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

All papers under Casey’s ORCID:

2024

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
Natalie R Davidson, Casey S Greene
eLife  ·  28 May 2024  ·  doi:10.7554/eLife.84855.3
Analysis of science journalism reveals gender and regional disparities in coverage
Natalie R. Davidson, Casey S. Greene
eLife Sciences Publications, Ltd  ·  17 May 2024  ·  doi:10.7554/eLife.84855.2
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
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
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

2023

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors
Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene
Genome Biology  ·  20 Oct 2023  ·  doi:10.1186/s13059-023-03077-7
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman
Cold Spring Harbor Laboratory  ·  11 Oct 2023  ·  doi:10.1101/2023.10.11.560955
Human Microbiome Compendium dataset
Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman
Zenodo  ·  11 Oct 2023  ·  doi:10.5281/zenodo.8186993
Analysis ofPseudomonas aeruginosatranscription in anex vivocystic fibrosis sputum model identifies metal restriction as a gene expression stimulus
Samuel L. Neff, Georgia Doing, Taylor Reiter, Thomas H. Hampton, Casey S. Greene, Deborah A. Hogan
Cold Spring Harbor Laboratory  ·  21 Aug 2023  ·  doi:10.1101/2023.08.21.554169
MousiPLIER: A Mouse Pathway-Level Information Extractor Model
Shuo Zhang, Benjamin J. Heil, Weiguang Mao, Maria Chikina, Casey S. Greene, Elizabeth A. Heller
Cold Spring Harbor Laboratory  ·  02 Aug 2023  ·  doi:10.1101/2023.07.31.551386
BuDDI:Bulk Deconvolution with Domain Invarianceto predict cell-type-specific perturbations from bulk
Natalie R. Davidson, Casey S. Greene
Cold Spring Harbor Laboratory  ·  22 Jul 2023  ·  doi:10.1101/2023.07.20.549951
Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry Estimates from Direct-to-Consumer Canine Genetic Tests
Halie M. Rando, Kiley Graim, Greg Hampikian, Casey S. Greene
Cold Spring Harbor Laboratory  ·  29 Jun 2023  ·  doi:10.1101/2023.06.28.546898
Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction
Jake Crawford, Maria Chikina, Casey S. Greene
Cold Spring Harbor Laboratory  ·  26 Jun 2023  ·  doi:10.1101/2023.06.26.546586
greenelab/phenoplier: a computational framework to integrate genetic studies with gene co-expression patterns
Milton Pividori, Casey Greene
Zenodo  ·  22 Jun 2023  ·  doi:10.5281/zenodo.8071382
greenelab/phenoplier: a computational framework to integrate genetic studies with gene co-expression patterns
Milton Pividori, Casey Greene
Zenodo  ·  22 Jun 2023  ·  doi:10.5281/zenodo.8044955
Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes
Ariel A. Hippen, Natalie R. Davidson, Mollie E. Barnard, Lukas M. Weber, Jason Gertz, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene
Cold Spring Harbor Laboratory  ·  15 Jun 2023  ·  doi:10.1101/2023.06.14.544991
Machine learning in rare disease
Jineta Banerjee, Jaclyn N. Taroni, Robert J. Allaway, Deepashree Venkatesh Prasad, Justin Guinney, Casey Greene
Nature Methods  ·  29 May 2023  ·  doi:10.1038/s41592-023-01886-z
Changing word meanings in biomedical literature reveal pandemics and new technologies
David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti, Casey S. Greene
BioData Mining  ·  05 May 2023  ·  doi:10.1186/s13040-023-00332-2
The Coming of Age of Nucleic Acid Vaccines during COVID-19
Halie M. Rando, Ronan Lordan, Likhitha Kolla, Elizabeth Sell, Alexandra J. Lee, …, Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen
mSystems  ·  27 Apr 2023  ·  doi:10.1128/msystems.00928-22
Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Halie M. Rando, Ronan Lordan, Alexandra J. Lee, Amruta Naik, Nils Wellhausen, …, Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen
mSystems  ·  27 Apr 2023  ·  doi:10.1128/msystems.00927-22
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
Nucleic Acids Research  ·  18 Apr 2023  ·  doi:10.1093/nar/gkad289
Data underlying OpenPBTA Manuscript Figures and Molecular Alterations
Joshua A. Shapiro, Krutika S. Gaonkar, Stephanie J. Spielman, Candace L. Savonen, Chante J. Bethell, …, Miguel A. Brown, Adam C. Resnick, Casey S. Greene, Jo Lynne Rokita, Jaclyn N. Taroni
Zenodo  ·  06 Apr 2023  ·  doi:10.5281/zenodo.7805407
The effect of non-linear signal in classification problems using gene expression
Benjamin J. Heil, Jake Crawford, Casey S. Greene
PLOS Computational Biology  ·  27 Mar 2023  ·  doi:10.1371/journal.pcbi.1010984
Biomonitoring and precision health in deep space supported by artificial intelligence
Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-min Park, …, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes
Nature Machine Intelligence  ·  23 Mar 2023  ·  doi:10.1038/s42256-023-00617-5
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Steven M. Foltz, Casey S. Greene, Jaclyn N. Taroni
Communications Biology  ·  25 Feb 2023  ·  doi:10.1038/s42003-023-04588-6
Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia
Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Taylor Reiter, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan
mSystems  ·  23 Feb 2023  ·  doi:10.1128/msystems.00341-22
Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14
Alexandra J. Lee, Georgia Doing, Samuel L. Neff, Taylor Reiter, Deborah A. Hogan, Casey S. Greene
mSystems  ·  23 Feb 2023  ·  doi:10.1128/msystems.00342-22
Analysis of science journalism reveals gender and regional disparities in coverage
Natalie R. Davidson, Casey S. Greene
eLife Sciences Publications, Ltd  ·  09 Feb 2023  ·  doi:10.7554/eLife.84855.1
Analysis of science journalism reveals gender and regional disparities in coverage
Natalie R. Davidson, Casey S. Greene
eLife Sciences Publications, Ltd  ·  09 Feb 2023  ·  doi:10.7554/eLife.84855
A publishing infrastructure for AI-assisted academic authoring
Milton Pividori, Casey S. Greene
Cold Spring Harbor Laboratory  ·  23 Jan 2023  ·  doi:10.1101/2023.01.21.525030
The probability of edge existence due to node degree: a baseline for network-based predictions
Michael Zietz, Daniel S. Himmelstein, Kyle Kloster, Christopher Williams, Michael W. Nagle, Casey S. Greene
Cold Spring Harbor Laboratory  ·  06 Jan 2023  ·  doi:10.1101/2023.01.05.522939
The Field-Dependent Nature of PageRank Values in Citation Networks
Benjamin J. Heil, Casey S. Greene
Cold Spring Harbor Laboratory  ·  06 Jan 2023  ·  doi:10.1101/2023.01.05.522943
Supporting data for "Hetnet connectivity search provides rapid insights into how two biomedical entities are related"
Himmelstein S Daniel, Zietz Michael, Rubinetti Vincent, Kloster Kyle, Heil J Benjamin, …, Nicholson N David, Hao Yun, Sullivan D Blair, Nagle W Michael, Greene S Casey
GigaScience Database  ·  01 Jan 2023  ·  doi:10.5524/102389

2022

Hetnet connectivity search provides rapid insights into how biomedical entities are related
Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, …, David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene
GigaScience  ·  28 Dec 2022  ·  doi:10.1093/gigascience/giad047
Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors
Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene
Cold Spring Harbor Laboratory  ·  05 Dec 2022  ·  doi:10.1101/2022.12.04.519045
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts
David N. Nicholson, Daniel S. Himmelstein, Casey S. Greene
BioData Mining  ·  18 Oct 2022  ·  doi:10.1186/s13040-022-00311-z
wenda_gpu: fast domain adaptation for genomic data
Ariel A Hippen, Jake Crawford, Jacob R Gardner, Casey S Greene
Bioinformatics  ·  04 Oct 2022  ·  doi:10.1093/bioinformatics/btac663
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses
Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene
Genomics, Proteomics & Bioinformatics  ·  01 Oct 2022  ·  doi:10.1016/j.gpb.2022.09.011
Changing word meanings in biomedical literature reveal pandemics and new technologies
David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti, Casey S. Greene
Cold Spring Harbor Laboratory  ·  28 Jun 2022  ·  doi:10.1101/2022.06.27.497742
GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent J. Carey, Casey S. Greene, Levi Waldron, Sean Davis
Nature Communications  ·  27 Jun 2022  ·  doi:10.1038/s41467-022-31411-3
Widespread redundancy in -omics profiles of cancer mutation states
Jake Crawford, Brock C. Christensen, Maria Chikina, Casey S. Greene
Genome Biology  ·  27 Jun 2022  ·  doi:10.1186/s13059-022-02705-y
The Effects of Nonlinear Signal on Expression-Based Prediction Performance
Benjamin J. Heil, Jake Crawford, Casey S. Greene
Cold Spring Harbor Laboratory  ·  26 Jun 2022  ·  doi:10.1101/2022.06.22.497194
An efficient not-only-linear correlation coefficient based on machine learning
Milton Pividori, Marylyn D. Ritchie, Diego H. Milone, Casey S. Greene
Cold Spring Harbor Laboratory  ·  17 Jun 2022  ·  doi:10.1101/2022.06.15.496326
Compendium-wide analysis of P. aeruginosa core and accessory genes reveal more nuanced transcriptional patterns
Alexandra J. Lee, Georgia Doing, Samuel L. Neff, Taylor Reiter, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  15 Apr 2022  ·  doi:10.1101/2022.04.14.488429
wenda_gpu: fast domain adaptation for genomic data
Ariel A. Hippen, Jake Crawford, Jacob R. Gardner, Casey S. Greene
Cold Spring Harbor Laboratory  ·  11 Apr 2022  ·  doi:10.1101/2022.04.09.487671
Ten quick tips for deep learning in biology
Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, …, Alexandr A. Kalinin, Brandon Signal, Benjamin J. Lengerich, Timothy J. Triche, Simina M. Boca
PLOS Computational Biology  ·  24 Mar 2022  ·  doi:10.1371/journal.pcbi.1009803
Ten simple rules for large-scale data processing
Arkarachai Fungtammasan, Alexandra Lee, Jaclyn Taroni, Kurt Wheeler, Chen-Shan Chin, Sean Davis, Casey Greene
PLOS Computational Biology  ·  10 Feb 2022  ·  doi:10.1371/journal.pcbi.1009757
Examining linguistic shifts between preprints and publications
David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene
PLOS Biology  ·  01 Feb 2022  ·  doi:10.1371/journal.pbio.3001470
Computationally efficient assembly of a Pseudomonas aeruginosa gene expression compendium
Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan
Cold Spring Harbor Laboratory  ·  25 Jan 2022  ·  doi:10.1101/2022.01.24.477642
Computational audits combat disparities in recognition
Ariel A. Hippen, Natalie R. Davidson, Casey S. Greene
Nature Human Behaviour  ·  17 Jan 2022  ·  doi:10.1038/s41562-021-01279-2

2021

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

2020

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

2019

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

2018

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

2017

A Pilot Characterization of the Human Chronobiome
Carsten Skarke, Nicholas F. Lahens, Seth D. Rhoades, Amy Campbell, Kyle Bittinger, …, Frederic D. Bushman, Casey S. Greene, Gregory R. Grant, Aalim M. Weljie, Garret A. FitzGerald
Scientific Reports  ·  07 Dec 2017  ·  doi:10.1038/s41598-017-17362-6
ADAGE signature analysis: differential expression analysis with data-defined gene sets
Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
BMC Bioinformatics  ·  22 Nov 2017  ·  doi:10.1186/s12859-017-1905-4
Machine Learning Analysis IdentifiesDrosophila Grunge/Atrophinas an Important Learning and Memory Gene Required for Memory Retention and Social Learning
Balint Z Kacsoh, Casey S Greene, Giovanni Bosco
G3 Genes|Genomes|Genetics  ·  01 Nov 2017  ·  doi:10.1534/g3.117.300172
Sci-Hub provides access to nearly all scholarly literature
Daniel S Himmelstein, Ariel R Romero, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
PeerJ  ·  12 Oct 2017  ·  doi:10.7287/peerj.preprints.3100v2
Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations
Genevieve L. Stein-O’Brien, Raman Arora, Aedin C. Culhane, Alexander V. Favorov, Lana X. Garmire, …, Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig
Cold Spring Harbor Laboratory  ·  02 Oct 2017  ·  doi:10.1101/196915
Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders
Gregory P. Way, Casey S. Greene
Cold Spring Harbor Laboratory  ·  11 Aug 2017  ·  doi:10.1101/174474
Implicating candidate genes at GWAS signals by leveraging topologically associating domains
Gregory P Way, Daniel W Youngstrom, Kurt D Hankenson, Casey S Greene, Struan FA Grant
European Journal of Human Genetics  ·  09 Aug 2017  ·  doi:10.1038/ejhg.2017.108
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules
Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Casey S. Greene, Jason H. Moore, Andrew J. Saykin, Li Shen
Bioinformatics  ·  20 Jul 2017  ·  doi:10.1093/bioinformatics/btx344
Sci-Hub provides access to nearly all scholarly literature
Daniel S Himmelstein, Ariel R Romero, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
PeerJ  ·  20 Jul 2017  ·  doi:10.7287/peerj.preprints.3100v1
Functional Network Community Detection Can Disaggregate and Filter Multiple Underlying Pathways in Enrichment Analyses
Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene
Cold Spring Harbor Laboratory  ·  20 Jul 2017  ·  doi:10.1101/166207
Privacy-preserving generative deep neural networks support clinical data sharing
Brett K. Beaulieu-Jones, Zhiwei Steven Wu, Chris Williams, Ran Lee, Sanjeev P. Bhavnani, James Brian Byrd, Casey S. Greene
Cold Spring Harbor Laboratory  ·  05 Jul 2017  ·  doi:10.1101/159756
Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks
Jie Tan, Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady, Barret Perchuk, Michael T. Laub, Deborah A. Hogan, Casey S. Greene
Cell Systems  ·  01 Jul 2017  ·  doi:10.1016/j.cels.2017.06.003
Machine learning analysis identifies Drosophila Grunge/Atrophin as an important learning and memory gene required for memory retention and social learning
Balint Z Kacsoh, Casey S. Greene, Giovanni Bosco
Cold Spring Harbor Laboratory  ·  29 Jun 2017  ·  doi:10.1101/157610
ADAGE signature analysis: differential expression analysis with data-defined gene sets
Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  27 Jun 2017  ·  doi:10.1101/156620
Data-Sharing Models
New England Journal of Medicine  ·  08 Jun 2017  ·  doi:10.1056/NEJMc1705477
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene
Cold Spring Harbor Laboratory  ·  08 Jun 2017  ·  doi:10.1101/147645
Opportunities and obstacles for deep learning in biology and medicine
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, …, Simina M. Boca, S. Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S. Greene
Cold Spring Harbor Laboratory  ·  28 May 2017  ·  doi:10.1101/142760
Celebrating parasites
Casey S Greene, Lana X Garmire, Jack A Gilbert, Marylyn D Ritchie, Lawrence E Hunter
Nature Genetics  ·  01 Apr 2017  ·  doi:10.1038/ng.3830
A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis
Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood, Romy B. Christmann, …, Christopher P. Denton, Monique E. Hinchcliff, Patricia A. Pioli, J. Matthew Mahoney, Michael L. Whitfield
Genome Medicine  ·  23 Mar 2017  ·  doi:10.1186/s13073-017-0417-1
Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously
Jaclyn N Taroni, Casey S Greene
Cold Spring Harbor Laboratory  ·  20 Mar 2017  ·  doi:10.1101/118349
Reproducibility of computational workflows is automated using continuous analysis
Brett K Beaulieu-Jones, Casey S Greene
Nature Biotechnology  ·  13 Mar 2017  ·  doi:10.1038/nbt.3780
Tell me your neighbors, and I will tell you what you are
Casey S. Greene
Science Translational Medicine  ·  08 Feb 2017  ·  doi:10.1126/scitranslmed.aam6058
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene
BMC Genomics  ·  06 Feb 2017  ·  doi:10.1186/s12864-017-3519-7
"Cross-platform normalization enables analysis of microarray and RNA-seq data simultaneously" - Fileset
Jaclyn Taroni, Casey Greene
figshare  ·  01 Jan 2017  ·  doi:10.6084/m9.figshare.5035997.v1
"Cross-platform normalization enables analysis of microarray and RNA-seq data simultaneously" - Fileset
Jaclyn Taroni, Casey Greene
figshare  ·  01 Jan 2017  ·  doi:10.6084/m9.figshare.5035997.v2
"Cross-platform normalization enables analysis of microarray and RNA-seq data simultaneously" - Fileset
Jaclyn Taroni, Casey Greene
figshare  ·  01 Jan 2017  ·  doi:10.6084/M9.FIGSHARE.5035997

2016

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

2015

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

2014

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

2013

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

2012

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

2011

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

2010

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

2009

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

2008

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

2006

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

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

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