and Stroke

+ + +
+
+ + + + + +
+ + +
+ + The Greene Lab in their natural Philadelphia habitat + + +
+ The Greene Lab in their natural Philadelphia habitat + +
+ +
+
+ + +
+ + + + + + + diff --git a/preview/pr-117/tools/index.html b/preview/pr-117/tools/index.html new file mode 100644 index 00000000..4c58ffff --- /dev/null +++ b/preview/pr-117/tools/index.html @@ -0,0 +1,1307 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Tools | The Greene Lab + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + +
+ +
+ + + + + + + + + + + + + +
+

+Tools

+ +

All of our software, tools, datasets, etc. are 100% open-source, and free for anyone around the world to use and modify. +We strive to make resources that are high quality in every aspect: +cleanly written, robustly constructed and tested, well-documented, easy-to-use, accessible, customizable, and as effective as possible in real-world use.

+ +
+
+ + + + + +
+ + + + +
+ + Adage + + +
+ + + Adage + + + + + + +

Adage helps you explore gene expression data and discover new insights from machine learning models. See how genes relate to each other, other genes, and how they are represented in machine learning signatures. View the activities of samples as a colored heatmap, and cluster them on the fly. Explore the genes that contribute to signatures, the experiments in which they vary the most, and the pathways they significantly overlap with.

+ + + + + + + +
+ +
+ + + +
+
+ +
+ + Preprint Similarity Search + + +
+ + + Preprint Similarity Search + + + + + + +

Preprint Similarity Search uses a machine learning model trained on 1.7 million PubMed Central open access documents to find similar papers and journals based on the textual content of your bioRxiv or medRxiv preprint. These results can be used as a starting point when searching for a place to publish your paper.

+ + + + + + + +
+ +
+ + + +
+
+ +
+ + Connectivity Search + + +
+ + + Connectivity Search + + + + + + +

Connectivity search allows you to find the most important paths connecting any two nodes in Hetionet, even when they are different types or not known to be related. If you want to investigate how the eye and breast cancer may be related, you can. Filter nodes by group, see computed significance data about paths, create graph visualizations with highlighted paths, and more.

+ + + + + + + +
+ +
+ + + +
+
+ +
+ + Manubot + + +
+ + + Manubot + + + + + + +

Manubot is a workflow and set of tools for the next generation of scholarly publishing. Write your manuscript in markdown, track it with git, automatically convert it to .html, .pdf, or .docx, and deploy it to your destination of choice.

+ + + + + + + +
+ +
+ + + +
+
+ +
+ + Lab Website Template + + +
+ + + Lab Website Template + + + + + + +

What this website is built on! An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more. Spend less time reinventing the wheel, and more time running your lab.

+ + + + + + + + + + + +
+
+
+ + + + + +
+ + +

More

+ +
+ + ponyo + + +
+ + + ponyo + + + + + + +

A method to simulate gene expression data using a generative neural network trained on existing gene expression data to learn a representation of expression patterns.

+ + + + + + + +
+ +
+ + + +
+
+ +
+ + hclust + + +
+ + + hclust + + + + + + +

A JavaScript npm package for agglomerative hierarchical clustering.

+ + + + + + + +
+ +
+ + + +
+
+ +
+ + Intro to SVGs + + +
+ + + Intro to SVGs + + + + + + +

An introduction to the Scalable Vector Graphics (SVG) image format, aimed at people in academia.

+ + + + + + + +
+ +
+ + + +
+
+ +
+ + SVG to PNG + + +
+ + + SVG to PNG + + + + + + +

Convert SVG to PNG right in your browser, reliably and correctly.

+ + + + + + + +
+ +
+ + + +
+
+
+ + + + + +
+ + +

Affiliated Organizations

+ +
+ + Childhood Cancer Data Lab + + +
+ + + Childhood Cancer Data Lab + + + + + + +

Turning researchers who fight childhood cancer into data wizards.

+ + + + +
+
+ +
+ + Hetio + + +
+ + + Hetio + + + + + + +

Hetnet-related research, tools, and datasets including Hetionet.

+ + + + +
+
+ +
+ + Manubot + + +
+ + + Manubot + + + + + + +

The next generation of scholarly publishing: open, collaborative, reproducible, free.

+ + + + +
+
+
+ + + + + +
+ + +

Legacy

+ +
+ + Tribe + + +
+ + + Tribe + + + + + + +

Seamlessly mine data across bioinformatics systems. Tribe stores the findings of your research as collections of genes.

+ + + + + + + +
+ +
+ + + +
+
+ +
+ + IMP + + +
+ + + IMP + + + + + + +

IMP helps researchers identify new gene-gene and gene-process associations that are supported by existing data but currently unannotated.

+ + + + +
+
+ +
+ + GIANT + + +
+ + + GIANT + + + + + + +

GIANT helps researchers identify which genes are working together in specific tissues. This tissue-specific lens into human biology helps researchers study complex human diseases.

+ + + + +
+
+ +
+ + Nano-dissection + + +
+ + + Nano-dissection + + + + + + +

Nano-dissection allows researchers to identify genes expressed in specific tissues and cell lineages from microarray data that are not resolved to the level of the cell lineage of interest.

+ + + + +
+
+
+ + +
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