A comparative analysis of the information content in long and short SAGE libraries. - Yi-Ju Li; Puting Xu; Xuejun Qin; Donald E. Schmechel; Christine M. Hulette; Jonathan L. Haines; Margaret A. Pericak-Vance; John R. Gilbert (BMC Bioinform., 2006)

Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data. - Tricia A. Thornton-Wells; Jason H. Moore; Jonathan L. Haines (BMC Bioinform., 2006)

PheKB.org: An Online Collaboration Tool for Phenotype Algorithm Research. - Joshua Pruitt; Peter Speltz; Jacqueline Kirby; Melissa A. Basford; Jonathan L. Haines; Joshua C. Denny (AMIA, 2012)

Genotype Correlation Analysis Reveals Pathway-Based Functional Disequilibrium and Potential Epistasis in the Human Interactome. - William S. Bush; Jonathan L. Haines (EvoApplications, 2014)

Size matters: How population size influences genotype-phenotype association studies in anonymized data. - Raymond Heatherly; Joshua C. Denny; Jonathan L. Haines; Dan M. Roden; Bradley A. Malin (J. Biomed. Informatics, 2014)

Mitochondrial Variation and the Risk of Age-Related Macular Degeneration Across Diverse Populations. - Nicole A. Restrepo; Sabrina L. Mitchell; Robert J. Goodloe; Deborah G. Murdock; Jonathan L. Haines; Dana C. Crawford (Pacific Symposium on Biocomputing, 2015)

Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models. - Jacob B. Hall; Jessica Cooke Bailey; Joshua Hoffman; Margaret A. Pericak-Vance; William K. Scott; Jaclyn Kovach; Stephen G. Schwartz; Anita Agarwal; Milam Brantley; Jonathan L. Haines; William S. Bush (BMC Bioinform., 2015)

Drug-drug Interaction Profiles of Medication Regimens Extracted from a De-identified Electronic Medical Records System. - Mariusz Butkiewicz; Nicole A. Restrepo; Jonathan L. Haines; Dana C. Crawford (CRI, 2016)

Pathway analysis by randomization incorporating structure - PARIS: an update. - Mariusz Butkiewicz; Jessica Cooke Bailey; Alex T. Frase; Scott M. Dudek; Brian L. Yaspan; Marylyn D. Ritchie; Sarah A. Pendergrass; Jonathan L. Haines (Bioinform., 2016)

Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model. - Jingchao Ni; Mehmet Koyutürk; Hanghang Tong; Jonathan L. Haines; Rong Xu; Xiang Zhang 001 (BMC Bioinform., 2016)

PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. - Jacqueline Kirby; Peter Speltz; Luke V. Rasmussen; Melissa A. Basford; Omri Gottesman; Peggy L. Peissig; Jennifer A. Pacheco; Gerard Tromp; Jyotishman Pathak; David S. Carrell; Stephen B. Ellis; Todd Lingren; et al. (J. Am. Medical Informatics Assoc., 2016)

Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants. - Mariusz Butkiewicz; Jonathan L. Haines; William S. Bush (Bioinform., 2017)

Functional annotation of genomic variants in studies of late-onset Alzheimer's disease. - Mariusz Butkiewicz; Elizabeth E. Blue; Yuk Yee Leung; Xueqiu Jian; Edoardo Marcora; Alan E. Renton; Amanda Kuzma; Li-San Wang; Daniel C. Koboldt; Jonathan L. Haines; William S. Bush (Bioinform., 2018)

Hadoop and PySpark for Reproducibility and Scalability of Genomic Sequencing Studies. - Nicholas R. Wheeler; Penelope Benchek; Brian W. Kunkle; Kara L. Hamilton-Nelson; MikeWarfe; Jeremy R. Fondran; Jonathan L. Haines; William S. Bush (PSB, 2020)

Automated identification of clinical features from sparsely annotated 3-dimensional medical imaging. - Nadav Rakocz; Jeffrey N. Chiang; Muneeswar G. Nittala; Giulia Corradetti; Liran Tiosano; Swetha Velaga; Michael Thompson; Brian L. Hill; Sriram Sankararaman; Jonathan L. Haines; Margaret A. Pericak-Vance; Dwight Stambolian; et al. (npj Digit. Medicine, 2021)