Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics. - Atul J. Butte; Rong Chen 006 (AMIA, 2006)

Methodologies for Extracting Functional Pharmacogenomic Experiments from International Repository. - Yi-An Lin; Annie P. Chiang; Ray Lin; Peggy Yao; Rong Chen 006; Atul J. Butte (AMIA, 2007)

GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed. - Rong Chen 006; Rohan Mallelwar; Ajit Thosar; Shivkumar Venkatasubrahmanyam; Atul J. Butte (BMC Bioinform., 2008)

Ontology-driven indexing of public datasets for translational bioinformatics. - Nigam H. Shah; Clément Jonquet; Annie P. Chiang; Atul J. Butte; Rong Chen 006; Mark A. Musen (BMC Bioinform., 2009)

Content-based microarray search using differential expression profiles. - Jesse M. Engreitz; Alexander A. Morgan; Joel Dudley; Rong Chen 006; Rahul Thathoo; Russ B. Altman; Atul J. Butte (BMC Bioinform., 2010)

Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions. - Rong Chen 006; Tara K. Sigdel; Li Li 062; Neeraja Kambham; Joel Dudley; Szu-chuan Hsieh; R. Bryan Klassen; Amery Chen; Tuyen Caohuu; Alexander A. Morgan; Hannah A. Valantine; Kiran K. Khush; et al. (PLoS Comput. Biol., 2010)

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets. - Silpa Suthram; Joel Dudley; Annie P. Chiang; Rong Chen 006; Trevor Hastie; Atul J. Butte (PLoS Comput. Biol., 2010)

The Reference Human Genome Demonstrates High Risk of Type 1 Diabetes and Other Disorders. - Rong Chen 006; Atul J. Butte (Pacific Symposium on Biocomputing, 2011)

Matching Cancer Genomes to Established Cell Lines for Personalized Oncology. - Joel Dudley; Rong Chen 006; Atul J. Butte (Pacific Symposium on Biocomputing, 2011)

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. - Jesse M. Engreitz; Rong Chen 006; Alexander A. Morgan; Joel Dudley; Rohan Mallelwar; Atul J. Butte (Bioinform., 2011)

Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. - Chirag J. Patel; Rong Chen 006; Atul J. Butte (Bioinform., 2012)

Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. - Alexander A. Morgan; Rong Chen 006; Atul J. Butte (J. Am. Medical Informatics Assoc., 2012)

Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases. - David Ruau; Joel Dudley; Rong Chen 006; Nicholas G. Phillips; Gary E. Swan; Laura Lazzeroni; J. David Clark; Atul J. Butte; Martin S. Angst (PLoS Comput. Biol., 2012)

Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical Records. - Li Li 062; David Ruau; Rong Chen 006; Susan C. Weber; Atul J. Butte (Pacific Symposium on Biocomputing, 2013)

An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships. - Benjamin S. Glicksberg; Li Li 062; Wei-Yi Cheng; Khader Shameer; Jörg Hakenberg; Rafael Castellanos; Meng Ma; Lisong Shi; Hardik Shah; Joel T. Dudley; Rong Chen 006 (Pacific Symposium on Biocomputing, 2015)

DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. - Wei-Yi Cheng; Jörg Hakenberg; Shuyu Dan Li; Rong Chen 006 (Bioinform., 2016)

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. - Benjamin S. Glicksberg; Li Li 062; Marcus A. Badgeley; Khader Shameer; Roman Kosoy; Noam D. Beckmann; Nam Pho; Jörg Hakenberg; Meng Ma; Kristin L. Ayers; Gabriel E. Hoffman; Shuyu Dan Li; et al. (Bioinform., 2016)

Integrating 400 million variants from 80, 000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. - Jörg Hakenberg; Wei-Yi Cheng; Philippe Thomas 002; Ying-Chih Wang; Andrew V. Uzilov; Rong Chen 006 (BMC Bioinform., 2016)

Identify Cancer Driver Genes Through Shared Mendelian Disease Pathogenic Variants and Cancer Somatic Mutations. - Meng Ma; Changchang Wang; Benjamin S. Glicksberg; Eric E. Schadt; Shuyu Dan Li; Rong Chen 006 (PSB, 2017)

Automated disease cohort selection using word embeddings from Electronic Health Records. - Benjamin S. Glicksberg; Riccardo Miotto; Kipp W. Johnson; Khader Shameer; Li Li 062; Rong Chen 006; Joel T. Dudley (PSB, 2018)

Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disorders. - Milo R. Smith; Benjamin S. Glicksberg; Li Li 062; Rong Chen 006; Hirofumi Morishita; Joel T. Dudley (PSB, 2018)

Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. - Khader Shameer; Benjamin S. Glicksberg; Rachel Hodos; Kipp W. Johnson; Marcus A. Badgeley; Ben Readhead; Max S. Tomlinson; Timothy O'Connor; Riccardo Miotto; Brian A. Kidd; Rong Chen 006; Avi Ma'ayan; et al. (Briefings Bioinform., 2018)

DxTree: a visual analytics tool for hierarchical representation of disease cohort counts for clinical trials. - Mingwei Zhang; Zongzhi Liu; Meng Ma; Kyeryoung Lee; Yun Mai; Scott Jones; Chris Gilman; Ying Ru; Matthew Deitz; Yunrou Gong; Xiang Zhou; Krish Ghosh; et al. (AMIA, 2020)

The Real-World Trend Analysis of Cancer Drugs Empowered by Natural Language Processing. - Meng Ma; Kyeryoung Lee; Yun Mai; Chris Gilman; Zongzhi Liu; Mingwei Zhang; Minghao Li; Arielle Redfern; Tommy Mullaney; Tony Prentice; Paul McDonagh; Qi Pan; et al. (AMIA, 2021)

Applying Bayesian hyperparameter optimization towards accurate and efficient topic modeling in clinical notes. - Minghao Li; Kyeryoung Lee; Zongzhi Liu; Meng Ma; Qi Pan; Rong Chen 006; Eric E. Schadt; Xiaoyan Wang (ICHI, 2021)