From c8fc74800adb78e8f0c48b915f3853ea430a2a8d Mon Sep 17 00:00:00 2001
From: cgreene <cgreene@users.noreply.github.com>
Date: Tue, 9 Jan 2024 18:50:43 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20greenela?=
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---
 2019/01/29/infant-in-arms.html                |   8 +-
 2019/04/06/the-harassment-tax.html            |   8 +-
 .../01/why-do-we-have-application-fees.html   |   8 +-
 2020/10/19/DL-workshop.html                   |   8 +-
 feed.xml                                      |   8 +-
 members/casey-greene.html                     |  16 +--
 research/index.html                           |  39 +++++++
 sitemap.xml                                   | 100 +++++++++---------
 8 files changed, 117 insertions(+), 78 deletions(-)

diff --git a/2019/01/29/infant-in-arms.html b/2019/01/29/infant-in-arms.html
index 1347637b..74604a86 100644
--- a/2019/01/29/infant-in-arms.html
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@@ -68,10 +68,10 @@
 
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diff --git a/2019/04/06/the-harassment-tax.html b/2019/04/06/the-harassment-tax.html
index ceb9b1f6..2eceb13e 100644
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@@ -68,10 +68,10 @@
 
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     "name": "The Harassment Tax",
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diff --git a/2019/05/01/why-do-we-have-application-fees.html b/2019/05/01/why-do-we-have-application-fees.html
index 26824a4a..e06ccde0 100644
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@@ -68,10 +68,10 @@
 
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diff --git a/2020/10/19/DL-workshop.html b/2020/10/19/DL-workshop.html
index 1d616a04..9a92dbd1 100644
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@@ -68,10 +68,10 @@
 
   <meta name="author" content="alex-lee">
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-  <meta property="og:updated_time" content="2024-01-09T17:59:52+00:00">
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diff --git a/feed.xml b/feed.xml
index bdcc9407..4d35c180 100644
--- a/feed.xml
+++ b/feed.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.2">Jekyll</generator><link href="/feed.xml" rel="self" type="application/atom+xml" /><link href="/" rel="alternate" type="text/html" /><updated>2024-01-09T18:01:04+00:00</updated><id>/feed.xml</id><title type="html">The Greene Lab</title><subtitle>Where data and biology meet</subtitle><entry><title type="html">Deep Learning in Biology Workshop</title><link href="/2020/10/19/DL-workshop.html" rel="alternate" type="text/html" title="Deep Learning in Biology Workshop" /><published>2020-10-19T00:00:00+00:00</published><updated>2024-01-09T17:59:52+00:00</updated><id>/2020/10/19/DL-workshop</id><content type="html" xml:base="/2020/10/19/DL-workshop.html"><![CDATA[<h2 id="discovering-the-beauty-of-math-and-the-fun-of-computer-science">Discovering the beauty of math and the fun of computer science</h2>
+<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.2">Jekyll</generator><link href="/feed.xml" rel="self" type="application/atom+xml" /><link href="/" rel="alternate" type="text/html" /><updated>2024-01-09T18:50:34+00:00</updated><id>/feed.xml</id><title type="html">The Greene Lab</title><subtitle>Where data and biology meet</subtitle><entry><title type="html">Deep Learning in Biology Workshop</title><link href="/2020/10/19/DL-workshop.html" rel="alternate" type="text/html" title="Deep Learning in Biology Workshop" /><published>2020-10-19T00:00:00+00:00</published><updated>2024-01-09T18:49:34+00:00</updated><id>/2020/10/19/DL-workshop</id><content type="html" xml:base="/2020/10/19/DL-workshop.html"><![CDATA[<h2 id="discovering-the-beauty-of-math-and-the-fun-of-computer-science">Discovering the beauty of math and the fun of computer science</h2>
 
 <p>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.
@@ -66,7 +66,7 @@ You can find my current research projects on my <a href="https://github.com/ajle
       " alt="figure image" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;" />
   </a>
   
-</figure>]]></content><author><name>alex-lee</name></author><category term="deep learning" /><category term="workshop" /><summary type="html"><![CDATA[Discovering the beauty of math and the fun of computer science]]></summary></entry><entry><title type="html">Why do we have application fees?</title><link href="/2019/05/01/why-do-we-have-application-fees.html" rel="alternate" type="text/html" title="Why do we have application fees?" /><published>2019-05-01T00:00:00+00:00</published><updated>2024-01-09T17:59:52+00:00</updated><id>/2019/05/01/why-do-we-have-application-fees</id><content type="html" xml:base="/2019/05/01/why-do-we-have-application-fees.html"><![CDATA[<h2 id="context">Context</h2>
+</figure>]]></content><author><name>alex-lee</name></author><category term="deep learning" /><category term="workshop" /><summary type="html"><![CDATA[Discovering the beauty of math and the fun of computer science]]></summary></entry><entry><title type="html">Why do we have application fees?</title><link href="/2019/05/01/why-do-we-have-application-fees.html" rel="alternate" type="text/html" title="Why do we have application fees?" /><published>2019-05-01T00:00:00+00:00</published><updated>2024-01-09T18:49:34+00:00</updated><id>/2019/05/01/why-do-we-have-application-fees</id><content type="html" xml:base="/2019/05/01/why-do-we-have-application-fees.html"><![CDATA[<h2 id="context">Context</h2>
 
 <p>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.
@@ -126,7 +126,7 @@ I am posting this to the blog in the hopes that another institution will find th
 
 <p><em>Update 5/1/19:</em></p>
 
-<p>After posting, I was pointed to <a href="http://dailynous.com/2017/10/04/carnegie-mellon-philosophy-eliminates-application-fee-guest-post-kevin-zollman/">CMU’s Department of Philosophy’s elimination of application fees in 2017</a>.</p>]]></content><author><name>casey-greene</name></author><summary type="html"><![CDATA[Context]]></summary></entry><entry><title type="html">The Harassment Tax</title><link href="/2019/04/06/the-harassment-tax.html" rel="alternate" type="text/html" title="The Harassment Tax" /><published>2019-04-06T00:00:00+00:00</published><updated>2024-01-09T17:59:52+00:00</updated><id>/2019/04/06/the-harassment-tax</id><content type="html" xml:base="/2019/04/06/the-harassment-tax.html"><![CDATA[<p><em>TL;DR: <a href="https://twitter.com/mhendr1cks/status/1112893604010262530">This twitter thread from Michael Hendricks</a> is on the money.</em></p>
+<p>After posting, I was pointed to <a href="http://dailynous.com/2017/10/04/carnegie-mellon-philosophy-eliminates-application-fee-guest-post-kevin-zollman/">CMU’s Department of Philosophy’s elimination of application fees in 2017</a>.</p>]]></content><author><name>casey-greene</name></author><summary type="html"><![CDATA[Context]]></summary></entry><entry><title type="html">The Harassment Tax</title><link href="/2019/04/06/the-harassment-tax.html" rel="alternate" type="text/html" title="The Harassment Tax" /><published>2019-04-06T00:00:00+00:00</published><updated>2024-01-09T18:49:34+00:00</updated><id>/2019/04/06/the-harassment-tax</id><content type="html" xml:base="/2019/04/06/the-harassment-tax.html"><![CDATA[<p><em>TL;DR: <a href="https://twitter.com/mhendr1cks/status/1112893604010262530">This twitter thread from Michael Hendricks</a> is on the money.</em></p>
 
 <p>In a recent article in Science about the National Academies developing a procedure to expel sexual harassers, Dr. Robert Weinberg (<a href="https://biology.mit.edu/profile/robert-a-weinberg/">Member, Whitehead Institute; and Daniel K. Ludwig Professor for Cancer Research in the Department of Biology at MIT</a>) 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.
@@ -169,7 +169,7 @@ The Chancellor of Vanderbilt University, Nick Zeppos, has failed to support her
 It conspicuously ignores Dr. McLaughlin, a <a href="http://news.mit.edu/2018/media-lab-disobedience-award-winners-announced-1128">winner of the MIT Disobedience Prize</a>.</p>
 
 <p>P.S. I gave a talk at UAB recently, where I <a href="https://upenn.box.com/s/hqnry3kd75hg5upjml2z82g4bocgbb9z">included some slides</a> (+ 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).</p>]]></content><author><name>casey-greene</name></author><summary type="html"><![CDATA[TL;DR: This twitter thread from Michael Hendricks is on the money.]]></summary></entry><entry><title type="html">Infant in arms: Some thoughts from a father traveling solo with an infant</title><link href="/2019/01/29/infant-in-arms.html" rel="alternate" type="text/html" title="Infant in arms: Some thoughts from a father traveling solo with an infant" /><published>2019-01-29T00:00:00+00:00</published><updated>2024-01-09T17:59:52+00:00</updated><id>/2019/01/29/infant-in-arms</id><content type="html" xml:base="/2019/01/29/infant-in-arms.html"><![CDATA[<h2 id="brief-context">Brief Context</h2>
+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).</p>]]></content><author><name>casey-greene</name></author><summary type="html"><![CDATA[TL;DR: This twitter thread from Michael Hendricks is on the money.]]></summary></entry><entry><title type="html">Infant in arms: Some thoughts from a father traveling solo with an infant</title><link href="/2019/01/29/infant-in-arms.html" rel="alternate" type="text/html" title="Infant in arms: Some thoughts from a father traveling solo with an infant" /><published>2019-01-29T00:00:00+00:00</published><updated>2024-01-09T18:49:34+00:00</updated><id>/2019/01/29/infant-in-arms</id><content type="html" xml:base="/2019/01/29/infant-in-arms.html"><![CDATA[<h2 id="brief-context">Brief Context</h2>
 
 <p>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.
diff --git a/members/casey-greene.html b/members/casey-greene.html
index 6a65b31b..b64c4661 100644
--- a/members/casey-greene.html
+++ b/members/casey-greene.html
@@ -794,8 +794,8 @@ <h3 id="2023">2023</h3>
     
     
 
-    <a href="https://doi.org/gsvhxn" class="citation-title">
-      Human Microbiome Compendium dataset
+    <a href="https://doi.org/gsvf5z" class="citation-title">
+      Integration of 168,000 samples reveals global patterns of the human gut microbiome
     </a>
 
     <div class="citation-authors" tabindex="0">
@@ -803,11 +803,11 @@ <h3 id="2023">2023</h3>
     </div>
 
     <div class="citation-details">
-      Zenodo
+      Cold Spring Harbor Laboratory
         ·  
       11 Oct 2023
         ·  
-      doi:10.5281/zenodo.8186993
+      doi:10.1101/2023.10.11.560955
     </div>
 
     
@@ -821,8 +821,8 @@ <h3 id="2023">2023</h3>
     
     
 
-    <a href="https://doi.org/gsvf5z" class="citation-title">
-      Integration of 168,000 samples reveals global patterns of the human gut microbiome
+    <a href="https://doi.org/gsvhxn" class="citation-title">
+      Human Microbiome Compendium dataset
     </a>
 
     <div class="citation-authors" tabindex="0">
@@ -830,11 +830,11 @@ <h3 id="2023">2023</h3>
     </div>
 
     <div class="citation-details">
-      Cold Spring Harbor Laboratory
+      Zenodo
         ·  
       11 Oct 2023
         ·  
-      doi:10.1101/2023.10.11.560955
+      doi:10.5281/zenodo.8186993
     </div>
 
     
diff --git a/research/index.html b/research/index.html
index 41e0e6dc..636d1189 100644
--- a/research/index.html
+++ b/research/index.html
@@ -707,6 +707,45 @@ <h1 id="research">
 
 <div class="search-info"></div>
 
+<h3 id="2024">2024</h3>
+
+<div class="citation">
+  
+    <a href="https://doi.org/gtcwqq" class="citation-image" aria-label="Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine">
+      <img src="https://private-user-images.githubusercontent.com/542643/294239653-924e038d-77d7-4bf0-aa80-7d532faa66fc.png" alt="Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine" loading="lazy" onerror="this.src = '/images/fallback.svg'; this.onerror = null;">
+    </a>
+  
+
+  <div class="citation-text">
+    
+    
+
+    <a href="https://doi.org/gtcwqq" class="citation-title">
+      Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine
+    </a>
+
+    <div class="citation-authors" data-tooltip="Laura K. Wiley, Jonathan A. Shortt, Emily R. Roberts, Jan Lowery, Elizabeth Kudron, Meng Lin, David Mayer, Melissa Wilson, Tonya M. Brunetti, Sameer Chavan, Tzu L. Phang, Nikita Pozdeyev, Joseph Lesny, Stephen J. Wicks, Ethan T. Moore, Joshua L. Morgenstern, Alanna N. Roff, Elise L. Shalowitz, Adrian Stewart, Cole Williams, Michelle N. Edelmann, Madelyne Hull, J. Tacker Patton, Lisen Axell, Lisa Ku, Yee Ming Lee, Jean Jirikowic, Anna Tanaka, Emily Todd, Sarah White, Brett Peterson, Emily Hearst, Richard Zane, Casey S. Greene, Rasika Mathias, Marilyn Coors, Matthew Taylor, Debashis Ghosh, Michael G. Kahn, Ian M. Brooks, Christina L. Aquilante, David Kao, Nicholas Rafaels, Kristy R. Crooks, Steve Hess, Kathleen C. Barnes, Christopher R. Gignoux " tabindex="0">
+      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
+    </div>
+
+    <div class="citation-details">
+      The American Journal of Human Genetics
+        ·  
+      01 Jan 2024
+        ·  
+      doi:10.1016/j.ajhg.2023.12.001
+    </div>
+
+    
+      
+
+      
+
+      
+    
+  </div>
+</div>
+
 <h3 id="2023">2023</h3>
 
 <div class="citation">
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