Research

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

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

2023

Molecular subtypes of high grade serous ovarian cancer across racial groups and gene expression platforms

Natalie R. Davidson, Mollie E. Barnard, Ariel A. Hippen, Amy Campbell, Courtney Johnson, ..., Lauren C. Peres, Jeffrey R. Marks, Joellen M. Schildkraut, Casey S. Greene, Jennifer A. Doherty

Cold Spring Harbor Laboratory   ·   04 Nov 2023   ·   doi:10.1101/2023.11.01.565179

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors

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

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

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 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

SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics

Halie M. Rando, Casey S. Greene, Michael P. Robson, Simina M. Boca, Nils Wellhausen, ..., Yusha Sun, Daniel S. Himmelstein, Jeremy P. Kamil, Jesse G. Meyer, Ariel I. Mundo

Manubot   ·   30 Jul 2023   ·   url:https://greenelab.github.io/covid19-review/

Preprint

Manubot

COVID19

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

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

Preprint

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

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

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

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

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

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

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

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

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

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

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

2022

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

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

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

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

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

Joshua A. Shapiro, Krutika S. Gaonkar, Candace L. Savonen, Stephanie J. Spielman, Chante J. Bethell, ..., Sabine Mueller, Adam C. Resnick, Casey S. Greene, Jo Lynne Rokita, Jaclyn N. Taroni

Cold Spring Harbor Laboratory   ·   16 Sep 2022   ·   doi:10.1101/2022.09.13.507832

GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases

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

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

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

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

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

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

Preprint

bioRxiv natural language processing machine learning

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

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

2021

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

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

Anthony R. Kerlavage, Anne C. Kirchhoff, Jaime M. Guidry Auvil, Norman E. Sharpless, Kara L. Davis, ..., Jack DiGiovanna, Adam C. Resnick, Eve R. Shalley, Sorena Nadaf, Warren A. Kibbe

JCO Clinical Cancer Informatics   ·   01 Dec 2021   ·   doi:10.1200/CCI.21.00040

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure

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

Binglan Li, Yogasudha Veturi, Anastasia Lucas, Yuki Bradford, Shefali S. Verma, ..., Yuan Luo, Milton Pividori, Hae Kyung Im, Casey S. Greene, Marylyn D. Ritchie

Cold Spring Harbor Laboratory   ·   26 Oct 2021   ·   10.1101/2021.10.21.21265225

A field guide to cultivating computational biology

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

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

Madison Cooley, Casey S. Greene, Davis Issac, Milton Pividori, Blair D. Sullivan

arXiv   ·   08 Sep 2021   ·   arxiv:2106.00657

Analysis of scientific society honors reveals disparities

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

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

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

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

Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, ..., Michael I. Love, Matthew E. Ritchie, Guo-Cheng Yuan, Aedin C. Culhane, Elana Fertig

Genome Biology   ·   05 Aug 2021   ·   doi:10.1186/s13059-021-02433-9

Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment

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

Natalie R. Davidson, Casey S. Greene

Cold Spring Harbor Laboratory   ·   22 Jun 2021   ·   doi:10.1101/2021.06.21.449261

Expanding and Remixing the Metadata Landscape

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

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

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

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

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

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

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

Manubot

Manuscript Source

Website

open science collaboration

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Qiwen Hu, Casey S Greene, Elizabeth A Heller

Nucleic Acids Research   ·   22 Apr 2020   ·   doi:10.1093/nar/gkaa248

Preprint

Source

genomics machine learning

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

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

Jake Crawford, Casey S. Greene

Cold Spring Harbor Laboratory   ·   21 Jan 2020   ·   doi:10.1101/2020.01.17.910703

Source

machine learning genomics

2019

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

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

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

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

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

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

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

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

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

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

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

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

Deanne M. Taylor, Bruce J. Aronow, Kai Tan, Kathrin Bernt, Nathan Salomonis, ..., Yi Xing, Sek Won Kong, Carsten G. Bönnemann, Kenneth D. Mandl, Peter S. White

Developmental Cell   ·   01 Apr 2019   ·   doi:10.1016/j.devcel.2019.03.001

Technologies to watch in 2019

Marissa Fessenden

Nature   ·   01 Jan 2019   ·   doi:10.1038/d41586-019-00218-6

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

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

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

YoSon Park, Casey S Greene

GigaScience   ·   01 Nov 2018   ·   doi:10.1093/gigascience/giy129

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

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

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*

Gary E. Weissman, Rebecca A. Hubbard, Lyle H. Ungar, Michael O. Harhay, Casey S. Greene, Blanca E. Himes, Scott D. Halpern

Critical Care Medicine   ·   01 Jul 2018   ·   doi:10.1097/CCM.0000000000003148

Metabolic pathways and immunometabolism in rare kidney diseases

Peter C Grayson, Sean Eddy, Jaclyn N Taroni, Yaíma L Lightfoot, Laura Mariani, ..., Brad Godfrey, Clemens D Cohen, Jeffrey Krischer, Matthias Kretzler, Peter A Merkel

Annals of the Rheumatic Diseases   ·   03 May 2018   ·   doi:10.1136/annrheumdis-2017-212935

A Multimodal Strategy Used by a Large c-di-GMP Network

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

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

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

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

Source

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

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.

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

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

Preprint

R package

Source

Updated app

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

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

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

Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Casey S. Greene, Jason H. Moore, Andrew J. Saykin, Li Shen

Bioinformatics   ·   20 Jul 2017   ·   doi:10.1093/bioinformatics/btx344

Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes

Jennifer Anne Doherty, Lauren Cole Peres, Chen Wang, Gregory P. Way, Casey S. Greene, Joellen M. Schildkraut

Current Epidemiology Reports   ·   10 Jul 2017   ·   doi:10.1007/s40471-017-0115-y

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks

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

Data-Sharing Models

[no author info]

New England Journal of Medicine   ·   08 Jun 2017   ·   doi:10.1056/NEJMc1705477

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

Preprint

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

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

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

2016

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

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

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

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

Casey S. Greene

Science Translational Medicine   ·   09 Nov 2016   ·   doi:10.1126/scitranslmed.aal0067

Zhou et al.

A stromal focus reveals tumor immune signatures

Casey S. Greene

Science Translational Medicine   ·   28 Sep 2016   ·   doi:10.1126/scitranslmed.aai8224

Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations

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

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

Gut check

Casey S. Greene

Science Translational Medicine   ·   17 Aug 2016   ·   doi:10.1126/scitranslmed.aah5494

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

Preprint

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

Casey S. Greene

Science Translational Medicine   ·   25 May 2016   ·   doi:10.1126/scitranslmed.aaf9196

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

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

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

Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene

mSystems   ·   23 Feb 2016   ·   doi:10.1128/mSystems.00025-15

Preprint

Source

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

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

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

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

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

Processed networks

Raw networks

App

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

App

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

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

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

Highlighted by Nature Reviews Genetics

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