An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming. - Casey S. Greene; Bill C. White; Jason H. Moore (PRIB, 2007)

Ant Colony Optimization for Genome-Wide Genetic Analysis. - Casey S. Greene; Bill C. White; Jason H. Moore (ANTS Conference, 2008)

Using expert knowledge in initialization for genome-wide analysis of epistasis using genetic programming. - Casey S. Greene; Bill C. White; Jason H. Moore (GECCO, 2008)

Nature-inspired algorithms for the genetic analysis of epistasis in common human diseases: Theoretical assessment of wrapper vs. filter approaches. - Casey S. Greene; Jeff Kiralis; Jason H. Moore (IEEE Congress on Evolutionary Computation, 2009)

Sensible initialization using expert knowledge for genome-wide analysis of epistasis using genetic programming. - Casey S. Greene; Bill C. White; Jason H. Moore (IEEE Congress on Evolutionary Computation, 2009)

Development and evaluation of an open-ended computational evolution system for the creation of digital organisms with complex genetic architecture. - Anna L. Tyler; Bill C. White; Casey S. Greene; Paul C. Andrews; Richard Cowper-Sallari; Jason H. Moore (IEEE Congress on Evolutionary Computation, 2009)

An Analysis of New Expert Knowledge Scaling Methods for Biologically Inspired Computing. - Jason M. Gilmore; Casey S. Greene; Peter C. Andrews; Jeff Kiralis; Jason H. Moore (ECAL (2), 2009)

An Open-Ended Computational Evolution Strategy for Evolving Parsimonious Solutions to Human Genetics Problems. - Casey S. Greene; Douglas P. Hill; Jason H. Moore (ECAL (1), 2009)

Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease. - Casey S. Greene; Jason M. Gilmore; Jeff Kiralis; Peter C. Andrews; Jason H. Moore (EvoBIO, 2009)

Environmental noise improves epistasis models of genetic data discovered using a computational evolution system. - Casey S. Greene; Douglas P. Hill; Jason H. Moore (GECCO, 2009)

Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions. - Casey S. Greene; Nadia M. Penrod; Jeff Kiralis; Jason H. Moore (BioData Min., 2009)

Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms Requires Strategies which Exploit Domain-Specific Knowledge. - Casey S. Greene; Jason H. Moore (Nature-Inspired Informatics for Intelligent Applications and Knowledge Discovery, 2010)

The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics. - Casey S. Greene; Daniel S. Himmelstein; Jeff Kiralis; Jason H. Moore (EvoBIO, 2010)

A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships. - Casey S. Greene; Daniel S. Himmelstein; Jason H. Moore (EvoBIO, 2010)

Artificial Immune Systems for Epistasis Analysis in Human Genetics. - Nadia M. Penrod; Casey S. Greene; Delaney Granizo-MacKenzie; Jason H. Moore (EvoBIO, 2010)

Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units. - Nicholas A. Sinnott-Armstrong; Casey S. Greene; Jason H. Moore (GECCO, 2010)

Enabling Personal Genomics with an Explicit Test of Epistasis. - Casey S. Greene; Daniel S. Himmelstein; Heather H. Nelson; Karl T. Kelsey; Scott M. Williams; Angeline S. Andrew; Margaret R. Karagas; Jason H. Moore (Pacific Symposium on Biocomputing, 2010)

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. - Casey S. Greene; Nicholas A. Sinnott-Armstrong; Daniel S. Himmelstein; Paul J. Park; Jason H. Moore; Brent T. Harris (Bioinform., 2010)

Evolving hard problems: Generating human genetics datasets with a complex etiology. - Daniel S. Himmelstein; Casey S. Greene; Jason H. Moore (BioData Min., 2011)

PILGRM: an interactive data-driven discovery platform for expert biologists. - Casey S. Greene; Olga G. Troyanskaya (Nucleic Acids Res., 2011)

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. - Aaron K. Wong; Christopher Y. Park; Casey S. Greene; Lars Ailo Bongo; Yuanfang Guan; Olga G. Troyanskaya (Nucleic Acids Res., 2012)

Chapter 2: Data-Driven View of Disease Biology. - Casey S. Greene; Olga G. Troyanskaya (PLoS Comput. Biol., 2012)

Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments. - Jie Tan; Gavin D. Grant; Michael L. Whitfield; Casey S. Greene (EvoBIO, 2013)

Session introduction. - Graciela Gonzalez 001; Kevin Bretonnel Cohen; Casey S. Greene; Udo Hahn; Maricel G. Kann; Robert Leaman; Nigam Shah; Jieping Ye (Pacific Symposium on Biocomputing, 2013)

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. - Christopher Y. Park; Aaron K. Wong; Casey S. Greene; Jessica Rowland; Yuanfang Guan; Lars Ailo Bongo; Rebecca D. Burdine; Olga G. Troyanskaya (PLoS Comput. Biol., 2013)

Identification of Novel Genetic Models of Glaucoma Using the "EMERGENT" Genetic Programming-Based Artificial Intelligence System. - Jason H. Moore; Casey S. Greene; Douglas P. Hill (GPTP, 2014)

Applications of Bioinformatics to Non-Coding RNAs in the Era of Next-Generation Sequencing. - Chao Cheng; Jason H. Moore; Casey S. Greene (Pacific Symposium on Biocomputing, 2014)

Session introduction. - Graciela Gonzalez 001; Kevin Bretonnel Cohen; Robert Leaman; Casey S. Greene; Nigam Shah; Maricel G. Kann; Jieping Ye (Pacific Symposium on Biocomputing, 2014)

Computational genetics analysis of grey matter density in Alzheimer's disease. - Amanda L. Zieselman; Jonathan M. Fisher; Ting Hu 001; Peter C. Andrews; Casey S. Greene; Li Shen 001; Andrew J. Saykin; Jason H. Moore (BioData Min., 2014)

Unsupervised Feature Construction and Knowledge Extraction from Genome-Wide Assays of Breast Cancer with Denoising Autoencoders. - Jie Tan; Matthew Ung; Chao Cheng; Casey S. Greene (Pacific Symposium on Biocomputing, 2015)

Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study. - Jiang Gui; Casey S. Greene; Con Sullivan; Walter Taylor; Jason H. Moore; Carol Kim (BioData Min., 2015)

Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms. - J. Matthew Mahoney; Jaclyn N. Taroni; Viktor Martyanov; Tammara A. Wood; Casey S. Greene; Patricia A. Pioli; Monique E. Hinchcliff; Michael L. Whitfield (PLoS Comput. Biol., 2015)

Computational Approaches to Study Microbes and Microbiomes. - Casey S. Greene; James A. Foster; Bruce A. Stanton; Deborah A. Hogan; Yana Bromberg (PSB, 2016)

Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. - Graciela Gonzalez 001; Tasnia Tahsin; Britton C. Goodale; Anna C. Greene; Casey S. Greene (Briefings Bioinform., 2016)

Adapting bioinformatics curricula for big data. - Anna C. Greene; Kristine A. Giffin; Casey S. Greene; Jason H. Moore (Briefings Bioinform., 2016)

Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology. - Daniel S. Himmelstein; Casey S. Greene; Jason H. Moore (BioData Min., 2016)

Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. - Ailin Song; Jingwen Yan; Sungeun Kim; Shannon L. Risacher; Aaron K. Wong; Andrew J. Saykin; Li Shen 001; Casey S. Greene (BioData Min., 2016)

Semi-supervised learning of the electronic health record for phenotype stratification. - Brett K. Beaulieu-Jones; Casey S. Greene (J. Biomed. Informatics, 2016)

No-Boundary Thinking in Bioinformatics. - Jason H. Moore; Steven F. Jennings; Casey S. Greene; Lawrence E. Hunter; Andy D. Perkins; ClarLynda R. Williams-DeVane; Donald C. Wunsch; Zhongming Zhao; Xiuzhen Huang (PSB, 2017)

Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. - Xiaohui Yao; Jingwen Yan; Kefei Liu 001; Sungeun Kim; Kwangsik Nho; Shannon L. Risacher; Casey S. Greene; Jason H. Moore; Andrew J. Saykin; Li Shen 001 (Bioinform., 2017)

ADAGE signature analysis: differential expression analysis with data-defined gene sets. - Jie Tan; Matt Huyck; Dongbo Hu; René A. Zelaya; Deborah A. Hogan; Casey S. Greene (BMC Bioinform., 2017)

Session Introduction. - Graciela Gonzalez-Hernandez; Abeed Sarker; Karen O'Connor; Casey S. Greene; Hongfang Liu (PSB, 2018)

Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. - Lia X. Harrington; Gregory P. Way; Jennifer A. Doherty; Casey S. Greene (PSB, 2018)

Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. - Gregory P. Way; Casey S. Greene (PSB, 2018)

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. - Kathleen M. Chen; Jie Tan; Gregory P. Way; Georgia Doing; Deborah A. Hogan; Casey S. Greene (BioData Min., 2018)

Text Mining and Machine Learning for Precision Medicine. - Graciela Gonzalez 001; Zhiyong Lu; Robert Leaman; Davy Weissenbacher; Mary Regina Boland; Yong Chen 016; Jingcheng Du; Juliane Fluck; Casey S. Greene; John H. Holmes; Aditya Kashyap; Rikke Linnemann Nielsen; et al. (PSB, 2019)

Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. - Qiwen Hu; Casey S. Greene (PSB, 2019)

Learning and Imputation for Mass-spec Bias Reduction (LIMBR). - Alexander M. Crowell; Casey S. Greene; Jennifer J. Loros; Jay C. Dunlap (Bioinform., 2019)

Open collaborative writing with Manubot. - Daniel S. Himmelstein; Vincent Rubinetti; David R. Slochower; Dongbo Hu; Venkat S. Malladi; Casey S. Greene; Anthony Gitter (PLoS Comput. Biol., 2019)

Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. - Madison Cooley; Casey S. Greene; Davis Issac; Milton Pividori; Blair D. Sullivan (ACDA, 2021)

An Open-Publishing Response to the COVID-19 Infodemic. - Halie M. Rando; Simina M. Boca; Lucy D'Agostino McGowan; Daniel S. Himmelstein; Michael P. Robson; Vincent Rubinetti; Ryan Velazquez; Casey S. Greene; Anthony Gitter (DISCO@JCDL, 2021)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

Ten Quick Tips for Deep Learning in Biology. - Benjamin D. Lee; Anthony Gitter; Casey S. Greene; Sebastian Raschka; Finlay Maguire; Alexander J. Titus; Michael D. Kessler; Alexandra J. Lee; Marc G. Chevrette; Paul Allen Stewart; Thiago Britto-Borges; Evan M. Cofer; et al. (CoRR, 2021)

Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health. - Ryan T. Scott; Erik L. Antonsen; Lauren M. Sanders; Jaden J. A. Hastings; Seung-Min Park; Graham Mackintosh; Robert J. Reynolds; Adrienne L. Hoarfrost; Aenor Sawyer; Casey S. Greene; Benjamin S. Glicksberg; Corey A. Theriot; et al. (CoRR, 2021)

Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs. - Lauren M. Sanders; Jason H. Yang; Ryan T. Scott; Amina Ann Qutub; Héctor García Martín; Daniel C. Berrios; Jaden J. A. Hastings; Jon Rask; Graham Mackintosh; Adrienne L. Hoarfrost; Stuart J. Chalk; John Kalantari; et al. (CoRR, 2021)

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. - Ariel A. Hippen; Matias M. Falco; Lukas M. Weber; Erdogan Pekcan Erkan; Kaiyang Zhang; Jennifer Anne Doherty; Anna Vähärautio; Casey S. Greene; Stephanie C. Hicks (PLoS Comput. Biol., 2021)

Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. - David N. Nicholson; Daniel S. Himmelstein; Casey S. Greene (BioData Min., 2022)

Ten simple rules for large-scale data processing. - Arkarachai Fungtammasan; Alexandra Lee; Jaclyn N. Taroni; Kurt Wheeler; Chen-Shan Chin; Sean Davis 001; Casey S. Greene (PLoS Comput. Biol., 2022)

Ten quick tips for deep learning in biology. - Benjamin D. Lee; Anthony Gitter; Casey S. Greene; Sebastian Raschka; Finlay Maguire; Alexander J. Titus; Michael D. Kessler; Alexandra J. Lee; Marc G. Chevrette; Paul Allen Stewart; Thiago Britto-Borges; Evan M. Cofer; et al. (PLoS Comput. Biol., 2022)

SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. - Alexandra J. Lee; Dallas L. Mould; Jake Crawford; Dongbo Hu; Rani K. Powers; Georgia Doing; James C. Costello; Deborah A. Hogan; Casey S. Greene (Genom. Proteom. Bioinform., 2022)

wenda_gpu: fast domain adaptation for genomic data. - Ariel A. Hippen; Jake Crawford; Jacob R. Gardner; Casey S. Greene (Bioinform., 2022)

Changing word meanings in biomedical literature reveal pandemics and new technologies. - David N. Nicholson; Faisal Alquaddoomi; Vincent Rubinetti; Casey S. Greene (BioData Min., 2023)

Biological research and self-driving labs in deep space supported by artificial intelligence. - Lauren M. Sanders; Ryan T. Scott; Jason H. Yang; Amina Ann Qutub; Héctor García Martín; Daniel C. Berrios; Jaden J. A. Hastings; Jon Rask; Graham Mackintosh; Adrienne L. Hoarfrost; Stuart J. Chalk; John Kalantari; et al. (Nat. Mac. Intell., 2023)

Biomonitoring and precision health in deep space supported by artificial intelligence. - Ryan T. Scott; Lauren M. Sanders; Erik L. Antonsen; Jaden J. A. Hastings; Seung-Min Park; Graham Mackintosh; Robert J. Reynolds; Adrienne L. Hoarfrost; Aenor Sawyer; Casey S. Greene; Benjamin S. Glicksberg; Corey A. Theriot; et al. (Nat. Mac. Intell., 2023)

The effect of non-linear signal in classification problems using gene expression. - Benjamin J. Heil; Jake Crawford; Casey S. Greene (PLoS Comput. Biol., 2023)

MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes. - Ricardo Avila; Vincent Rubinetti; Xinghua Zhou; Dongbo Hu; Zhongchao Qian; Marco Alvarado Cano; Everaldo Rodrigo Rodolpho; Ginger Tsueng; Casey S. Greene; Chunlei Wu (Nucleic Acids Res., 2023)

A publishing infrastructure for Artificial Intelligence (AI)-assisted academic authoring. - Milton Pividori; Casey S. Greene (J. Am. Medical Informatics Assoc., 2024)

Best holdout assessment is sufficient for cancer transcriptomic model selection. - Jake Crawford; Maria Chikina; Casey S. Greene (Patterns, 2024)

BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. - Natalie R. Davidson; Fan Zhang; Casey S. Greene (PLoS Comput. Biol., 2025)