Casey S. Greene

Also affiliated with Alex's Lemonade Stand Foundation, University of Colorado Anschutz Medical Campus

Biochemistry, Genetics and Molecular BiologyMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

16.0Author DataRank

Indexed papers

109in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 109 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

PeerJ(2016)10.7717/peerj.1621

Top 6%

3.8DataRank

Top 6%105 citations

Jie Tan, Casey S. Greene, Jeffrey Thompson

Papers

Driven by 424 papers — median percentile 0. Top paper: “Opportunities and obstacles for deep learning in biology and medicine”.

Opportunities and obstacles for deep learning in biology and medicine

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/142760

N/A

11.2DataRank · unranked

310 citations

Daniel S. Himmelstein, Brett K. Beaulieu‐Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way +31 more

Semi-supervised learning of the electronic health record for phenotype stratification

Journal of Biomedical Informatics(2016)10.1016/j.jbi.2016.10.007

N/A

8.5DataRank · unranked

198 citations

Casey S. Greene, Brett K. Beaulieu‐Jones

Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery

Briefings in Bioinformatics(2015)10.1093/bib/bbv087

N/A

7.3DataRank · unranked

166 citations

Tasnia Tahsin, Britton C. Goodale, Anna C. Greene, Casey S. Greene, Graciela Gonzalez‐Hernandez +1 more

Reproducibility of computational workflows is automated using continuous analysis

Nature Biotechnology(2017)10.1038/nbt.3780

N/A

7.0DataRank · unranked

161 citations

Casey S. Greene, Brett K. Beaulieu‐Jones

Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing

Nature Human Behaviour(2020)10.1038/s41562-020-00944-2

N/A

6.7DataRank · unranked

129 citations

Han Altae-Tran, James Briggs, Xin Jin, Glen McGee, Andy Shi +33 more

Metabolic pathways and immunometabolism in rare kidney diseases

Annals of the Rheumatic Diseases(2018)10.1136/annrheumdis-2017-212935

N/A

5.5DataRank · unranked

186 citations

Sean Eddy, Jaclyn N. Taroni, Yaíma L. Lightfoot, Laura Mariani, Hemang Parikh +9 more

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

Cell Reports(2018)10.1016/j.celrep.2018.03.046

N/A

5.5DataRank · unranked

186 citations

Francisco Sanchez-Vega, Konnor C. La, Joshua Armenia, Walid K. Chatila, Augustin Luna +869 more

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

Nucleic Acids Research(2012)10.1093/nar/gks458

N/A

5.5DataRank · unranked

137 citations

Christopher Y. Park, Casey S. Greene, Lars A. Bongo, Yuanfang Guan, Olga G. Troyanskaya +2 more

Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions

BioData Mining(2009)10.1186/1756-0381-2-5

N/A

5.0DataRank · unranked

149 citations

Nadia M. Penrod, Jeff Kiralis, Jason H. Moore, Casey S. Greene

Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/174474

N/A

5.0DataRank · unranked

103 citations

Casey S. Greene, Gregory P. Way

Immune landscapes associated with different glioblastoma molecular subtypes

Acta Neuropathologica Communications(2019)10.1186/s40478-019-0803-6

N/A

4.8DataRank · unranked

227 citations

Timothy M. Lynch, Yingtao Bi, Carolina Cocito, Gregory P. Way, Sharmistha Pal +13 more

MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease

Cell Systems(2019)10.1016/j.cels.2019.04.003

N/A

4.7DataRank · unranked

138 citations

Peter C. Grayson, Qiwen Hu, Sean Eddy, Matthias Kretzler, Peter A. Merkel +2 more

Responsible, practical genomic data sharing that accelerates research

Nature Reviews Genetics(2020)10.1038/s41576-020-0257-5

N/A

4.7DataRank · unranked

147 citations

Anna C. Greene, Deepashree Venkatesh Prasad, Xiaoqian Jiang, Casey S. Greene, James Brian Byrd

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

Bioinformatics(2010)10.1093/bioinformatics/btq009

N/A

4.7DataRank · unranked

84 citations

Nicholas A Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, Brent T. Harris +2 more

Open collaborative writing with Manubot

PLOS Computational Biology(2019)10.1371/journal.pcbi.1007128

N/A

4.2DataRank · unranked

83 citations

Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene +2 more

Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay*

Critical Care Medicine(2018)10.1097/ccm.0000000000003148

N/A

4.2DataRank · unranked

91 citations

Rebecca A. Hubbard, Lyle H. Ungar, Michael O. Harhay, Casey S. Greene, Blanca E. Himes +3 more

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual

Genome Biology(2021)10.1186/s13059-020-02207-9

N/A

4.2DataRank · unranked

149 citations

Yadav Wagley, James A. Pippin, Ahmed Elhakeem, Gregory P. Way, Matthew C. Pahl +29 more

Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes

Current Epidemiology Reports(2017)10.1007/s40471-017-0115-y

N/A

4.1DataRank · unranked

107 citations

Chen Wang, Gregory P. Way, Casey S. Greene, Joellen M. Schildkraut, Lauren C. Peres +1 more

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

PeerJ(2016)10.7717/peerj.1621

Top 6%

3.8DataRank

Top 6%105 citations

Jie Tan, Casey S. Greene, Jeffrey Thompson

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

mSystems(2021)10.1128/msystems.00122-21

N/A

3.0DataRank · unranked

123 citations

Diane N. Rafizadeh, Casey S. Greene, Bharath Ramsundar

Sci-Hub provides access to nearly all scholarly literature

Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt)(2017)10.7287/peerj.preprints.3100v1

Top 8%

2.9DataRank

Top 8%39 citations

Ariel Rodriguez Romero, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S. Greene, Daniel S. Himmelstein

Ant Colony Optimization for Genome-Wide Genetic Analysis

Lecture notes in computer science(2008)10.1007/978-3-540-87527-7_4

N/A

2.7DataRank · unranked

54 citations

Bill C. White, Jason H. Moore, Casey S. Greene

Accelerating epistasis analysis in human genetics with consumer graphics hardware

BMC Research Notes(2009)10.1186/1756-0500-2-149

N/A

2.6DataRank · unranked

46 citations

Casey S. Greene, Fabio Cancare, Jason H. Moore, Nicholas A. Sinnott‐Armstrong, Nicholas A Sinnott-Armstrong

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

Cell Systems(2017)10.1016/j.cels.2017.06.003

N/A

2.6DataRank · unranked

102 citations

Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kyle C. Cady, Barret Perchuk +5 more

Celebrating parasites

Nature Genetics(2017)10.1038/ng.3830

N/A

2.4DataRank · unranked

40 citations

Lana X. Garmire, Jack A. Gilbert, Marylyn D. Ritchie, Lawrence E. Hunter, Casey S. Greene

Machine learning in rare disease

Nature Methods(2023)10.1038/s41592-023-01886-z

N/A

2.4DataRank · unranked

113 citations

Jaclyn N. Taroni, Robert J. Allaway, Deepashree Venkatesh Prasad, Gustavo Stolovitzky, Casey S. Greene +1 more

ENABLING PERSONAL GENOMICS WITH AN EXPLICIT TEST OF EPISTASIS

Biocomputing 2010(2009)10.1142/9789814295291_0035

N/A

2.0DataRank · unranked

51 citations

Daniel S. Himmelstein, HEATHER H. NELSON, KARL T. KELSEY, SCOTT M. WILLIAMS, ANGELINE S. ANDREW +3 more

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

PLoS Computational Biology(2013)10.1371/journal.pcbi.1002957

N/A

1.9DataRank · unranked

70 citations

Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars A. Bongo +4 more

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

Journal of Bacteriology(2018)10.1128/jb.00703-17

N/A

1.8DataRank · unranked

67 citations

Alan J. Collins, Georgia Doing, Jaclyn N. Taroni, Timothy J. Gauvin, Casey S. Greene +3 more

Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE)

Clinical Cancer Research(2020)10.1158/1078-0432.ccr-20-0103

N/A

1.8DataRank · unranked

76 citations

Joshy George, Chen Wang, Timothy Budden, Tuan Zea Tan, Derek S. Chiu +134 more

Bayesian deep learning for single-cell analysis

Nature Methods(2018)10.1038/s41592-018-0230-9

N/A

1.5DataRank · unranked

29 citations

Casey S. Greene, Gregory P. Way

Integration of 168,000 samples reveals global patterns of the human gut microbiome

Cell(2025)10.1016/j.cell.2024.12.017

Top 14%

1.5DataRank

Top 14%107 citations

Samantha P. Graham, Vincent Rubinetti, Mansooreh Ahmadian, Parker Hicks, Ashwin Chetty +10 more

Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

GigaScience(2021)10.1093/gigascience/giab062

N/A

1.5DataRank · unranked

44 citations

Ariel A. Hippen Anderson, Peter F. Hickey, Kristofer C. Berrett, Jason Gertz, Jennifer Anne Doherty +3 more

Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.1917576117

N/A

1.4DataRank · unranked

69 citations

John H. Hammond, Fangfang Zhong, Xiaolei Chen, Caitlin H. Kowalski, Alexandra J. Lee +6 more

Evolving hard problems: Generating human genetics datasets with a complex etiology

BioData Mining(2011)10.1186/1756-0381-4-21

N/A

1.4DataRank · unranked

27 citations

Casey S. Greene, Jason H. Moore, Daniel S. Himmelstein

Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes

G3 Genes|Genomes|Genetics(2016)10.1534/g3.116.033514

Top 15%

1.4DataRank

Top 15%50 citations

James Rudd, Chen Wang, Habib Hamidi, Brooke L. Fridley, Gottfried E. Konecny +4 more

Building an international consortium for tracking coronavirus health status

Nature Medicine(2020)10.1038/s41591-020-0929-x

N/A

1.4DataRank · unranked

33 citations

Feng Zhang, Xihong Lin, Gary King, Ophir Shalem, Smadar Shilo +54 more

Biomonitoring and precision health in deep space supported by artificial intelligence

Nature Machine Intelligence(2023)10.1038/s42256-023-00617-5

N/A

1.3DataRank · unranked

57 citations

Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung Min Park, Graham Mackintosh +51 more

A field guide to cultivating computational biology

PLOS Biology(2021)10.1371/journal.pbio.3001419

N/A

1.3DataRank · unranked

22 citations

Casey S. Greene, Piero Carninci, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley +11 more

Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer’s disease: a study of ADNI cohorts

BioData Mining(2016)10.1186/s13040-016-0082-8

N/A

1.3DataRank · unranked

35 citations

Ailin Song, Jingwen Yan, Sungeun Kim, Aaron K. Wong, Andrew J. Saykin +3 more

OpenPBTA: The Open Pediatric Brain Tumor Atlas

Cell Genomics(2023)10.1016/j.xgen.2023.100340

Top 16%

1.3DataRank

Top 16%62 citations

Krutika S. Gaonkar, Stephanie J. Spielman, Candace L. Savonen, Chanté J. Bethell, Run Jin +61 more

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

Genome Biology(2023)10.1186/s13059-023-03077-7

N/A

1.3DataRank · unranked

44 citations

Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer Anne Doherty +3 more

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Cell(2018)10.1016/j.cell.2018.03.035

N/A

1.2DataRank · unranked

3322 citations

Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, Konnor C. La +891 more

Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease

Lecture Notes in Computer Science(2009)10.1007/978-3-642-01184-9_9

N/A

1.2DataRank · unranked

23 citations

Jason M. Gilmore, Jeff Kiralis, Peter C. Andrews, Jason H. Moore, Casey S. Greene

Analysis of ISCB honorees and keynotes reveals disparities

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.14.927251

N/A

1.2DataRank · unranked

12 citations

Daniel S. Himmelstein, Ariel A. Hippen Anderson, Matthew R. Gazzara, Casey S. Greene, Trang T. Le

Opportunities and obstacles for deep learning in biology and medicine

Journal of The Royal Society Interface(2018)10.1098/rsif.2017.0387

N/A

1.2DataRank · unranked

2203 citations

Daniel S. Himmelstein, Brett K. Beaulieu‐Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way +31 more

Biological research and self-driving labs in deep space supported by artificial intelligence

Nature Machine Intelligence(2023)10.1038/s42256-023-00618-4

N/A

1.1DataRank · unranked

48 citations

Ryan T. Scott, Jason H. Yang, Héctor García Martín, Daniel C. Berrios, Jaden J. A. Hastings +54 more

Understanding multicellular function and disease with human tissue-specific networks

Nature Genetics(2015)10.1038/ng.3259

N/A

1.0DataRank · unranked

925 citations

Krishnan, Arjun, Aaron K. Wong, Emanuela Ricciotti, Daniel S. Himmelstein, Ran Zhang +12 more

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

European Journal of Human Genetics(2017)10.1038/ejhg.2017.108

N/A

1.0DataRank · unranked

24 citations

Daniel W. Youngstrom, Kurt D. Hankenson, Casey S. Greene, Struan F.A. Grant, Gregory P. Way

ADAGE analysis of publicly available gene expression data collections illuminates Pseudomonas aeruginosa-host interactions

bioRxiv (Cold Spring Harbor Laboratory)(2015)10.1101/030650

N/A

0.969DataRank · unranked

10 citations

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

Correcting for experiment-specific variability in expression compendia can remove underlying signals

GigaScience(2020)10.1093/gigascience/giaa117

N/A

0.962DataRank · unranked

25 citations

YoSon Park, Georgia Doing, Deborah A. Hogan, Casey S. Greene, Alexandra J. Lee

Transparency and reproducibility in artificial intelligence

Nature(2020)10.1038/s41586-020-2766-y

N/A

0.929DataRank · unranked

487 citations

George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, Massive Analysis Quality Control (MAQC) Society Board of Directors, Matthias Fischer +26 more

Expanding and Remixing the Metadata Landscape

Trends in Cancer(2021)10.1016/j.trecan.2020.10.011

N/A

0.899DataRank · unranked

9 citations

Casey S. Greene, Ariel A. Hippen Anderson

Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States

medRxiv(2020)10.1101/2020.06.09.20126813

N/A

0.869DataRank · unranked

10 citations

Han Altae-Tran, James Briggs, Xin Jin, Glen McGee, Andy Shi +33 more

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

Nature Communications(2015)10.1038/ncomms9019

N/A

0.860DataRank · unranked

309 citations

Younghun Han, George F. Mells, Yafang Li, Gideon M. Hirschfield, Casey S. Greene +518 more

Failure to Replicate a Genetic Association May Provide Important Clues About Genetic Architecture

PLoS ONE(2009)10.1371/journal.pone.0005639

N/A

0.844DataRank · unranked

276 citations

Nadia M. Penrod, SCOTT M. WILLIAMS, Jason H. Moore, Casey S. Greene

An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming

Lecture notes in computer science(2007)10.1007/978-3-540-75286-8_4

N/A

0.842DataRank · unranked

33 citations

Bill C. White, Jason H. Moore, Casey S. Greene

Constructing knowledge graphs and their biomedical applications

Computational and Structural Biotechnology Journal(2020)10.1016/j.csbj.2020.05.017

N/A

0.838DataRank · unranked

266 citations

Casey S. Greene, David N. Nicholson

Enter the Matrix: Factorization Uncovers Knowledge from Omics

Trends in Genetics(2018)10.1016/j.tig.2018.07.003

N/A

0.837DataRank · unranked

264 citations

Raman Arora, Alexander V. Favorov, Lana X. Garmire, Casey S. Greene, Loyal A. Goff +7 more

Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units

Proceedings of the 12th annual conference on Genetic and evolutionary computation(2010)10.1145/1830483.1830523

N/A

0.824DataRank · unranked

12 citations

Casey S. Greene, Jason H. Moore, Nicholas A. Sinnott‐Armstrong, Nicholas A Sinnott-Armstrong

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

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.04.519045

N/A

0.815DataRank · unranked

9 citations

Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer Anne Doherty +3 more

Reproducibility standards for machine learning in the life sciences

Nature Methods(2021)10.1038/s41592-021-01256-7

N/A

0.808DataRank · unranked

218 citations

Michael M. Hoffman, Jeffrey R. Marks, Su-In Lee, Casey S. Greene, Stephanie C. Hicks +1 more

Characterizing Long COVID: Deep Phenotype of a Complex Condition

eBioMedicine(2021)10.1016/j.ebiom.2021.103722

N/A

0.802DataRank · unranked

209 citations

Nicole A. Vasilevsky, Leigh C Carmody, Diane N. Rafizadeh, Alfred J Anzalone, Marc D. Basson +53 more

The probability of edge existence due to node degree: a baseline for network-based predictions

GigaScience(2024)10.1093/gigascience/giae001

N/A

0.792DataRank · unranked

19 citations

Daniel S. Himmelstein, Kyle Kloster, Christopher K. I. Williams, Michael W. Nagle, Casey S. Greene +1 more

Publisher Correction: Building an international consortium for tracking coronavirus health status

Nature Medicine(2020)10.1038/s41591-020-0983-4

N/A

0.788DataRank · unranked

1 citations

Feng Zhang, Xihong Lin, Gary King, Ophir Shalem, Smadar Shilo +54 more

New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

G3 Genes|Genomes|Genetics(2019)10.1534/g3.118.200867

N/A

0.772DataRank · unranked

26 citations

Stephen Barton, Yuxiang Jiang, Naihui Zhou, Sean D. Mooney, Iddo Friedberg +5 more

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

Nature Methods(2015)10.1038/nmeth.3249

N/A

0.769DataRank · unranked

167 citations

Aaron K. Wong, Krishnan, Arjun, Sietse Aukema, Alicja Tadych, Ran Zhang +10 more

Sci-Hub provides access to nearly all scholarly literature

Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt)(2017)10.7287/peerj.preprints.3100v2

Top 27%

0.756DataRank

Top 27%8 citations

Ariel Rodriguez Romero, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S. Greene, Daniel S. Himmelstein

Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms

PLoS Computational Biology(2015)10.1371/journal.pcbi.1004005

N/A

0.755DataRank · unranked

152 citations

Jaclyn N. Taroni, Viktor Martyanov, Casey S. Greene, Patricia A. Pioli, Michael L. Whitfield +3 more

Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1

Genes(2020)10.3390/genes11020226

N/A

0.751DataRank · unranked

21 citations

Robert J. Allaway, Jaclyn N. Taroni, Aaron Baker, Xiaochun Zhang, Chang In Moon +7 more

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

BioData Mining(2018)10.1186/s13040-018-0175-7

N/A

0.726DataRank · unranked

15 citations

Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan, Casey S. Greene +1 more

Prognostic gene expression signature for high-grade serous ovarian cancer

Annals of Oncology(2020)10.1016/j.annonc.2020.05.019

N/A

0.718DataRank · unranked

119 citations

S. Chen, Blake Gilks, C. Wang, S.C.Y. Leung, V. Chow +387 more

Application of Traditional Vaccine Development Strategies to SARS-CoV-2

mSystems(2023)10.1128/msystems.00927-22

N/A

0.718DataRank · unranked

22 citations

Alexandra J. Lee, Elizabeth Sell, Likhitha Kolla, Anthony Gitter, Casey S. Greene +32 more

The Coming of Age of Nucleic Acid Vaccines during COVID-19

mSystems(2023)10.1128/msystems.00928-22

N/A

0.709DataRank · unranked

22 citations

Ronan Lordan, Likhitha Kolla, Elizabeth Sell, Alexandra J. Lee, Nils Wellhausen +46 more

SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses

Genomics, Proteomics & Bioinformatics(2022)10.1016/j.gpb.2022.09.011

N/A

0.705DataRank · unranked

9 citations

Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing +4 more

ADAGE signature analysis: differential expression analysis with data-defined gene sets

BMC Bioinformatics(2017)10.1186/s12859-017-1905-4

N/A

0.700DataRank · unranked

24 citations

Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene +1 more

Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations

Current Genetic Medicine Reports(2016)10.1007/s40142-016-0102-5

N/A

0.681DataRank · unranked

9 citations

Jaclyn N. Taroni, Casey S. Greene, Krishnan, Arjun

Privacy-preserving generative deep neural networks support clinical data sharing

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/159756

N/A

0.675DataRank · unranked

89 citations

Zhiwei Steven Wu, Chris Williams, Ran Lee, Sanjeev P. Bhavnani, James Brian Byrd +2 more

A Pilot Characterization of the Human Chronobiome

Scientific Reports(2017)10.1038/s41598-017-17362-6

N/A

0.666DataRank · unranked

84 citations

Nicholas F. Lahens, Seth D. Rhoades, Amy Campbell, Kyle Bittinger, Aubrey Bailey +12 more

Building an International Consortium for Tracking Coronavirus Health Status

medRxiv(2020)10.1101/2020.04.02.20051284

N/A

0.661DataRank · unranked

13 citations

Feng Zhang, Xihong Lin, Gary King, Ophir Shalem, Smadar Shilo +52 more

Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders

Biocomputing 2018(2017)10.1142/9789813235533_0008

N/A

0.652DataRank · unranked

76 citations

Casey S. Greene, Gregory P. Way

A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC

Nature Cancer(2022)10.1038/s43018-022-00450-6

N/A

0.648DataRank · unranked

74 citations

Michael W. Knitz, Junxiao Hu, Eric T. Clambey, Jennifer Backus, Andrew Dumit +29 more

Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

Cancer Research(2021)10.1158/0008-5472.can-20-3892

N/A

0.606DataRank · unranked

56 citations

Miles Piper, Andrew Goodspeed, Shiv Bhuvane, Jason S. Williams, Shilpa Bhatia +32 more

UNSUPERVISED FEATURE CONSTRUCTION AND KNOWLEDGE EXTRACTION FROM GENOME-WIDE ASSAYS OF BREAST CANCER WITH DENOISING AUTOENCODERS

Biocomputing 2015(2014)10.1142/9789814644730_0014

N/A

0.593DataRank · unranked

51 citations

MATTHEW UNG, Chao Cheng, Casey S. Greene, Jie Tan

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Communications Biology(2023)10.1038/s42003-023-04588-6

N/A

0.593DataRank · unranked

51 citations

Casey S. Greene, Jaclyn N. Taroni, Steven M. Foltz

Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine

The American Journal of Human Genetics(2024)10.1016/j.ajhg.2023.12.001

N/A

0.571DataRank · unranked

44 citations

Jonathan A. Shortt, Emily R. Roberts, Joe A. Lesny, Elizabeth Kudron, Meng Lin +49 more

Ten quick tips for deep learning in biology

PLOS Computational Biology(2022)10.1371/journal.pcbi.1009803

N/A

0.550DataRank · unranked

38 citations

Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus +16 more

Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality

Cell Reports(2021)10.1016/j.celrep.2021.108917

N/A

0.538DataRank · unranked

35 citations

Michael V. Gonzalez, Krutika S. Gaonkar, Komal S. Rathi, Patricia Young, Sherjeel Arif +19 more

Specific histone modifications associate with alternative exon selection during mammalian development

Nucleic Acids Research(2020)10.1093/nar/gkaa248

N/A

0.529DataRank · unranked

33 citations

Casey S. Greene, Elizabeth A. Heller, Qiwen Hu

Ability of epistatic interactions of cytokine single‐nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patients

Arthritis Care & Research(2008)10.1002/art.23836

N/A

0.529DataRank · unranked

33 citations

Francesca Cappiello, Jason H. Moore, Morena Barili, Casey S. Greene, Raffaella Scorza +2 more

Integration of 168,000 samples reveals global patterns of the human gut microbiome

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.11.560955

Top 37%

0.526DataRank

Top 37%11 citations

Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis +2 more

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

Nature Communications(2022)10.1038/s41467-022-31411-3

N/A

0.523DataRank · unranked

14 citations

Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni +5 more

A New Tableau Representation for Supersymmetric Schur Functions

Journal of Algebra(1994)10.1006/jabr.1994.1361

N/A

0.520DataRank · unranked

31 citations

I. P. Goulden, Casey S. Greene, I. Goulden

A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma

BMC Genomics(2017)10.1186/s12864-017-3519-7

N/A

0.510DataRank · unranked

29 citations

Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Casey S. Greene, Yolanda Sánchez +1 more

Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules

Bioinformatics(2017)10.1093/bioinformatics/btx344

N/A

0.489DataRank · unranked

25 citations

Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher +6 more

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

mSystems(2021)10.1128/msystems.00095-21

N/A

0.489DataRank · unranked

25 citations

Adam L. MacLean, Alexandra J. Lee, Bharath Ramsundar, Vikas Bansal, Michael P. Robson +24 more

Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms

Nature Communications(2023)10.1038/s41467-023-41057-4

N/A

0.483DataRank · unranked

24 citations

Sumei Lu, Binglan Li, Chun Su, Matthew E. Johnson, Wei‐Qi Wei +12 more

Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.06.371963

N/A

0.479DataRank · unranked

6 citations

Ariel A. Hippen Anderson, Peter F. Hickey, Kristofer C. Berrett, Jason Gertz, Jennifer Anne Doherty +3 more

Missing cell types in single-cell references impact deconvolution of bulk data but are detectable

Genome Biology(2025)10.1186/s13059-025-03506-9

N/A

0.479DataRank · unranked

16 citations

Natalie R. Davidson, Laurie Grieshober, Weishan Li, Stephanie C. Hicks, Jennifer Anne Doherty +2 more

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.03.433798

N/A

0.478DataRank · unranked

6 citations

Matías Marín Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty +4 more

Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/573782

N/A

0.476DataRank · unranked

9 citations

Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene, Gregory P. Way

Characterizing Long COVID: Deep Phenotype of a Complex Condition

medRxiv(2021)10.1101/2021.06.23.21259416

N/A

0.470DataRank · unranked

22 citations

Madeline A Rock, Nicole A. Vasilevsky, Leigh C Carmody, Diane N. Rafizadeh, Alfred J Anzalone +53 more

Sensible Initialization of a Computational Evolution System Using Expert Knowledge for Epistasis Analysis in Human Genetics

Evolutionary Learning and Optimization(2010)10.1007/978-3-642-12834-9_10

N/A

0.464DataRank · unranked

10 citations

Casey S. Greene, Douglas P. Hill, Jason H. Moore, Douglas Hill, Joshua L. Payne

Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14

mSystems(2022)10.1128/msystems.00342-22

N/A

0.457DataRank · unranked

10 citations

Georgia Doing, Samuel L. Neff, Taylor Reiter, Deborah A. Hogan, Casey S. Greene +1 more

Integrative Systems Biology for Data-Driven Knowledge Discovery

Seminars in Nephrology(2010)10.1016/j.semnephrol.2010.07.002

N/A

0.457DataRank · unranked

20 citations

Olga G. Troyanskaya, Casey S. Greene

LTR Retrotransposon-Gene Associations in Drosophila melanogaster

Journal of Molecular Evolution(2006)10.1007/s00239-004-0312-4

N/A

0.457DataRank · unranked

20 citations

Casey S. Greene, Judson A. Lewis, Vikram Bhattacharjee, John F. McDonald, Eric Ganko +1 more

Learning and Imputation for Mass-spec Bias Reduction (LIMBR)

Bioinformatics(2018)10.1093/bioinformatics/bty828

N/A

0.449DataRank · unranked

19 citations

Casey S. Greene, Jennifer J Loros, Jay C Dunlap, Jennifer Loros, Jay Dunlap +1 more

Environmental Sensing of Expert Knowledge in a Computational Evolution System for Complex Problem Solving in Human Genetics

Genetic and Evolutionary Computation(2009)10.1007/978-1-4419-1626-6_2

N/A

0.445DataRank · unranked

12 citations

Douglas P. Hill, Jason H. Moore, Douglas Hill, Casey S. Greene

A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships

Lecture Notes in Computer Science(2010)10.1007/978-3-642-12211-8_7

N/A

0.441DataRank · unranked

3 citations

Daniel S. Himmelstein, Jason H. Moore, Casey S. Greene

Ten simple rules for large-scale data processing

PLoS Computational Biology(2022)10.1371/journal.pcbi.1009757

N/A

0.441DataRank · unranked

8 citations

Alexandra J. Lee, Jaclyn N. Taroni, K. Wheeler, Chen-Shan Chin, Sean Davis +2 more

Community-wide hackathons to identify central themes in single-cell multi-omics

Genome Biology(2021)10.1186/s13059-021-02433-9

N/A

0.436DataRank · unranked

15 citations

Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb +26 more

Examining linguistic shifts between preprints and publications

PLOS Biology(2022)10.1371/journal.pbio.3001470

N/A

0.434DataRank · unranked

17 citations

Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene +1 more

Evaluating deep variational autoencoders trained on pan-cancer gene expression

arXiv (Cornell University)(2017)10.48550/arxiv.1711.04828

N/A

0.434DataRank · unranked

17 citations

Casey S. Greene, Gregory P. Way

Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

Cancer Epidemiology, Biomarkers & Prevention(2024)10.1158/1055-9965.epi-24-0113

Top 43%

0.432DataRank

Top 43%11 citations

Mollie E. Barnard, Ariel A. Hippen Anderson, Amy Campbell, Courtney E. Johnson, Gregory P. Way +9 more

Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics

Biocomputing 2019(2018)10.1142/9789813279827_0033

N/A

0.425DataRank · unranked

16 citations

Casey S. Greene, Qiwen Hu

Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum

Microbiology Spectrum(2024)10.1128/spectrum.03157-23

N/A

0.417DataRank · unranked

10 citations

Georgia Doing, Taylor Reiter, Thomas H. Hampton, Casey S. Greene, Deborah A. Hogan +1 more

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

PLoS ONE(2013)10.1371/journal.pone.0069678

N/A

0.416DataRank · unranked

15 citations

Chrystal M. Chadwick, Lorrie M. Mandell, John C. Hu, Joanne M. O’Hara, Robert N. Brey +6 more

Extensions of the Erdös‐Ko‐Rado Theorem

Studies in Applied Mathematics(1976)10.1002/sapm19765511

N/A

0.406DataRank · unranked

14 citations

G. O. H. Katona, D. J. Kleitman, Casey S. Greene, Gyula O. H. Katona, Daniel J. Kleitman

Computational genetics analysis of grey matter density in Alzheimer’s disease

BioData Mining(2014)10.1186/1756-0381-7-17

N/A

0.400DataRank · unranked

9 citations

Jonathan M Fisher, Ting Hu, Peter C. Andrews, Casey S. Greene, Li Shen +6 more

A parasite's perspective on data sharing

GigaScience(2018)10.1093/gigascience/giy129

N/A

0.396DataRank · unranked

13 citations

Casey S. Greene, Ariel I. Mundo

Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning

Annual Review of Biomedical Data Science(2019)10.1146/annurev-biodatasci-072018-021348

N/A

0.373DataRank · unranked

11 citations

Casey S. Greene, Gregory P. Way

The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors

(2024)10.1101/2024.04.19.590243

Top 48%

0.373DataRank

Top 48%11 citations

Joshua A. Shapiro, Stephanie J. Spielman, David S. Mejia, Deepashree Venkatesh Prasad, Nozomi Ichihara +9 more

Biologically Informed Neural Networks Predict Drug Responses

Cancer Cell(2020)10.1016/j.ccell.2020.10.014

N/A

0.373DataRank · unranked

11 citations

James C. Costello, Casey S. Greene

The probability of edge existence due to node degree: a baseline for network-based predictions

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.05.522939

N/A

0.365DataRank · unranked

5 citations

Daniel S. Himmelstein, Kyle Kloster, Christopher K. I. Williams, Michael W. Nagle, Casey S. Greene +1 more

OpenPBTA: An Open Pediatric Brain Tumor Atlas

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.13.507832

Top 49%

0.363DataRank

Top 49%7 citations

Krutika S. Gaonkar, Candace L. Savonen, Stephanie J. Spielman, Chanté J. Bethell, Run Jin +59 more

Sensible initialization using expert knowledge for genome-wide analysis of epistasis using genetic programming

2009 IEEE Congress on Evolutionary Computation(2009)10.1109/cec.2009.4983093

N/A

0.360DataRank · unranked

10 citations

Bill C. White, Jason H. Moore, Casey S. Greene

The effect of non-linear signal in classification problems using gene expression

PLOS Computational Biology(2023)10.1371/journal.pcbi.1010984

N/A

0.360DataRank · unranked

10 citations

Jake Crawford, Casey S. Greene, Benjamin J. Heil

Polygenic risk score for type 2 diabetes shows context-dependent effects across populations

Nature Communications(2025)10.1038/s41467-025-63546-4

N/A

0.345DataRank · unranked

9 citations

Yanwei Cai, Daeeun Kim, Roelof A. J. Smit, Zhe Wang, Kruthika R. Iyer +169 more

Widespread redundancy in -omics profiles of cancer mutation states

Genome Biology(2022)10.1186/s13059-022-02705-y

N/A

0.345DataRank · unranked

9 citations

Brock C. Christensen, Maria Chikina, Casey S. Greene, Jake Crawford

Analysis of science journalism reveals gender and regional disparities in coverage

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.21.449261

N/A

0.345DataRank · unranked

9 citations

Casey S. Greene, Natalie R. Davidson

Some results on sperner families

Journal of Combinatorial Theory, Series A(1979)10.1016/0097-3165(79)90073-6

N/A

0.345DataRank · unranked

9 citations

Casey S. Greene, A. J. W. Hilton

Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.13.904771

N/A

0.344DataRank · unranked

6 citations

Robert J. Allaway, Jaclyn N. Taroni, Aaron Baker, Xiaochun Zhang, Chang In Moon +7 more

Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia

mSystems(2023)10.1128/msystems.00341-22

Top 51%

0.342DataRank

Top 51%6 citations

Alexandra J. Lee, Samuel L. Neff, Taylor Reiter, Jacob D. Holt, BRUCE A. STANTON +3 more

Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer

JCO Clinical Cancer Informatics(2021)10.1200/cci.21.00040

N/A

0.341DataRank · unranked

4 citations

Anne C. Kirchhoff, Jaime M. Guidry Auvil, Norman E. Sharpless, Kara L. Davis, Karlyne M. Reilly +26 more

Building a Vertically-Integrated Genomic Learning Health System: The Colorado Center for Personalized Medicine Biobank

medRxiv(2022)10.1101/2022.06.09.22276222

N/A

0.330DataRank · unranked

8 citations

Jonathan A. Shortt, Emily R. Roberts, Joe A. Lesny, Elizabeth Kudron, Meng Lin +50 more

Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health

arXiv (Cornell University)(2021)10.48550/arxiv.2112.12554

N/A

0.330DataRank · unranked

8 citations

Erik L. Antonsen, Lauren M. Sanders, Jaden J. A. Hastings, Seung Min Park, Graham Mackintosh +51 more

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/078659

N/A

0.314DataRank · unranked

4 citations

Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady +5 more

A generalization of Sperner's theorem

Journal of the Australian Mathematical Society(1981)10.1017/s1446788700024290

N/A

0.312DataRank · unranked

7 citations

P. Frankl, A. J. W. Hilton, Péter Frankl, Casey S. Greene, D. E. Daykin

Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning

ScholarlyCommons (University of Pennsylvania)(2018)10.7287/peerj.preprints.27229v1

N/A

0.312DataRank · unranked

7 citations

Casey S. Greene, Gregory P. Way

Computationally efficient assembly of a Pseudomonas aeruginos a gene expression compendium

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.24.477642

Top 54%

0.310DataRank

Top 54%5 citations

Alexandra J. Lee, Samuel L. Neff, Jacob D. Holt, BRUCE A. STANTON, Casey S. Greene +2 more

Analytical Code for "Cross-population analysis of high-grade serous ovarian cancer reveals only two robust subtypes"

Zenodo (CERN European Organization for Nuclear Research)(2015)10.5281/zenodo.32906

Top 54%

0.305DataRank

Top 54%3 citations

James Rudd, Casey S. Greene, Gregory P. Way

Hetnet connectivity search provides rapid insights into how biomedical entities are related

GigaScience(2022)10.1093/gigascience/giad047

N/A

0.292DataRank · unranked

6 citations

Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, Faisal Alquaddoomi +7 more

An efficient, not-only-linear correlation coefficient based on clustering

Cell Systems(2024)10.1016/j.cels.2024.08.005

N/A

0.292DataRank · unranked

6 citations

Marylyn D. Ritchie, Diego H. Milone, Casey S. Greene, Milton Pividori

Teaching undergraduate dental students about TMJ disorders: survey and proposal

Journal of Dental Education(1973)10.1002/j.0022-0337.1973.37.4.tb00669.x

N/A

0.292DataRank · unranked

6 citations

Casey S. Greene, C.S. Greene

Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/118349

N/A

0.292DataRank · unranked

6 citations

Casey S. Greene, Jaclyn N. Taroni

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping

medRxiv(2020)10.1101/2020.02.17.20024133

N/A

0.290DataRank · unranked

5 citations

Yadav Wagley, James A. Pippin, Ahmed Elhakeem, Gregory P. Way, Shana E. McCormack +28 more

Embracing study heterogeneity for finding genetic interactions in large‐scale research consortia

Genetic Epidemiology(2019)10.1002/gepi.22262

N/A

0.274DataRank · unranked

5 citations

Jing Huang, Ryan J. Urbanowicz, Kun Chen, Elisabetta Manduchi, Casey S. Greene +4 more

gene-ontology: Initial zenodo release

Zenodo (CERN European Organization for Nuclear Research)(2015)10.5281/zenodo.21711

Top 58%

0.271DataRank

Top 58%4 citations

Casey S. Greene, Venkat S. Malladi, Frederic Bastian, Sergio E. Baranzini, Daniel S. Himmelstein

Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts

BioData Mining(2022)10.1186/s13040-022-00311-z

N/A

0.269DataRank · unranked

5 citations

Daniel S. Himmelstein, Casey S. Greene, David N. Nicholson

Sperner Families and Partitions of A Partially Ordered Set

Combinatorics(1975)10.1007/978-94-010-1826-5_15

N/A

0.269DataRank · unranked

5 citations

Casey S. Greene

Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/196915

N/A

0.269DataRank · unranked

5 citations

Raman Arora, Aedín C. Culhane, Alexander V. Favorov, Lana X. Garmire, Casey S. Greene +7 more

Many direct-to-consumer canine genetic tests can identify the breed of purebred dogs

Journal of the American Veterinary Medical Association(2024)10.2460/javma.23.07.0372

N/A

0.269DataRank · unranked

5 citations

Kiley Graim, Greg Hampikian, Casey S. Greene, Diane N. Rafizadeh

Identification of Novel Genetic Models of Glaucoma Using the “EMERGENT” Genetic Programming-Based Artificial Intelligence System

Genetic and Evolutionary Computation(2015)10.1007/978-3-319-16030-6_2

N/A

0.269DataRank · unranked

5 citations

Casey S. Greene, Douglas P. Hill, Douglas Hill, Jason H. Moore

Voices in methods development

Nature Methods(2019)10.1038/s41592-019-0585-6

N/A

0.269DataRank · unranked

5 citations

Rosalind Mott Firenze, Clifford Brangwynne, Ibrahim I. Cissé, Oliver Fiehn, Petra Fromme +44 more

Inflammatory and JAK-STAT Pathways as Shared Molecular Targets for ANCA-Associated Vasculitis and Nephrotic Syndrome

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/427898

N/A

0.269DataRank · unranked

5 citations

Viji Nair, Laura H. Mariani, Felix H. Eichinger, John Hartman, Huateng Huang +17 more

ADAGE signature analysis: differential expression analysis with data-defined gene sets

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/156620

N/A

0.268DataRank · unranked

3 citations

Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene +1 more

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

(2015)10.7287/peerj.preprints.1460v1

Top 59%

0.261DataRank

Top 59%4 citations

Jie Tan, Casey S. Greene, Jeffrey Thompson

COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES

Biocomputing 2016(2015)10.1142/9789814749411_0051

N/A

0.241DataRank · unranked

4 citations

JAMES A. FOSTER, BRUCE A. STANTON, Deborah A. Hogan, YANA BROMBERG, Casey S. Greene

Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.05.450786

N/A

0.241DataRank · unranked

4 citations

Sumei Lu, Binglan Li, Chun Su, Matthew E. Johnson, Wei-Qi Wei +14 more

Widespread redundancy in -omics profiles of cancer mutation states

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.27.466140

N/A

0.241DataRank · unranked

4 citations

Brock C. Christensen, Maria Chikina, Casey S. Greene, Jake Crawford

Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.14.544991

N/A

0.241DataRank · unranked

4 citations

Natalie R. Davidson, Mollie E. Barnard, Lukas M. Weber, Jason Gertz, Jennifer Anne Doherty +3 more

Correction for Rando et al., “Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure”

mSystems(2022)10.1128/msystems.01447-21

N/A

0.241DataRank · unranked

4 citations

Adam L. MacLean, Alexandra J. Lee, Bharath Ramsundar, Vikas Bansal, Michael P. Robson +23 more

Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs

arXiv (Cornell University)(2021)10.48550/arxiv.2112.12582

N/A

0.241DataRank · unranked

4 citations

Jason H. Yang, Ryan T. Scott, Amina A. Qutub, Héctor García Martín, Daniel C. Berrios +51 more

Tribe: The collaborative platform for reproducible web-based analysis of gene sets

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/055913

N/A

0.241DataRank · unranked

4 citations

Aaron K. Wong, Alex T. Frase, Marylyn D. Ritchie, Casey S. Greene, Alex Frase +1 more

Highly connected genes contain more SNPs

Zenodo (CERN European Organization for Nuclear Research)(2015)10.5281/zenodo.30105

N/A

0.241DataRank · unranked

4 citations

Casey S. Greene, Daniel S. Himmelstein

TEXT AND DATA MINING FOR BIOMEDICAL DISCOVERY- SESSION INTRODUCTION

Biocomputing 2014(2013)10.1142/9789814583220_0030

N/A

0.241DataRank · unranked

4 citations

Kevin Bretonnel Cohen, Casey S. Greene, Maricel G. Kann, Robert Leaman, Nigam Shah +4 more

Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data

medRxiv(2021)10.1101/2021.10.21.21265225

N/A

0.241DataRank · unranked

4 citations

Yogasudha Veturi, Anastasia Lucas, Yuki Bradford, Shefali S. Verma, Anurag Verma +14 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.01.565179

Top 61%

0.241DataRank

Top 61%4 citations

Mollie E. Barnard, Ariel A. Hippen Anderson, Amy Campbell, Courtney E. Johnson, Gregory P. Way +9 more

Using expert knowledge in initialization for genome-wide analysis of epistasis using genetic programming

Proceedings of the 10th annual conference on Genetic and evolutionary computation(2008)10.1145/1389095.1389158

N/A

0.241DataRank · unranked

4 citations

Bill C. White, Jason H. Moore, Casey S. Greene

Leveraging global gene expression patterns to predict expression of unmeasured genes

BMC Genomics(2015)10.1186/s12864-015-2250-5

N/A

0.241DataRank · unranked

4 citations

René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene, Jennifer Anne Doherty +1 more

Artificial Immune Systems for Epistasis Analysis in Human Genetics

Lecture Notes in Computer Science(2010)10.1007/978-3-642-12211-8_17

N/A

0.222DataRank · unranked

3 citations

Casey S. Greene, Delaney Granizo-MacKenzie, Jason H. Moore, Nadia M. Penrod

Solving complex problems in human genetics using GP

ACM SIGEVOlution(2008)10.1145/1527063.1527064

N/A

0.208DataRank · unranked

3 citations

Jason H. Moore, Casey S. Greene

Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction

Bioinformatics Advances(2024)10.1093/bioadv/vbae004

N/A

0.208DataRank · unranked

3 citations

Maria Chikina, Casey S. Greene, Jake Crawford

Reproducible Computational Workflows with Continuous Analysis

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/056473

N/A

0.208DataRank · unranked

3 citations

Casey S. Greene, Brett K. Beaulieu‐Jones

Analysis of science journalism reveals gender and regional disparities in coverage

eLife(2024)10.7554/elife.84855

N/A

0.208DataRank · unranked

3 citations

Casey S. Greene, Natalie R. Davidson

BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk

PLOS Computational Biology(2025)10.1371/journal.pcbi.1012742

N/A

0.208DataRank · unranked

3 citations

Fan Zhang, Casey S. Greene, Natalie R. Davidson

A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/075382

N/A

0.204DataRank · unranked

2 citations

Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Casey S. Greene, Yolanda Sánchez +1 more

Key points for good clinical practice in the field of temporomandibular disorders

Nederlands Tijdschrift Voor Tandheelkunde(2025)10.5177/ntvt.2025.06.24131

N/A

0.165DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/730085

N/A

0.165DataRank · unranked

2 citations

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N/A

0.165DataRank · unranked

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(2023)10.64628/aai.hccx6qejf

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0.165DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.14.488429

N/A

0.165DataRank · unranked

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0.165DataRank · unranked

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Specific histone modifications associate with alternative exon selection during mammalian development

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/361816

N/A

0.165DataRank · unranked

2 citations

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(2018)10.7554/elife.32822.022

N/A

0.165DataRank · unranked

2 citations

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0.165DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.31.551386

N/A

0.165DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.03.066597

N/A

0.165DataRank · unranked

2 citations

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0.165DataRank

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eLife(2024)10.7554/elife.84855.3

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Zenodo (CERN European Organization for Nuclear Research)(2015)10.5281/zenodo.32087

N/A

0.104DataRank · unranked

1 citations

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0.104DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/062695

N/A

0.104DataRank · unranked

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2009 IEEE Congress on Evolutionary Computation(2009)10.1109/cec.2009.4983027

N/A

0.104DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.12.945642

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0.104DataRank · unranked

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0.104DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.24.445440

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2014 8th International Conference on Systems Biology (ISB)(2014)10.1109/isb.2014.6990733

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0.104DataRank · unranked

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0.104DataRank · unranked

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arXiv (Cornell University)(2021)10.48550/arxiv.2104.11364

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0.104DataRank · unranked

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0.104DataRank · unranked

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0.104DataRank · unranked

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0.104DataRank · unranked

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0.104DataRank · unranked

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Tell me your neighbors, and I will tell you what you are

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TEXT AND DATA MINING FOR BIOMEDICAL DISCOVERY

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bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/198481

N/A

0.104DataRank · unranked

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Node connectivity measurements for Hetionet v1.0 metapaths

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0.104DataRank · unranked

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0.104DataRank · unranked

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0.104DataRank · unranked

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(2018)10.7287/peerj.preprints.27229

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0.104DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/301242

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0.104DataRank · unranked

1 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.26.546586

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0.104DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.17.910703

N/A

0.104DataRank · unranked

1 citations

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Integrated Phosphoproteomics and Transcriptional Classifiers Reveal Hidden RAS Signaling Dynamics in Multiple Myeloma

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/563312

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0.104DataRank · unranked

1 citations

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Zenodo (CERN European Organization for Nuclear Research)(2015)10.5281/zenodo.32852

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arXiv (Cornell University)(2022)10.48550/arxiv.2203.13946

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Reviewer #1 (Public Review): Analysis of science journalism reveals gender and regional disparities in coverage

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0DataRank · unranked

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Reproducible Computational Workflows with Continuous Analysis

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0DataRank · unranked

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(2023)10.1158/0008-5472.24895378

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Back Cover Image

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(2024)10.1158/1055-9965.26423545

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greedy-geneset-selection: GGS 1.0.1

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Relief-based bioinformatics methods for the analysis of epistasis in genetic association studies.

(2009)10.1349/ddlp.303

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Reviewer #2 (Public Review): Analysis of science journalism reveals gender and regional disparities in coverage

(2023)10.7554/elife.84855.1.sa0

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Human Microbiome Compendium dataset

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eADAGE-1.0.0

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Imp 1.0 Filtered Human Functional Network

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TCGA Pan-Cancer sample, expression, and mutation data for Project Cognoma

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Figshare(2025)10.1158/0008-5472.28917763

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Figure S2 from Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

(2023)10.1158/0008-5472.24895399

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Figure S1 from Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

(2023)10.1158/0008-5472.24895402.v1

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Figure S3 from Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

(2023)10.1158/0008-5472.24895396

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Additional file 11: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d2

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Additional file 20: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d12

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Supplemental Figure 2 from Genomic Characterization of High-Grade Serous Ovarian Carcinoma Reveals Distinct Somatic Features in Black Individuals

Figshare(2025)10.1158/0008-5472.28917793

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Supplementary Table S2 from An Analytic Pipeline to Obtain Reliable Genetic Ancestry Estimates from Tumor-Derived RNA Sequencing Data

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(2024)10.1158/1055-9965.26423554

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UNC Libraries(2025)10.17615/96cj-z232

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Supplementary Table S4 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

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(2024)10.1158/1055-9965.c.7380196.v1

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Additional file 15: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

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Additional file 31: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.05.522941

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eLife(2024)10.7554/elife.84855.2

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(2025)10.1158/0008-5472.28917796

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Additional file 3 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

(2020)10.6084/m9.figshare.12285506

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Supplementary Figure S1 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

(2024)10.1158/1055-9965.26423617

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bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/166207

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Cancer Epidemiology, Biomarkers & Prevention(2025)10.1158/1055-9965.epi-25-0371

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Additional file 19: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d10

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Supplementary Figure S16 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

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Supplemental Table 8 from Genomic Characterization of High-Grade Serous Ovarian Carcinoma Reveals Distinct Somatic Features in Black Individuals

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Additional file 21: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

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(2023)10.1158/0008-5472.24895390

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(2024)10.1158/1055-9965.26423602

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.05.522943

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arXiv (Cornell University)(2022)10.48550/arxiv.2210.07247

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Additional file 14: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

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medRxiv(2025)10.1101/2025.01.21.25320918

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(2025)10.1158/1055-9965.c.8012108

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Supplementary Figure S7 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

(2024)10.1158/1055-9965.26423575

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(2024)10.1158/1055-9965.26423557

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(2024)10.1158/1055-9965.26423563

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(2025)10.1158/1055-9965.30517304

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Input data from "The Effects of Nonlinear Signal on Expression-Based Prediction Performance"

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Supplementary Figure S2 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

(2024)10.1158/1055-9965.26423593

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(2019)10.7554/elife.45133.053

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Additional file 3: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d26

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Figshare(2015)10.6084/m9.figshare.c.3607190_d3

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(2024)10.1158/1055-9965.26423608

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Additional file 18: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

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Additional file 9: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

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Supplementary Figure S3 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

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Additional file 4 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

Figshare(2020)10.6084/m9.figshare.12285512

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Additional file 32: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

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Additional file 7: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

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Expression Data From "A Novel Multi-Network Approach Reveals Tissue-Specific Cellular Modulators Of Fibrosis In Systemic Sclerosis, Pulmonary Fibrosis, And Pulmonary Arterial Hypertension"

Zenodo (CERN European Organization for Nuclear Research)(2016)10.5281/zenodo.216614

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Figshare(2025)10.1158/0008-5472.28917760

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(2025)10.1158/0008-5472.c.7798939

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(2024)10.1158/1055-9965.26423605

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Figshare(2023)10.1158/0008-5472.24895378.v1

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Figshare(2025)10.1158/0008-5472.28917790

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Figure S6 from Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

(2023)10.1158/0008-5472.24895387

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Figshare(2025)10.1158/0008-5472.28917778

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Additional file 27: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d19

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Figshare(2018)10.6084/m9.figshare.6739592

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Figshare(2025)10.1158/1055-9965.30517313

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Additional file 6 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

Figshare(2020)10.6084/m9.figshare.12285518

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Figshare(2024)10.1158/1055-9965.26423575.v1

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Additional file 25: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d17

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Figshare(2025)10.1158/0008-5472.28917751

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Figshare(2017)10.6084/m9.figshare.c.3684217_d4

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Figure S4 from Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

Figshare(2023)10.1158/0008-5472.24895393.v1

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Zenodo (CERN European Organization for Nuclear Research)(2017)10.5281/zenodo.822470

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(2023)10.64628/aao.d3uduttgh

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.21.554169

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Figshare(2025)10.1158/1055-9965.30517319

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Supplementary Table S7 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

Figshare(2024)10.1158/1055-9965.26423545.v1

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PMC(2016)10.6084/m9.figshare.c.3643697

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(2023)10.1158/0008-5472.24895393

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(2024)10.1158/1055-9965.26423569

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Additional file 2: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d22

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Figshare(2025)10.1158/0008-5472.28917769

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Supplemental Figure 5 from Genomic Characterization of High-Grade Serous Ovarian Carcinoma Reveals Distinct Somatic Features in Black Individuals

Figshare(2025)10.1158/0008-5472.28917784

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arXiv (Cornell University)(2021)10.48550/arxiv.2106.00657

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Figshare(2024)10.1158/1055-9965.26423581.v1

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Figshare(2025)10.1158/0008-5472.28917766

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Figshare(2024)10.1158/1055-9965.26423614.v1

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Supplementary Figure S8 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms

Figshare(2024)10.1158/1055-9965.26423572.v1

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Figure S1 from Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

(2023)10.1158/0008-5472.24895402

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Additional file 24: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d16

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Data from Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer

(2023)10.1158/0008-5472.c.6994537.v1

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Additional file 28: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d20

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Additional file 6: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

Figshare(2017)10.6084/m9.figshare.c.3723766_d29

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(2023)10.1158/0008-5472.24895384

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