All Stories

  1. Deconvolved tumor adipocyte proportions and high grade serous ovarian carcinoma survival

    Article • January 2026, openRxiv

    Professor Casey Greene

  2. Data from Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race

    Article • November 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  3. Supplementary Figure 1 from Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race

    Article • November 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  4. Supplementary Figure 2 from Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race

    Article • November 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  5. Supplementary Figure 3 from Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race

    Article • November 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  6. Supplementary Table 1 from Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race

    Article • November 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  7. Supplementary Table 2 from Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race

    Article • November 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  8. Supplementary Table 3 from Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race

    Article • November 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  9. Characterizing intra- and inter-tumor heterogeneity in Ovarian high-grade serous carcinoma subtypes using single-cell and spatial transcriptomics

    Article • September 2025, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  10. Homologous recombination deficiency and survival in ovarian high-grade serous carcinoma by self-reported race

    Article • Cancer Epidemiology Biomarkers & Prevention, September 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  11. Data from An Analytic Pipeline to Obtain Reliable Genetic Ancestry Estimates from Tumor-Derived RNA Sequencing Data

    Article • September 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  12. Supplementary Figure S1 from An Analytic Pipeline to Obtain Reliable Genetic Ancestry Estimates from Tumor-Derived RNA Sequencing Data

    Article • September 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  13. Supplementary Table S1 from An Analytic Pipeline to Obtain Reliable Genetic Ancestry Estimates from Tumor-Derived RNA Sequencing Data

    Article • September 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

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

    Article • September 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  15. Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution

    Article • August 2025, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  16. An Analytic Pipeline to Obtain Reliable Genetic Ancestry Estimates from Tumor-Derived RNA Sequencing Data

    Article • Cancer Epidemiology Biomarkers & Prevention, July 2025, American Association for Cancer Research (AACR)

    Professor Casey Greene

  17. Research turns hope into reality

    Article • eLife, March 2025, eLife

    Professor Casey Greene

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

    Article • PLoS Computational Biology, January 2025, PLOS

    Professor Casey Greene

  19. Latent spaces for tumour transcriptomes

    Article • Nature Biomedical Engineering, December 2024, Springer Science + Business Media

    Professor Casey Greene

  20. Best holdout assessment is sufficient for cancer transcriptomic model selection

    Article • Patterns, December 2024, Elsevier

    Professor Casey Greene

  21. A publishing infrastructure for Artificial Intelligence (AI)-assisted academic authoring

    Article • Journal of the American Medical Informatics Association, June 2024, Oxford University Press (OUP)

    Professor Casey Greene

  22. Analysis of science journalism reveals gender and regional disparities in coverage

    Article • eLife, May 2024, eLife

    Professor Casey Greene

  23. Analysis of science journalism reveals gender and regional disparities in coverage

    Article • eLife, May 2024, eLife

    Professor Casey Greene

  24. MousiPLIER: A Mouse Pathway-Level Information Extractor Model

    Article • eNeuro, May 2024, Society for Neuroscience

    Professor Casey Greene

  25. Analysis of science journalism reveals gender and regional disparities in coverage

    Article • May 2024, eLife

    Professor Casey Greene

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

    Article • Journal of the American Veterinary Medical Association, May 2024, American Veterinary Medical Association (AVMA)

    Professor Casey Greene

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

    Article • April 2024, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • April 2024, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Microbiology Spectrum, April 2024, ASM Journals

    Professor Casey Greene

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

    Article • The American Journal of Human Genetics, January 2024, Elsevier

    Professor Casey Greene

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

    Article • Bioinformatics Advances, January 2024, Oxford University Press (OUP)

    Professor Casey Greene

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

    Article • GigaScience, January 2024, Oxford University Press (OUP)

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Genome Biology, October 2023, Springer Science + Business Media

    Professor Casey Greene, Lukas Weber

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

    Article • October 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Nature Communications, September 2023, Springer Science + Business Media

    Professor Casey Greene

  37. Analysis ofPseudomonas aeruginosatranscription in anex vivocystic fibrosis sputum model identifies metal restriction as a gene expression stimulus

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  38. MousiPLIER: A Mouse Pathway-Level Information Extractor Model

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  39. BuDDI:Bulk Deconvolution with Domain Invarianceto predict cell-type-specific perturbations from bulk

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  40. OpenPBTA: The Open Pediatric Brain Tumor Atlas

    Article • Cell Genomics, July 2023, Elsevier

    Professor Casey Greene

  41. Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry Estimates from Direct-to-Consumer Canine Genetic Tests

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Lukas Weber

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

    Article • Cell Reports, June 2023, Elsevier

    Professor Casey Greene

  45. Machine learning in rare disease

    Article • Nature Chemical Biology, May 2023, Springer Science + Business Media

    Professor Casey Greene

  46. Changing word meanings in biomedical literature reveal pandemics and new technologies

    Article • BioData Mining, May 2023, Springer Science + Business Media

    Professor Casey Greene

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

    Article • mSystems, April 2023, ASM Journals

    Professor Casey Greene

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

    Article • mSystems, April 2023, ASM Journals

    Professor Casey Greene

  49. MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes

    Article • Nucleic Acids Research, April 2023, Oxford University Press (OUP)

    Professor Casey Greene

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

    Article • PLoS Computational Biology, March 2023, PLOS

    Professor Casey Greene

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

    Article • Nature Machine Intelligence, March 2023, Springer Science + Business Media

    Professor Casey Greene

  52. Biomonitoring and precision health in deep space supported by artificial intelligence

    Article • Nature Machine Intelligence, March 2023, Springer Science + Business Media

    Professor Casey Greene

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

    Article • Communications Biology, February 2023, Springer Science + Business Media

    Professor Casey Greene

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

    Article • mSystems, February 2023, ASM Journals

    Professor Casey Greene

  55. Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia

    Article • mSystems, February 2023, ASM Journals

    Professor Casey Greene

  56. Analysis of science journalism reveals gender and regional disparities in coverage

    Article • February 2023, eLife

    Professor Casey Greene

  57. A publishing infrastructure for AI-assisted academic authoring

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

  60. The Field-Dependent Nature of PageRank Values in Citation Networks

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Nature Cancer, December 2022, Springer Science + Business Media

    Professor Casey Greene

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

    Article • GigaScience, December 2022, Oxford University Press (OUP)

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • December 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Lukas Weber

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

    Article • Nature Cancer, November 2022, Springer Science + Business Media

    Professor Casey Greene

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

    Article • BioData Mining, October 2022, Springer Science + Business Media

    Professor Casey Greene, Mr Daniel S Himmelstein

  66. wenda_gpu: fast domain adaptation for genomic data

    Article • Bioinformatics, October 2022, Oxford University Press (OUP)

    Professor Casey Greene

  67. SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses

    Article • Genomics Proteomics & Bioinformatics, October 2022, Oxford University Press (OUP)

    Professor Casey Greene

  68. OpenPBTA: An Open Pediatric Brain Tumor Atlas

    Article • September 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  69. Changing word meanings in biomedical literature reveal pandemics and new technologies

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Nature Communications, June 2022, Springer Science + Business Media

    Professor Casey Greene

  71. Widespread redundancy in -omics profiles of cancer mutation states

    Article • Genome Biology, June 2022, Springer Science + Business Media

    Professor Casey Greene

  72. The Effects of Nonlinear Signal on Expression-Based Prediction Performance

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  73. An efficient not-only-linear correlation coefficient based on machine learning

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  75. Compendium-wide analysis of P. aeruginosa core and accessory genes reveal more nuanced transcriptional patterns

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  76. wenda_gpu: fast domain adaptation for genomic data

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  77. Ten quick tips for deep learning in biology

    Article • PLoS Computational Biology, March 2022, PLOS

    Professor Casey Greene

  78. Ten simple rules for large-scale data processing

    Article • PLoS Computational Biology, February 2022, PLOS

    Professor Casey Greene

  79. Examining linguistic shifts between preprints and publications

    Article • PLoS Biology, February 2022, PLOS

    Professor Casey Greene

  80. Computationally efficient assembly of a Pseudomonas aeruginosa gene expression compendium

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  81. Computational audits combat disparities in recognition

    Article • Nature Human Behaviour, January 2022, Springer Science + Business Media

    Professor Casey Greene

  82. Using genome-wide expression compendia to study microorganisms

    Article • Computational and Structural Biotechnology Journal, January 2022, Elsevier

    Professor Casey Greene

  83. Identification and Development of Therapeutics for COVID-19

    Article • mSystems, December 2021, ASM Journals

    Professor Casey Greene

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

    Article • JCO Clinical Cancer Informatics, December 2021, American Society of Clinical Oncology (ASCO)

    Professor Casey Greene

  85. Characterizing Long COVID: Deep Phenotype of a Complex Condition

    Article • EBioMedicine, December 2021, Elsevier

    Professor Casey Greene

  86. Human Intrigue: Meta-analysis approaches for big questions with big data while shaking up the peer review process

    Article • November 2021, World Scientific Pub Co Pte Lt

    Professor Casey Greene

  87. Widespread redundancy in -omics profiles of cancer mutation states

    Article • October 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • October 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  89. A field guide to cultivating computational biology

    Article • PLoS Biology, October 2021, PLOS

    Piero Carninci, Dr Anne Carpenter, Professor Casey Greene

  90. Analysis of scientific society honors reveals disparities

    Article • Cell Systems, September 2021, Elsevier

    Professor Casey Greene

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

    Article • GigaScience, September 2021, Oxford University Press (OUP)

    Professor Casey Greene, Lukas Weber

  92. Reproducibility standards for machine learning in the life sciences

    Article • Nature Chemical Biology, August 2021, Springer Science + Business Media

    Professor Casey Greene

  93. Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics

    Article • Genome Biology, August 2021, Springer Science + Business Media

    Professor Casey Greene

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

    Article • PLoS Computational Biology, August 2021, PLOS

    Professor Casey Greene, Lukas Weber

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

    Article • Genome Biology, August 2021, Springer Science + Business Media

    Professor Casey Greene

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

    Article • July 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  97. Characterizing Long COVID: Deep Phenotype of a Complex Condition

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • mSystems, June 2021, ASM Journals

    Professor Casey Greene

  99. Analysis of science journalism reveals gender and regional disparities in coverage

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  100. GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases

    Article • May 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  101. Generative neural networks separate common and specific transcriptional responses

    Article • May 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  102. Linguistic Analysis of the bioRxiv Preprint Landscape

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Lukas Weber

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

    Article • Cell Reports, March 2021, Elsevier

    Professor Casey Greene

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

    Article • Cancer Research, February 2021, American Association for Cancer Research (AACR)

    Professor Casey Greene

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

    Article • Genome Biology, January 2021, Springer Science + Business Media

    Professor Casey Greene

  107. 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, Lukas Weber

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

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

    Professor Casey Greene

  109. Expanding and Remixing the Metadata Landscape

    Article • Trends in Cancer, November 2020, Elsevier

    Professor Casey Greene

  110. Biologically Informed Neural Networks Predict Drug Responses

    Article • Cancer Cell, November 2020, Elsevier

    Professor Casey Greene

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

    Article • Clinical Cancer Research, October 2020, American Association for Cancer Research (AACR)

    Professor Casey Greene

  112. Transparency and reproducibility in artificial intelligence

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

    Professor Casey Greene

  113. Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research

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

    Professor Casey Greene

  114. Prognostic gene expression signature for high-grade serous ovarian cancer

    Article • Annals of Oncology, September 2020, Elsevier

    Professor Casey Greene

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

    Article • Nature Human Behaviour, August 2020, Springer Science + Business Media

    Professor Casey Greene

  116. The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment

    Article • Journal of the American Medical Informatics Association, August 2020, Oxford University Press (OUP)

    Megan Coffee, Professor Casey Greene

  117. Responsible, practical genomic data sharing that accelerates research

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

    Professor Casey Greene

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

    Article • Nature Reports Stem Cells, June 2020, Springer Science + Business Media

    Professor Casey Greene

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

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  120. Building an international consortium for tracking coronavirus health status

    Article • Nature Reports Stem Cells, June 2020, Springer Science + Business Media

    Professor Casey Greene

  121. Incorporating biological structure into machine learning models in biomedicine

    Article • Current Opinion in Biotechnology, June 2020, Elsevier

    Professor Casey Greene

  122. Recommendations to enhance rigor and reproducibility in biomedical research

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

    Professor Casey Greene

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

    Article • May 2020, Springer Science + Business Media

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Nucleic Acids Research, April 2020, Oxford University Press (OUP)

    Professor Casey Greene

  126. Analysis of ISCB honorees and keynotes reveals disparities

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

  127. Building an International Consortium for Tracking Coronavirus Health Status

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  128. 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

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

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  130. Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  131. 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

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

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  133. 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

  134. Constructing knowledge graphs and their biomedical applications

    Article • Computational and Structural Biotechnology Journal, January 2020, Elsevier

    Professor Casey Greene

  135. Immune landscapes associated with different glioblastoma molecular subtypes

    Article • Acta Neuropathologica Communications, November 2019, Springer Science + Business Media

    Manoj kandpal, Professor Casey Greene

  136. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Article • November 2019, Springer Science + Business Media

    Dr Tunca Dogan, Professor Casey Greene, Dr Christophe Dessimoz

  137. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

    Article • Cell Reports, November 2019, Elsevier

    Professor Casey Greene

  138. 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

  139. 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

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

    Article • Genetic Epidemiology, October 2019, Wiley

    Professor Casey Greene

  141. Voices in methods development

    Article • Nature Chemical Biology, September 2019, Springer Science + Business Media

    Professor Casey Greene

  142. 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

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

    Article • Annual Review of Biomedical Data Science, July 2019, Annual Reviews

    Professor Casey Greene

  144. Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing

    Article • Circulation Cardiovascular Quality and Outcomes, July 2019, Wolters Kluwer Health

    Professor Casey Greene

  145. Open collaborative writing with Manubot

    Article • PLoS Computational Biology, June 2019, PLOS

    Professor Casey Greene, Mr Daniel S Himmelstein

  146. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan, Dr Christophe Dessimoz, Professor Casey Greene

  147. Show me the models

    Article • Nature Biotechnology, May 2019, Springer Science + Business Media

    Professor Casey Greene

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

    Article • Cell Systems, May 2019, Elsevier

    Professor Casey Greene

  149. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

    Article • Developmental Cell, April 2019, Elsevier

    Professor Casey Greene

  150. 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

  151. Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design

    Article • March 2019, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  153. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

    Article • SSRN Electronic Journal, January 2019, Elsevier

    Professor Casey Greene

  154. Bayesian deep learning for single-cell analysis

    Article • Nature Chemical Biology, November 2018, Springer Science + Business Media

    Professor Casey Greene

  155. 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

  156. A Parasite's Perspective on Data Sharing

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

    Professor Casey Greene

  157. Enter the Matrix: Factorization Uncovers Knowledge from Omics

    Article • Trends in Genetics, October 2018, Elsevier

    Professor Casey Greene

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

    Article • September 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

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

    Professor Casey Greene

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

    Article • September 2018, PeerJ

    Professor Casey Greene

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

    Article • September 2018, PeerJ

    Professor Casey Greene

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

    Article • September 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  164. 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

  165. Metabolic pathways and immunometabolism in rare kidney diseases

    Article • Annals of the Rheumatic Diseases, August 2018, Elsevier

    Professor Casey Greene

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

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  167. 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

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

    Article • Critical Care Medicine, July 2018, Wolters Kluwer Health

    Professor Casey Greene

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

    Article • April 2018, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  170. Opportunities and obstacles for deep learning in biology and medicine

    Article • Journal of The Royal Society Interface, April 2018, Royal Society Publishing

    Mr Daniel S Himmelstein, Professor Casey Greene

  171. 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

  172. Oncogenic Signaling Pathways in The Cancer Genome Atlas

    Article • Cell, April 2018, Elsevier

    Professor Casey Greene, Renumathy Dhanasekaran, Dr Ronald E Warnick

  173. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

    Article • Cell Reports, April 2018, Elsevier

    Renumathy Dhanasekaran, Professor Casey Greene

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

    Article • eLife, February 2018, eLife

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • February 2018, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • Journal of Bacteriology, January 2018, ASM Journals

    Professor Casey Greene

  177. A Pilot Characterization of the Human Chronobiome

    Article • Scientific Reports, December 2017, Nature

    Professor Casey Greene

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

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

    Professor Casey Greene

  179. Advances in Text Mining and Visualization for Precision Medicine

    Article • November 2017, World Scientific Pub Co Pte Lt

    Professor Casey Greene

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

    Article • November 2017, World Scientific Pub Co Pte Lt

    Professor Casey Greene

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

    Article • November 2017, World Scientific Pub Co Pte Lt

    Professor Casey Greene

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

    Article • October 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

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

    Article • October 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

  184. A Multimodal Strategy Used By A Large c-di-GMP Network

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  185. 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

  186. 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

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

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

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

    Professor Casey Greene

  189. 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

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

    Article • July 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

  191. 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

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

    Article • July 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • Cell Systems, July 2017, Elsevier

    Professor Casey Greene

  194. 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

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

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  197. Data-Sharing Models

    Article • The New England Journal of Medicine and Surgery and the Collateral Branches of Science, June 2017, New England Journal of Medicine (NEJM/MMS)

    Professor Casey Greene

  198. 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

  199. Celebrating parasites

    Article • Nature Genetics, April 2017, Nature

    Professor Casey Greene

  200. 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

  201. 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

  202. Reproducibility of computational workflows is automated using continuous analysis

    Article • Nature Biotechnology, March 2017, Nature

    Professor Casey Greene

  203. 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

  204. 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

  205. Cheap-seq

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

    Professor Casey Greene

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

    Article • Journal of Biomedical Informatics, December 2016, Elsevier

    Professor Casey Greene

  207. NO-BOUNDARY THINKING IN BIOINFORMATICS

    Article • November 2016, World Scientific Pub Co Pte Lt

    Professor Casey Greene

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

    Article • November 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  209. How to know what we dont

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

    Professor Casey Greene

  210. 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

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

    Article • October 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  212. A stromal focus reveals tumor immune signatures

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

    Professor Casey Greene

  213. 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

  214. 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, Professor Giorgio Valentini

  215. Gut check

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

    Professor Casey Greene

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

    Article • July 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Arjun Krishnan

  217. The future is unsupervised

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

    Professor Casey Greene

  218. 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

  219. 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

  220. Reproducible Computational Workflows with Continuous Analysis

    Article • June 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

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

    Article • May 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  222. Nothing but a hound dog

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

    Professor Casey Greene

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

    Article • May 2016, Cold Spring Harbor Laboratory Press

    Professor Casey Greene

  224. CoINcIDE: All together now

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

    Professor Casey Greene

  225. 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

  226. 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

  227. 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

  228. 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

  229. 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

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

    Article • PeerJ, January 2016, PeerJ

    Professor Casey Greene

  231. 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

  232. 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

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

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

    Professor Casey Greene

  234. 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

  235. 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

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

    Article • October 2015, PeerJ

    Professor Casey Greene

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

    Article • October 2015, PeerJ

    Professor Casey Greene

  238. 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

  239. 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

  240. 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

  241. 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

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

    Article • Nature Genetics, April 2015, Nature

    Mr Daniel S Himmelstein, Professor Casey Greene

  243. Adapting bioinformatics curricula for big data

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

    Professor Casey Greene

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

    Article • Nature Chemical Biology, January 2015, Nature

    Professor Casey Greene

  245. 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

  246. 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

  247. Big Data Bioinformatics

    Article • Journal of Cellular Physiology, August 2014, Wiley

    Professor Casey Greene

  248. 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

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

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

    Professor Casey Greene

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

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

    Professor Casey Greene

  251. 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

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

    Article • PLoS Computational Biology, March 2013, PLOS

    Professor Casey Greene

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

    Article • January 2013, Springer Science + Business Media

    Professor Casey Greene

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

    Article • PLoS Computational Biology, December 2012, PLOS

    Professor Casey Greene

  255. 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

  256. 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

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

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

    Professor Casey Greene

  258. 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

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

    Article • January 2011, Springer Science + Business Media

    Professor Casey Greene

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

    Article • January 2011, Springer Science + Business Media

    Professor Casey Greene

  261. Integrative Systems Biology for Data-Driven Knowledge Discovery

    Article • Seminars in Nephrology, September 2010, Elsevier

    Professor Casey Greene

  262. 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

  263. The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics

    Article • January 2010, Springer Science + Business Media

    Mr Daniel S Himmelstein, Professor Casey Greene

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

    Article • January 2010, Springer Science + Business Media

    Mr Daniel S Himmelstein, Professor Casey Greene

  265. 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

  266. Artificial Immune Systems for Epistasis Analysis in Human Genetics

    Article • January 2010, Springer Science + Business Media

    Professor Casey Greene

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

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

    Professor Casey Greene

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

    Article • PLOS One, June 2009, PLOS

    Professor Casey Greene

  269. 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

  270. 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

  271. 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

  272. 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

  273. 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

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

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

    Professor Casey Greene

  275. 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

  276. Solving complex problems in human genetics using GP

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

    Professor Casey Greene

  277. LTR Retrotransposon-Gene Associations in Drosophila melanogaster

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

    Professor Casey Greene

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

    Article • IGI Global

    Professor Casey Greene

  279. Ant Colony Optimization for Genome-Wide Genetic Analysis

    Article • Springer Science + Business Media

    Professor Casey Greene

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

    Article • Dartmouth College Library Press

    Professor Casey Greene

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

    Article • Springer Science + Business Media

    Professor Casey Greene