ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules. - Anthony A. Philippakis; Fangxue Sherry He; Martha L. Bulyk (Pacific Symposium on Biocomputing, 2005)

Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells. - Anthony A. Philippakis; Brian W. Busser; Stephen S. Gisselbrecht; Fangxue Sherry He; Beatriz Estrada; Alan M. Michelson; Martha L. Bulyk (PLoS Comput. Biol., 2006)

Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. - Anthony A. Philippakis; Aaron M. Qureshi; Michael F. Berger; Martha L. Bulyk (J. Comput. Biol., 2008)

Predicting the binding preference of transcription factors to individual DNA k-mers. - Trevis M. Alleyne; Lourdes Peña Castillo; Gwenael Badis; Shaheynoor Talukder; Michael F. Berger; Andrew R. Gehrke; Anthony A. Philippakis; Martha L. Bulyk; Quaid Morris; Timothy R. Hughes (Bioinform., 2009)

The All of Us Research Program Researcher Portal: Innovative access to Unprecendented Data. - Andrea H. Ramirez; Anthony A. Philippakis; Gonçalo R. Abecasis; Paul A. Harris; Joshua C. Denny (AMIA, 2017)

The All of Us Research Program Researcher Workbench Phenotype Library: Five Disease Implementations. - Izabelle P. Humes; Roxana Loperena-Cortes; Melissa A. Basford; Kelsey R. Mayo; Joseph DiPaolo; David J. Schlueter; Jun Qian; Wei-Qi Wei; Robert J. Carroll; David Glazer; Paul A. Harris; Anthony A. Philippakis; et al. (AMIA, 2020)

The All of Us Research Program Researcher Workbench: Cloud based access and analytics to advance precision medicine. - Andrea H. Ramirez; Kelsey R. Mayo; Robert J. Carroll; Karthik Muthuraman; Melissa A. Basford; David Glazer; Paul A. Harris; Anthony A. Philippakis; Dan M. Roden (AMIA, 2020)

A structural variation reference for medical and population genetics. - Ryan L. Collins; Harrison Brand; Konrad J. Karczewski; Xuefang Zhao; Jessica Alföldi; Laurent C. Francioli; Amit V. Khera; Chelsea Lowther; Laura D. Gauthier; Harold Wang; Nicholas A. Watts; Matthew Solomonson; et al. (Nat., 2020)

Selection of 51 predictors from 13, 782 candidate multimodal features using machine learning improves coronary artery disease prediction. - Saaket Agrawal; Marcus D. R. Klarqvist; Connor Emdin; Aniruddh P. Patel; Manish D. Paranjpe; Patrick T. Ellinor; Anthony A. Philippakis; Kenney Ng; Puneet Batra; Amit V. Khera (Patterns, 2021)

Assessing the Robustness and Internal Consistency of the Pooled Cohort Equations. - Uri Kartoun; Shaan Khurshid; BC Kwon; Aniruddh P. Patel; Akl Fahed; Puneet Batra; Anthony A. Philippakis; Steven A. Lubitz; Amit V. Khera; Patrick T. Ellinor; Vibha Anand; Kenney Ng (AMIA, 2022)

STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis. - Sheila M. Gaynor; Kenneth E. Westerman; Lea L. Ackovic; Xihao Li; Zilin Li; Alisa Manning; Anthony A. Philippakis; Xihong Lin (Bioinform., 2022)

Cohort design and natural language processing to reduce bias in electronic health records research. - Shaan Khurshid; Christopher Reeder; Lia X. Harrington; Pulkit Singh; Gopal Sarma; Samuel F. Friedman; Paolo Di Achille; Nathaniel Diamant; Jonathan W. Cunningham; Ashby C. Turner; Emily S. Lau; Julian S. Haimovich; et al. (npj Digit. Medicine, 2022)

The All of Us Research Program: Data quality, utility, and diversity. - Andrea H. Ramirez; Lina M. Sulieman; David J. Schlueter; Alese E. Halvorson; Jun Qian; Francis Ratsimbazafy; Roxana Loperena-Cortes; Kelsey R. Mayo; Melissa A. Basford; Nicole Deflaux; Karthik Muthuraman; Karthik Natarajan; et al. (Patterns, 2022)

Unsupervised deep learning of electrocardiograms enables scalable human disease profiling. - Samuel F. Friedman; Shaan Khurshid; Rachael A. Venn; Xin Wang; Nathaniel Diamant; Paolo Di Achille; Lu-Chen Weng; Seung Hoan Choi; Christopher Reeder; James P. Pirruccello; Pulkit Singh; Emily S. Lau; et al. (npj Digit. Medicine, 2025)