diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db
index 74a72484..c7f96d4a 100644
Binary files a/_cite/.cache/cache.db and b/_cite/.cache/cache.db differ
diff --git a/_data/citations.yaml b/_data/citations.yaml
index 1b95c3d5..7d53d5d6 100644
--- a/_data/citations.yaml
+++ b/_data/citations.yaml
@@ -13,45 +13,98 @@
member: casey-greene
plugin: orcid.py
file: orcid.yaml
-- id: doi:10.7554/eLife.84855
- title: Analysis of science journalism reveals gender and regional disparities in
- coverage
+- id: doi:10.5281/zenodo.8186993
+ title: Human Microbiome Compendium dataset
authors:
- - Natalie R. Davidson
+ - Richard J. Abdill
+ - Samantha P. Graham
+ - Vincent Rubinetti
+ - Frank W. Albert
- Casey S. Greene
- publisher: eLife Sciences Publications, Ltd
- date: '2023-02-09'
- link: https://doi.org/10.7554/elife.84855
+ - Sean Davis
+ - Ran Blekhman
+ publisher: Zenodo
+ date: '2023-10-11'
+ link: https://doi.org/gsvhxn
orcid: 0000-0001-8713-9213
member: casey-greene
plugin: orcid.py
file: orcid.yaml
-- id: doi:10.7554/eLife.84855.3
- title: Analysis of science journalism reveals gender and regional disparities in
- coverage
+- id: doi:10.1016/j.ajhg.2023.12.001
+ title: 'Building a vertically integrated genomic learning health system: The biobank
+ at the Colorado Center for Personalized Medicine'
authors:
- - Natalie R Davidson
- - Casey S Greene
- publisher: eLife
- date: '2024-05-28'
- link: https://doi.org/gtw9dx
+ - 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
+ publisher: The American Journal of Human Genetics
+ date: '2024-01-01'
+ link: https://doi.org/gtcwqq
orcid: 0000-0001-8713-9213
member: casey-greene
- plugin: orcid.py
- file: orcid.yaml
-- id: doi:10.7554/eLife.84855.2
- title: Analysis of science journalism reveals gender and regional disparities in
- coverage
+ plugin: sources.py
+ file: sources.yaml
+ image: https://private-user-images.githubusercontent.com/542643/294239653-924e038d-77d7-4bf0-aa80-7d532faa66fc.png
+- id: doi:10.1101/2023.06.28.546898
+ title: Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry
+ Estimates from Direct-to-Consumer Canine Genetic Tests
authors:
- - Natalie R. Davidson
+ - Halie M. Rando
+ - Kiley Graim
+ - Greg Hampikian
- Casey S. Greene
- publisher: eLife Sciences Publications, Ltd
- date: '2024-05-17'
- link: https://doi.org/gtvsrt
+ publisher: Cold Spring Harbor Laboratory
+ date: '2023-06-29'
+ link: https://doi.org/10.1101/2023.06.28.546898
orcid: 0000-0001-8713-9213
member: casey-greene
- plugin: orcid.py
- file: orcid.yaml
+ plugin: sources.py
+ file: sources.yaml
+ image: https://user-images.githubusercontent.com/8975841/250271905-4eed44ba-528a-4a61-a4ec-fa90d51e61f9.jpg
- id: doi:10.1101/2024.04.25.590992
title: Missing cell types in single-cell references impact deconvolution of bulk
data but are detectable
@@ -70,6 +123,37 @@
member: casey-greene
plugin: orcid.py
file: orcid.yaml
+- id: doi:10.1101/2023.07.31.551386
+ title: 'MousiPLIER: A Mouse Pathway-Level Information Extractor Model'
+ authors:
+ - Shuo Zhang
+ - Benjamin J. Heil
+ - Weiguang Mao
+ - Maria Chikina
+ - Casey S. Greene
+ - Elizabeth A. Heller
+ publisher: Cold Spring Harbor Laboratory
+ date: '2023-08-02'
+ link: https://doi.org/10.1101/2023.07.31.551386
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: sources.py
+ file: sources.yaml
+ image: https://user-images.githubusercontent.com/542643/262141715-23a165d3-0156-4ba0-afc6-0ef260c46d7c.png
+- id: doi:10.1093/bioadv/vbae004
+ title: "Optimizer\u2019s dilemma: optimization strongly influences model selection\
+ \ in transcriptomic prediction"
+ authors:
+ - Jake Crawford
+ - Maria Chikina
+ - Casey S Greene
+ publisher: Bioinformatics Advances
+ date: '2024-01-01'
+ link: https://doi.org/gtdh5z
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
- id: doi:10.1128/spectrum.03157-23
title: "Pseudomonas aeruginosa\n transcriptome analysis of metal\
\ restriction in\n ex vivo\n cystic fibrosis sputum"
@@ -87,33 +171,26 @@
member: casey-greene
plugin: orcid.py
file: orcid.yaml
-- id: doi:10.5281/zenodo.8186993
- title: Human Microbiome Compendium dataset
+- id: doi:10.1101/2024.04.19.590243
+ title: 'The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools
+ for single-cell transcriptomics of pediatric tumors'
authors:
- - Richard J. Abdill
- - Samantha P. Graham
- - Vincent Rubinetti
- - Frank W. Albert
+ - Allegra G. Hawkins
+ - Joshua A. Shapiro
+ - Stephanie J. Spielman
+ - David S. Mejia
+ - Deepashree Venkatesh Prasad
+ - Nozomi Ichihara
+ - Arkadii Yakovets
+ - Kurt G. Wheeler
+ - Chante J. Bethell
+ - Steven M. Foltz
+ - "Jennifer O\u2019Malley"
- Casey S. Greene
- - Sean Davis
- - Ran Blekhman
- publisher: Zenodo
- date: '2023-10-11'
- link: https://doi.org/gsvhxn
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: orcid.py
- file: orcid.yaml
-- id: doi:10.1093/bioadv/vbae004
- title: "Optimizer\u2019s dilemma: optimization strongly influences model selection\
- \ in transcriptomic prediction"
- authors:
- - Jake Crawford
- - Maria Chikina
- - Casey S Greene
- publisher: Bioinformatics Advances
- date: '2024-01-01'
- link: https://doi.org/gtdh5z
+ - Jaclyn N. Taroni
+ publisher: Cold Spring Harbor Laboratory
+ date: '2024-04-24'
+ link: https://doi.org/gt6s6h
orcid: 0000-0001-8713-9213
member: casey-greene
plugin: orcid.py
@@ -128,255 +205,127 @@
member: casey-greene
plugin: orcid.py
file: orcid.yaml
-- id: doi:10.1186/s13059-023-03077-7
- title: Performance of computational algorithms to deconvolve heterogeneous bulk
- ovarian tumor tissue depends on experimental factors
- authors:
- - Ariel A. Hippen
- - Dalia K. Omran
- - Lukas M. Weber
- - Euihye Jung
- - Ronny Drapkin
- - Jennifer A. Doherty
- - Stephanie C. Hicks
- - Casey S. Greene
- publisher: Genome Biology
- date: '2023-10-20'
- link: https://doi.org/gswt6v
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/211156536-a2179f50-9d88-4b80-bb01-6247941bbe4b.png
- buttons:
- - type: preprint
- link: https://doi.org/10.1101/2022.12.04.519045
-- id: doi:10.1101/2023.10.11.560955
- title: Integration of 168,000 samples reveals global patterns of the human gut microbiome
- authors:
- - Richard J. Abdill
- - Samantha P. Graham
- - Vincent Rubinetti
- - Frank W. Albert
- - Casey S. Greene
- - Sean Davis
- - Ran Blekhman
- publisher: Cold Spring Harbor Laboratory
- date: '2023-10-11'
- link: https://doi.org/gsvf5z
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/274611735-0b4d7372-d935-4a0d-b3a3-909012346b35.png
-- id: doi:10.1101/2023.08.21.554169
- title: Analysis ofPseudomonas aeruginosatranscription in anex vivocystic
- fibrosis sputum model identifies metal restriction as a gene expression stimulus
- authors:
- - Samuel L. Neff
- - Georgia Doing
- - Taylor Reiter
- - Thomas H. Hampton
- - Casey S. Greene
- - Deborah A. Hogan
- publisher: Cold Spring Harbor Laboratory
- date: '2023-08-21'
- link: https://doi.org/10.1101/2023.08.21.554169
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/274611350-b55a8531-8fee-4125-8054-4db365ab8009.png
-- id: doi:10.1101/2023.07.31.551386
- title: 'MousiPLIER: A Mouse Pathway-Level Information Extractor Model'
+- id: doi:10.5281/zenodo.8044955
+ title: 'greenelab/phenoplier: a computational framework to integrate genetic studies
+ with gene co-expression patterns'
authors:
- - Shuo Zhang
- - Benjamin J. Heil
- - Weiguang Mao
- - Maria Chikina
- - Casey S. Greene
- - Elizabeth A. Heller
- publisher: Cold Spring Harbor Laboratory
- date: '2023-08-02'
- link: https://doi.org/10.1101/2023.07.31.551386
+ - Milton Pividori
+ - Casey Greene
+ publisher: Zenodo
+ date: '2023-06-22'
+ link: https://doi.org/10.5281/zenodo.8044955
orcid: 0000-0001-8713-9213
member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/262141715-23a165d3-0156-4ba0-afc6-0ef260c46d7c.png
-- id: doi:10.1101/2023.07.20.549951
- title: BuDDI:Bulk Deconvolution with Domain Invarianceto predict cell-type-specific
- perturbations from bulk
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.5281/zenodo.7805407
+ title: Data underlying OpenPBTA Manuscript Figures and Molecular Alterations
authors:
- - Natalie R. Davidson
- - Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2023-07-22'
- link: https://doi.org/10.1101/2023.07.20.549951
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/262144782-78a11c8e-1b10-44e0-85ec-1b709cfd94e4.png
-- id: doi:10.1093/nar/gkad289
- title: 'MyGeneset.info: an interactive and programmatic platform for community-curated
- and user-created collections of genes'
- authors:
- - Ricardo Avila
- - Vincent Rubinetti
- - Xinghua Zhou
- - Dongbo Hu
- - Zhongchao Qian
- - Marco Alvarado Cano
- - Everaldo Rodolpho
- - Ginger Tsueng
- - Casey Greene
- - Chunlei Wu
- publisher: Nucleic Acids Research
- date: '2023-04-18'
- link: https://doi.org/10.1093/nar/gkad289
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/232873400-6146a32d-b11b-4514-8b26-14c6e4d6bcac.jpeg
-- id: doi:10.1101/2023.06.28.546898
- title: Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry
- Estimates from Direct-to-Consumer Canine Genetic Tests
- authors:
- - Halie M. Rando
- - Kiley Graim
- - Greg Hampikian
+ - Joshua A. Shapiro
+ - Krutika S. Gaonkar
+ - Stephanie J. Spielman
+ - Candace L. Savonen
+ - Chante J. Bethell
+ - Run Jin
+ - Komal S. Rathi
+ - Yuankun Zhu
+ - Laura E. Egolf
+ - Bailey K. Farrow
+ - Daniel P. Miller
+ - Yang Yang
+ - Tejaswi Koganti
+ - Nighat Noureen
+ - Mateusz P. Koptyra
+ - Nhat Duong
+ - Mariarita Santi
+ - Jung Kim
+ - Shannon Robins
+ - Phillip B. Storm
+ - Stephen C. Mack
+ - Jena V. Lilly
+ - Hongbo M. Xie
+ - Payal Jain
+ - Pichai Raman
+ - Brian R. Rood
+ - Rishi R. Lulla
+ - Javad Nazarian
+ - Adam A. Kraya
+ - Zalman Vaksman
+ - Allison P. Heath
+ - Cassie Kline
+ - Laura Scolaro
+ - Angela N. Viaene
+ - Xiaoyan Huang
+ - Gregory P. Way
+ - Steven M. Foltz
+ - Bo Zhang
+ - Anna R. Poetsch
+ - Sabine Mueller
+ - Brian M. Ennis
+ - Michael Prados
+ - Sharon J. Diskin
+ - Siyuan Zheng
+ - Yiran Guo
+ - Shrivats Kannan
+ - Angela J. Waanders
+ - Ashley S. Margol
+ - Meen Chul Kim
+ - Derek Hanson
+ - Nicholas Van Kuren
+ - Jessica Wong
+ - Rebecca S. Kaufman
+ - Noel Coleman
+ - Christopher Blackden
+ - Kristina A. Cole
+ - Jennifer L. Mason
+ - Peter J. Madsen
+ - Carl J. Koschmann
+ - Douglas R. Stewart
+ - Eric Wafula
+ - Miguel A. Brown
+ - Adam C. Resnick
- Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2023-06-29'
- link: https://doi.org/10.1101/2023.06.28.546898
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/8975841/250271905-4eed44ba-528a-4a61-a4ec-fa90d51e61f9.jpg
-- id: doi:10.1093/gigascience/giad047
- title: Hetnet connectivity search provides rapid insights into how biomedical entities
- are related
- authors:
- - Daniel S Himmelstein
- - Michael Zietz
- - Vincent Rubinetti
- - Kyle Kloster
- - Benjamin J Heil
- - Faisal Alquaddoomi
- - Dongbo Hu
- - David N Nicholson
- - Yun Hao
- - Blair D Sullivan
- - Michael W Nagle
- - Casey S Greene
- publisher: GigaScience
- date: '2022-12-28'
- link: https://doi.org/10.1093/gigascience/giad047
+ - Jo Lynne Rokita
+ - Jaclyn N. Taroni
+ publisher: Zenodo
+ date: '2023-04-06'
+ link: https://doi.org/10.5281/zenodo.7805407
orcid: 0000-0001-8713-9213
member: casey-greene
plugin: orcid.py
file: orcid.yaml
-- id: doi:10.1101/2023.06.26.546586
- title: "Optimizer\u2019s dilemma: optimization strongly influences model selection\
- \ in transcriptomic prediction"
+- id: doi:10.1101/2023.08.21.554169
+ title: Analysis ofPseudomonas aeruginosatranscription in anex vivocystic
+ fibrosis sputum model identifies metal restriction as a gene expression stimulus
authors:
- - Jake Crawford
- - Maria Chikina
+ - Samuel L. Neff
+ - Georgia Doing
+ - Taylor Reiter
+ - Thomas H. Hampton
- Casey S. Greene
+ - Deborah A. Hogan
publisher: Cold Spring Harbor Laboratory
- date: '2023-06-26'
- link: https://doi.org/10.1101/2023.06.26.546586
+ date: '2023-08-21'
+ link: https://doi.org/10.1101/2023.08.21.554169
orcid: 0000-0001-8713-9213
member: casey-greene
plugin: sources.py
file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/252371308-1ae174fe-1eb6-47c4-882b-5a3b982bc533.png
-- id: doi:10.5281/zenodo.8044955
- title: 'greenelab/phenoplier: a computational framework to integrate genetic studies
- with gene co-expression patterns'
- authors:
- - Milton Pividori
- - Casey Greene
- publisher: Zenodo
- date: '2023-06-22'
- link: https://doi.org/10.5281/zenodo.8044955
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: orcid.py
- file: orcid.yaml
-- id: doi:10.5281/zenodo.8071382
- title: 'greenelab/phenoplier: a computational framework to integrate genetic studies
- with gene co-expression patterns'
+ image: https://user-images.githubusercontent.com/542643/274611350-b55a8531-8fee-4125-8054-4db365ab8009.png
+- id: doi:10.7554/ELIFE.84855
+ title: Analysis of science journalism reveals gender and regional disparities in
+ coverage
authors:
- - ' Milton Pividori'
- - ' Casey Greene'
- publisher: Zenodo
- date: '2023-06-22'
- link: https://doi.org/gsdcgn
+ - Natalie R Davidson
+ - Casey S Greene
+ publisher: eLife
+ date: '2024-05-28'
+ link: https://doi.org/grrw83
orcid: 0000-0001-8713-9213
member: casey-greene
plugin: orcid.py
file: orcid.yaml
-- id: doi:10.1101/2023.06.14.544991
- title: Deconvolution reveals compositional differences in high-grade serous ovarian
- cancer subtypes
- authors:
- - Ariel A. Hippen
- - Natalie R. Davidson
- - Mollie E. Barnard
- - Lukas M. Weber
- - Jason Gertz
- - Jennifer A. Doherty
- - Stephanie C. Hicks
- - Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2023-06-15'
- link: https://doi.org/10.1101/2023.06.14.544991
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/252370773-d74c01ff-8230-4e0b-815a-48a2dfa05c9a.png
-- id: doi:10.1038/s41592-023-01886-z
- title: Machine learning in rare disease
- authors:
- - Jineta Banerjee
- - Jaclyn N. Taroni
- - Robert J. Allaway
- - Deepashree Venkatesh Prasad
- - Justin Guinney
- - Casey Greene
- publisher: Nature Methods
- date: '2023-05-29'
- link: https://doi.org/10.1038/s41592-023-01886-z
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/262425906-9b6e243a-c371-44dd-849c-5a2ce240a99b.png
-- id: doi:10.1186/s13040-023-00332-2
- title: Changing word meanings in biomedical literature reveal pandemics and new
- technologies
- authors:
- - David N. Nicholson
- - Faisal Alquaddoomi
- - Vincent Rubinetti
- - Casey S. Greene
- publisher: BioData Mining
- date: '2023-05-05'
- link: https://doi.org/10.1186/s13040-023-00332-2
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://user-images.githubusercontent.com/542643/179368710-0f832059-fc60-410c-b9bf-43d1cf381f18.png
- buttons:
- - type: preprint
- link: https://doi.org/10.1101/2022.06.27.497742
-- id: doi:10.1128/msystems.00927-22
+- id: doi:10.48550/arXiv.2208.08907
title: Application of Traditional Vaccine Development Strategies to SARS-CoV-2
authors:
- Halie M. Rando
@@ -386,265 +335,151 @@
- Nils Wellhausen
- Elizabeth Sell
- Likhitha Kolla
+ - COVID-19 Review Consortium
- Anthony Gitter
- Casey S. Greene
- - Vikas Bansal
- - John P. Barton
- - Simina M. Boca
- - Joel D. Boerckel
- - Christian Brueffer
- - James Brian Byrd
- - Stephen Capone
- - Shikta Das
- - Anna Ada Dattoli
- - John J. Dziak
- - Jeffrey M. Field
- - Soumita Ghosh
- - Anthony Gitter
- - Rishi Raj Goel
- - Casey S. Greene
- - Marouen Ben Guebila
- - Daniel S. Himmelstein
- - Fengling Hu
- - Nafisa M. Jadavji
- - Jeremy P. Kamil
- - Sergey Knyazev
- - Likhitha Kolla
- - Alexandra J. Lee
- - Ronan Lordan
- - Tiago Lubiana
- - Temitayo Lukan
- - Adam L. MacLean
- - David Mai
- - Serghei Mangul
- - David Manheim
- - "Lucy D\u2019Agostino McGowan"
- - Jesse G. Meyer
- - Ariel I. Mundo
- - Amruta Naik
- - YoSon Park
- - Dimitri Perrin
- - Yanjun Qi
- - Diane N. Rafizadeh
- - Bharath Ramsundar
- - Halie M. Rando
- - Sandipan Ray
- - Michael P. Robson
- - Vincent Rubinetti
- - Elizabeth Sell
- - Lamonica Shinholster
- - Ashwin N. Skelly
- - Yuchen Sun
- - Yusha Sun
- - Gregory L. Szeto
- - Ryan Velazquez
- - Jinhui Wang
- - Nils Wellhausen
- publisher: mSystems
- date: '2023-04-27'
- link: https://doi.org/10.1128/msystems.00927-22
- orcid: 0000-0001-8713-9213
- member: casey-greene
- plugin: sources.py
- file: sources.yaml
- image: https://greenelab.github.io/covid19-review/images/N000-overview.png
- tags:
- - COVID19
-- id: doi:10.1128/msystems.00928-22
- title: The Coming of Age of Nucleic Acid Vaccines during COVID-19
- authors:
- - Halie M. Rando
- - Ronan Lordan
- - Likhitha Kolla
- - Elizabeth Sell
- - Alexandra J. Lee
- - Nils Wellhausen
- - Amruta Naik
- - Jeremy P. Kamil
- - Anthony Gitter
- - Casey S. Greene
- - John P. Barton
- - Simina M. Boca
- - Joel D. Boerckel
- - Christian Brueffer
- - James Brian Byrd
- - Stephen Capone
- - Shikta Capone
- - Anna Ada Dattoli
- - John J. Dziak
- - Jeffrey M. Field
- - Soumita Ghosh
- - Anthony Gitter
- - Rishi Raj Goel
- - Casey S. Greene
- - Marouen Ben Guebila
- - Daniel S. Himmelstein
- - Fengling Hu
- - Nafisa M. Jadavji
- - Jeremy P. Kamil
- - Sergey Knyazev
- - Likhitha Kolla
- - Alexandra J. Lee
- - Ronan Lordan
- - Tiago Lubiana
- - Temitayo Lukan
- - Adam L. MacLean
- - David Mai
- - Serghei Mangul
- - David Manheim
- - "Lucy D\u2019Agostino McGowan"
- - Jesse G. Meyer
- - Ariel I. Mundo
- - Amruta Naik
- - YoSon Park
- - Dimitri Perrin
- - Yanjun Qi
- - Diane N. Rafizadeh
- - Bharath Ramsundar
- - Halie M. Rando
- - Sandipan Ray
- - Michael P. Robson
- - Vincent Rubinetti
- - Elizabeth Sell
- - Lamonica Shinholster
- - Ashwin N. Skelly
- - Yuchen Sun
- - Yusha Sun
- - Gregory L. Szeto
- - Ryan Velazquez
- - Jinhui Wang
- - Nils Wellhausen
- publisher: mSystems
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publisher: Cold Spring Harbor Laboratory
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-- id: doi:10.5281/zenodo.4677667
- title: Response to NOT-OD-21-066 - Racial EDI in Biomedical Research Workforce
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+ title: 'wenda_gpu: fast domain adaptation for genomic data'
authors:
- - Monica Munoz-Torres
- - Melissa Haendel
- - Sean Davis
- - Lawrence Hunter
- - Andrew Neumann
- - Nicole Vasilevsky
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- - Shawn T. O'Neil
- - Matthew H. Brush
- publisher: Zenodo
- date: '2021-04-09'
- link: https://doi.org/10.5281/zenodo.4677667
+ - Ariel A. Hippen
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+ - Jacob R. Gardner
+ - Casey S. Greene
+ publisher: Cold Spring Harbor Laboratory
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- - open science
- - machine learning
-- id: doi:10.1101/2021.03.04.433874
- title: Linguistic Analysis of the bioRxiv Preprint Landscape
+- id: doi:10.48550/arxiv.2104.11364
+ title: A field guide to cultivating computational biology
authors:
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- - Vincent Rubinetti
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- - Lawrence E. Hunter
- - Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
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+ - Piero Carnici
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+ - Luigi Marchionni
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+ - Gregory P Way
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+ - Elana J Fertig
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-- id: doi:10.1101/2021.03.03.433798
- title: 'miQC: An adaptive probabilistic framework for quality control of single-cell
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+- id: doi:10.48550/arxiv.2109.08633
+ title: An Open-Publishing Response to the COVID-19 Infodemic
authors:
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- - Matias M. Falco
- - Lukas M. Weber
- - Erdogan Pekcan Erkan
- - Kaiyang Zhang
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+ - Ryan Velazquez
+ - COVID-19 Review Consortium
- Casey S. Greene
- - Stephanie C. Hicks
- publisher: Cold Spring Harbor Laboratory
- date: '2021-03-03'
- link: https://doi.org/10.1101/2021.03.03.433798
+ - Anthony Gitter
+ publisher: arXiv
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-- id: doi:10.1186/s13059-020-02021-3
- title: Compressing gene expression data using multiple latent space dimensionalities
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+- id: doi:10.1016/j.cels.2021.07.007
+ title: Analysis of scientific society honors reveals disparities
authors:
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- - Michael Zietz
- - Vincent Rubinetti
+ - Trang T. Le
- Daniel S. Himmelstein
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- publisher: Genome Biology
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+ publisher: Cell Systems
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- Casey S. Greene
- - Stephanie C. Hicks
- publisher: Cold Spring Harbor Laboratory
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- link: https://doi.org/10.1101/2020.11.06.371963
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+ - Michael I. Love
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+ - Guo-Cheng Yuan
+ - Aedin C. Culhane
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- - Georgia Doing
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-- id: doi:10.1038/s41576-020-0257-5
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+- id: doi:10.48550/arxiv.2112.12582
+ title: 'Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and
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authors:
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- - Anna C. Greene
- - Deepashree Venkatesh Prasad
- - Xiaoqian Jiang
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- Casey S. Greene
- publisher: Nature Reviews Genetics
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+ - Prachi Kothiyal
+ - Ashish Mahabal
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+ - Christopher E. Mason
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+ - Jerry G. Myers
+ - Charlotte Nelson
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+ - Patricia Parsons-Wingerter
+ - R. K. Prabhu
+ - Robert J. Reynolds
+ - Amanda Saravia-Butler
+ - Suchi Saria
+ - Aenor Sawyer
+ - Nitin Kumar Singh
+ - Frank Soboczenski
+ - Michael Snyder
+ - Karthik Soman
+ - Corey A. Theriot
+ - David Van Valen
+ - Kasthuri Venkateswaran
+ - Liz Warren
+ - Liz Worthey
+ - Marinka Zitnik
+ - Sylvain V. Costes
+ publisher: arXiv
+ date: '2021-01-01'
+ link: https://doi.org/gt6s6v
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-- id: doi:10.1038/s41586-020-2766-y
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+- id: doi:10.48550/arxiv.2112.12554
+ title: 'Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision
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authors:
- - Benjamin Haibe-Kains
- - George Alexandru Adam
- - Ahmed Hosny
- - Farnoosh Khodakarami
- - Thakkar Shraddha
- - Rebecca Kusko
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- - Joaquin Dopazo
- - Cesare Furlanello
- - Levi Waldron
- - Bo Wang
- - Chris McIntosh
- - Anna Goldenberg
- - Anshul Kundaje
+ - Ryan T. Scott
+ - Erik L. Antonsen
+ - Lauren M. Sanders
+ - Jaden J. A. Hastings
+ - Seung-min Park
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- Casey S. Greene
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- publisher: Nature
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+ - Amanda Saravia-Butler
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+ - David Van Valen
+ - Kasthuri Venkateswaran
+ - Liz Warren
+ - Liz Worthey
+ - Jason H. Yang
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+ title: 'Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics,
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+ - Anthony R. Kerlavage
+ - Anne C. Kirchhoff
+ - Jaime M. Guidry Auvil
+ - Norman E. Sharpless
+ - Kara L. Davis
+ - Karlyne Reilly
+ - Gregory Reaman
+ - Lynne Penberthy
+ - Dennis Deapen
+ - Amie Hwang
+ - Eric B. Durbin
+ - Sara L. Gallotto
+ - Richard Aplenc
+ - Samuel L. Volchenboum
+ - Allison P. Heath
+ - Bruce J. Aronow
+ - Jinghui Zhang
+ - Olena Vaske
+ - Todd A. Alonzo
+ - Paul C. Nathan
+ - Jenny N. Poynter
+ - Greg Armstrong
+ - Erin E. Hahn
+ - Karen J. Wernli
+ - Casey Greene
+ - Jack DiGiovanna
+ - Adam C. Resnick
+ - Eve R. Shalley
+ - Sorena Nadaf
+ - Warren A. Kibbe
+ publisher: JCO Clinical Cancer Informatics
+ date: '2021-12-01'
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+ image: https://user-images.githubusercontent.com/542643/131275719-cc94220d-35c9-4608-a1ca-26116dff6b0c.png
+- id: doi:10.1101/2021.06.23.21259416
+ title: 'Characterizing Long COVID: Deep Phenotype of a Complex Condition'
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-- id: doi:10.1093/gigascience/giaa056
- title: Recommendations to enhance rigor and reproducibility in biomedical research
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- - Lana X Garmire
- - Serghei Mangul
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+ - Melanie Loth
+ - Chen Meng
+ - Wancen Mu
+ - Vera Pancaldi
+ - Kris Sankaran
+ - Dario Righelli
+ - Amrit Singh
+ - Joshua S. Sodicoff
+ - "Genevieve L. Stein-O\u2019Brien"
+ - Ayshwarya Subramanian
+ - Joshua D. Welch
+ - Yue You
+ - Ricard Argelaguet
+ - Vincent J. Carey
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+ - Matthew E. Ritchie
+ - Guo-Cheng Yuan
+ - Aedin C. Culhane
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+ publisher: Genome Biology
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- - Elaine R. Mardis
- - Michael D. McLellan
- - Christopher A. Miller
- - Heather K. Schmidt
- - Richard K. Wilson
- - Daniel Crain
- - Erin Curley
- - Johanna Gardner
- - Kevin Lau
- - David Mallery
- - Scott Morris
- - Joseph Paulauskis
- - Robert Penny
- - Candace Shelton
- - Troy Shelton
- - Mark Sherman
- - Eric Thompson
- - Peggy Yena
- - Jay Bowen
- - Julie M. Gastier-Foster
- - Mark Gerken
- - Kristen M. Leraas
- - Tara M. Lichtenberg
- - Nilsa C. Ramirez
- - Lisa Wise
- - Erik Zmuda
- - Niall Corcoran
- - Tony Costello
- - Christopher Hovens
- - Andre L. Carvalho
- - Ana C. de Carvalho
- - "Jos\xE9 H. Fregnani"
- - Adhemar Longatto-Filho
- - Rui M. Reis
- - Cristovam Scapulatempo-Neto
- - Henrique C.S. Silveira
- - Daniel O. Vidal
- - Andrew Burnette
- - Jennifer Eschbacher
- - Beth Hermes
- - Ardene Noss
- - Rosy Singh
- - Matthew L. Anderson
- - Patricia D. Castro
- - Michael Ittmann
- - David Huntsman
- - Bernard Kohl
- - Xuan Le
- - Richard Thorp
- - Chris Andry
- - Elizabeth R. Duffy
- - Vladimir Lyadov
- - Oxana Paklina
- - Galiya Setdikova
- - Alexey Shabunin
- - Mikhail Tavobilov
- - Christopher McPherson
- - Ronald Warnick
- - Ross Berkowitz
- - Daniel Cramer
- - Colleen Feltmate
- - Neil Horowitz
- - Adam Kibel
- - Michael Muto
- - Chandrajit P. Raut
- - Andrei Malykh
- - Jill S. Barnholtz-Sloan
- - Wendi Barrett
- - Karen Devine
- - Jordonna Fulop
- - Quinn T. Ostrom
- - Kristen Shimmel
- - Yingli Wolinsky
- - Andrew E. Sloan
- - Agostino De Rose
- - Felice Giuliante
- - Marc Goodman
- - Beth Y. Karlan
- - Curt H. Hagedorn
- - John Eckman
- - Jodi Harr
- - Jerome Myers
- - Kelinda Tucker
- - Leigh Anne Zach
- - Brenda Deyarmin
- - Hai Hu
- - Leonid Kvecher
- - Caroline Larson
- - Richard J. Mural
- - Stella Somiari
- - Ales Vicha
- - Tomas Zelinka
- - Joseph Bennett
- - Mary Iacocca
- - Brenda Rabeno
- - Patricia Swanson
- - Mathieu Latour
- - Louis Lacombe
- - "Bernard T\xEAtu"
- - Alain Bergeron
- - Mary McGraw
- - Susan M. Staugaitis
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- - Timothy Wang
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- - Olga Voronina
- - Laurence Desjardins
- - Odette Mariani
- - Sergio Roman-Roman
- - Xavier Sastre
- - Marc-Henri Stern
- - Feixiong Cheng
- - Sabina Signoretti
- - Andrew Berchuck
- - Darell Bigner
- - Eric Lipp
- - Jeffrey Marks
- - Shannon McCall
- - Roger McLendon
- - Angeles Secord
- - Alexis Sharp
- - Madhusmita Behera
- - Daniel J. Brat
- - Amy Chen
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- - Seth Force
- - Fadlo Khuri
- - Kelly Magliocca
- - Shishir Maithel
- - Jeffrey J. Olson
- - Taofeek Owonikoko
- - Alan Pickens
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- - Dong M. Shin
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- - Hongzheng Zhang
- - Wil Eijckenboom
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- - Leendert Looijenga
- - Wolter Oosterhuis
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- - Kim E. van Kessel
- - Ellen C. Zwarthoff
- - Chiara Calatozzolo
- - Lucia Cuppini
- - Stefania Cuzzubbo
- - Francesco DiMeco
- - Gaetano Finocchiaro
- - Luca Mattei
- - Alessandro Perin
- - Bianca Pollo
- - Chu Chen
- - John Houck
- - Pawadee Lohavanichbutr
- - Arndt Hartmann
- - Christine Stoehr
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- - "Armando L\xF3pez Guillermo"
- - Nguyen Van Bang
- - Phan Thi Hanh
- - Bui Duc Phu
- - Yufang Tang
- - Howard Colman
- - Kimberley Evason
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- - Hani Gabra
- - Hartmut Juhl
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- - Serghei Stepa
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- publisher: Cell Reports
- date: '2018-04-01'
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- - type: source
- link: https://github.com/greenelab/pancancer/blob/master/ras_analysis.sh
-- id: doi:10.6084/M9.FIGSHARE.6982919
- title: MultiPLIER Fileset
- authors:
- - Jaclyn Taroni
- - Casey Greene
- publisher: figshare
- date: '2019-01-01'
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-- id: doi:10.6084/m9.figshare.6982919.v1
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- - Casey Greene
- publisher: figshare
- date: '2018-01-01'
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-- id: doi:10.1016/j.cell.2018.03.035
- title: Oncogenic Signaling Pathways in The Cancer Genome Atlas
- authors:
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- - Angeles Secord
- - Alexis Sharp
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- - Klaus-Peter Janssen
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- - J. Bradley Elder
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- - William E. Grizzle
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- - Mark Nelson
- - Oliver Bathe
- - Peter R. Carroll
- - June M. Chan
- - Philip Disaia
- - Pat Glenn
- - Robin K. Kelley
- - Charles N. Landen
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- - Jeffry Simko
- - Karen Smith-McCune
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- - Kevin Roggin
- - Ashley Fehrenbach
- - Ady Kendler
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- - Antonio Jimeno
- - Francis Carey
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- - Rita Sigmund
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- - Howard G. Rosenthal
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- - Joan Walker
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- - Jeffey Moyer
- - Lisa Peterson
- - Mark Prince
- - Laura Rozek
- - Gregory Wolf
- - Rayleen Bowman
- - Kwun M. Fong
- - Ian Yang
- - Robert Korst
- - W. Kimryn Rathmell
- - J. Leigh Fantacone-Campbell
- - Jeffrey A. Hooke
- - Albert J. Kovatich
- - Craig D. Shriver
- - John DiPersio
- - Bettina Drake
- - Ramaswamy Govindan
- - Sharon Heath
- - Timothy Ley
- - Brian Van Tine
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- - Jung Il Lee
- - "Nat\xE1lia D. Aredes"
- - Armaz Mariamidze
- publisher: Cell
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-- id: doi:10.1186/s12859-017-1905-4
- title: 'ADAGE signature analysis: differential expression analysis with data-defined
- gene sets'
- authors:
- - Jie Tan
- - Matthew Huyck
- - Dongbo Hu
- - "Ren\xE9 A. Zelaya"
- - Deborah A. Hogan
- - Casey S. Greene
- publisher: BMC Bioinformatics
- date: '2017-11-22'
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- text: Updated app
-- id: doi:10.7287/peerj.preprints.3100v2
- title: Sci-Hub provides access to nearly all scholarly literature
- authors:
- - Daniel S Himmelstein
- - Ariel R Romero
- - Stephen R McLaughlin
- - Bastian Greshake Tzovaras
- - Casey S Greene
- publisher: PeerJ
- date: '2017-10-12'
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-- id: doi:10.1101/196915
- title: 'Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations'
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- - Raman Arora
- - Aedin C. Culhane
- - Alexander V. Favorov
- - Lana X. Garmire
- - Casey S. Greene
- - Loyal A. Goff
- - Yifeng Li
- - Aloune Ngom
- - Michael F. Ochs
- - Yanxun Xu
- - Elana J. Fertig
- publisher: Cold Spring Harbor Laboratory
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-- id: doi:10.1101/174474
- title: Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes
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- authors:
- - Gregory P. Way
- - Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2017-08-11'
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-- id: doi:10.1101/166207
- title: Functional Network Community Detection Can Disaggregate and Filter Multiple
- Underlying Pathways in Enrichment Analyses
- authors:
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- - Gregory P. Way
- - Jennifer A. Doherty
- - Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2017-07-20'
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- member: casey-greene
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-- id: doi:10.7287/peerj.preprints.3100v1
- title: Sci-Hub provides access to nearly all scholarly literature
- authors:
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- - Ariel R Romero
- - Stephen R McLaughlin
- - Bastian Greshake Tzovaras
- - Casey S Greene
- publisher: PeerJ
- date: '2017-07-20'
- link: https://doi.org/10.7287/peerj.preprints.3100v1
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- member: casey-greene
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-- id: doi:10.7287/peerj.preprints.3100
- title: Sci-Hub provides access to nearly all scholarly literature
- authors:
- - Daniel S Himmelstein
- - Ariel R Romero
- - Jacob G Levernier
- - Thomas A Munro
- - Stephen R McLaughlin
- - Bastian Greshake Tzovaras
- - Casey S Greene
- publisher: PeerJ
- date: '2018-02-02'
- link: https://doi.org/10.7287/peerj.preprints.3100
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- member: casey-greene
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-- id: doi:10.1101/159756
- title: Privacy-preserving generative deep neural networks support clinical data
- sharing
- authors:
- - Brett K. Beaulieu-Jones
- - Zhiwei Steven Wu
- - Chris Williams
- - Ran Lee
- - Sanjeev P. Bhavnani
- - James Brian Byrd
- - Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2017-07-05'
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-- id: doi:10.1101/157610
- title: Machine learning analysis identifies Drosophila Grunge/Atrophin as
- an important learning and memory gene required for memory retention and social
- learning
- authors:
- - Balint Z Kacsoh
- - Casey S. Greene
- - Giovanni Bosco
- publisher: Cold Spring Harbor Laboratory
- date: '2017-06-29'
- link: https://doi.org/10.1101/157610
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-- id: doi:10.1101/156620
- title: 'ADAGE signature analysis: differential expression analysis with data-defined
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- authors:
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- - Matthew Huyck
- - Dongbo Hu
- - "Ren\xE9 A. Zelaya"
- - Deborah A. Hogan
- - Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2017-06-27'
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-- id: doi:10.1101/147645
- title: 'PathCORE-T: identifying and visualizing globally co-occurring pathways in
- large transcriptomic compendia'
- authors:
- - Kathleen M. Chen
- - Jie Tan
- - Gregory P. Way
- - Georgia Doing
- - Deborah A. Hogan
- - Casey S. Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2017-06-08'
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-- id: doi:10.1101/142760
- title: Opportunities and obstacles for deep learning in biology and medicine
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- - Daniel S. Himmelstein
- - Brett K. Beaulieu-Jones
- - Alexandr A. Kalinin
- - Brian T. Do
- - Gregory P. Way
- - Enrico Ferrero
- - Paul-Michael Agapow
- - Michael Zietz
- - Michael M. Hoffman
- - Wei Xie
- - Gail L. Rosen
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- - Jack Lanchantin
- - Stephen Woloszynek
- - Anne E. Carpenter
- - Avanti Shrikumar
- - Jinbo Xu
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- - Christopher A. Lavender
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- - Amr M. Alexandari
- - Zhiyong Lu
- - David J. Harris
- - Dave DeCaprio
- - Yanjun Qi
- - Anshul Kundaje
- - Yifan Peng
- - Laura K. Wiley
- - Marwin H.S. Segler
- - Simina M. Boca
- - S. Joshua Swamidass
- - Austin Huang
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- publisher: Cold Spring Harbor Laboratory
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-- id: doi:10.1038/nbt.3780
- title: Reproducibility of computational workflows is automated using continuous
- analysis
- authors:
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- - Casey S Greene
- publisher: Nature Biotechnology
- date: '2017-03-13'
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-- id: doi:10.1101/118349
- title: Cross-Platform Normalization Enables Machine Learning Model Training On Microarray
- And RNA-Seq Data Simultaneously
- authors:
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- - Casey S Greene
- publisher: Cold Spring Harbor Laboratory
- date: '2017-03-20'
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-- id: doi:10.6084/M9.FIGSHARE.5035997
- title: '"Cross-platform normalization enables analysis of microarray and RNA-seq
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- - Casey Greene
- publisher: figshare
- date: '2017-01-01'
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-- id: doi:10.6084/m9.figshare.5035997.v2
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-- id: doi:10.6084/m9.figshare.5035997.v1
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- publisher: figshare
- date: '2017-01-01'
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-- id: doi:10.1186/s12864-017-3519-7
- title: A machine learning classifier trained on cancer transcriptomes detects NF1
- inactivation signal in glioblastoma
- authors:
- - Gregory P. Way
- - Robert J. Allaway
- - Stephanie J. Bouley
- - Camilo E. Fadul
- - Yolanda Sanchez
- - Casey S. Greene
- publisher: BMC Genomics
- date: '2017-02-06'
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-- id: doi:10.1186/s13073-017-0417-1
- title: A novel multi-network approach reveals tissue-specific cellular modulators
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- - Casey S. Greene
- - Viktor Martyanov
- - Tammara A. Wood
- - Romy B. Christmann
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- - Robert A. Lafyatis
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- - Monique E. Hinchcliff
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-- id: doi:10.1038/s41598-017-17362-6
- title: A Pilot Characterization of the Human Chronobiome
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- - Nicholas F. Lahens
- - Seth D. Rhoades
- - Amy Campbell
- - Kyle Bittinger
- - Aubrey Bailey
- - Christian Hoffmann
- - Randal S. Olson
- - Lihong Chen
- - Guangrui Yang
- - Thomas S. Price
- - Jason H. Moore
- - Frederic D. Bushman
- - Casey S. Greene
- - Gregory R. Grant
- - Aalim M. Weljie
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- publisher: Scientific Reports
- date: '2017-12-07'
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-- id: doi:10.1038/ng.3830
- title: Celebrating parasites
- authors:
- - Casey S Greene
- - Lana X Garmire
- - Jack A Gilbert
- - Marylyn D Ritchie
- - Lawrence E Hunter
- publisher: Nature Genetics
- date: '2017-04-01'
- link: https://doi.org/10.1038/ng.3830
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-- id: doi:10.1093/hmg/ddv440
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-- id: doi:10.1371/journal.pcbi.1004005
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-- id: doi:10.1186/s13040-015-0050-8
- title: Testing multiple hypotheses through IMP weighted FDR based on a genetic functional
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- - Casey S. Greene
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- date: '2015-06-01'
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-- id: doi:10.1038/ng.3259
- title: Understanding multicellular function and disease with human tissue-specific
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-- id: doi:10.1002/jcp.24662
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-- id: doi:10.1186/gm550
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-- id: doi:10.1109/ISB.2014.6990733
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-- id: doi:10.1101/gr.155697.113
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-- id: doi:10.1371/journal.pcbi.1002957
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-- id: doi:10.1371/journal.pone.0069678
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-- id: doi:10.1007/978-3-642-37189-9_2
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-- id: doi:10.1093/nar/gks458
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-- id: doi:10.1007/978-3-642-21314-4_36
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-- id: doi:10.1007/978-3-642-21283-3_39
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-- id: doi:10.1186/1756-0381-4-21
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-- id: doi:10.1093/nar/gkr440
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-- id: wosuid:WOS:000411479100034
- title: Enabling personal genomics with an explicit test of epistasis
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-- id: wosuid:MEDLINE:19908385
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-- id: doi:10.1145/1830483.1830523
- title: Fast genome-wide epistasis analysis using ant colony optimization for multifactor
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- publisher: Proceedings of the 12th annual conference on Genetic and evolutionary
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-- id: doi:10.1016/j.semnephrol.2010.07.002
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-- id: doi:10.1093/bioinformatics/btq009
- title: Multifactor dimensionality reduction for graphics processing units enables
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-- id: wosuid:WOS:000272540600026
- title: A Computational Evolution System for Open-Ended Automated Learning of Complex
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- publisher: Genetic Epidemiology
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-- id: doi:10.1186/1756-0500-2-149
- title: Accelerating epistasis analysis in human genetics with consumer graphics
- hardware
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- publisher: BMC Research Notes
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-- id: wosuid:WOS:000272540600064
- title: Computationally Efficient Relief-based Algorithms for Detecting Epistasis
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- authors: []
- publisher: Genetic Epidemiology
- date: '2022-05-24'
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-- id: doi:10.1109/CEC.2009.4983308
- title: Development and evaluation of an open-ended computational evolution system
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-- id: doi:10.1145/1569901.1570160
- title: Environmental noise improves epistasis models of genetic data discovered
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- publisher: Proceedings of the 11th Annual conference on Genetic and evolutionary
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-- id: doi:10.1371/journal.pone.0005639
- title: Failure to Replicate a Genetic Association May Provide Important Clues About
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- publisher: PLoS ONE
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-- id: doi:10.1109/CEC.2009.4983027
- title: 'Nature-inspired algorithms for the genetic analysis of epistasis in common
- human diseases: Theoretical assessment of wrapper vs. filter approaches'
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- publisher: 2009 IEEE Congress on Evolutionary Computation
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-- id: doi:10.1007/978-3-642-01184-9_9
- title: Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis
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- - Jason M. Gilmore
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- - Peter C. Andrews
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- publisher: Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
- date: '2009-01-01'
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-- id: doi:10.1109/CEC.2009.4983093
- title: Sensible initialization using expert knowledge for genome-wide analysis of
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- publisher: 2009 IEEE Congress on Evolutionary Computation
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-- id: doi:10.4018/978-1-60566-705-8.ch007
- title: Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms
- Requires Strategies which Exploit Domain-Specific Knowledge
- authors:
- - Casey S. Greene
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- publisher: Nature-Inspired Informatics for Intelligent Applications and Knowledge
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- date: ''
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-- id: doi:10.1186/1756-0381-2-5
- title: Spatially Uniform ReliefF (SURF) for computationally-efficient filtering
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- - Nadia M Penrod
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- publisher: BioData Mining
- date: '2009-09-22'
- link: https://doi.org/10.1186/1756-0381-2-5
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-- id: doi:10.1145/1527063.1527064
- title: Solving complex problems in human genetics using GP
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- publisher: ACM SIGEVOlution
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-- id: doi:10.1002/art.23836
- title: "Ability of epistatic interactions of cytokine single\u2010nucleotide polymorphisms\
- \ to predict susceptibility to disease subsets in systemic sclerosis patients"
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-- id: doi:10.1349/ddlp.303
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-- id: doi:10.1016/j.ajhg.2023.12.001
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- - Shilpa Bhatia
- - Andy V. Phan
- - Benjamin Van Court
- - Kathryn L. Zolman
- - "Brisa Pe\xF1a"
- - Ayman J. Oweida
- - Sara Zakem
- - Cheryl Meguid
- - Michael W. Knitz
- - Laurel Darragh
- - Thomas E. Bickett
- - Jacob Gadwa
- - Luisa Mestroni
- - Matthew R.G. Taylor
- - Kimberly R. Jordan
- - Peter Dempsey
- - M. Scott Lucia
- - Martin D. McCarter
- - Marco Del Chiaro
- - Wells A. Messersmith
- - Richard D. Schulick
- - Karyn A. Goodman
- - Michael J. Gough
- - Casey S. Greene
- - James C. Costello
- - Antonio Galveo Neto
- - David Lagares
- - Kirk C. Hansen
- - Adrie Van Bokhoven
- - Sana D. Karam
- publisher: Cancer Research
- date: '2021-02-01'
- link: https://doi.org/10.1158/0008-5472.can-20-3892
- image: https://user-images.githubusercontent.com/542643/107096146-4ba21b80-67c7-11eb-9358-eb2e0ffd927c.png
- tags:
- - cancer
- plugin: sources.py
- file: sources.yaml
-- id: doi:10.1128/mSystems.00095-21
- title: Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis
- of Viral Genomics and Structure
- authors:
- - Halie M. Rando
- - Adam L. MacLean
- - Alexandra J. Lee
- - Ronan Lordan
- - Sandipan Ray
- - Vikas Bansal
- - Ashwin N. Skelly
- - Elizabeth Sell
- - John J. Dziak
- - Lamonica Shinholster
- - "Lucy D\u2019Agostino McGowan"
- - Marouen Ben Guebila
- - Nils Wellhausen
- - Sergey Knyazev
- - Simina M. Boca
- - Stephen Capone
- - Yanjun Qi
- - YoSon Park
- - David Mai
- - Yuchen Sun
- - Joel D. Boerckel
- - Christian Brueffer
- - James Brian Byrd
- - Jeremy P. Kamil
- - Jinhui Wang
- - Ryan Velazquez
- - Gregory L. Szeto
- - John P. Barton
- - Rishi Raj Goel
- - Serghei Mangul
- - Tiago Lubiana
- - Anthony Gitter
- - Casey S. Greene
- publisher: mSystems
- date: '2021-10-26'
- link: https://doi.org/10.1128/msystems.00095-21
- image: https://greenelab.github.io/covid19-review/images/N000-overview.png
- tags:
- - COVID19
- plugin: sources.py
- file: sources.yaml
-- id: doi:10.1016/j.ccell.2020.10.014
- title: Biologically Informed Neural Networks Predict Drug Responses
- authors:
- - Casey S. Greene
- - James C. Costello
- publisher: Cancer Cell
- date: '2020-11-01'
- link: https://doi.org/10.1016/j.ccell.2020.10.014
- image: https://user-images.githubusercontent.com/542643/97004985-cb072a00-150b-11eb-9d4b-765ec1893a11.png
- tags:
- - cancer
- - machine learning
- plugin: sources.py
- file: sources.yaml
-- id: url:https://greenelab.github.io/covid19-review/
- title: 'SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics'
- authors:
- - Halie M. Rando
- - Casey S. Greene
- - Michael P. Robson
- - Simina M. Boca
- - Nils Wellhausen
- - Ronan Lordan
- - Christian Brueffer
- - Sandipan Ray
- - Lucy D\'Agostino McGowan
- - Anthony Gitter
- - Anna Ada Dattoli
- - Ryan Velazquez
- - John P. Barton
- - Jeffrey M. Field
- - Bharath Ramsundar
- - Adam L. MacLean
- - Alexandra J. Lee
- - Immunology Institute of the Icahn School Medicine
- - Fengling Hu
- - Nafisa M. Jadavji
- - Elizabeth Sell
- - Vincent Rubinetti
- - Jinhui Wang
- - Diane N. Rafizadeh
- - Ashwin N. Skelly
- - Marouen Ben Guebila
- - Likhitha Kolla
- - David Manheim
- - Soumita Ghosh
- - James Brian Byrd
- - YoSon Park
- - Vikas Bansal
- - Stephen Capone
- - John J. Dziak
- - Yuchen Sun
- - Yanjun Qi
- - Lamonica Shinholster
- - Temitayo Lukan
- - Sergey Knyazev
- - Dimitri Perrin
- - Serghei Mangul
- - Shikta Das
- - Gregory L. Szeto
- - Tiago Lubiana
- - David Mai
- - COVID-19 Review Consortium
- - Rishi Raj Goel
- - Joel D. Boerckel
- - Amruta Naik
- - Yusha Sun
- - Daniel S. Himmelstein
- - Jeremy P. Kamil
- - Jesse G. Meyer
- - Ariel I. Mundo
- publisher: Manubot
- date: '2023-07-30'
- link: https://greenelab.github.io/covid19-review/
- image: https://greenelab.github.io/covid19-review/images/N000-overview.png
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- - type: preprint
- - type: manubot
- link: https://greenelab.github.io/covid19-review/
- tags:
- - COVID19
- plugin: sources.py
- file: sources.yaml
-- id: doi:10.1093/jamia/ocaa196
- title: 'The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure,
- and deployment'
- authors:
- - Melissa A Haendel
- - Christopher G Chute
- - Tellen D Bennett
- - David A Eichmann
- - Justin Guinney
- - Warren A Kibbe
- - Philip R O Payne
- - Emily R Pfaff
- - Peter N Robinson
- - Joel H Saltz
- - Heidi Spratt
- - Christine Suver
- - John Wilbanks
- - Adam B Wilcox
- - Andrew E Williams
- - Chunlei Wu
- - Clair Blacketer
- - Robert L Bradford
- - James J Cimino
- - Marshall Clark
- - Evan W Colmenares
- - Patricia A Francis
- - Davera Gabriel
- - Alexis Graves
- - Raju Hemadri
- - Stephanie S Hong
- - George Hripscak
- - Dazhi Jiao
- - Jeffrey G Klann
- - Kristin Kostka
- - Adam M Lee
- - Harold P Lehmann
- - Lora Lingrey
- - Robert T Miller
- - Michele Morris
- - Shawn N Murphy
- - Karthik Natarajan
- - Matvey B Palchuk
- - Usman Sheikh
- - Harold Solbrig
- - Shyam Visweswaran
- - Anita Walden
- - Kellie M Walters
- - Griffin M Weber
- - Xiaohan Tanner Zhang
- - Richard L Zhu
- - Benjamin Amor
- - Andrew T Girvin
- - Amin Manna
- - Nabeel Qureshi
- - Michael G Kurilla
- - Sam G Michael
- - Lili M Portilla
- - Joni L Rutter
- - Christopher P Austin
- - Ken R Gersing
- publisher: Journal of the American Medical Informatics Association
- date: '2020-08-17'
- link: https://doi.org/10.1093/jamia/ocaa196
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- tags:
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- plugin: sources.py
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-- id: doi:10.1038/s41562-020-00944-2
- title: Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and
- testing
- authors:
- - William E. Allen
- - Han Altae-Tran
- - James Briggs
- - Xin Jin
- - Glen McGee
- - Andy Shi
- - Rumya Raghavan
- - Mireille Kamariza
- - Nicole Nova
- - Albert Pereta
- - Chris Danford
- - Amine Kamel
- - Patrik Gothe
- - Evrhet Milam
- - Jean Aurambault
- - Thorben Primke
- - Weijie Li
- - Josh Inkenbrandt
- - Tuan Huynh
- - Evan Chen
- - Christina Lee
- - Michael Croatto
- - Helen Bentley
- - Wendy Lu
- - Robert Murray
- - Mark Travassos
- - Brent A. Coull
- - John Openshaw
- - Casey S. Greene
- - Ophir Shalem
- - Gary King
- - Ryan Probasco
- - David R. Cheng
- - Ben Silbermann
- - Feng Zhang
- - Xihong Lin
- publisher: Nature Human Behaviour
- date: '2020-08-26'
- link: https://doi.org/10.1038/s41562-020-00944-2
- image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41562-020-00944-2/MediaObjects/41562_2020_944_Fig1_HTML.png
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- tags:
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- plugin: sources.py
- file: sources.yaml
-- id: doi:10.1016/j.annonc.2020.05.019
- title: Prognostic gene expression signature for high-grade serous ovarian cancer
- authors:
- - J. Millstein
- - T. Budden
- - E.L. Goode
- - M.S. Anglesio
- - A. Talhouk
- - M.P. Intermaggio
- - H.S. Leong
- - S. Chen
- - W. Elatre
- - B. Gilks
- - T. Nazeran
- - M. Volchek
- - R.C. Bentley
- - C. Wang
- - D.S. Chiu
- - S. Kommoss
- - S.C.Y. Leung
- - J. Senz
- - A. Lum
- - V. Chow
- - H. Sudderuddin
- - R. Mackenzie
- - J. George
- - S. Fereday
- - J. Hendley
- - N. Traficante
- - H. Steed
- - J.M. Koziak
- - "M. K\xF6bel"
- - I.A. McNeish
- - T. Goranova
- - D. Ennis
- - G. Macintyre
- - D. Silva De Silva
- - "T. Ram\xF3n y Cajal"
- - "J. Garc\xEDa-Donas"
- - S. Hernando Polo
- - G.C. Rodriguez
- - K.L. Cushing-Haugen
- - H.R. Harris
- - C.S. Greene
- - R.A. Zelaya
- - S. Behrens
- - R.T. Fortner
- - P. Sinn
- - E. Herpel
- - J. Lester
- - "J. Lubi\u0144ski"
- - O. Oszurek
- - "A. To\u0142oczko"
- - C. Cybulski
- - J. Menkiszak
- - C.L. Pearce
- - M.C. Pike
- - C. Tseng
- - J. Alsop
- - V. Rhenius
- - H. Song
- - M. Jimenez-Linan
- - A.M. Piskorz
- - A. Gentry-Maharaj
- - C. Karpinskyj
- - M. Widschwendter
- - N. Singh
- - C.J. Kennedy
- - R. Sharma
- - P.R. Harnett
- - B. Gao
- - S.E. Johnatty
- - R. Sayer
- - J. Boros
- - S.J. Winham
- - G.L. Keeney
- - S.H. Kaufmann
- - M.C. Larson
- - H. Luk
- - B.Y. Hernandez
- - P.J. Thompson
- - L.R. Wilkens
- - M.E. Carney
- - B. Trabert
- - J. Lissowska
- - L. Brinton
- - M.E. Sherman
- - C. Bodelon
- - S. Hinsley
- - L.A. Lewsley
- - R. Glasspool
- - S.N. Banerjee
- - E.A. Stronach
- - P. Haluska
- - I. Ray-Coquard
- - S. Mahner
- - B. Winterhoff
- - D. Slamon
- - D.A. Levine
- - L.E. Kelemen
- - J. Benitez
- - J. Chang-Claude
- - J. Gronwald
- - A.H. Wu
- - U. Menon
- - M.T. Goodman
- - J.M. Schildkraut
- - N. Wentzensen
- - R. Brown
- - A. Berchuck
- - G. Chenevix-Trench
- - A. deFazio
- - S.A. Gayther
- - "M.J. Garc\xEDa"
- - M.J. Henderson
- - M.A. Rossing
- - A. Beeghly-Fadiel
- - P.A. Fasching
- - S. Orsulic
- - B.Y. Karlan
- - G.E. Konecny
- - D.G. Huntsman
- - D.D. Bowtell
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- - J.A. Doherty
- - P.D.P. Pharoah
- - S.J. Ramus
- - D. Bowtell
- - G. Chenevix-Trench
- - A. Green
- - P. Webb
- - A. DeFazio
- - D. Gertig
- - N. Traficante
- - S. Fereday
- - S. Moore
- - J. Hung
- - K. Harrap
- - T. Sadkowsky
- - N. Pandeya
- - M. Malt
- - A. Mellon
- - R. Robertson
- - T. Vanden Bergh
- - M. Jones
- - P. Mackenzie
- - J. Maidens
- - K. Nattress
- - Y.E. Chiew
- - A. Stenlake
- - H. Sullivan
- - B. Alexander
- - P. Ashover
- - S. Brown
- - T. Corrish
- - L. Green
- - L. Jackman
- - K. Ferguson
- - K. Martin
- - A. Martyn
- - B. Ranieri
- - J. White
- - V. Jayde
- - P. Mamers
- - L. Bowes
- - L. Galletta
- - D. Giles
- - J. Hendley
- - K. Alsop
- - T. Schmidt
- - H. Shirley
- - C. Ball
- - C. Young
- - S. Viduka
- - Hoa Tran
- - Sanela Bilic
- - Lydia Glavinas
- - Julia Brooks
- - R. Stuart-Harris
- - F. Kirsten
- - J. Rutovitz
- - P. Clingan
- - A. Glasgow
- - A. Proietto
- - S. Braye
- - G. Otton
- - J. Shannon
- - T. Bonaventura
- - J. Stewart
- - S. Begbie
- - M. Friedlander
- - D. Bell
- - S. Baron-Hay
- - A. Ferrier,a
- - G. Gard
- - D. Nevell
- - N. Pavlakis
- - S. Valmadre
- - B. Young
- - C. Camaris
- - R. Crouch
- - L. Edwards
- - N. Hacker
- - D. Marsden
- - G. Robertson
- - P. Beale
- - J. Beith
- - J. Carter
- - C. Dalrymple
- - R. Houghton
- - P. Russell
- - M. Links
- - J. Grygiel
- - J. Hill
- - A. Brand
- - K. Byth
- - R. Jaworski
- - P. Harnett
- - R. Sharma
- - G. Wain
- - B. Ward
- - D. Papadimos
- - A. Crandon
- - M. Cummings
- - K. Horwood
- - A. Obermair
- - L. Perrin
- - D. Wyld
- - J. Nicklin
- - M. Davy
- - M.K. Oehler
- - C. Hall
- - T. Dodd
- - T. Healy
- - K. Pittman
- - D. Henderson
- - J. Miller
- - J. Pierdes
- - P. Blomfield
- - D. Challis
- - R. McIntosh
- - A. Parker
- - B. Brown
- - R. Rome
- - D. Allen
- - P. Grant
- - S. Hyde
- - R. Laurie
- - M. Robbie
- - D. Healy
- - T. Jobling
- - T. Manolitsas
- - J. McNealage
- - P. Rogers
- - B. Susil
- - E. Sumithran
- - I. Simpson
- - K. Phillips
- - D. Rischin
- - S. Fox
- - D. Johnson
- - S. Lade
- - M. Loughrey
- - "N. O\u2019Callaghan"
- - W. Murray
- - P. Waring
- - V. Billson
- - J. Pyman
- - D. Neesham
- - M. Quinn
- - C. Underhill
- - R. Bell
- - L.F. Ng
- - R. Blum
- - V. Ganju
- - I. Hammond
- - Y. Leung
- - A. McCartney
- - M. Buck
- - I. Haviv
- - D. Purdie
- - D. Whiteman
- - N. Zeps
- publisher: Annals of Oncology
- date: '2020-09-01'
- link: https://doi.org/10.1016/j.annonc.2020.05.019
- image: https://ars.els-cdn.com/content/image/1-s2.0-S0923753420398410-gr3.jpg
- tags:
- - ovarian cancer
- - genomics
- plugin: sources.py
- file: sources.yaml
-- id: doi:10.1038/s41591-020-0929-x
- title: Building an international consortium for tracking coronavirus health status
- authors:
- - Eran Segal
- - Feng Zhang
- - Xihong Lin
- - Gary King
- - Ophir Shalem
- - Smadar Shilo
- - William E. Allen
- - Faisal Alquaddoomi
- - Han Altae-Tran
- - Simon Anders
- - Ran Balicer
- - Tal Bauman
- - Ximena Bonilla
- - Gisel Booman
- - Andrew T. Chan
- - Ori Cohen
- - Silvano Coletti
- - Natalie Davidson
- - Yuval Dor
- - David A. Drew
- - Olivier Elemento
- - Georgina Evans
- - Phil Ewels
- - Joshua Gale
- - Amir Gavrieli
- - Benjamin Geiger
- - Yonatan H. Grad
- - Casey S. Greene
- - Iman Hajirasouliha
- - Roman Jerala
- - Andre Kahles
- - Olli Kallioniemi
- - Ayya Keshet
- - Ljupco Kocarev
- - Gregory Landua
- - Tomer Meir
- - Aline Muller
- - Long H. Nguyen
- - Matej Oresic
- - Svetlana Ovchinnikova
- - Hedi Peterson
- - Jana Prodanova
- - Jay Rajagopal
- - "Gunnar R\xE4tsch"
- - Hagai Rossman
- - Johan Rung
- - Andrea Sboner
- - Alexandros Sigaras
- - Tim Spector
- - Ron Steinherz
- - Irene Stevens
- - Jaak Vilo
- - Paul Wilmes
- publisher: Nature Medicine
- date: '2020-06-02'
- link: https://doi.org/10.1038/s41591-020-0929-x
- image: https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fs41591-020-0929-x/MediaObjects/41591_2020_929_Fig2_HTML.png?as=webp
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- - type: preprint
- link: https://www.medrxiv.org/content/10.1101/2020.04.02.20051284v1
- plugin: sources.py
- file: sources.yaml
-- id: doi:10.1158/1078-0432.CCR-20-0103
- title: Development and Validation of the Gene Expression Predictor of High-grade
- Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE)
- authors:
- - Aline Talhouk
- - Joshy George
- - Chen Wang
- - Timothy Budden
- - Tuan Zea Tan
- - Derek S. Chiu
- - Stefan Kommoss
- - Huei San Leong
- - Stephanie Chen
- - Maria P. Intermaggio
- - Blake Gilks
- - Tayyebeh M. Nazeran
- - Mila Volchek
- - Wafaa Elatre
- - Rex C. Bentley
- - Janine Senz
- - Amy Lum
- - Veronica Chow
- - Hanwei Sudderuddin
- - Robertson Mackenzie
- - Samuel C.Y. Leong
- - Geyi Liu
- - Dustin Johnson
- - Billy Chen
- - AOCS Group
- - Jennifer Alsop
- - Susana N. Banerjee
- - Sabine Behrens
- - Clara Bodelon
- - Alison H. Brand
- - Louise Brinton
- - Michael E. Carney
- - Yoke-Eng Chiew
- - Kara L. Cushing-Haugen
- - Cezary Cybulski
- - Darren Ennis
- - Sian Fereday
- - "Ren\xE9e T. Fortner"
- - "Jes\xFAs Garc\xEDa-Donas"
- - Aleksandra Gentry-Maharaj
- - Rosalind Glasspool
- - Teodora Goranova
- - Casey S. Greene
- - Paul Haluska
- - Holly R. Harris
- - Joy Hendley
- - Brenda Y. Hernandez
- - Esther Herpel
- - Mercedes Jimenez-Linan
- - Chloe Karpinskyj
- - Scott H. Kaufmann
- - Gary L. Keeney
- - Catherine J. Kennedy
- - "Martin K\xF6bel"
- - Jennifer M. Koziak
- - Melissa C. Larson
- - Jenny Lester
- - Liz-Anne Lewsley
- - Jolanta Lissowska
- - "Jan Lubi\u0144ski"
- - Hugh Luk
- - Geoff Macintyre
- - Sven Mahner
- - Iain A. McNeish
- - Janusz Menkiszak
- - Nikilyn Nevins
- - Ana Osorio
- - Oleg Oszurek
- - "Jos\xE9 Palacios"
- - Samantha Hinsley
- - Celeste L. Pearce
- - Malcolm C. Pike
- - Anna M. Piskorz
- - Isabelle Ray-Coquard
- - Valerie Rhenius
- - Cristina Rodriguez-Antona
- - Raghwa Sharma
- - Mark E. Sherman
- - Dilrini De Silva
- - Naveena Singh
- - Peter Sinn
- - Dennis Slamon
- - Honglin Song
- - Helen Steed
- - Euan A. Stronach
- - Pamela J. Thompson
- - "Aleksandra To\u0142oczko"
- - Britton Trabert
- - Nadia Traficante
- - Chiu-Chen Tseng
- - Martin Widschwendter
- - Lynne R. Wilkens
- - Stacey J. Winham
- - Boris Winterhoff
- - Alicia Beeghly-Fadiel
- - Javier Benitez
- - Andrew Berchuck
- - James D. Brenton
- - Robert Brown
- - Jenny Chang-Claude
- - Georgia Chenevix-Trench
- - Anna deFazio
- - Peter A. Fasching
- - "Mar\xEDa J. Garc\xEDa"
- - Simon A. Gayther
- - Marc T. Goodman
- - Jacek Gronwald
- - Michelle J. Henderson
- - Beth Y. Karlan
- - Linda E. Kelemen
- - Usha Menon
- - Sandra Orsulic
- - Paul D.P. Pharoah
- - Nicolas Wentzensen
- - Anna H. Wu
- - Joellen M. Schildkraut
- - Mary Anne Rossing
- - Gottfried E. Konecny
- - David G. Huntsman
- - Ruby Yun-Ju Huang
- - Ellen L. Goode
- - Susan J. Ramus
- - Jennifer A. Doherty
- - David D. Bowtell
- - Michael S. Anglesio
- publisher: Clinical Cancer Research
- date: '2020-10-15'
- link: https://doi.org/10.1158/1078-0432.ccr-20-0103
- image: https://user-images.githubusercontent.com/542643/91751846-6e366580-eb93-11ea-854d-8f4bb210a46b.png
- tags:
- - ovarian cancer
- - genomics
- plugin: sources.py
- file: sources.yaml
-- id: doi:10.1093/nar/gkaa248
- title: Specific histone modifications associate with alternative exon selection
- during mammalian development
- authors:
- - Qiwen Hu
- - Casey S Greene
- - Elizabeth A Heller
- publisher: Nucleic Acids Research
- date: '2020-04-22'
- link: https://doi.org/10.1093/nar/gkaa248
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-- id: doi:10.1016/j.csbj.2020.05.017
- title: Constructing knowledge graphs and their biomedical applications
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+ title: Pseudomonas aeruginosa lasRmutant fitness in microoxia is supported
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authors:
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- Casey S. Greene
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-- id: doi:10.1038/s41592-019-0585-6
- title: Voices in methods development
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-- id: doi:10.1146/annurev-biodatasci-072018-021348
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-- id: doi:10.1161/CIRCOUTCOMES.118.005122
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-- id: doi:10.1038/s41587-019-0143-x
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- - Kathrin Bernt
- - Nathan Salomonis
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- - Marissa Fessenden
- publisher: Nature
- date: '2019-01-01'
- link: https://doi.org/10.1038/d41586-019-00218-6
- image: https://media.nature.com/lw800/magazine-assets/d41586-019-00218-6/d41586-019-00218-6_16402666.jpg
+ - "Genevieve L. Stein-O\u2019Brien"
+ - Raman Arora
+ - Aedin C. Culhane
+ - Alexander V. Favorov
+ - Lana X. Garmire
+ - Casey S. Greene
+ - Loyal A. Goff
+ - Yifeng Li
+ - Aloune Ngom
+ - Michael F. Ochs
+ - Yanxun Xu
+ - Elana J. Fertig
+ publisher: Trends in Genetics
+ date: '2018-10-01'
+ link: https://doi.org/10.1016/j.tig.2018.07.003
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: sources.py
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+ link: https://doi.org/10.1101/196915
+- id: doi:10.1016/j.celrep.2018.03.076
+ title: Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The
+ Cancer Genome Atlas
+ authors:
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+ - Linghua Wang
+ - Michael T. Zimmermann
+ - Nyasha Chambwe
+ - Galen F. Gao
+ - Andrew D. Cherniack
+ - Huihui Fan
+ - Hui Shen
+ - Gregory P. Way
+ - Casey S. Greene
+ - Yuexin Liu
+ - Rehan Akbani
+ - Bin Feng
+ - Lawrence A. Donehower
+ - Chase Miller
+ - Yang Shen
+ - Mostafa Karimi
+ - Haoran Chen
+ - Pora Kim
+ - Peilin Jia
+ - Eve Shinbrot
+ - Shaojun Zhang
+ - Jianfang Liu
+ - Hai Hu
+ - Matthew H. Bailey
+ - Christina Yau
+ - Denise Wolf
+ - Zhongming Zhao
+ - John N. Weinstein
+ - Lei Li
+ - Li Ding
+ - Gordon B. Mills
+ - Peter W. Laird
+ - David A. Wheeler
+ - Ilya Shmulevich
+ - Raymond J. Monnat
+ - Yonghong Xiao
+ - Chen Wang
+ - Samantha J. Caesar-Johnson
+ - John A. Demchok
+ - Ina Felau
+ - Melpomeni Kasapi
+ - Martin L. Ferguson
+ - Carolyn M. Hutter
+ - Heidi J. Sofia
+ - Roy Tarnuzzer
+ - Zhining Wang
+ - Liming Yang
+ - Jean C. Zenklusen
+ - Jiashan (Julia) Zhang
+ - Sudha Chudamani
+ - Jia Liu
+ - Laxmi Lolla
+ - Rashi Naresh
+ - Todd Pihl
+ - Qiang Sun
+ - Yunhu Wan
+ - Ye Wu
+ - Juok Cho
+ - Timothy DeFreitas
+ - Scott Frazer
+ - Nils Gehlenborg
+ - Gad Getz
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+ - Jaegil Kim
+ - Michael S. Lawrence
+ - Pei Lin
+ - Sam Meier
+ - Michael S. Noble
+ - Gordon Saksena
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+ - Hailei Zhang
+ - Brady Bernard
+ - Nyasha Chambwe
+ - Varsha Dhankani
+ - Theo Knijnenburg
+ - Roger Kramer
+ - Kalle Leinonen
+ - Yuexin Liu
+ - Michael Miller
+ - Sheila Reynolds
+ - Ilya Shmulevich
+ - Vesteinn Thorsson
+ - Wei Zhang
+ - Rehan Akbani
+ - Bradley M. Broom
+ - Apurva M. Hegde
+ - Zhenlin Ju
+ - Rupa S. Kanchi
+ - Anil Korkut
+ - Jun Li
+ - Han Liang
+ - Shiyun Ling
+ - Wenbin Liu
+ - Yiling Lu
+ - Gordon B. Mills
+ - Kwok-Shing Ng
+ - Arvind Rao
+ - Michael Ryan
+ - Jing Wang
+ - John N. Weinstein
+ - Jiexin Zhang
+ - Adam Abeshouse
+ - Joshua Armenia
+ - Debyani Chakravarty
+ - Walid K. Chatila
+ - Ino de Bruijn
+ - Jianjiong Gao
+ - Benjamin E. Gross
+ - Zachary J. Heins
+ - Ritika Kundra
+ - Konnor La
+ - Marc Ladanyi
+ - Augustin Luna
+ - Moriah G. Nissan
+ - Angelica Ochoa
+ - Sarah M. Phillips
+ - Ed Reznik
+ - Francisco Sanchez-Vega
+ - Chris Sander
+ - Nikolaus Schultz
+ - Robert Sheridan
+ - S. Onur Sumer
+ - Yichao Sun
+ - Barry S. Taylor
+ - Jioajiao Wang
+ - Hongxin Zhang
+ - Pavana Anur
+ - Myron Peto
+ - Paul Spellman
+ - Christopher Benz
+ - Joshua M. Stuart
+ - Christopher K. Wong
+ - Christina Yau
+ - D. Neil Hayes
+ - Joel S. Parker
+ - Matthew D. Wilkerson
+ - Adrian Ally
+ - Miruna Balasundaram
+ - Reanne Bowlby
+ - Denise Brooks
+ - Rebecca Carlsen
+ - Eric Chuah
+ - Noreen Dhalla
+ - Robert Holt
+ - Steven J.M. Jones
+ - Katayoon Kasaian
+ - Darlene Lee
+ - Yussanne Ma
+ - Marco A. Marra
+ - Michael Mayo
+ - Richard A. Moore
+ - Andrew J. Mungall
+ - Karen Mungall
+ - A. Gordon Robertson
+ - Sara Sadeghi
+ - Jacqueline E. Schein
+ - Payal Sipahimalani
+ - Angela Tam
+ - Nina Thiessen
+ - Kane Tse
+ - Tina Wong
+ - Ashton C. Berger
+ - Rameen Beroukhim
+ - Andrew D. Cherniack
+ - Carrie Cibulskis
+ - Stacey B. Gabriel
+ - Galen F. Gao
+ - Gavin Ha
+ - Matthew Meyerson
+ - Steven E. Schumacher
+ - Juliann Shih
+ - Melanie H. Kucherlapati
+ - Raju S. Kucherlapati
+ - Stephen Baylin
+ - Leslie Cope
+ - Ludmila Danilova
+ - Moiz S. Bootwalla
+ - Phillip H. Lai
+ - Dennis T. Maglinte
+ - David J. Van Den Berg
+ - Daniel J. Weisenberger
+ - J. Todd Auman
+ - Saianand Balu
+ - Tom Bodenheimer
+ - Cheng Fan
+ - Katherine A. Hoadley
+ - Alan P. Hoyle
+ - Stuart R. Jefferys
+ - Corbin D. Jones
+ - Shaowu Meng
+ - Piotr A. Mieczkowski
+ - Lisle E. Mose
+ - Amy H. Perou
+ - Charles M. Perou
+ - Jeffrey Roach
+ - Yan Shi
+ - Janae V. Simons
+ - Tara Skelly
+ - Matthew G. Soloway
+ - Donghui Tan
+ - Umadevi Veluvolu
+ - Huihui Fan
+ - Toshinori Hinoue
+ - Peter W. Laird
+ - Hui Shen
+ - Wanding Zhou
+ - Michelle Bellair
+ - Kyle Chang
+ - Kyle Covington
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+ - Richard A. Gibbs
+ - Robert Glenn
+ - Walker Hale
+ - Yi Han
+ - Jianhong Hu
+ - Viktoriya Korchina
+ - Sandra Lee
+ - Lora Lewis
+ - Wei Li
+ - Xiuping Liu
+ - Margaret Morgan
+ - Donna Morton
+ - Donna Muzny
+ - Jireh Santibanez
+ - Margi Sheth
+ - Eve Shinbrot
+ - Linghua Wang
+ - Min Wang
+ - David A. Wheeler
+ - Liu Xi
+ - Fengmei Zhao
+ - Julian Hess
+ - Elizabeth L. Appelbaum
+ - Matthew Bailey
+ - Matthew G. Cordes
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+ - Michael D. McLellan
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+ - Kevin Lau
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+ - Kristen M. Leraas
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+ - Nilsa C. Ramirez
+ - Lisa Wise
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+ - Leigh Anne Zach
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+ - Richard J. Mural
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+ - Timothy Wang
+ - Olga Potapova
+ - Olga Voronina
+ - Laurence Desjardins
+ - Odette Mariani
+ - Sergio Roman-Roman
+ - Xavier Sastre
+ - Marc-Henri Stern
+ - Feixiong Cheng
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+ - Darell Bigner
+ - Eric Lipp
+ - Jeffrey Marks
+ - Shannon McCall
+ - Roger McLendon
+ - Angeles Secord
+ - Alexis Sharp
+ - Madhusmita Behera
+ - Daniel J. Brat
+ - Amy Chen
+ - Keith Delman
+ - Seth Force
+ - Fadlo Khuri
+ - Kelly Magliocca
+ - Shishir Maithel
+ - Jeffrey J. Olson
+ - Taofeek Owonikoko
+ - Alan Pickens
+ - Suresh Ramalingam
+ - Dong M. Shin
+ - Gabriel Sica
+ - Erwin G. Van Meir
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+ - Wil Eijckenboom
+ - Ad Gillis
+ - Esther Korpershoek
+ - Leendert Looijenga
+ - Wolter Oosterhuis
+ - Hans Stoop
+ - Kim E. van Kessel
+ - Ellen C. Zwarthoff
+ - Chiara Calatozzolo
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+ - Stefania Cuzzubbo
+ - Francesco DiMeco
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+ - Marta Aymerich
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+ - "Armando L\xF3pez Guillermo"
+ - Nguyen Van Bang
+ - Phan Thi Hanh
+ - Bui Duc Phu
+ - Yufang Tang
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+ - Kimberley Evason
+ - Peter R. Dottino
+ - John A. Martignetti
+ - Hani Gabra
+ - Hartmut Juhl
+ - Teniola Akeredolu
+ - Serghei Stepa
+ - Dave Hoon
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+ - Erik Castle
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+ - Carmen Behrens
+ - Jolanta Bondaruk
+ - Russell Broaddus
+ - Bogdan Czerniak
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+ - Charles Guo
+ - Alexander J. Lazar
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+ - Funda Meric-Bernstam
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+ - Patricia Troncoso
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+ - Candace Carter
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+ - Kenneth Lee
+ - Georgina Long
+ - Graham Mann
+ - Michael Quinn
+ - Robyn Saw
+ - Richard Scolyer
+ - Kerwin Shannon
+ - Andrew Spillane
+ - Jonathan Stretch
+ - Maria Synott
+ - John Thompson
+ - James Wilmott
+ - Hikmat Al-Ahmadie
+ - Timothy A. Chan
+ - Ronald Ghossein
+ - Anuradha Gopalan
+ - Douglas A. Levine
+ - Victor Reuter
+ - Samuel Singer
+ - Bhuvanesh Singh
+ - Nguyen Viet Tien
+ - Thomas Broudy
+ - Cyrus Mirsaidi
+ - Praveen Nair
+ - Paul Drwiega
+ - Judy Miller
+ - Jennifer Smith
+ - Howard Zaren
+ - Joong-Won Park
+ - Nguyen Phi Hung
+ - Electron Kebebew
+ - W. Marston Linehan
+ - Adam R. Metwalli
+ - Karel Pacak
+ - Peter A. Pinto
+ - Mark Schiffman
+ - Laura S. Schmidt
+ - Cathy D. Vocke
+ - Nicolas Wentzensen
+ - Robert Worrell
+ - Hannah Yang
+ - Marc Moncrieff
+ - Chandra Goparaju
+ - Jonathan Melamed
+ - Harvey Pass
+ - Natalia Botnariuc
+ - Irina Caraman
+ - Mircea Cernat
+ - Inga Chemencedji
+ - Adrian Clipca
+ - Serghei Doruc
+ - Ghenadie Gorincioi
+ - Sergiu Mura
+ - Maria Pirtac
+ - Irina Stancul
+ - Diana Tcaciuc
+ - Monique Albert
+ - Iakovina Alexopoulou
+ - Angel Arnaout
+ - John Bartlett
+ - Jay Engel
+ - Sebastien Gilbert
+ - Jeremy Parfitt
+ - Harman Sekhon
+ - George Thomas
+ - Doris M. Rassl
+ - Robert C. Rintoul
+ - Carlo Bifulco
+ - Raina Tamakawa
+ - Walter Urba
+ - Nicholas Hayward
+ - Henri Timmers
+ - Anna Antenucci
+ - Francesco Facciolo
+ - Gianluca Grazi
+ - Mirella Marino
+ - Roberta Merola
+ - Ronald de Krijger
+ - Anne-Paule Gimenez-Roqueplo
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+ - Simone Chevalier
+ - Ginette McKercher
+ - Kivanc Birsoy
+ - Gene Barnett
+ - Cathy Brewer
+ - Carol Farver
+ - Theresa Naska
+ - Nathan A. Pennell
+ - Daniel Raymond
+ - Cathy Schilero
+ - Kathy Smolenski
+ - Felicia Williams
+ - Carl Morrison
+ - Jeffrey A. Borgia
+ - Michael J. Liptay
+ - Mark Pool
+ - Christopher W. Seder
+ - Kerstin Junker
+ - Larsson Omberg
+ - Mikhail Dinkin
+ - George Manikhas
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+ - Maria Consiglia Bragazzi
+ - Vincenzo Cardinale
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+ - David Chesla
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+ - Renumathy Dhanasekaran
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+ - Klaus-Peter Janssen
+ - Julia Slotta-Huspenina
+ - Mohamed H. Abdel-Rahman
+ - Dina Aziz
+ - Sue Bell
+ - Colleen M. Cebulla
+ - Amy Davis
+ - Rebecca Duell
+ - J. Bradley Elder
+ - Joe Hilty
+ - Bahavna Kumar
+ - James Lang
+ - Norman L. Lehman
+ - Randy Mandt
+ - Phuong Nguyen
+ - Robert Pilarski
+ - Karan Rai
+ - Lynn Schoenfield
+ - Kelly Senecal
+ - Paul Wakely
+ - Paul Hansen
+ - Ronald Lechan
+ - James Powers
+ - Arthur Tischler
+ - William E. Grizzle
+ - Katherine C. Sexton
+ - Alison Kastl
+ - Joel Henderson
+ - Sima Porten
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+ - Oliver Bathe
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+ - Philip Disaia
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+ - Scott VandenBerg
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+ - Aaron Bossler
+ - Joseph Galbraith
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+ - Deqin Ma
+ - Mohammed Milhem
+ - Rita Sigmund
+ - Andrew K. Godwin
+ - Rashna Madan
+ - Howard G. Rosenthal
+ - Clement Adebamowo
+ - Sally N. Adebamowo
+ - Alex Boussioutas
+ - David Beer
+ - Thomas Giordano
+ - Anne-Marie Mes-Masson
+ - Fred Saad
+ - Therese Bocklage
+ - Lisa Landrum
+ - Robert Mannel
+ - Kathleen Moore
+ - Katherine Moxley
+ - Russel Postier
+ - Joan Walker
+ - Rosemary Zuna
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+ - Federico Valdivieso
+ - Rajiv Dhir
+ - James Luketich
+ - Edna M. Mora Pinero
+ - Mario Quintero-Aguilo
+ - Carlos Gilberto Carlotti
+ - "Jose Sebasti\xE3o Dos Santos"
+ - Rafael Kemp
+ - Ajith Sankarankuty
+ - Daniela Tirapelli
+ - James Catto
+ - Kathy Agnew
+ - Elizabeth Swisher
+ - Jenette Creaney
+ - Bruce Robinson
+ - Carl Simon Shelley
+ - Eryn M. Godwin
+ - Sara Kendall
+ - Cassaundra Shipman
+ - Carol Bradford
+ - Thomas Carey
+ - Andrea Haddad
+ - Jeffey Moyer
+ - Lisa Peterson
+ - Mark Prince
+ - Laura Rozek
+ - Gregory Wolf
+ - Rayleen Bowman
+ - Kwun M. Fong
+ - Ian Yang
+ - Robert Korst
+ - W. Kimryn Rathmell
+ - J. Leigh Fantacone-Campbell
+ - Jeffrey A. Hooke
+ - Albert J. Kovatich
+ - Craig D. Shriver
+ - John DiPersio
+ - Bettina Drake
+ - Ramaswamy Govindan
+ - Sharon Heath
+ - Timothy Ley
+ - Brian Van Tine
+ - Peter Westervelt
+ - Mark A. Rubin
+ - Jung Il Lee
+ - "Nat\xE1lia D. Aredes"
+ - Armaz Mariamidze
+ publisher: Cell Reports
+ date: '2018-04-01'
+ link: https://doi.org/10.1016/j.celrep.2018.03.076
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publisher: Critical Care Medicine
date: '2018-07-01'
link: https://doi.org/10.1097/ccm.0000000000003148
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image: https://www.ncbi.nlm.nih.gov/pmc/articles/instance/6005735/bin/nihms951452f2.jpg
+- id: doi:10.1101/427898
+ title: Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated
+ Vasculitis and Nephrotic Syndrome
+ authors:
+ - Sean Eddy
+ - Viji Nair
+ - Laura H. Mariani
+ - Felix H. Eichinger
+ - John Hartman
+ - Huateng Huang
+ - Hemang Parikh
+ - Jaclyn N. Taroni
+ - Maja T. Lindenmeyer
+ - Wenjun Ju
+ - Casey S. Greene
+ - Peter C. Grayson
+ - Brad Godfrey
+ - Clemens D. Cohen
+ - Matt G. Sampson
+ - Richard A. Lafayette
+ - Jeffrey Krischer
+ - Peter A. Merkel
+ - Matthias Kretzler
+ publisher: Cold Spring Harbor Laboratory
+ date: '2018-09-27'
+ link: https://doi.org/gkwxhp
+ orcid: 0000-0001-8713-9213
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+- id: doi:10.1016/j.celrep.2018.03.046
+ title: Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer
+ Genome Atlas
+ authors:
+ - Gregory P. Way
+ - Francisco Sanchez-Vega
+ - Konnor La
+ - Joshua Armenia
+ - Walid K. Chatila
+ - Augustin Luna
+ - Chris Sander
+ - Andrew D. Cherniack
+ - Marco Mina
+ - Giovanni Ciriello
+ - Nikolaus Schultz
+ - Yolanda Sanchez
+ - Casey S. Greene
+ - Samantha J. Caesar-Johnson
+ - John A. Demchok
+ - Ina Felau
+ - Melpomeni Kasapi
+ - Martin L. Ferguson
+ - Carolyn M. Hutter
+ - Heidi J. Sofia
+ - Roy Tarnuzzer
+ - Zhining Wang
+ - Liming Yang
+ - Jean C. Zenklusen
+ - Jiashan (Julia) Zhang
+ - Sudha Chudamani
+ - Jia Liu
+ - Laxmi Lolla
+ - Rashi Naresh
+ - Todd Pihl
+ - Qiang Sun
+ - Yunhu Wan
+ - Ye Wu
+ - Juok Cho
+ - Timothy DeFreitas
+ - Scott Frazer
+ - Nils Gehlenborg
+ - Gad Getz
+ - David I. Heiman
+ - Jaegil Kim
+ - Michael S. Lawrence
+ - Pei Lin
+ - Sam Meier
+ - Michael S. Noble
+ - Gordon Saksena
+ - Doug Voet
+ - Hailei Zhang
+ - Brady Bernard
+ - Nyasha Chambwe
+ - Varsha Dhankani
+ - Theo Knijnenburg
+ - Roger Kramer
+ - Kalle Leinonen
+ - Yuexin Liu
+ - Michael Miller
+ - Sheila Reynolds
+ - Ilya Shmulevich
+ - Vesteinn Thorsson
+ - Wei Zhang
+ - Rehan Akbani
+ - Bradley M. Broom
+ - Apurva M. Hegde
+ - Zhenlin Ju
+ - Rupa S. Kanchi
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+ image: https://media.springernature.com/w306/springer-static/cover/book/978-3-642-37189-9.jpg
+- id: doi:10.1111/j.1749-6632.2011.06383.x
+ title: Accurate evaluation and analysis of functional genomics data and methods
+ authors:
+ - Casey S. Greene
+ - Olga G. Troyanskaya
+ publisher: Annals of the New York Academy of Sciences
+ date: '2012-01-23'
+ link: https://doi.org/10.1111/j.1749-6632.2011.06383.x
+ orcid: 0000-0001-8713-9213
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+- id: doi:10.1371/journal.pcbi.1002816
+ title: 'Chapter 2: Data-Driven View of Disease Biology'
+ authors:
+ - Casey S. Greene
+ - Olga G. Troyanskaya
+ publisher: PLoS Computational Biology
+ date: '2012-12-27'
+ link: https://doi.org/10.1371/journal.pcbi.1002816
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
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+ image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1002816.g004
+- id: doi:10.1093/nar/gks458
+ title: 'IMP: a multi-species functional genomics portal for integration, visualization
+ and prediction of protein functions and networks'
+ authors:
+ - Aaron K. Wong
+ - Christopher Y. Park
+ - Casey S. Greene
+ - Lars A. Bongo
+ - Yuanfang Guan
+ - Olga G. Troyanskaya
+ publisher: Nucleic Acids Research
+ date: '2012-06-07'
+ link: https://doi.org/10.1093/nar/gks458
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: sources.py
+ file: sources.yaml
+ image: https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/Issue/40/W1/1/m_cover.gif?Expires=1601999470&Signature=Q2NOjEoX0jcl9eWLTHkXNaCRT2TNG3fWyJCMInmS2TIOqI5F0IvesRQm4Whc6JC~wzeR9Tjy25OxhJkIYEDBSYu9v4MVrA34r5POVBDcw2zCnNP-3G7CNaFar8g9N5AjzuxsC93tWtq7XUSd3NV4fC5BoyblYb9OYXVUfLIvy-GIYp4D6-wdgs1SyqaDcDrANy~VpQJdNn4Hs0wMLMfd1zcPFvbK-~DFEZ6joshnHYHRbECR7is7a-~-JYqeSqDS2~ZH2cwYO3heAgicnuC0sFltn7DJb8CLTLnpiaHs6yFpyHuKv-XOnVh7zcX~rFnvJEgFmDlUNDEHYAuvsFzwQQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA
+- id: doi:10.1007/978-3-642-21314-4_36
+ title: An Analysis of New Expert Knowledge Scaling Methods for Biologically Inspired
+ Computing
+ authors:
+ - Jason M. Gilmore
+ - Casey S. Greene
+ - Peter C. Andrews
+ - Jeff Kiralis
+ - Jason H. Moore
+ publisher: Advances in Artificial Life. Darwin Meets von Neumann
+ date: '2011-01-01'
+ link: https://doi.org/10.1007/978-3-642-21314-4_36
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1007/978-3-642-21283-3_39
+ title: An Open-Ended Computational Evolution Strategy for Evolving Parsimonious
+ Solutions to Human Genetics Problems
+ authors:
+ - Casey S. Greene
+ - Douglas P. Hill
+ - Jason H. Moore
+ publisher: Advances in Artificial Life. Darwin Meets von Neumann
+ date: '2011-01-01'
+ link: https://doi.org/10.1007/978-3-642-21283-3_39
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1186/1756-0381-4-21
+ title: 'Evolving hard problems: Generating human genetics datasets with a complex
+ etiology'
+ authors:
+ - Daniel S Himmelstein
+ - Casey S Greene
+ - Jason H Moore
+ publisher: BioData Mining
+ date: '2011-07-07'
+ link: https://doi.org/10.1186/1756-0381-4-21
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1093/nar/gkr440
+ title: 'PILGRM: an interactive data-driven discovery platform for expert biologists'
+ authors:
+ - C. S. Greene
+ - O. G. Troyanskaya
+ publisher: Nucleic Acids Research
+ date: '2011-06-07'
+ link: https://doi.org/10.1093/nar/gkr440
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1007/978-3-642-12211-8_7
+ title: A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease
+ Relationships
+ authors:
+ - Casey S. Greene
+ - Daniel S. Himmelstein
+ - Jason H. Moore
+ publisher: Lecture Notes in Computer Science
+ date: '2010-01-01'
+ link: https://doi.org/czh822
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: wosuid:WOS:000411479100034
+ title: Enabling personal genomics with an explicit test of epistasis
+ authors: []
+ publisher: Pacific Symposium on Biocomputing 2010, PSB 2010
+ date: '2024-08-07'
+ link: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000411479100034&KeyUID=WOS:000411479100034
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: wosuid:MEDLINE:19908385
+ title: Enabling personal genomics with an explicit test of epistasis.
+ authors: []
+ publisher: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
+ date: '2022-05-24'
+ link: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:19908385&KeyUID=MEDLINE:19908385
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1145/1830483.1830523
+ title: Fast genome-wide epistasis analysis using ant colony optimization for multifactor
+ dimensionality reduction analysis on graphics processing units
+ authors:
+ - Nicholas A. Sinnott-Armstrong
+ - Casey S. Greene
+ - Jason H. Moore
+ publisher: Proceedings of the 12th annual conference on Genetic and evolutionary
+ computation
+ date: '2010-07-07'
+ link: https://doi.org/10.1145/1830483.1830523
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1016/j.semnephrol.2010.07.002
+ title: Integrative Systems Biology for Data-Driven Knowledge Discovery
+ authors:
+ - Casey S. Greene
+ - Olga G. Troyanskaya
+ publisher: Seminars in Nephrology
+ date: '2010-09-01'
+ link: https://doi.org/10.1016/j.semnephrol.2010.07.002
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1093/bioinformatics/btq009
+ title: Multifactor dimensionality reduction for graphics processing units enables
+ genome-wide testing of epistasis in sporadic ALS
+ authors:
+ - Casey S. Greene
+ - Nicholas A. Sinnott-Armstrong
+ - Daniel S. Himmelstein
+ - Paul J. Park
+ - Jason H. Moore
+ - Brent T. Harris
+ publisher: Bioinformatics
+ date: '2010-01-16'
+ link: https://doi.org/10.1093/bioinformatics/btq009
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: wosuid:WOS:000272540600026
+ title: A Computational Evolution System for Open-Ended Automated Learning of Complex
+ Genetic Relationships
+ authors: []
+ publisher: Genetic Epidemiology
+ date: '2022-05-24'
+ link: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000272540600026&KeyUID=WOS:000272540600026
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1186/1756-0500-2-149
+ title: Accelerating epistasis analysis in human genetics with consumer graphics
+ hardware
+ authors:
+ - Nicholas A Sinnott-Armstrong
+ - Casey S Greene
+ - Fabio Cancare
+ - Jason H Moore
+ publisher: BMC Research Notes
+ date: '2009-07-24'
+ link: https://doi.org/10.1186/1756-0500-2-149
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: wosuid:WOS:000272540600064
+ title: Computationally Efficient Relief-based Algorithms for Detecting Epistasis
+ in Genome-wide Association Studies
+ authors: []
+ publisher: Genetic Epidemiology
+ date: '2022-05-24'
+ link: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000272540600064&KeyUID=WOS:000272540600064
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1109/CEC.2009.4983308
+ title: Development and evaluation of an open-ended computational evolution system
+ for the creation of digital organisms with complex genetic architecture
+ authors:
+ - Anna L. Tyler
+ - Bill C. White
+ - Casey S. Greene
+ - Peter C. Andrews
+ - Richard Cowper-Sa
+ - Jason H. Moore
+ publisher: 2009 IEEE Congress on Evolutionary Computation
+ date: '2009-05-01'
+ link: https://doi.org/10.1109/cec.2009.4983308
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1145/1569901.1570160
+ title: Environmental noise improves epistasis models of genetic data discovered
+ using a computational evolution system
+ authors:
+ - Casey S. Greene
+ - Douglas P. Hill
+ - Jason H. Moore
+ publisher: Proceedings of the 11th Annual conference on Genetic and evolutionary
+ computation
+ date: '2009-07-08'
+ link: https://doi.org/10.1145/1569901.1570160
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1371/journal.pone.0005639
+ title: Failure to Replicate a Genetic Association May Provide Important Clues About
+ Genetic Architecture
+ authors:
+ - Casey S. Greene
+ - Nadia M. Penrod
+ - Scott M. Williams
+ - Jason H. Moore
+ publisher: PLoS ONE
+ date: '2009-06-02'
+ link: https://doi.org/10.1371/journal.pone.0005639
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1109/CEC.2009.4983027
+ title: 'Nature-inspired algorithms for the genetic analysis of epistasis in common
+ human diseases: Theoretical assessment of wrapper vs. filter approaches'
+ authors:
+ - Casey S. Greene
+ - Jeff Kiralis
+ - Jason H. Moore
+ publisher: 2009 IEEE Congress on Evolutionary Computation
+ date: '2009-05-01'
+ link: https://doi.org/10.1109/cec.2009.4983027
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1007/978-3-642-01184-9_9
+ title: Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis
+ of Epistasis in Human Disease
+ authors:
+ - Casey S. Greene
+ - Jason M. Gilmore
+ - Jeff Kiralis
+ - Peter C. Andrews
+ - Jason H. Moore
+ publisher: Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
+ date: '2009-01-01'
+ link: https://doi.org/10.1007/978-3-642-01184-9_9
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1109/CEC.2009.4983093
+ title: Sensible initialization using expert knowledge for genome-wide analysis of
+ epistasis using genetic programming
+ authors:
+ - Casey S. Greene
+ - Bill C. White
+ - Jason H. Moore
+ publisher: 2009 IEEE Congress on Evolutionary Computation
+ date: '2009-05-01'
+ link: https://doi.org/10.1109/cec.2009.4983093
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.4018/978-1-60566-705-8.ch007
+ title: Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms
+ Requires Strategies which Exploit Domain-Specific Knowledge
+ authors:
+ - Casey S. Greene
+ - Jason H. Moore
+ publisher: Nature-Inspired Informatics for Intelligent Applications and Knowledge
+ Discovery
+ date: ''
+ link: https://doi.org/10.4018/978-1-60566-705-8.ch007
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1186/1756-0381-2-5
+ title: Spatially Uniform ReliefF (SURF) for computationally-efficient filtering
+ of gene-gene interactions
+ authors:
+ - Casey S Greene
+ - Nadia M Penrod
+ - Jeff Kiralis
+ - Jason H Moore
+ publisher: BioData Mining
+ date: '2009-09-22'
+ link: https://doi.org/10.1186/1756-0381-2-5
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1145/1527063.1527064
+ title: Solving complex problems in human genetics using GP
+ authors:
+ - Casey S. Greene
+ - Jason H. Moore
+ publisher: ACM SIGEVOlution
+ date: '2008-07-01'
+ link: https://doi.org/10.1145/1527063.1527064
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1002/art.23836
+ title: "Ability of epistatic interactions of cytokine single\u2010nucleotide polymorphisms\
+ \ to predict susceptibility to disease subsets in systemic sclerosis patients"
+ authors:
+ - Lorenzo Beretta
+ - Francesca Cappiello
+ - Jason H. Moore
+ - Morena Barili
+ - Casey S. Greene
+ - Raffaella Scorza
+ publisher: Arthritis & Rheumatism
+ date: '2008-07-15'
+ link: https://doi.org/10.1002/art.23836
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1007/978-3-540-87527-7_4
+ title: Ant Colony Optimization for Genome-Wide Genetic Analysis
+ authors:
+ - Casey S. Greene
+ - Bill C. White
+ - Jason H. Moore
+ publisher: Ant Colony Optimization and Swarm Intelligence
+ date: ''
+ link: https://doi.org/10.1007/978-3-540-87527-7_4
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: wosuid:WOS:000260871600142
+ title: Multifactor Dimensionality Reduction 2.0
+ authors: []
+ publisher: Genetic Epidemiology
+ date: '2022-05-24'
+ link: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000260871600142&KeyUID=WOS:000260871600142
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1007/978-3-540-75286-8_4
+ title: An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis
+ Using Genetic Programming
+ authors:
+ - Casey S. Greene
+ - Bill C. White
+ - Jason H. Moore
+ publisher: Lecture Notes in Computer Science
+ date: ''
+ link: https://doi.org/bf26rr
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1007/s00239-004-0312-4
+ title: LTR Retrotransposon-Gene Associations in Drosophila melanogaster
+ authors:
+ - Eric W. Ganko
+ - Casey S. Greene
+ - Judson A. Lewis
+ - Vikram Bhattacharjee
+ - John F. McDonald
+ publisher: Journal of Molecular Evolution
+ date: '2006-01-01'
+ link: https://doi.org/10.1007/s00239-004-0312-4
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1349/ddlp.303
+ title: Relief-based bioinformatics methods for the analysis of epistasis in genetic
+ association studies.
+ authors:
+ - Casey Stephen. Greene
+ publisher: Dartmouth College Library Press
+ date: ''
+ link: https://doi.org/10.1349/ddlp.303
+ orcid: 0000-0001-8713-9213
+ member: casey-greene
+ plugin: orcid.py
+ file: orcid.yaml
+- id: doi:10.1101/2023.06.26.546586
+ title: "Optimizer\u2019s dilemma: optimization strongly influences model selection\
+ \ in transcriptomic prediction"
+ authors:
+ - Jake Crawford
+ - Maria Chikina
+ - Casey S. Greene
+ publisher: Cold Spring Harbor Laboratory
+ date: '2023-06-26'
+ link: https://doi.org/10.1101/2023.06.26.546586
+ image: https://user-images.githubusercontent.com/542643/252371308-1ae174fe-1eb6-47c4-882b-5a3b982bc533.png
+ plugin: sources.py
+ file: sources.yaml
+- id: doi:10.1128/msystems.00928-22
+ title: The Coming of Age of Nucleic Acid Vaccines during COVID-19
+ authors:
+ - Halie M. Rando
+ - Ronan Lordan
+ - Likhitha Kolla
+ - Elizabeth Sell
+ - Alexandra J. Lee
+ - Nils Wellhausen
+ - Amruta Naik
+ - Jeremy P. Kamil
+ - Anthony Gitter
+ - Casey S. Greene
+ - John P. Barton
+ - Simina M. Boca
+ - Joel D. Boerckel
+ - Christian Brueffer
+ - James Brian Byrd
+ - Stephen Capone
+ - Shikta Capone
+ - Anna Ada Dattoli
+ - John J. Dziak
+ - Jeffrey M. Field
+ - Soumita Ghosh
+ - Anthony Gitter
+ - Rishi Raj Goel
+ - Casey S. Greene
+ - Marouen Ben Guebila
+ - Daniel S. Himmelstein
+ - Fengling Hu
+ - Nafisa M. Jadavji
+ - Jeremy P. Kamil
+ - Sergey Knyazev
+ - Likhitha Kolla
+ - Alexandra J. Lee
+ - Ronan Lordan
+ - Tiago Lubiana
+ - Temitayo Lukan
+ - Adam L. MacLean
+ - David Mai
+ - Serghei Mangul
+ - David Manheim
+ - "Lucy D\u2019Agostino McGowan"
+ - Jesse G. Meyer
+ - Ariel I. Mundo
+ - Amruta Naik
+ - YoSon Park
+ - Dimitri Perrin
+ - Yanjun Qi
+ - Diane N. Rafizadeh
+ - Bharath Ramsundar
+ - Halie M. Rando
+ - Sandipan Ray
+ - Michael P. Robson
+ - Vincent Rubinetti
+ - Elizabeth Sell
+ - Lamonica Shinholster
+ - Ashwin N. Skelly
+ - Yuchen Sun
+ - Yusha Sun
+ - Gregory L. Szeto
+ - Ryan Velazquez
+ - Jinhui Wang
+ - Nils Wellhausen
+ publisher: mSystems
+ date: '2023-04-27'
+ link: https://doi.org/10.1128/msystems.00928-22
+ image: https://greenelab.github.io/covid19-review/images/N000-overview.png
+ tags:
+ - COVID19
+ plugin: sources.py
+ file: sources.yaml
+- id: doi:10.1101/2023.01.05.522941
+ title: Hetnet connectivity search provides rapid insights into how two biomedical
+ entities are related
+ authors:
+ - Daniel S. Himmelstein
+ - Michael Zietz
+ - Vincent Rubinetti
+ - Kyle Kloster
+ - Benjamin J. Heil
+ - Faisal Alquaddoomi
+ - Dongbo Hu
+ - David N. Nicholson
+ - Yun Hao
+ - Blair D. Sullivan
+ - Michael W. Nagle
+ - Casey S. Greene
+ publisher: Cold Spring Harbor Laboratory
+ date: '2023-01-07'
+ link: https://doi.org/10.1101/2023.01.05.522941
+ image: https://user-images.githubusercontent.com/542643/211341569-e465826a-4cb1-41ea-a66f-162f420ea968.png
+ plugin: sources.py
+ file: sources.yaml
+- id: doi:10.1101/2023.01.05.522939
+ title: 'The probability of edge existence due to node degree: a baseline for network-based
+ predictions'
+ authors:
+ - Michael Zietz
+ - Daniel S. Himmelstein
+ - Kyle Kloster
+ - Christopher Williams
+ - Michael W. Nagle
+ - Casey S. Greene
+ publisher: Cold Spring Harbor Laboratory
+ date: '2023-01-06'
+ link: https://doi.org/10.1101/2023.01.05.522939
+ image: https://user-images.githubusercontent.com/542643/211156151-21a97245-c17b-4a94-ae72-76d6cf66a535.png
+ plugin: sources.py
+ file: sources.yaml
+- id: doi:10.1128/msystems.00927-22
+ title: Application of Traditional Vaccine Development Strategies to SARS-CoV-2
+ authors:
+ - Halie M. Rando
+ - Ronan Lordan
+ - Alexandra J. Lee
+ - Amruta Naik
+ - Nils Wellhausen
+ - Elizabeth Sell
+ - Likhitha Kolla
+ - Anthony Gitter
+ - Casey S. Greene
+ - Vikas Bansal
+ - John P. Barton
+ - Simina M. Boca
+ - Joel D. Boerckel
+ - Christian Brueffer
+ - James Brian Byrd
+ - Stephen Capone
+ - Shikta Das
+ - Anna Ada Dattoli
+ - John J. Dziak
+ - Jeffrey M. Field
+ - Soumita Ghosh
+ - Anthony Gitter
+ - Rishi Raj Goel
+ - Casey S. Greene
+ - Marouen Ben Guebila
+ - Daniel S. Himmelstein
+ - Fengling Hu
+ - Nafisa M. Jadavji
+ - Jeremy P. Kamil
+ - Sergey Knyazev
+ - Likhitha Kolla
+ - Alexandra J. Lee
+ - Ronan Lordan
+ - Tiago Lubiana
+ - Temitayo Lukan
+ - Adam L. MacLean
+ - David Mai
+ - Serghei Mangul
+ - David Manheim
+ - "Lucy D\u2019Agostino McGowan"
+ - Jesse G. Meyer
+ - Ariel I. Mundo
+ - Amruta Naik
+ - YoSon Park
+ - Dimitri Perrin
+ - Yanjun Qi
+ - Diane N. Rafizadeh
+ - Bharath Ramsundar
+ - Halie M. Rando
+ - Sandipan Ray
+ - Michael P. Robson
+ - Vincent Rubinetti
+ - Elizabeth Sell
+ - Lamonica Shinholster
+ - Ashwin N. Skelly
+ - Yuchen Sun
+ - Yusha Sun
+ - Gregory L. Szeto
+ - Ryan Velazquez
+ - Jinhui Wang
+ - Nils Wellhausen
+ publisher: mSystems
+ date: '2023-04-27'
+ link: https://doi.org/10.1128/msystems.00927-22
+ image: https://greenelab.github.io/covid19-review/images/N000-overview.png
+ tags:
+ - COVID19
+ plugin: sources.py
+ file: sources.yaml
+- id: doi:10.1093/bioinformatics/btac663
+ title: 'wenda_gpu: fast domain adaptation for genomic data'
+ authors:
+ - Ariel A Hippen
+ - Jake Crawford
+ - Jacob R Gardner
+ - Casey S Greene
+ publisher: Bioinformatics
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