All Stories

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

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • GigaScience, November 2020, Oxford University Press (OUP)

    Professor Casey Greene

  3. Expanding and Remixing the Metadata Landscape

    Article • Trends in Cancer, November 2020, Elsevier

    Professor Casey Greene

  4. Transparency and reproducibility in artificial intelligence

    Article • Nature, October 2020, Springer Science + Business Media

    Professor Casey Greene

  5. Responsible, practical genomic data sharing that accelerates research

    Article • Nature Reviews Genetics, July 2020, Springer Science + Business Media

    Professor Casey Greene

  6. Incorporating biological structure into machine learning models in biomedicine

    Article • Current Opinion in Biotechnology, June 2020, Elsevier

    Professor Casey Greene

  7. Recommendations to enhance rigor and reproducibility in biomedical research

    Article • GigaScience, June 2020, Oxford University Press (OUP)

    Professor Casey Greene

  8. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

    Article • May 2020, Springer Science + Business Media

    Professor Casey Greene

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

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  10. Analysis of ISCB honorees and keynotes reveals disparities

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Genes, February 2020, MDPI AG

    Professor Casey Greene

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

    Article • Proceedings of the National Academy of Sciences, January 2020, Proceedings of the National Academy of Sciences

    Professor Casey Greene

  13. Graph biased feature selection of genes is better than random for many genes

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  15. Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma

    Article • Blood Advances, October 2019, American Society of Hematology

    Professor Casey Greene

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

    Article • October 2019, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  17. Reusing label functions to extract multiple types of biomedical relationships from biomedical abstracts at scale

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

  18. Open collaborative writing with Manubot

    Article • PLoS Computational Biology, June 2019, PLOS

    Professor Casey Greene, Mr Daniel S Himmelstein

  19. Sequential compression across latent space dimensions enhances gene expression signatures

    Article • March 2019, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  21. Bayesian deep learning for single-cell analysis

    Article • Nature Methods, November 2018, Springer Science + Business Media

    Professor Casey Greene

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

    Article • G3 Genes Genomes Genetics, November 2018, Genetics Society of America

    Professor Casey Greene

  23. A Parasite's Perspective on Data Sharing

    Article • GigaScience, November 2018, Oxford University Press (OUP)

    Professor Casey Greene

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

    Article • Bioinformatics, September 2018, Oxford University Press (OUP)

    Professor Casey Greene

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

    Article • September 2018, PeerJ

    Professor Casey Greene

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

    Article • September 2018, PeerJ

    Professor Casey Greene

  27. New Drosophila long-term memory genes revealed by assessing computational function prediction methods.

    Article • September 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  28. MultiPLIER: a transfer learning framework reveals systemic features of rare autoimmune disease

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  30. Specific histone modifications associate with alternative exon selection during mammalian development

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • BioData Mining, July 2018, Springer Science + Business Media

    Professor Casey Greene

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

    Article • April 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Cell Reports, April 2018, Elsevier

    Professor Casey Greene, Renumathy Dhanasekaran, Dr Ronald E Warnick

  34. Oncogenic Signaling Pathways in The Cancer Genome Atlas

    Article • Cell, April 2018, Elsevier

    Professor Casey Greene, Renumathy Dhanasekaran, Dr Ronald E Warnick

  35. Research: Sci-Hub provides access to nearly all scholarly literature

    Article • eLife, February 2018, eLife

    Professor Casey Greene, Mr Daniel S Himmelstein

  36. Sci-Hub provides access to nearly all scholarly literature

    Article • February 2018, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • Journal of Bacteriology, January 2018, ASM Journals

    Professor Casey Greene

  38. A Pilot Characterization of the Human Chronobiome

    Article • Scientific Reports, December 2017, Nature

    Professor Casey Greene

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

    Article • BMC Bioinformatics, November 2017, Springer Science + Business Media

    Professor Casey Greene

  40. Sci-Hub provides access to nearly all scholarly literature

    Article • October 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

  41. Sci-Hub provides access to nearly all scholarly literature

    Article • October 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

  42. Enter the matrix: Interpreting unsupervised feature learning with matrix decomposition to discover hidden knowledge in high-throughput omics data

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  43. Machine Learning Analysis Identifies Drosophila Grunge/Atrophin as an Important Learning and Memory Gene Required for Memory Retention and Social Learning

    Article • G3 Genes Genomes Genetics, September 2017, Genetics Society of America

    Professor Casey Greene

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

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  45. Implicating candidate genes at GWAS signals by leveraging topologically associating domains

    Article • European Journal of Human Genetics, August 2017, Nature

    Professor Casey Greene

  46. Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses

    Article • July 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  47. Sci-Hub provides access to nearly all scholarly literature

    Article • July 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • Bioinformatics, July 2017, Oxford University Press (OUP)

    Professor Casey Greene

  49. Privacy-preserving generative deep neural networks support clinical data sharing

    Article • July 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Cell Systems, July 2017, Elsevier

    Professor Casey Greene

  51. Machine learning analysis identifies Drosophila Grunge/Atrophin as an important learning and memory gene required for memory retention and social learning.

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  53. PathCORE: Visualizing globally co-occurring pathways in large transcriptomic compendia

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  54. Data-Sharing Models

    Article • New England Journal of Medicine, June 2017, New England Journal of Medicine (NEJM/MMS)

    Professor Casey Greene

  55. Opportunities And Obstacles For Deep Learning In Biology And Medicine

    Article • May 2017, Cold Spring Harbor Laboratory Press

    Mr Daniel S Himmelstein, Professor Casey Greene

  56. Celebrating parasites

    Article • Nature Genetics, April 2017, Nature

    Professor Casey Greene

  57. A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

    Article • Genome Medicine, March 2017, Springer Science + Business Media

    Professor Casey Greene

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

    Article • March 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  59. Reproducibility of computational workflows is automated using continuous analysis

    Article • Nature Biotechnology, March 2017, Nature

    Professor Casey Greene

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

    Article • Science Translational Medicine, February 2017, American Association for the Advancement of Science

    Professor Casey Greene

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

    Article • BMC Genomics, February 2017, Springer Science + Business Media

    Professor Casey Greene

  62. Cheap-seq

    Article • Science Translational Medicine, December 2016, American Association for the Advancement of Science

    Professor Casey Greene

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

    Article • Journal of Biomedical Informatics, December 2016, Elsevier

    Professor Casey Greene

  64. Implicating candidate genes at GWAS signals by leveraging topologically associating domains

    Article • November 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  65. How to know what we dont

    Article • Science Translational Medicine, November 2016, American Association for the Advancement of Science

    Professor Casey Greene

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

    Article • G3 Genes Genomes Genetics, October 2016, Genetics Society of America

    Professor Casey Greene

  67. System-wide automatic extraction of functional signatures in Pseudomonas aeruginosa with eADAGE

    Article • October 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  68. A stromal focus reveals tumor immune signatures

    Article • Science Translational Medicine, September 2016, American Association for the Advancement of Science

    Professor Casey Greene

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

    Article • September 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  70. An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    Article • September 2016, Springer Science + Business Media

    Professor Casey Greene, Dr Christophe Dessimoz, Dr Tunca Dogan

  71. Gut check

    Article • Science Translational Medicine, August 2016, American Association for the Advancement of Science

    Professor Casey Greene

  72. Integrative networks illuminate biological factors underlying gene-disease associations

    Article • July 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Arjun Krishnan

  73. The future is unsupervised

    Article • Science Translational Medicine, July 2016, American Association for the Advancement of Science

    Professor Casey Greene

  74. Pathway and network-based strategies to translate genetic discoveries into effective therapies

    Article • Human Molecular Genetics, June 2016, Oxford University Press (OUP)

    Professor Casey Greene

  75. Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression

    Article • PLoS Biology, June 2016, PLOS

    Professor Casey Greene, Cameron R Currie

  76. Reproducible Computational Workflows with Continuous Analysis

    Article • June 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • May 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  78. Nothing but a hound dog

    Article • Science Translational Medicine, May 2016, American Association for the Advancement of Science

    Professor Casey Greene

  79. Pathway and network-based strategies to translate genetic discoveries into effective therapies

    Article • May 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  80. CoINcIDE: All together now

    Article • Science Translational Medicine, April 2016, American Association for the Advancement of Science

    Professor Casey Greene

  81. Genetic Association–Guided Analysis of Gene Networks for the Study of Complex Traits

    Article • Circulation Cardiovascular Genetics, April 2016, Wolters Kluwer Health

    Mr Daniel S Himmelstein, Professor Casey Greene

  82. 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

    Article • Oncotarget, March 2016, Impact Journals, LLC

    Professor Casey Greene

  83. Semi-Supervised Learning of the Electronic Health Record with Denoising Autoencoders for Phenotype Stratification

    Article • February 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  84. A Novel Multi-network Approach Reveals Tissue-specific Cellular Modulators of Fibrosis in Systemic Sclerosis, Pulmonary Fibrosis and Pulmonary Arterial Hypertension

    Article • February 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  85. Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology

    Article • BioData Mining, February 2016, Springer Science + Business Media

    Professor Casey Greene

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

    Article • PeerJ, January 2016, PeerJ

    Professor Casey Greene

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

    Article • BioData Mining, January 2016, Springer Science + Business Media

    Professor Casey Greene

  88. ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

    Article • mSystems, January 2016, ASM Journals

    Professor Casey Greene

  89. Leveraging global gene expression patterns to predict expression of unmeasured genes

    Article • BMC Genomics, December 2015, Springer Science + Business Media

    Professor Casey Greene

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

    Article • November 2015, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  91. Comprehensive cross-population analysis of high-grade serous ovarian cancer supports no more than three subtypes

    Article • October 2015, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • October 2015, PeerJ

    Professor Casey Greene

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

    Article • October 2015, PeerJ

    Professor Casey Greene

  94. 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

    Article • Human Molecular Genetics, October 2015, Oxford University Press (OUP)

    Professor Casey Greene

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

    Article • Briefings in Bioinformatics, September 2015, Oxford University Press (OUP)

    Professor Casey Greene

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

    Article • Nature Communications, September 2015, Nature

    Professor Casey Greene

  97. Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study

    Article • BioData Mining, June 2015, Springer Science + Business Media

    Professor Casey Greene

  98. Understanding multicellular function and disease with human tissue-specific networks

    Article • Nature Genetics, April 2015, Nature

    Mr Daniel S Himmelstein, Professor Casey Greene

  99. Adapting bioinformatics curricula for big data

    Article • Briefings in Bioinformatics, March 2015, Oxford University Press (OUP)

    Professor Casey Greene

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

    Article • Nature Methods, January 2015, Nature

    Professor Casey Greene

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

    Article • PLoS Computational Biology, January 2015, PLOS

    Professor Casey Greene

  102. Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study

    Article • October 2014, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Casey Greene

  103. Big Data Bioinformatics

    Article • Journal of Cellular Physiology, August 2014, Wiley

    Professor Casey Greene

  104. Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity

    Article • Genome Medicine, January 2014, Springer Science + Business Media

    Professor Casey Greene

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

    Article • BioData Mining, January 2014, Springer Science + Business Media

    Professor Casey Greene

  106. Defining cell-type specificity at the transcriptional level in human disease

    Article • Genome Research, August 2013, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  107. 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

    Article • PLoS ONE, August 2013, PLOS

    Dr Nicholas J Mantis, Professor Casey Greene

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

    Article • PLoS Computational Biology, March 2013, PLOS

    Professor Casey Greene

  109. Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments

    Article • January 2013, Springer Science + Business Media

    Professor Casey Greene

  110. Chapter 2: Data-Driven View of Disease Biology

    Article • PLoS Computational Biology, December 2012, PLOS

    Professor Casey Greene

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

    Article • Nucleic Acids Research, June 2012, Oxford University Press (OUP)

    Professor Casey Greene

  112. Accurate evaluation and analysis of functional genomics data and methods

    Article • Annals of the New York Academy of Sciences, January 2012, Wiley

    Professor Casey Greene

  113. PILGRM: an interactive data-driven discovery platform for expert biologists

    Article • Nucleic Acids Research, June 2011, Oxford University Press (OUP)

    Professor Casey Greene

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

    Article • BioData Mining, January 2011, Springer Science + Business Media

    Mr Daniel S Himmelstein, Professor Casey Greene

  115. An Open-Ended Computational Evolution Strategy for Evolving Parsimonious Solutions to Human Genetics Problems

    Article • January 2011, Springer Science + Business Media

    Professor Casey Greene

  116. An Analysis of New Expert Knowledge Scaling Methods for Biologically Inspired Computing

    Article • January 2011, Springer Science + Business Media

    Professor Casey Greene

  117. Integrative Systems Biology for Data-Driven Knowledge Discovery

    Article • Seminars in Nephrology, September 2010, Elsevier

    Professor Casey Greene

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

    Article • Bioinformatics, January 2010, Oxford University Press (OUP)

    Mr Daniel S Himmelstein, Professor Casey Greene

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

    Article • January 2010, ACM (Association for Computing Machinery)

    Professor Casey Greene

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

    Article • BioData Mining, September 2009, Springer Science + Business Media

    Professor Casey Greene

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

    Article • PLoS ONE, June 2009, PLOS

    Professor Casey Greene

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

    Article • May 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Casey Greene

  123. Nature-inspired algorithms for the genetic analysis of epistasis in common human diseases: Theoretical assessment of wrapper vs. filter approaches

    Article • May 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Casey Greene

  124. Development and evaluation of an open-ended computational evolution system for the creation of digital organisms with complex genetic architecture

    Article • May 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Casey Greene

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

    Article • January 2009, Springer Science + Business Media

    Professor Casey Greene

  126. Environmental noise improves epistasis models of genetic data discovered using a computational evolution system

    Article • January 2009, ACM (Association for Computing Machinery)

    Professor Casey Greene

  127. Accelerating epistasis analysis in human genetics with consumer graphics hardware

    Article • BMC Research Notes, January 2009, Springer Science + Business Media

    Professor Casey Greene

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

    Article • Arthritis & Rheumatism, July 2008, Wiley

    Professor Casey Greene

  129. Solving complex problems in human genetics using GP

    Article • ACM SIGEVOlution, July 2008, ACM (Association for Computing Machinery)

    Professor Casey Greene

  130. LTR Retrotransposon-Gene Associations in Drosophila melanogaster

    Article • Journal of Molecular Evolution, January 2006, Springer Science + Business Media

    Professor Casey Greene

  131. Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms Requires Strategies which Exploit Domain-Specific Knowledge

    Article • IGI Global

    Professor Casey Greene

  132. Ant Colony Optimization for Genome-Wide Genetic Analysis

    Article • Springer Science + Business Media

    Professor Casey Greene

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

    Article • Dartmouth College Library Press

    Professor Casey Greene