Research

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

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

2025

BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk
BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk
Natalie R. Davidson, Fan Zhang, Casey S. Greene
PLOS Computational Biology  ·  17 Jan 2025  ·  doi:10.1371/journal.pcbi.1012742
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Mansooreh Ahmadian, Parker Hicks, …, Arjun Krishnan, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman
Cell  ·  01 Jan 2025  ·  doi:10.1016/j.cell.2024.12.017

2024

Latent spaces for tumour transcriptomes
Latent spaces for tumour transcriptomes
Adriana Ivich, Casey S. Greene
Nature Biomedical Engineering  ·  17 Dec 2024  ·  doi:10.1038/s41551-024-01322-3
Best holdout assessment is sufficient for cancer transcriptomic model selection
Best holdout assessment is sufficient for cancer transcriptomic model selection
Jake Crawford, Maria Chikina, Casey S. Greene
Patterns  ·  01 Dec 2024  ·  doi:10.1016/j.patter.2024.101115
A publishing infrastructure for Artificial Intelligence AI -assisted academic authoring
A publishing infrastructure for Artificial Intelligence (AI)-assisted academic authoring
Milton Pividori, Casey S Greene
Journal of the American Medical Informatics Association  ·  14 Jun 2024  ·  doi:10.1093/jamia/ocae139
Analysis of science journalism reveals gender and regional disparities in coverage
Analysis of science journalism reveals gender and regional disparities in coverage
Natalie R Davidson, Casey S Greene
eLife  ·  28 May 2024  ·  doi:10.7554/ELIFE.84855
MousiPLIER: A Mouse Pathway-Level Information Extractor Model
MousiPLIER: A Mouse Pathway-Level Information Extractor Model
Shuo Zhang, Benjamin J. Heil, Weiguang Mao, Maria Chikina, Casey S. Greene, Elizabeth A. Heller
eneuro  ·  24 May 2024  ·  doi:10.1523/ENEURO.0313-23.2024
Many direct-to-consumer canine genetic tests can identify the breed of purebred dogs
Many direct-to-consumer canine genetic tests can identify the breed of purebred dogs
Halie M. Rando, Kiley Graim, Greg Hampikian, Casey S. Greene
Journal of the American Veterinary Medical Association  ·  01 May 2024  ·  doi:10.2460/javma.23.07.0372
Missing cell types in single-cell references impact deconvolution of bulk data but are detectable
Missing cell types in single-cell references impact deconvolution of bulk data but are detectable
Adriana Ivich, Natalie R. Davidson, Laurie Grieshober, Weishan Li, Stephanie C. Hicks, Jennifer A. Doherty, Casey S. Greene
Cold Spring Harbor Laboratory  ·  28 Apr 2024  ·  doi:10.1101/2024.04.25.590992
The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors
The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors
Allegra G. Hawkins, Joshua A. Shapiro, Stephanie J. Spielman, David S. Mejia, Deepashree Venkatesh Prasad, …, Chante J. Bethell, Steven M. Foltz, Jennifer O’Malley, Casey S. Greene, Jaclyn N. Taroni
Cold Spring Harbor Laboratory  ·  24 Apr 2024  ·  doi:10.1101/2024.04.19.590243
i Pseudomonas aeruginosa i transcriptome analysis of metal restriction in i ex vivo i cystic fibrosis sputum
Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum
Samuel L. Neff, Georgia Doing, Taylor Reiter, Thomas H. Hampton, Casey S. Greene, Deborah A. Hogan
Microbiology Spectrum  ·  22 Feb 2024  ·  doi:10.1128/spectrum.03157-23
SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics
SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics
Halie M. Rando, Casey S. Greene, Michael P. Robson, Simina M. Boca, Nils Wellhausen, …, Yusha Sun, Daniel S. Himmelstein, Jeremy P. Kamil, Jesse G. Meyer, Ariel I. Mundo
Manubot  ·  02 Feb 2024  ·  url:https://greenelab.github.io/covid19-review/
Preprint
Manubot
covid19
The probability of edge existence due to node degree: a baseline for network-based predictions
The probability of edge existence due to node degree: a baseline for network-based predictions
Michael Zietz, Daniel S Himmelstein, Kyle Kloster, Christopher Williams, Michael W Nagle, Casey S Greene
GigaScience  ·  01 Jan 2024  ·  doi:10.1093/gigascience/giae001
Optimizer s dilemma: optimization strongly influences model selection in transcriptomic prediction
Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction
Jake Crawford, Maria Chikina, Casey S Greene
Bioinformatics Advances  ·  01 Jan 2024  ·  doi:10.1093/bioadv/vbae004
Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine
Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine
Laura K. Wiley, Jonathan A. Shortt, Emily R. Roberts, Jan Lowery, Elizabeth Kudron, …, Nicholas Rafaels, Kristy R. Crooks, Steve Hess, Kathleen C. Barnes, Christopher R. Gignoux
The American Journal of Human Genetics  ·  01 Jan 2024  ·  doi:10.1016/j.ajhg.2023.12.001

2023

Molecular subtypes of high-grade serous ovarian cancer across racial groups and gene expression platforms
Molecular subtypes of high-grade serous ovarian cancer across racial groups and gene expression platforms
Natalie R. Davidson, Mollie E. Barnard, Ariel A. Hippen, Amy Campbell, Courtney E. Johnson, …, Lauren C. Peres, Jeffrey R. Marks, Joellen M. Schildkraut, Casey S. Greene, Jennifer A. Doherty
Cold Spring Harbor Laboratory  ·  04 Nov 2023  ·  doi:10.1101/2023.11.01.565179
Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors
Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors
Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene
Genome Biology  ·  20 Oct 2023  ·  doi:10.1186/s13059-023-03077-7
Preprint
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman
Cold Spring Harbor Laboratory  ·  11 Oct 2023  ·  doi:10.1101/2023.10.11.560955
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
Milton Pividori, Sumei Lu, Binglan Li, Chun Su, Matthew E. Johnson, …, Benjamin F. Voight, Carsten Skarke, Marylyn D. Ritchie, Struan F. A. Grant, Casey S. Greene
Nature Communications  ·  09 Sep 2023  ·  doi:10.1038/s41467-023-41057-4
Preprint
gene-modules twas gwas complex-traits drugs
Analysis of i Pseudomonas aeruginosa i transcription in an i ex vivo i cystic fibrosis sputum model identifies metal restriction as a gene expression stimulus
Analysis ofPseudomonas aeruginosatranscription in anex vivocystic fibrosis sputum model identifies metal restriction as a gene expression stimulus
Samuel L. Neff, Georgia Doing, Taylor Reiter, Thomas H. Hampton, Casey S. Greene, Deborah A. Hogan
Cold Spring Harbor Laboratory  ·  21 Aug 2023  ·  doi:10.1101/2023.08.21.554169
MousiPLIER: A Mouse Pathway-Level Information Extractor Model
MousiPLIER: A Mouse Pathway-Level Information Extractor Model
Shuo Zhang, Benjamin J. Heil, Weiguang Mao, Maria Chikina, Casey S. Greene, Elizabeth A. Heller
Cold Spring Harbor Laboratory  ·  02 Aug 2023  ·  doi:10.1101/2023.07.31.551386
BuDDI: i Bulk Deconvolution with Domain Invariance i to predict cell-type-specific perturbations from bulk
BuDDI:Bulk Deconvolution with Domain Invarianceto predict cell-type-specific perturbations from bulk
Natalie R. Davidson, Fan Zhang, Casey S. Greene
Cold Spring Harbor Laboratory  ·  22 Jul 2023  ·  doi:10.1101/2023.07.20.549951
OpenPBTA: The Open Pediatric Brain Tumor Atlas
OpenPBTA: The Open Pediatric Brain Tumor Atlas
Joshua A. Shapiro, Krutika S. Gaonkar, Stephanie J. Spielman, Candace L. Savonen, Chante J. Bethell, …, Miguel A. Brown, Adam C. Resnick, Casey S. Greene, Jo Lynne Rokita, Jaclyn N. Taroni
Cell Genomics  ·  01 Jul 2023  ·  doi:10.1016/j.xgen.2023.100340
Is a Picture Worth 1,000 SNPs Effects of User-Submitted Photographs on Ancestry Estimates from Direct-to-Consumer Canine Genetic Tests
Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry Estimates from Direct-to-Consumer Canine Genetic Tests
Halie M. Rando, Kiley Graim, Greg Hampikian, Casey S. Greene
Cold Spring Harbor Laboratory  ·  29 Jun 2023  ·  doi:10.1101/2023.06.28.546898
Optimizer s dilemma: optimization strongly influences model selection in transcriptomic prediction
Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction
Jake Crawford, Maria Chikina, Casey S. Greene
Cold Spring Harbor Laboratory  ·  26 Jun 2023  ·  doi:10.1101/2023.06.26.546586
Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes
Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes
Ariel A. Hippen, Natalie R. Davidson, Mollie E. Barnard, Lukas M. Weber, Jason Gertz, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene
Cold Spring Harbor Laboratory  ·  15 Jun 2023  ·  doi:10.1101/2023.06.14.544991
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality
Mai T. Dang, Michael V. Gonzalez, Krutika S. Gaonkar, Komal S. Rathi, Patricia Young, …, Candace Savonen, Fernanda Mafra, Hakon Hakonarson, Tom Curran, Malay Haldar
Cell Reports  ·  01 Jun 2023  ·  doi:10.1016/j.celrep.2023.112600
Machine learning in rare disease
Machine learning in rare disease
Jineta Banerjee, Jaclyn N. Taroni, Robert J. Allaway, Deepashree Venkatesh Prasad, Justin Guinney, Casey Greene
Nature Methods  ·  29 May 2023  ·  doi:10.1038/s41592-023-01886-z
Changing word meanings in biomedical literature reveal pandemics and new technologies
Changing word meanings in biomedical literature reveal pandemics and new technologies
David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti, Casey S. Greene
BioData Mining  ·  05 May 2023  ·  doi:10.1186/s13040-023-00332-2
Preprint
The Coming of Age of Nucleic Acid Vaccines during COVID-19
The Coming of Age of Nucleic Acid Vaccines during COVID-19
Halie M. Rando, Ronan Lordan, Likhitha Kolla, Elizabeth Sell, Alexandra J. Lee, …, Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen
mSystems  ·  27 Apr 2023  ·  doi:10.1128/msystems.00928-22
covid19
Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Halie M. Rando, Ronan Lordan, Alexandra J. Lee, Amruta Naik, Nils Wellhausen, …, Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen
mSystems  ·  27 Apr 2023  ·  doi:10.1128/msystems.00927-22
covid19
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
Nucleic Acids Research  ·  18 Apr 2023  ·  doi:10.1093/nar/gkad289
The effect of non-linear signal in classification problems using gene expression
The effect of non-linear signal in classification problems using gene expression
Benjamin J. Heil, Jake Crawford, Casey S. Greene
PLOS Computational Biology  ·  27 Mar 2023  ·  doi:10.1371/journal.pcbi.1010984
Preprint
Source
Manubot
machine-learning gene-expression nonlinear-relationships
Biomonitoring and precision health in deep space supported by artificial intelligence
Biomonitoring and precision health in deep space supported by artificial intelligence
Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-min Park, …, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes
Nature Machine Intelligence  ·  23 Mar 2023  ·  doi:10.1038/s42256-023-00617-5
Preprint
Biological research and self-driving labs in deep space supported by artificial intelligence
Biological research and self-driving labs in deep space supported by artificial intelligence
Lauren M. Sanders, Ryan T. Scott, Jason H. Yang, Amina Ann Qutub, Hector Garcia Martin, …, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes
Nature Machine Intelligence  ·  23 Mar 2023  ·  doi:10.1038/s42256-023-00618-4
Preprint
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Steven M. Foltz, Casey S. Greene, Jaclyn N. Taroni
Communications Biology  ·  25 Feb 2023  ·  doi:10.1038/s42003-023-04588-6
Preprint
Source
Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia
Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia
Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Taylor Reiter, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan
mSystems  ·  23 Feb 2023  ·  doi:10.1128/msystems.00341-22
Preprint
Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14
Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14
Alexandra J. Lee, Georgia Doing, Samuel L. Neff, Taylor Reiter, Deborah A. Hogan, Casey S. Greene
mSystems  ·  23 Feb 2023  ·  doi:10.1128/msystems.00342-22
Preprint
Source
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, …, David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene
Cold Spring Harbor Laboratory  ·  07 Jan 2023  ·  doi:10.1101/2023.01.05.522941
The probability of edge existence due to node degree: a baseline for network-based predictions
The probability of edge existence due to node degree: a baseline for network-based predictions
Michael Zietz, Daniel S. Himmelstein, Kyle Kloster, Christopher Williams, Michael W. Nagle, Casey S. Greene
Cold Spring Harbor Laboratory  ·  06 Jan 2023  ·  doi:10.1101/2023.01.05.522939
The Field-Dependent Nature of PageRank Values in Citation Networks
The Field-Dependent Nature of PageRank Values in Citation Networks
Benjamin J. Heil, Casey S. Greene
Cold Spring Harbor Laboratory  ·  06 Jan 2023  ·  doi:10.1101/2023.01.05.522943
Supporting data for Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Supporting data for "Hetnet connectivity search provides rapid insights into how two biomedical entities are related"
Himmelstein S Daniel, Zietz Michael, Rubinetti Vincent, Kloster Kyle, Heil J Benjamin, …, Nicholson N David, Hao Yun, Sullivan D Blair, Nagle W Michael, Greene S Casey
GigaScience Database  ·  01 Jan 2023  ·  doi:10.5524/102389

2022

Hetnet connectivity search provides rapid insights into how biomedical entities are related
Hetnet connectivity search provides rapid insights into how biomedical entities are related
Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, …, David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene
GigaScience  ·  28 Dec 2022  ·  doi:10.1093/gigascience/giad047
Author Correction: A phase I Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC
Author Correction: A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC
Laurel B. Darragh, Michael M. Knitz, Junxiao Hu, Eric T. Clambey, Jennifer Backus, …, Antonio Jimeno, Angelo D’Alessandro, David Raben, Jessica D. McDermott, Sana D. Karam
Nature Cancer  ·  28 Dec 2022  ·  doi:10.1038/s43018-022-00507-6
Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors
Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors
Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene
Cold Spring Harbor Laboratory  ·  05 Dec 2022  ·  doi:10.1101/2022.12.04.519045
A phase I Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC
A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC
Laurel B. Darragh, Michael M. Knitz, Junxiao Hu, Eric T. Clambey, Jennifer Backus, …, Antonio Jimeno, Angelo D’Alessandro, David Raben, Jessica D. McDermott, Sana D. Karam
Nature Cancer  ·  25 Nov 2022  ·  doi:10.1038/s43018-022-00450-6
Source
Discerning asthma endotypes through comorbidity mapping
Discerning asthma endotypes through comorbidity mapping
Gengjie Jia, Xue Zhong, Hae Kyung Im, Nathan Schoettler, Milton Pividori, …, Michiaki Kubo, Nancy J. Cox, Carole Ober, Andrey Rzhetsky, Julian Solway
Nature Communications  ·  07 Nov 2022  ·  doi:10.1038/s41467-022-33628-8
asthma asthma-endotypes asthma-comorbidities
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts
David N. Nicholson, Daniel S. Himmelstein, Casey S. Greene
BioData Mining  ·  18 Oct 2022  ·  doi:10.1186/s13040-022-00311-z
Preprint
Manubot
Source
knowledge-graphs open-science
wenda gpu: fast domain adaptation for genomic data
wenda_gpu: fast domain adaptation for genomic data
Ariel A Hippen, Jake Crawford, Jacob R Gardner, Casey S Greene
Bioinformatics  ·  04 Oct 2022  ·  doi:10.1093/bioinformatics/btac663
Preprint
Source
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses
Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene
Genomics, Proteomics & Bioinformatics  ·  01 Oct 2022  ·  doi:10.1016/j.gpb.2022.09.011
Preprint
OpenPBTA: An Open Pediatric Brain Tumor Atlas
OpenPBTA: An Open Pediatric Brain Tumor Atlas
Joshua A. Shapiro, Krutika S. Gaonkar, Candace L. Savonen, Stephanie J. Spielman, Chante J. Bethell, …, Sabine Mueller, Adam C. Resnick, Casey S. Greene, Jo Lynne Rokita, Jaclyn N. Taroni
Cold Spring Harbor Laboratory  ·  16 Sep 2022  ·  doi:10.1101/2022.09.13.507832
Widespread redundancy in -omics profiles of cancer mutation states
Widespread redundancy in -omics profiles of cancer mutation states
Jake Crawford, Brock C. Christensen, Maria Chikina, Casey S. Greene
Genome Biology  ·  27 Jun 2022  ·  doi:10.1186/s13059-022-02705-y
Source
Preprint
GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases
GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent J. Carey, Casey S. Greene, Levi Waldron, Sean Davis
Nature Communications  ·  27 Jun 2022  ·  doi:10.1038/s41467-022-31411-3
Preprint
The Effects of Nonlinear Signal on Expression-Based Prediction Performance
The Effects of Nonlinear Signal on Expression-Based Prediction Performance
Benjamin J. Heil, Jake Crawford, Casey S. Greene
Cold Spring Harbor Laboratory  ·  26 Jun 2022  ·  doi:10.1101/2022.06.22.497194
An efficient not-only-linear correlation coefficient based on machine learning
An efficient not-only-linear correlation coefficient based on machine learning
Milton Pividori, Marylyn D. Ritchie, Diego H. Milone, Casey S. Greene
Cold Spring Harbor Laboratory  ·  17 Jun 2022  ·  doi:10.1101/2022.06.15.496326
correlation-coefficient nonlinear-relationships gene-expression
Building a Vertically-Integrated Genomic Learning Health System: The Colorado Center for Personalized Medicine Biobank
Building a Vertically-Integrated Genomic Learning Health System: The Colorado Center for Personalized Medicine Biobank
Laura K Wiley, Jonathan A Shortt, Emily R Roberts, Jan Lowery, Elizabeth Kudron, …, Nicholas Rafaels, Kristy Crooks, Steve Hess, Kathleen C Barnes, Christopher R Gignoux
Cold Spring Harbor Laboratory  ·  14 Jun 2022  ·  doi:10.1101/2022.06.09.22276222
Ten Quick Tips for Deep Learning in Biology
Ten Quick Tips for Deep Learning in Biology
Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, …, Alexandr A. Kalinin, Beth Signal, Benjamin J. Lengerich, Timothy J. Triche, Simina M. Boca
arXiv  ·  04 May 2022  ·  arxiv:2105.14372
Molecular and Serologic Diagnostic Technologies for SARS-CoV-2
Molecular and Serologic Diagnostic Technologies for SARS-CoV-2
Halie M. Rando, Christian Brueffer, Ronan Lordan, Anna Ada Dattoli, David Manheim, …, David Mai, Nils Wellhausen, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene
arXiv  ·  29 Apr 2022  ·  arxiv:2204.12598
covid19
Compendium-wide analysis of i P. aeruginosa i core and accessory genes reveal more nuanced transcriptional patterns
Compendium-wide analysis of P. aeruginosa core and accessory genes reveal more nuanced transcriptional patterns
Alexandra J. Lee, Georgia Doing, Samuel L. Neff, Taylor Reiter, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  15 Apr 2022  ·  doi:10.1101/2022.04.14.488429
wenda gpu: fast domain adaptation for genomic data
wenda_gpu: fast domain adaptation for genomic data
Ariel A. Hippen, Jake Crawford, Jacob R. Gardner, Casey S. Greene
Cold Spring Harbor Laboratory  ·  11 Apr 2022  ·  doi:10.1101/2022.04.09.487671
Ten simple rules for large-scale data processing
Ten simple rules for large-scale data processing
Arkarachai Fungtammasan, Alexandra Lee, Jaclyn Taroni, Kurt Wheeler, Chen-Shan Chin, Sean Davis, Casey Greene
PLOS Computational Biology  ·  10 Feb 2022  ·  doi:10.1371/journal.pcbi.1009757
Examining linguistic shifts between preprints and publications
Examining linguistic shifts between preprints and publications
David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene
PLOS Biology  ·  01 Feb 2022  ·  doi:10.1371/journal.pbio.3001470
Preprint
biorxiv natural-language-processing machine-learning
Computationally efficient assembly of a i Pseudomonas aeruginos i a gene expression compendium
Computationally efficient assembly of a Pseudomonas aeruginosa gene expression compendium
Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan
Cold Spring Harbor Laboratory  ·  25 Jan 2022  ·  doi:10.1101/2022.01.24.477642
Computational audits combat disparities in recognition
Computational audits combat disparities in recognition
Ariel A. Hippen, Natalie R. Davidson, Casey S. Greene
Nature Human Behaviour  ·  17 Jan 2022  ·  doi:10.1038/s41562-021-01279-2
Using genome-wide expression compendia to study microorganisms
Using genome-wide expression compendia to study microorganisms
Alexandra J. Lee, Taylor Reiter, Georgia Doing, Julia Oh, Deborah A. Hogan, Casey S. Greene
Computational and Structural Biotechnology Journal  ·  01 Jan 2022  ·  doi:10.1016/j.csbj.2022.08.012
Preprint
Molecular and Serologic Diagnostic Technologies for SARS-CoV-2
Molecular and Serologic Diagnostic Technologies for SARS-CoV-2
Halie M. Rando, Christian Brueffer, Ronan Lordan, Anna Ada Dattoli, David Manheim, …, David Mai, Nils Wellhausen, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene
arXiv  ·  01 Jan 2022  ·  doi:10.48550/arXiv.2204.12598

2021

Identification and Development of Therapeutics for COVID-19
Identification and Development of Therapeutics for COVID-19
Halie M. Rando, Nils Wellhausen, Soumita Ghosh, Alexandra J. Lee, Anna Ada Dattoli, …, Rishi Raj Goel, YoSon Park, Simina M. Boca, Anthony Gitter, Casey S. Greene
mSystems  ·  21 Dec 2021  ·  doi:10.1128/mSystems.00233-21
covid19
Characterizing Long COVID: Deep Phenotype of a Complex Condition
Characterizing Long COVID: Deep Phenotype of a Complex Condition
Rachel R Deer, Madeline A Rock, Nicole Vasilevsky, Leigh Carmody, Halie Rando, …, Umit Topaloglu, George D. Vavougios, Liwei Wang, Melissa A Haendel, Peter N Robinson
eBioMedicine  ·  01 Dec 2021  ·  doi:10.1016/j.ebiom.2021.103722
Preprint
covid19
Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer
Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer
Anthony R. Kerlavage, Anne C. Kirchhoff, Jaime M. Guidry Auvil, Norman E. Sharpless, Kara L. Davis, …, Jack DiGiovanna, Adam C. Resnick, Eve R. Shalley, Sorena Nadaf, Warren A. Kibbe
JCO Clinical Cancer Informatics  ·  01 Dec 2021  ·  doi:10.1200/CCI.21.00040
Human Intrigue: Meta-analysis approaches for big questions with big data while shaking up the peer review process
Human Intrigue: Meta-analysis approaches for big questions with big data while shaking up the peer review process
Carly A. Bobak, Meghan Muse, Kristine A. Giffin, Derek A. Williamson, Casey S. Greene, Jason H. Moore, Dennis P. Wall
Biocomputing 2022  ·  28 Nov 2021  ·  doi:10.1142/9789811250477_0015
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
Halie M. Rando, Adam L. MacLean, Alexandra J. Lee, Ronan Lordan, Sandipan Ray, …, Rishi Raj Goel, Serghei Mangul, Tiago Lubiana, Anthony Gitter, Casey S. Greene
mSystems  ·  26 Oct 2021  ·  doi:10.1128/mSystems.00095-21
covid19
Multi-ancestry gene-trait connection landscape using electronic health record EHR linked biobank data
Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data
Binglan Li, Yogasudha Veturi, Anastasia Lucas, Yuki Bradford, Shefali S. Verma, …, Yuan Luo, Milton Pividori, Hae Kyung Im, Casey S. Greene, Marylyn D. Ritchie
Cold Spring Harbor Laboratory  ·  26 Oct 2021  ·  10.1101/2021.10.21.21265225
Multi-ancestry gene-trait connection landscape using electronic health record EHR linked biobank data
Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data
Binglan Li, Yogasudha Veturi, Anastasia Lucas, Yuki Bradford, Shefali S. Verma, …, Yuan Luo, Milton Pividori, Hae Kyung Im, Casey S. Greene, Marylyn D. Ritchie
Cold Spring Harbor Laboratory  ·  26 Oct 2021  ·  doi:10.1101/2021.10.21.21265225
A field guide to cultivating computational biology
A field guide to cultivating computational biology
Gregory P. Way, Casey S. Greene, Piero Carninci, Benilton S. Carvalho, Michiel de Hoon, …, Suzanne S. Sindi, Fabian J. Theis, Jean Y. H. Yang, Anne E. Carpenter, Elana J. Fertig
PLOS Biology  ·  07 Oct 2021  ·  doi:10.1371/journal.pbio.3001419
Preprint
An Open-Publishing Response to the COVID-19 Infodemic
An Open-Publishing Response to the COVID-19 Infodemic
Halie M. Rando, Simina M. Boca, Lucy D’Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, Anthony Gitter
Digital Infrastructures for Scholarly Content Objects 2021  ·  30 Sep 2021  ·  url:http://ceur-ws.org/Vol-2976/paper-2.pdf
covid19
Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition
Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition
Madison Cooley, Casey S. Greene, Davis Issac, Milton Pividori, Blair D. Sullivan
arXiv  ·  08 Sep 2021  ·  arxiv:2106.00657
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design
Lukas M Weber, Ariel A Hippen, Peter F Hickey, Kristofer C Berrett, Jason Gertz, Jennifer Anne Doherty, Casey S Greene, Stephanie C Hicks
GigaScience  ·  01 Sep 2021  ·  doi:10.1093/gigascience/giab062
Preprint
cancer single-cell ovarian-cancer
Analysis of scientific society honors reveals disparities
Analysis of scientific society honors reveals disparities
Trang T. Le, Daniel S. Himmelstein, Ariel A. Hippen, Matthew R. Gazzara, Casey S. Greene
Cell Systems  ·  01 Sep 2021  ·  doi:10.1016/j.cels.2021.07.007
Preprint
Manubot
iscb-diversity
wiki-nationality-estimate
pubmedpy
machine-learning diversity
Reproducibility standards for machine learning in the life sciences
Reproducibility standards for machine learning in the life sciences
Benjamin J. Heil, Michael M. Hoffman, Florian Markowetz, Su-In Lee, Casey S. Greene, Stephanie C. Hicks
Nature Methods  ·  30 Aug 2021  ·  doi:10.1038/s41592-021-01256-7
reproducibility machine-learning
Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics
Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics
Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, …, Michael I. Love, Matthew E. Ritchie, Guo-Cheng Yuan, Aedin C. Culhane, Elana Fertig
Genome Biology  ·  25 Aug 2021  ·  doi:10.1186/s13059-021-02468-y
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks
PLOS Computational Biology  ·  24 Aug 2021  ·  doi:10.1371/journal.pcbi.1009290
Preprint
single-cell qc ovarian-cancer cancer
Community-wide hackathons to identify central themes in single-cell multi-omics
Community-wide hackathons to identify central themes in single-cell multi-omics
Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, …, Michael I. Love, Matthew E. Ritchie, Guo-Cheng Yuan, Aedin C. Culhane, Elana Fertig
Genome Biology  ·  05 Aug 2021  ·  doi:10.1186/s13059-021-02433-9
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
Milton Pividori, Sumei Lu, Binglan Li, Chun Su, Matthew E. Johnson, …, Benjamin F. Voight, Carsten Skarke, Marylyn D. Ritchie, Struan F.A. Grant, Casey S. Greene
Cold Spring Harbor Laboratory  ·  06 Jul 2021  ·  doi:10.1101/2021.07.05.450786
Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment
Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment
Ronan Lordan, Halie M. Rando, Casey S. Greene
mSystems  ·  29 Jun 2021  ·  doi:10.1128/mSystems.00122-21
covid19
Analysis of science journalism reveals gender and regional disparities in coverage
Analysis of science journalism reveals gender and regional disparities in coverage
Natalie R. Davidson, Casey S. Greene
Cold Spring Harbor Laboratory  ·  22 Jun 2021  ·  doi:10.1101/2021.06.21.449261
GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases
GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent Carey, Casey Greene, Levi Waldron, Sean Davis
Cold Spring Harbor Laboratory  ·  27 May 2021  ·  doi:10.1101/2021.05.26.445900
Generative neural networks separate common and specific transcriptional responses
Generative neural networks separate common and specific transcriptional responses
Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  24 May 2021  ·  doi:10.1101/2021.05.24.445440
Expanding and Remixing the Metadata Landscape
Expanding and Remixing the Metadata Landscape
Ariel A. Hippen, Casey S. Greene
Trends in Cancer  ·  01 Apr 2021  ·  doi:10.1016/j.trecan.2020.10.011
cancer open-science machine-learning
Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information
Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information
Halie M. Rando, Tellen D. Bennett, James Brian Byrd, Carolyn Bramante, Tiffany J. Callahan, …, Joel H. Saltz, Anthony Solomonides, Anupam Sule, Umit Topaloglu, Melissa A. Haendel
Cold Spring Harbor Laboratory  ·  26 Mar 2021  ·  doi:10.1101/2021.03.20.21253896
Preprint
covid19
Linguistic Analysis of the bioRxiv Preprint Landscape
Linguistic Analysis of the bioRxiv Preprint Landscape
David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene
Cold Spring Harbor Laboratory  ·  04 Mar 2021  ·  doi:10.1101/2021.03.04.433874
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks
Cold Spring Harbor Laboratory  ·  03 Mar 2021  ·  doi:10.1101/2021.03.03.433798
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality
Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality
Mai T. Dang, Michael V. Gonzalez, Krutika S. Gaonkar, Komal S. Rathi, Patricia Young, …, Candace Savonen, Fernanda Mafra, Hakon Hakonarson, Tom Curran, Malay Haldar
Cell Reports  ·  01 Mar 2021  ·  doi:10.1016/j.celrep.2021.108917
Preprint
genomics rare-diseases
Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer
Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer
Adam C. Mueller, Miles Piper, Andrew Goodspeed, Shiv Bhuvane, Jason S. Williams, …, Antonio Galveo Neto, David Lagares, Kirk C. Hansen, Adrie Van Bokhoven, Sana D. Karam
Cancer Research  ·  01 Feb 2021  ·  doi:10.1158/0008-5472.CAN-20-3892
cancer
Exploiting the GTEx resources to decipher the mechanisms at GWAS loci
Exploiting the GTEx resources to decipher the mechanisms at GWAS loci
Alvaro N. Barbeira, Rodrigo Bonazzola, Eric R. Gamazon, Yanyu Liang, YoSon Park, …, Ayellet V. Segrè, Christopher D. Brown, Tuuli Lappalainen, Xiaoquan Wen, Hae Kyung Im
Genome Biology  ·  26 Jan 2021  ·  doi:10.1186/s13059-020-02252-4
Preprint
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual
Diana L. Cousminer, Yadav Wagley, James A. Pippin, Ahmed Elhakeem, Gregory P. Way, …, Benjamin F. Voight, Andrew D. Wells, Babette S. Zemel, Kurt D. Hankenson, Struan F. A. Grant
Genome Biology  ·  04 Jan 2021  ·  doi:10.1186/s13059-020-02207-9
Preprint
genetics
Ten Quick Tips for Deep Learning in Biology
Ten Quick Tips for Deep Learning in Biology
Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, …, Alexandr A. Kalinin, Beth Signal, Benjamin J. Lengerich, Timothy J. Triche, Simina M. Boca
arXiv  ·  01 Jan 2021  ·  doi:10.48550/arxiv.2105.14372
Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition
Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition
Madison Cooley, Casey S. Greene, Davis Issac, Milton Pividori, Blair D. Sullivan
arXiv  ·  01 Jan 2021  ·  doi:10.48550/arxiv.2106.00657
Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health
Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health
Ryan T. Scott, Erik L. Antonsen, Lauren M. Sanders, Jaden J. A. Hastings, Seung-min Park, …, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes
arXiv  ·  01 Jan 2021  ·  doi:10.48550/arxiv.2112.12554
Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs
Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs
Lauren M. Sanders, Jason H. Yang, Ryan T. Scott, Amina Ann Qutub, Hector Garcia Martin, …, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V. Costes
arXiv  ·  01 Jan 2021  ·  doi:10.48550/arxiv.2112.12582

2020

Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128
Manubot
Manuscript Source
Website
open-science collaboration
Correcting for experiment-specific variability in expression compendia can remove underlying signals
Correcting for experiment-specific variability in expression compendia can remove underlying signals
Alexandra J Lee, YoSon Park, Georgia Doing, Deborah A Hogan, Casey S Greene
GigaScience  ·  01 Nov 2020  ·  doi:10.1093/gigascience/giaa117
Preprint
simulate-expression-compendia
genomics machine-learning data-integration
Biologically Informed Neural Networks Predict Drug Responses
Biologically Informed Neural Networks Predict Drug Responses
Casey S. Greene, James C. Costello
Cancer Cell  ·  01 Nov 2020  ·  doi:10.1016/j.ccell.2020.10.014
cancer machine-learning
Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE PrOTYPE
Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE)
Aline Talhouk, Joshy George, Chen Wang, Timothy Budden, Tuan Zea Tan, …, Ellen L. Goode, Susan J. Ramus, Jennifer A. Doherty, David D. Bowtell, Michael S. Anglesio
Clinical Cancer Research  ·  15 Oct 2020  ·  doi:10.1158/1078-0432.CCR-20-0103
ovarian-cancer genomics
Transparency and reproducibility in artificial intelligence
Transparency and reproducibility in artificial intelligence
Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, Thakkar Shraddha, …, Robert Tibshirani, Trevor Hastie, John P. A. Ioannidis, John Quackenbush, Hugo J. W. L. Aerts
Nature  ·  14 Oct 2020  ·  doi:10.1038/s41586-020-2766-y
arXiv
Transcriptomic signatures across human tissues identify functional rare genetic variation
Transcriptomic signatures across human tissues identify functional rare genetic variation
Nicole M. Ferraro, Benjamin J. Strober, Jonah Einson, Nathan S. Abell, Francois Aguet, …, Helen M. Moore, Concepcion R. Nierras, Abhi K. Rao, Jimmie B. Vaught, Simona Volpi
Science  ·  11 Sep 2020  ·  doi:10.1126/science.aaz5900
Preprint
PhenomeXcan: Mapping the genome to the phenome through the transcriptome
PhenomeXcan: Mapping the genome to the phenome through the transcriptome
Milton Pividori, Padma S. Rajagopal, Alvaro Barbeira, Yanyu Liang, Owen Melia, Lisa Bastarache, YoSon Park, GTEx Consortium, Xiaoquan Wen, Hae K. Im
Science Advances  ·  11 Sep 2020  ·  doi:10.1126/sciadv.aba2083
Preprint
Source
twas predixcan uk-biobank
Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx
Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx
Nicole R. Gay, Michael Gloudemans, Margaret L. Antonio, Nathan S. Abell, Brunilda Balliu, …, Christopher D. Brown, Hae Kyung Im, Tuuli Lappalainen, Xiaoquan Wen, Stephen B. Montgomery
Genome Biology  ·  11 Sep 2020  ·  doi:10.1186/s13059-020-02113-0
Preprint
Prognostic gene expression signature for high-grade serous ovarian cancer
Prognostic gene expression signature for high-grade serous ovarian cancer
J. Millstein, T. Budden, E.L. Goode, M.S. Anglesio, A. Talhouk, …, M. Buck, I. Haviv, D. Purdie, D. Whiteman, N. Zeps
Annals of Oncology  ·  01 Sep 2020  ·  doi:10.1016/j.annonc.2020.05.019
ovarian-cancer genomics
Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research
Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research
Jaqueline J Brito, Jun Li, Jason H Moore, Casey S Greene, Nicole A Nogoy, Lana X Garmire, Serghei Mangul
GigaScience  ·  01 Sep 2020  ·  doi:10.1093/gigascience/giaa103
Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing
Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing
William E. Allen, Han Altae-Tran, James Briggs, Xin Jin, Glen McGee, …, Ryan Probasco, David R. Cheng, Ben Silbermann, Feng Zhang, Xihong Lin
Nature Human Behaviour  ·  26 Aug 2020  ·  doi:10.1038/s41562-020-00944-2
Preprint
covid19
The National COVID Cohort Collaborative N3C : Rationale, design, infrastructure, and deployment
The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment
Melissa A Haendel, Christopher G Chute, Tellen D Bennett, David A Eichmann, Justin Guinney, …, Sam G Michael, Lili M Portilla, Joni L Rutter, Christopher P Austin, Ken R Gersing
Journal of the American Medical Informatics Association  ·  17 Aug 2020  ·  doi:10.1093/jamia/ocaa196
covid19
Responsible, practical genomic data sharing that accelerates research
Responsible, practical genomic data sharing that accelerates research
James Brian Byrd, Anna C. Greene, Deepashree Venkatesh Prasad, Xiaoqian Jiang, Casey S. Greene
Nature Reviews Genetics  ·  21 Jul 2020  ·  doi:10.1038/s41576-020-0257-5
open-science data-sharing
Publisher Correction: Building an international consortium for tracking coronavirus health status
Publisher Correction: Building an international consortium for tracking coronavirus health status
Eran Segal, Feng Zhang, Xihong Lin, Gary King, Ophir Shalem, …, Tim Spector, Ron Steinherz, Irene Stevens, Jaak Vilo, Paul Wilmes
Nature Medicine  ·  26 Jun 2020  ·  doi:10.1038/s41591-020-0983-4
Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States
Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States
William E. Allen, Han Altae-Tran, James Briggs, Xin Jin, Glen McGee, …, Ryan Probasco, David R. Cheng, Ben Silbermann, Feng Zhang, Xihong Lin
Cold Spring Harbor Laboratory  ·  11 Jun 2020  ·  doi:10.1101/2020.06.09.20126813
Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE PrOTYPE .
Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE).
Aline Talhouk, Joshy George, Chen Wang, Timothy Budden, Tuan Zea Tan, …, Ellen L Goode, Susan J Ramus, Jennifer A Doherty, David D Bowtell, Michael S Anglesio
American Association for Cancer Research (AACR)  ·  04 Jun 2020  ·  doi:10.17863/cam.53202
Constructing knowledge graphs and their biomedical applications
Constructing knowledge graphs and their biomedical applications
David N. Nicholson, Casey S. Greene
Computational and Structural Biotechnology Journal  ·  02 Jun 2020  ·  doi:10.1016/j.csbj.2020.05.017
Manubot
knowledge-graphs
Building an international consortium for tracking coronavirus health status
Building an international consortium for tracking coronavirus health status
Eran Segal, Feng Zhang, Xihong Lin, Gary King, Ophir Shalem, …, Tim Spector, Ron Steinherz, Irene Stevens, Jaak Vilo, Paul Wilmes
Nature Medicine  ·  02 Jun 2020  ·  doi:10.1038/s41591-020-0929-x
Preprint
Recommendations to enhance rigor and reproducibility in biomedical research
Recommendations to enhance rigor and reproducibility in biomedical research
Jaqueline J Brito, Jun Li, Jason H Moore, Casey S Greene, Nicole A Nogoy, Lana X Garmire, Serghei Mangul
GigaScience  ·  01 Jun 2020  ·  doi:10.1093/gigascience/giaa056
Manubot
arXiv
Incorporating biological structure into machine learning models in biomedicine
Incorporating biological structure into machine learning models in biomedicine
Jake Crawford, Casey S Greene
Current Opinion in Biotechnology  ·  01 Jun 2020  ·  doi:10.1016/j.copbio.2019.12.021
Manubot
arXiv
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Genome Biology  ·  11 May 2020  ·  doi:10.1186/s13059-020-02021-3
Preprint
Source
Website
machine-learning genomics
Specific histone modifications associate with alternative exon selection during mammalian development
Specific histone modifications associate with alternative exon selection during mammalian development
Qiwen Hu, Casey S Greene, Elizabeth A Heller
Nucleic Acids Research  ·  22 Apr 2020  ·  doi:10.1093/nar/gkaa248
Preprint
Source
genomics machine-learning
Analysis of ISCB honorees and keynotes reveals disparities
Analysis of ISCB honorees and keynotes reveals disparities
Trang T. Le, Daniel S. Himmelstein, Ariel A. Hippen Anderson, Matthew R. Gazzara, Casey S. Greene
Cold Spring Harbor Laboratory  ·  14 Apr 2020  ·  doi:10.1101/2020.04.14.927251
Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1
Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1
Jineta Banerjee, Robert J Allaway, Jaclyn N Taroni, Aaron Baker, Xiaochun Zhang, …, Jaishri O Blakeley, Justin Guinney, Angela Hirbe, Casey S Greene, Sara JC Gosline
Genes  ·  21 Feb 2020  ·  doi:10.3390/genes11020226
Preprint
Source
machine-learning rare-diseases
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping
Diana L. Cousminer, Yadav Wagley, James A. Pippin, Ahmed Elhakeem, Gregory P. Way, …, Benjamin F. Voight, Andrew D. Wells, Babette S. Zemel, Kurt Hankenson, Struan F. A. Grant
Cold Spring Harbor Laboratory  ·  20 Feb 2020  ·  doi:10.1101/2020.02.17.20024133
Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment
Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment
Mai T. Dang, Michael Gonzalez, Krutika S. Gaonkar, Komal S. Rathi, Patricia Young, …, Casey S. Greene, Candace Savonen, Hakon Hakonarson, Tom Curran, Malay Haldar
Cold Spring Harbor Laboratory  ·  13 Feb 2020  ·  doi:10.1101/2020.02.12.945642
i Pseudomonas aeruginosa lasR i mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin
Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin
Michelle E. Clay, John H. Hammond, Fangfang Zhong, Xiaolei Chen, Caitlin H. Kowalski, …, Monique S. Porter, Thomas H. Hampton, Casey S. Greene, Ekaterina V. Pletneva, Deborah A. Hogan
Proceedings of the National Academy of Sciences  ·  24 Jan 2020  ·  doi:10.1073/pnas.1917576117
Preprint
Graph biased feature selection of genes is better than random for many genes
Graph biased feature selection of genes is better than random for many genes
Jake Crawford, Casey S. Greene
Cold Spring Harbor Laboratory  ·  21 Jan 2020  ·  doi:10.1101/2020.01.17.910703
Source
machine-learning genomics
The importance of transparency and reproducibility in artificial intelligence research
The importance of transparency and reproducibility in artificial intelligence research
Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, MAQC Society Board, …, Robert Tibshirani, Trevor Hastie, John P. A. Ioannidis, John Quackenbush, Hugo J. W. L. Aerts
arXiv  ·  01 Jan 2020  ·  doi:10.48550/arxiv.2003.00898
Supporting data for Correcting for experiment-specific variability in expression compendia can remove underlying signals
Supporting data for "Correcting for experiment-specific variability in expression compendia can remove underlying signals"
Lee J Alexandra, Park YoSon, Doing Georgia, Hogan A Deborah, Greene S Casey
GigaScience Database  ·  01 Jan 2020  ·  doi:10.5524/100796
Recommendations to enhance rigor and reproducibility in biomedical research
Recommendations to enhance rigor and reproducibility in biomedical research
Jaqueline J. Brito, Jun Li, Jason H. Moore, Casey S. Greene, Nicole A. Nogoy, Lana X. Garmire, Serghei Mangul
arXiv  ·  01 Jan 2020  ·  doi:10.48550/arxiv.2001.05127

2019

Immune landscapes associated with different glioblastoma molecular subtypes
Immune landscapes associated with different glioblastoma molecular subtypes
Maria Martinez-Lage, Timothy M. Lynch, Yingtao Bi, Carolina Cocito, Gregory P. Way, …, Donald M. O’Rourke, Jeffrey P. Greenfield, Casey S. Greene, Ramana V. Davuluri, Nadia Dahmane
Acta Neuropathologica Communications  ·  29 Nov 2019  ·  doi:10.1186/s40478-019-0803-6
Source
Package
Zenodo
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, …, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg
Genome Biology  ·  19 Nov 2019  ·  doi:10.1186/s13059-019-1835-8
Preprint
Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design
Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design
Jo Lynne Rokita, Komal S. Rathi, Maria F. Cardenas, Kristen A. Upton, Joy Jayaseelan, …, Malcolm A. Smith, Richard B. Lock, Pichai Raman, David A. Wheeler, John M. Maris
Cell Reports  ·  01 Nov 2019  ·  doi:10.1016/j.celrep.2019.09.071
Preprint
Intermediate data
Classifier
Processed data
Source
Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma
Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma
Yu-Hsiu T. Lin, Gregory P. Way, Benjamin G. Barwick, Margarette C. Mariano, Makeba Marcoulis, Ian D. Ferguson, Christoph Driessen, Lawrence H. Boise, Casey S. Greene, Arun P. Wiita
Blood Advances  ·  29 Oct 2019  ·  doi:10.1182/bloodadvances.2019000303
Preprint
Classifier
Long non-coding RNA gene regulation and trait associations across human tissues
Long non-coding RNA gene regulation and trait associations across human tissues
O. M. de Goede, N. M. Ferraro, D. C. Nachun, A. S. Rao, F. Aguet, …, H. K. Im, K. G. Ardlie, T. Quertermous, K. Kirkegaard, S. B. Montgomery
Cold Spring Harbor Laboratory  ·  04 Oct 2019  ·  doi:10.1101/793091
Preprint
Embracing study heterogeneity for finding genetic interactions in large scale research consortia
Embracing study heterogeneity for finding genetic interactions in large‐scale research consortia
Yulun Liu, Jing Huang, Ryan J. Urbanowicz, Kun Chen, Elisabetta Manduchi, Casey S. Greene, Jason H. Moore, Paul Scheet, Yong Chen
Genetic Epidemiology  ·  04 Oct 2019  ·  doi:10.1002/gepi.22262
YETI2 Software
The GTEx Consortium atlas of genetic regulatory effects across human tissues
The GTEx Consortium atlas of genetic regulatory effects across human tissues
François Aguet, Alvaro N Barbeira, Rodrigo Bonazzola, Andrew Brown, Stephane E Castel, …, Barbara E Stranger, Hae Kyung Im, Alexis Battle, Kristin G Ardlie, Tuuli Lappalainen
Cold Spring Harbor Laboratory  ·  03 Oct 2019  ·  doi:10.1101/787903
Preprint
Voices in methods development
Voices in methods development
Polina Anikeeva, Edward Boyden, Clifford Brangwynne, Ibrahim I. Cissé, Oliver Fiehn, …, Hong-Wei Wang, Chengqi Yi, Peng Yin, Magdalena Zernicka-Goetz, Xiaowei Zhuang
Nature Methods  ·  27 Sep 2019  ·  doi:10.1038/s41592-019-0585-6
Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning
Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning
Gregory P. Way, Casey S. Greene
Annual Review of Biomedical Data Science  ·  20 Jul 2019  ·  doi:10.1146/annurev-biodatasci-072018-021348
Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing
Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing
Brett K. Beaulieu-Jones, Zhiwei Steven Wu, Chris Williams, Ran Lee, Sanjeev P. Bhavnani, James Brian Byrd, Casey S. Greene
Circulation: Cardiovascular Quality and Outcomes  ·  01 Jul 2019  ·  doi:10.1161/CIRCOUTCOMES.118.005122
Preprint
Source
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Naihui Zhou, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee, Balint Z Kacsoh, …, Claire O’Donovan, Sean D Mooney, Casey S Greene, Predrag Radivojac, Iddo Friedberg
Cold Spring Harbor Laboratory  ·  29 May 2019  ·  doi:10.1101/653105
Show me the models
Show me the models
Casey S. Greene
Nature Biotechnology  ·  28 May 2019  ·  doi:10.1038/s41587-019-0143-x
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease
Jaclyn N. Taroni, Peter C. Grayson, Qiwen Hu, Sean Eddy, Matthias Kretzler, Peter A. Merkel, Casey S. Greene
Cell Systems  ·  01 May 2019  ·  doi:10.1016/j.cels.2019.04.003
Source
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution
Deanne M. Taylor, Bruce J. Aronow, Kai Tan, Kathrin Bernt, Nathan Salomonis, …, Yi Xing, Sek Won Kong, Carsten G. Bönnemann, Kenneth D. Mandl, Peter S. White
Developmental Cell  ·  01 Apr 2019  ·  doi:10.1016/j.devcel.2019.03.001
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Cold Spring Harbor Laboratory  ·  11 Mar 2019  ·  doi:10.1101/573782
Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design
Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design
Jo Lynne Rokita, Komal S. Rathi, Maria F. Cardenas, Kristen A. Upton, Joy Jayaseelan, …, Malcolm A. Smith, Richard B. Lock, Pichai Raman, David A. Wheeler, John M. Maris
Cold Spring Harbor Laboratory  ·  06 Mar 2019  ·  doi:10.1101/566455
Technologies to watch in 2019
Technologies to watch in 2019
Marissa Fessenden
Nature  ·  23 Jan 2019  ·  doi:10.1038/d41586-019-00218-6
New i Drosophila i Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods
NewDrosophilaLong-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods
Balint Z Kacsoh, Stephen Barton, Yuxiang Jiang, Naihui Zhou, Sean D Mooney, Iddo Friedberg, Predrag Radivojac, Casey S Greene, Giovanni Bosco
G3 Genes|Genomes|Genetics  ·  01 Jan 2019  ·  doi:10.1534/g3.118.200867
Preprint
Incorporating biological structure into machine learning models in biomedicine
Incorporating biological structure into machine learning models in biomedicine
Jake Crawford, Casey S. Greene
arXiv  ·  01 Jan 2019  ·  doi:10.48550/arxiv.1910.06738

2018

Bayesian deep learning for single-cell analysis
Bayesian deep learning for single-cell analysis
Gregory P. Way, Casey S. Greene
Nature Methods  ·  30 Nov 2018  ·  doi:10.1038/s41592-018-0230-9
Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics
Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics
Qiwen Hu, Casey S. Greene
Biocomputing 2019  ·  01 Nov 2018  ·  doi:10.1142/9789813279827_0033
A parasite s perspective on data sharing
A parasite's perspective on data sharing
YoSon Park, Casey S Greene
GigaScience  ·  01 Nov 2018  ·  doi:10.1093/gigascience/giy129
Enter the Matrix: Factorization Uncovers Knowledge from Omics
Enter the Matrix: Factorization Uncovers Knowledge from Omics
Genevieve L. Stein-O’Brien, Raman Arora, Aedin C. Culhane, Alexander V. Favorov, Lana X. Garmire, …, Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig
Trends in Genetics  ·  01 Oct 2018  ·  doi:10.1016/j.tig.2018.07.003
Preprint
Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome
Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome
Sean Eddy, Viji Nair, Laura H. Mariani, Felix H. Eichinger, John Hartman, …, Matt G. Sampson, Richard A. Lafayette, Jeffrey Krischer, Peter A. Merkel, Matthias Kretzler
Cold Spring Harbor Laboratory  ·  27 Sep 2018  ·  doi:10.1101/427898
Learning and Imputation for Mass-spec Bias Reduction LIMBR
Learning and Imputation for Mass-spec Bias Reduction (LIMBR)
Alexander M Crowell, Casey S Greene, Jennifer J Loros, Jay C Dunlap
Bioinformatics  ·  24 Sep 2018  ·  doi:10.1093/bioinformatics/bty828
Preprint
Source
Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning
Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning
Gregory P Way, Casey S Greene
PeerJ  ·  20 Sep 2018  ·  doi:10.7287/peerj.preprints.27229v1
New Drosophila long-term memory genes revealed by assessing computational function prediction methods
New Drosophila long-term memory genes revealed by assessing computational function prediction methods
Balint Z. Kacsoh, Stephen Barton, Yuxiang Jiang, Naihui Zhou, Sean D. Mooney, Iddo Friedberg, Predrag Radivojac, Casey S. Greene, Giovanni Bosco
Cold Spring Harbor Laboratory  ·  11 Sep 2018  ·  doi:10.1101/414565
Metabolic pathways and immunometabolism in rare kidney diseases
Metabolic pathways and immunometabolism in rare kidney diseases
Peter C Grayson, Sean Eddy, Jaclyn N Taroni, Yaíma L Lightfoot, Laura Mariani, …, Brad Godfrey, Clemens D Cohen, Jeffrey Krischer, Matthias Kretzler, Peter A Merkel
Annals of the Rheumatic Diseases  ·  01 Aug 2018  ·  doi:10.1136/annrheumdis-2017-212935
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene
BioData Mining  ·  03 Jul 2018  ·  doi:10.1186/s13040-018-0175-7
Preprint
Analysis
Software
Server
Crosstalk correction
Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay
Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay*
Gary E. Weissman, Rebecca A. Hubbard, Lyle H. Ungar, Michael O. Harhay, Casey S. Greene, Blanca E. Himes, Scott D. Halpern
Critical Care Medicine  ·  01 Jul 2018  ·  doi:10.1097/CCM.0000000000003148
A Multimodal Strategy Used by a Large c-di-GMP Network
A Multimodal Strategy Used by a Large c-di-GMP Network
Kurt M. Dahlstrom, Alan J. Collins, Georgia Doing, Jaclyn N. Taroni, Timothy J. Gauvin, Casey S. Greene, Deborah A. Hogan, George A. O’Toole
Journal of Bacteriology  ·  15 Apr 2018  ·  doi:10.1128/JB.00703-17
Preprint
Opportunities and obstacles for deep learning in biology and medicine
Opportunities and obstacles for deep learning in biology and medicine
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, …, Simina M. Boca, S. Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S. Greene
Journal of The Royal Society Interface  ·  01 Apr 2018  ·  doi:10.1098/rsif.2017.0387
Preprint
Source
Oncogenic Signaling Pathways in The Cancer Genome Atlas
Oncogenic Signaling Pathways in The Cancer Genome Atlas
Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, …, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell  ·  01 Apr 2018  ·  doi:10.1016/j.cell.2018.03.035
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas
Gregory P. Way, Francisco Sanchez-Vega, Konnor La, Joshua Armenia, Walid K. Chatila, …, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports  ·  01 Apr 2018  ·  doi:10.1016/j.celrep.2018.03.046
Source
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Theo A. Knijnenburg, Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, …, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports  ·  01 Apr 2018  ·  doi:10.1016/j.celrep.2018.03.076
Source for ML portion
Sci-Hub provides access to nearly all scholarly literature
Sci-Hub provides access to nearly all scholarly literature
Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
eLife  ·  01 Mar 2018  ·  doi:10.7554/eLife.32822
Preprint
Manubot
Manuscript source
Analyses source
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses
Lia X Harrington, Gregory P Way, Jennifer A Doherty, Casey S Greene
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  ·  01 Jan 2018  ·  pmc:PMC5760988
Preprint
Source
Advances in Text Mining and Visualization for Precision Medicine.
Advances in Text Mining and Visualization for Precision Medicine.
Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O’Connor, Casey Greene, Hongfang Liu
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  ·  01 Jan 2018  ·  pubmed:29218914

2017

A Pilot Characterization of the Human Chronobiome
A Pilot Characterization of the Human Chronobiome
Carsten Skarke, Nicholas F. Lahens, Seth D. Rhoades, Amy Campbell, Kyle Bittinger, …, Frederic D. Bushman, Casey S. Greene, Gregory R. Grant, Aalim M. Weljie, Garret A. FitzGerald
Scientific Reports  ·  07 Dec 2017  ·  doi:10.1038/s41598-017-17362-6
ADAGE signature analysis: differential expression analysis with data-defined gene sets
ADAGE signature analysis: differential expression analysis with data-defined gene sets
Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
BMC Bioinformatics  ·  22 Nov 2017  ·  doi:10.1186/s12859-017-1905-4
Preprint
R package
Source
Updated app
Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders
Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders
Gregory P. Way, Casey S. Greene
Biocomputing 2018  ·  17 Nov 2017  ·  doi:10.1142/9789813235533_0008
Preprint
Source
Advances in Text Mining and Visualization for Precision Medicine
Advances in Text Mining and Visualization for Precision Medicine
Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O’Connor, Casey Greene, Hongfang Liu
Biocomputing 2018  ·  17 Nov 2017  ·  doi:10.1142/9789813235533_0051
Machine Learning Analysis Identifies i Drosophila Grunge Atrophin i as an Important Learning and Memory Gene Required for Memory Retention and Social Learning
Machine Learning Analysis IdentifiesDrosophila Grunge/Atrophinas an Important Learning and Memory Gene Required for Memory Retention and Social Learning
Balint Z Kacsoh, Casey S Greene, Giovanni Bosco
G3 Genes|Genomes|Genetics  ·  01 Nov 2017  ·  doi:10.1534/g3.117.300172
Preprint
A Multimodal Strategy Used By A Large c-di-GMP Network
A Multimodal Strategy Used By A Large c-di-GMP Network
Kurt M. Dahlstrom, Alan J. Collins, Georgia Doing, Jacyln N Taroni, Timothy J. Gauvin, Casey S. Greene, Deborah A. Hogan, George A. O’Toole
Cold Spring Harbor Laboratory  ·  04 Oct 2017  ·  doi:10.1101/198481
Enter the matrix: factorization uncovers knowledge from omics Names Affiliations
Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations
Genevieve L. Stein-O’Brien, Raman Arora, Aedin C. Culhane, Alexander V. Favorov, Lana X. Garmire, …, Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig
Cold Spring Harbor Laboratory  ·  02 Oct 2017  ·  doi:10.1101/196915
Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders
Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders
Gregory P. Way, Casey S. Greene
Cold Spring Harbor Laboratory  ·  11 Aug 2017  ·  doi:10.1101/174474
Implicating candidate genes at GWAS signals by leveraging topologically associating domains
Implicating candidate genes at GWAS signals by leveraging topologically associating domains
Gregory P Way, Daniel W Youngstrom, Kurt D Hankenson, Casey S Greene, Struan FA Grant
European Journal of Human Genetics  ·  09 Aug 2017  ·  doi:10.1038/ejhg.2017.108
Preprint
Source
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules
Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Casey S. Greene, Jason H. Moore, Andrew J. Saykin, Li Shen
Bioinformatics  ·  20 Jul 2017  ·  doi:10.1093/bioinformatics/btx344
Functional Network Community Detection Can Disaggregate and Filter Multiple Underlying Pathways in Enrichment Analyses
Functional Network Community Detection Can Disaggregate and Filter Multiple Underlying Pathways in Enrichment Analyses
Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene
Cold Spring Harbor Laboratory  ·  20 Jul 2017  ·  doi:10.1101/166207
Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes
Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes
Jennifer Anne Doherty, Lauren Cole Peres, Chen Wang, Gregory P. Way, Casey S. Greene, Joellen M. Schildkraut
Current Epidemiology Reports  ·  10 Jul 2017  ·  doi:10.1007/s40471-017-0115-y
Privacy-preserving generative deep neural networks support clinical data sharing
Privacy-preserving generative deep neural networks support clinical data sharing
Brett K. Beaulieu-Jones, Zhiwei Steven Wu, Chris Williams, Ran Lee, Sanjeev P. Bhavnani, James Brian Byrd, Casey S. Greene
Cold Spring Harbor Laboratory  ·  05 Jul 2017  ·  doi:10.1101/159756
Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks
Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks
Jie Tan, Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady, Barret Perchuk, Michael T. Laub, Deborah A. Hogan, Casey S. Greene
Cell Systems  ·  01 Jul 2017  ·  doi:10.1016/j.cels.2017.06.003
Preprint
Source
Machine learning analysis identifies i Drosophila Grunge Atrophin i as an important learning and memory gene required for memory retention and social learning
Machine learning analysis identifiesDrosophila Grunge/Atrophinas an important learning and memory gene required for memory retention and social learning
Balint Z Kacsoh, Casey S. Greene, Giovanni Bosco
Cold Spring Harbor Laboratory  ·  29 Jun 2017  ·  doi:10.1101/157610
ADAGE signature analysis: differential expression analysis with data-defined gene sets
ADAGE signature analysis: differential expression analysis with data-defined gene sets
Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  27 Jun 2017  ·  doi:10.1101/156620
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  08 Jun 2017  ·  doi:10.1101/147645
Data-Sharing Models
Data-Sharing Models
New England Journal of Medicine  ·  08 Jun 2017  ·  doi:10.1056/NEJMc1705477
Opportunities and obstacles for deep learning in biology and medicine
Opportunities and obstacles for deep learning in biology and medicine
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, …, Simina M. Boca, S. Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S. Greene
Cold Spring Harbor Laboratory  ·  28 May 2017  ·  doi:10.1101/142760
Celebrating parasites
Celebrating parasites
Casey S Greene, Lana X Garmire, Jack A Gilbert, Marylyn D Ritchie, Lawrence E Hunter
Nature Genetics  ·  01 Apr 2017  ·  doi:10.1038/ng.3830
A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis
A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis
Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood, Romy B. Christmann, …, Christopher P. Denton, Monique E. Hinchcliff, Patricia A. Pioli, J. Matthew Mahoney, Michael L. Whitfield
Genome Medicine  ·  23 Mar 2017  ·  doi:10.1186/s13073-017-0417-1
Preprint
Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously
Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously
Jaclyn N Taroni, Casey S Greene
Cold Spring Harbor Laboratory  ·  20 Mar 2017  ·  doi:10.1101/118349
Reproducibility of computational workflows is automated using continuous analysis
Reproducibility of computational workflows is automated using continuous analysis
Brett K Beaulieu-Jones, Casey S Greene
Nature Biotechnology  ·  13 Mar 2017  ·  doi:10.1038/nbt.3780
Preprint
Source
Tell me your neighbors, and I will tell you what you are
Tell me your neighbors, and I will tell you what you are
Casey S. Greene
Science Translational Medicine  ·  08 Feb 2017  ·  doi:10.1126/scitranslmed.aam6058
Khurana et al.
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene
BMC Genomics  ·  06 Feb 2017  ·  doi:10.1186/s12864-017-3519-7
Preprint
Source
Package
Evaluating deep variational autoencoders trained on pan-cancer gene expression
Evaluating deep variational autoencoders trained on pan-cancer gene expression
Gregory P. Way, Casey S. Greene
arXiv  ·  01 Jan 2017  ·  doi:10.48550/arxiv.1711.04828

2016

Cheap-seq
Cheap-seq
Casey S. Greene
Science Translational Medicine  ·  21 Dec 2016  ·  doi:10.1126/scitranslmed.aal3701
Tatlow et al.
Semi-supervised learning of the electronic health record for phenotype stratification
Semi-supervised learning of the electronic health record for phenotype stratification
Brett K. Beaulieu-Jones, Casey S. Greene
Journal of Biomedical Informatics  ·  01 Dec 2016  ·  doi:10.1016/j.jbi.2016.10.007
Preprint
Source
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes
Gregory P Way, James Rudd, Chen Wang, Habib Hamidi, Brooke L Fridley, Gottfried E Konecny, Ellen L Goode, Casey S Greene, Jennifer A Doherty
G3 Genes|Genomes|Genetics  ·  01 Dec 2016  ·  doi:10.1534/g3.116.033514
Preprint
Source
Package
NO-BOUNDARY THINKING IN BIOINFORMATICS
NO-BOUNDARY THINKING IN BIOINFORMATICS
JASON H. MOORE, STEVEN F. JENNINGS, CASEY S. GREENE, LAWRENCE E. HUNTER, ANDY D. PERKINS, CLARLYNDA WILLIAMS-DEVANE, DONALD C. WUNSCH, ZHONGMING ZHAO, XIUZHEN HUANG
Biocomputing 2017  ·  22 Nov 2016  ·  doi:10.1142/9789813207813_0060
How to know what we don t
How to know what we don’t
Casey S. Greene
Science Translational Medicine  ·  09 Nov 2016  ·  doi:10.1126/scitranslmed.aal0067
Zhou et al.
Unsupervised extraction of stable expression signatures from public compendia with eADAGE
Unsupervised extraction of stable expression signatures from public compendia with eADAGE
Jie Tan, Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady, Barret Perchuk, Michael T. Laub, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  03 Oct 2016  ·  doi:10.1101/078659
A stromal focus reveals tumor immune signatures
A stromal focus reveals tumor immune signatures
Casey S. Greene
Science Translational Medicine  ·  28 Sep 2016  ·  doi:10.1126/scitranslmed.aai8224
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene
Cold Spring Harbor Laboratory  ·  15 Sep 2016  ·  doi:10.1101/075382
Integrative Networks Illuminate Biological Factors Underlying Gene Disease Associations
Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations
Arjun Krishnan, Jaclyn N. Taroni, Casey S. Greene
Current Genetic Medicine Reports  ·  09 Sep 2016  ·  doi:10.1007/s40142-016-0102-5
Preprint
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur, Daniel D’Andrea, …, Burkhard Rost, Casey S. Greene, Sean D. Mooney, Iddo Friedberg, Predrag Radivojac
Genome Biology  ·  07 Sep 2016  ·  doi:10.1186/s13059-016-1037-6
Preprint
Integrative networks illuminate biological factors underlying gene-disease associations
Integrative networks illuminate biological factors underlying gene-disease associations
Arjun Krishnan, Jaclyn N. Taroni, Casey S. Greene
Cold Spring Harbor Laboratory  ·  28 Aug 2016  ·  doi:10.1101/062695
Gut check
Gut check
Casey S. Greene
Science Translational Medicine  ·  17 Aug 2016  ·  doi:10.1126/scitranslmed.aah5494
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes
Gregory P. Way, James Rudd, Chen Wang, Habib Hamidi, Brooke L. Fridley, Gottfried Konecny, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty
Cold Spring Harbor Laboratory  ·  12 Jul 2016  ·  doi:10.1101/030239
The future is unsupervised
The future is unsupervised
Casey S. Greene
Science Translational Medicine  ·  06 Jul 2016  ·  doi:10.1126/scitranslmed.aag3101
Pathway and network-based strategies to translate genetic discoveries into effective therapies
Pathway and network-based strategies to translate genetic discoveries into effective therapies
Casey S. Greene, Benjamin F. Voight
Human Molecular Genetics  ·  23 Jun 2016  ·  doi:10.1093/hmg/ddw160
Preprint
Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression
Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression
Adam J. Book, Gina R. Lewin, Bradon R. McDonald, Taichi E. Takasuka, Evelyn Wendt-Pienkowski, Drew T. Doering, Steven Suh, Kenneth F. Raffa, Brian G. Fox, Cameron R. Currie
PLOS Biology  ·  08 Jun 2016  ·  doi:10.1371/journal.pbio.1002475
Reproducible Computational Workflows with Continuous Analysis
Reproducible Computational Workflows with Continuous Analysis
Brett K. Beaulieu-Jones, Casey S. Greene
Cold Spring Harbor Laboratory  ·  01 Jun 2016  ·  doi:10.1101/056473
Tribe: The collaborative platform for reproducible web-based analysis of gene sets
Tribe: The collaborative platform for reproducible web-based analysis of gene sets
René A. Zelaya, Aaron K. Wong, Alex T. Frase, Marylyn D. Ritchie, Casey S. Greene
Cold Spring Harbor Laboratory  ·  27 May 2016  ·  doi:10.1101/055913
Preprint
Tribe server
Tribe web app
Nothing but a hound dog
Nothing but a hound dog
Casey S. Greene
Science Translational Medicine  ·  25 May 2016  ·  doi:10.1126/scitranslmed.aaf9196
Pathway and network-based strategies to translate genetic discoveries into effective therapies
Pathway and network-based strategies to translate genetic discoveries into effective therapies
Casey S. Greene, Benjamin F. Voight
Cold Spring Harbor Laboratory  ·  03 May 2016  ·  doi:10.1101/051524
CoINcIDE: All together now
CoINcIDE: All together now
Casey S. Greene
Science Translational Medicine  ·  13 Apr 2016  ·  doi:10.1126/scitranslmed.aaf6940
Genetic Association Guided Analysis of Gene Networks for the Study of Complex Traits
Genetic Association–Guided Analysis of Gene Networks for the Study of Complex Traits
Casey S. Greene, Daniel S. Himmelstein
Circulation: Cardiovascular Genetics  ·  01 Apr 2016  ·  doi:10.1161/CIRCGENETICS.115.001181
Source
Full text (free)
Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites
Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites
Robert J. Allaway, Dawn A. Fischer, Francine B. de Abreu, Timothy B. Gardner, Stuart R. Gordon, …, Gregory J. Tsongalis, Arief A. Suriawinata, Casey S. Greene, Yolanda Sanchez, Kerrington D. Smith
Oncotarget  ·  25 Feb 2016  ·  doi:10.18632/oncotarget.7718
Source
ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions
ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions
Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene
mSystems  ·  23 Feb 2016  ·  doi:10.1128/mSystems.00025-15
Preprint
Source
Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification
Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification
Brett K. Beaulieu-Jones, Casey S. Greene
Cold Spring Harbor Laboratory  ·  18 Feb 2016  ·  doi:10.1101/039800
A Novel Multi-network Approach Reveals Tissue-specific Cellular Modulators of Fibrosis in Systemic Sclerosis, Pulmonary Fibrosis and Pulmonary Arterial Hypertension
A Novel Multi-network Approach Reveals Tissue-specific Cellular Modulators of Fibrosis in Systemic Sclerosis, Pulmonary Fibrosis and Pulmonary Arterial Hypertension
Jaclyn N Taroni, Casey S Greene, Viktor Martyanov, Tammara A Wood, Romy Christmann, …, Christopher P Denton, Monique E Hinchcliff, Patricia A Pioli, J. Matthew Mahoney, Michael L Whitfield
Cold Spring Harbor Laboratory  ·  06 Feb 2016  ·  doi:10.1101/038950
Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology
Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology
Daniel S. Himmelstein, Casey S. Greene, Jason H. Moore
BioData Mining  ·  03 Feb 2016  ·  doi:10.1186/s13040-016-0085-5
Cross-platform normalization of microarray and RNA-seq data for machine learning applications
Cross-platform normalization of microarray and RNA-seq data for machine learning applications
Jeffrey A. Thompson, Jie Tan, Casey S. Greene
PeerJ  ·  21 Jan 2016  ·  doi:10.7717/peerj.1621
Preprint
R package
Source
Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer s disease: a study of ADNI cohorts
Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer’s disease: a study of ADNI cohorts
Ailin Song, Jingwen Yan, Sungeun Kim, Shannon Leigh Risacher, Aaron K. Wong, Andrew J. Saykin, Li Shen, Casey S. Greene
BioData Mining  ·  19 Jan 2016  ·  doi:10.1186/s13040-016-0082-8
Source
COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES
COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES
Casey S Greene, James A Foster, Bruce A Stanton, Deborah A Hogan, Yana Bromberg
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  ·  01 Jan 2016  ·  pmc:PMC4832978
PDF

2015

Leveraging global gene expression patterns to predict expression of unmeasured genes
Leveraging global gene expression patterns to predict expression of unmeasured genes
James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty
BMC Genomics  ·  01 Dec 2015  ·  doi:10.1186/s12864-015-2250-5
Source
ADAGE analysis of publicly available gene expression data collections illuminates i Pseudomonas aeruginosa-host i interactions
ADAGE analysis of publicly available gene expression data collections illuminatesPseudomonas aeruginosa-hostinteractions
Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  05 Nov 2015  ·  doi:10.1101/030650
Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions
Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions
David C. Qian, Jinyoung Byun, Younghun Han, Casey S. Greene, John K. Field, …, Fredrick R. Schumacher, Rosalind A. Eeles, Douglas F. Easton, Daniela Seminara, Christopher I. Amos
Human Molecular Genetics  ·  19 Oct 2015  ·  doi:10.1093/hmg/ddv440
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery
Graciela H. Gonzalez, Tasnia Tahsin, Britton C. Goodale, Anna C. Greene, Casey S. Greene
Briefings in Bioinformatics  ·  29 Sep 2015  ·  doi:10.1093/bib/bbv087
International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways
International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways
Heather J. Cordell, Younghun Han, George F. Mells, Yafang Li, Gideon M. Hirschfield, …, Pietro Invernizzi, Michael F. Seldin, Richard N. Sandford, Christopher I. Amos, Katherine A. Siminovitch
Nature Communications  ·  22 Sep 2015  ·  doi:10.1038/ncomms9019
Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study
Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study
Jiang Gui, Casey S. Greene, Con Sullivan, Walter Taylor, Jason H. Moore, Carol Kim
BioData Mining  ·  01 Jun 2015  ·  doi:10.1186/s13040-015-0050-8
Understanding multicellular function and disease with human tissue-specific networks
Understanding multicellular function and disease with human tissue-specific networks
Casey S Greene, Arjun Krishnan, Aaron K Wong, Emanuela Ricciotti, Rene A Zelaya, …, Daniel I Chasman, Garret A FitzGerald, Kara Dolinski, Tilo Grosser, Olga G Troyanskaya
Nature Genetics  ·  27 Apr 2015  ·  doi:10.1038/ng.3259
Processed networks
Raw networks
App
Adapting bioinformatics curricula for big data
Adapting bioinformatics curricula for big data
Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore
Briefings in Bioinformatics  ·  30 Mar 2015  ·  doi:10.1093/bib/bbv018
Targeted exploration and analysis of large cross-platform human transcriptomic compendia
Targeted exploration and analysis of large cross-platform human transcriptomic compendia
Qian Zhu, Aaron K Wong, Arjun Krishnan, Miriam R Aure, Alicja Tadych, …, Lars A Bongo, Vessela N Kristensen, Moses Charikar, Kai Li, Olga G Troyanskaya
Nature Methods  ·  12 Jan 2015  ·  doi:10.1038/nmeth.3249
App
Targeted exploration and analysis of large cross-platform human transcriptomic compendia
Targeted exploration and analysis of large cross-platform human transcriptomic compendia
Qian Zhu, Aaron K Wong, Arjun Krishnan, Miriam R Aure, Alicja Tadych, …, Lars A Bongo, Vessela N Kristensen, Moses Charikar, Kai Li, Olga G Troyanskaya
Nature Methods  ·  12 Jan 2015  ·  doi:10.1038/NMETH.3249
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
J. Matthew Mahoney, Jaclyn Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield
PLoS Computational Biology  ·  08 Jan 2015  ·  doi:10.1371/journal.pcbi.1004005
Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders
Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders
Jie Tan, Matthew Ung, Chao Cheng, Casey S Greene
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  ·  01 Jan 2015  ·  pmc:PMC4299935
Source

2014

Big Data Bioinformatics
Big Data Bioinformatics
Casey S. Greene, Jie Tan, Matthew Ung, Jason H. Moore, Chao Cheng
Journal of Cellular Physiology  ·  27 Aug 2014  ·  doi:10.1002/jcp.24662
Computational genetics analysis of grey matter density in Alzheimer s disease
Computational genetics analysis of grey matter density in Alzheimer’s disease
Amanda L Zieselman, Jonathan M Fisher, Ting Hu, Peter C Andrews, Casey S Greene, Li Shen, Andrew J Saykin, Jason H Moore
BioData Mining  ·  22 Aug 2014  ·  doi:10.1186/1756-0381-7-17
Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity
Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity
Nadia M Penrod, Casey S Greene, Jason H Moore
Genome Medicine  ·  30 Apr 2014  ·  doi:10.1186/gm550

2013

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

2012

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

2011

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

2010

Integrative Systems Biology for Data-Driven Knowledge Discovery
Integrative Systems Biology for Data-Driven Knowledge Discovery
Casey S. Greene, Olga G. Troyanskaya
Seminars in Nephrology  ·  01 Sep 2010  ·  doi:10.1016/j.semnephrol.2010.07.002
Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units
Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units
Nicholas A. Sinnott-Armstrong, Casey S. Greene, Jason H. Moore
Proceedings of the 12th annual conference on Genetic and evolutionary computation  ·  07 Jul 2010  ·  doi:10.1145/1830483.1830523
Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS
Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS
Casey S. Greene, Nicholas A. Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, Brent T. Harris
Bioinformatics  ·  16 Jan 2010  ·  doi:10.1093/bioinformatics/btq009
The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics
The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics
Casey S. Greene, Daniel S. Himmelstein, Jeff Kiralis, Jason H. Moore
Lecture Notes in Computer Science  ·  01 Jan 2010  ·  doi:10.1007/978-3-642-12211-8_16
Artificial Immune Systems for Epistasis Analysis in Human Genetics
Artificial Immune Systems for Epistasis Analysis in Human Genetics
Nadia M. Penrod, Casey S. Greene, Delaney Granizo-MacKenzie, Jason H. Moore
Lecture Notes in Computer Science  ·  01 Jan 2010  ·  doi:10.1007/978-3-642-12211-8_17
A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships
A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships
Casey S. Greene, Daniel S. Himmelstein, Jason H. Moore
Lecture Notes in Computer Science  ·  01 Jan 2010  ·  doi:10.1007/978-3-642-12211-8_7

2009

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

2008

Solving complex problems in human genetics using GP
Solving complex problems in human genetics using GP
Casey S. Greene, Jason H. Moore
ACM SIGEVOlution  ·  01 Jul 2008  ·  doi:10.1145/1527063.1527064
Ability of epistatic interactions of cytokine single nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patients
Ability of epistatic interactions of cytokine single‐nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patients
Lorenzo Beretta, Francesca Cappiello, Jason H. Moore, Morena Barili, Casey S. Greene, Raffaella Scorza
Arthritis Care & Research  ·  24 Jun 2008  ·  doi:10.1002/art.23836

2006

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

Relief-based bioinformatics methods for the analysis of epistasis in genetic association studies.
Relief-based bioinformatics methods for the analysis of epistasis in genetic association studies.
Casey Stephen. Greene
Dartmouth College Library Press  ·  [no date info]  ·  doi:10.1349/ddlp.303
An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming
An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming
Casey S. Greene, Bill C. White, Jason H. Moore
Lecture Notes in Computer Science  ·  [no date info]  ·  doi:10.1007/978-3-540-75286-8_4
Ant Colony Optimization for Genome-Wide Genetic Analysis
Ant Colony Optimization for Genome-Wide Genetic Analysis
Casey S. Greene, Bill C. White, Jason H. Moore
Lecture Notes in Computer Science  ·  [no date info]  ·  doi:10.1007/978-3-540-87527-7_4
Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms Requires Strategies which Exploit Domain-Specific Knowledge
Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms Requires Strategies which Exploit Domain-Specific Knowledge
Casey S. Greene, Jason H. Moore
Nature-Inspired Informatics for Intelligent Applications and Knowledge Discovery  ·  [no date info]  ·  doi:10.4018/978-1-60566-705-8.ch007