GEL: a novel genotype calling algorithm using empirical likelihood. - Dan L. Nicolae; Xiaolin Wu 002; Kazuaki Miyake; Nancy J. Cox (Bioinform., 2006)

SCAN: SNP and copy number annotation. - Eric R. Gamazon; Wei Zhang 253; Anuar Konkashbaev; Shiwei Duan; Emily O. Kistner; Dan L. Nicolae; M. Eileen Dolan; Nancy J. Cox (Bioinform., 2010)

Systems Pharmacogenomics-Bridging the Gap. - Marylyn D. Ritchie; Nancy J. Cox; Cheng Cheng; Scott Weiss; Teri E. Klein; Russ B. Altman (Pacific Symposium on Biocomputing, 2012)

Research and applications: Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. - Younghee Lee; Haiquan Li; Jianrong Li; Ellen Rebman; Ikbel Achour; Kelly Regan; Eric R. Gamazon; James L. Chen; Xinan Holly Yang; Nancy J. Cox; Yves A. Lussier (J. Am. Medical Informatics Assoc., 2013)

SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. - Wei Zhang 253; Eric R. Gamazon; Xu Zhang; Anuar Konkashbaev; Cong Liu; Keely L. Szilágyi; M. Eileen Dolan; Nancy J. Cox (Database J. Biol. Databases Curation, 2015)

A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis. - Rui Chen 021; Qiang Wei; Xiaowei Zhan; Xue Zhong; James S. Sutcliffe; Nancy J. Cox; Edwin H. Cook Jr.; Chun Li; Wei Chen 074; Bingshan Li (Bioinform., 2015)

Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes. - Vassily Trubetskoy; Alex A. Rodriguez; Uptal J. Dave; Nicholas Campbell; Emily L. Crawford; Edwin H. Cook Jr.; James S. Sutcliffe; Ian T. Foster; Ravi K. Madduri; Nancy J. Cox; Lea K. Davis (Bioinform., 2015)

Global circulation patterns of seasonal influenza viruses vary with antigenic drift. - Trevor Bedford; Steven Riley; Ian G. Barr; Shobha Broor; Mandeep Chadha; Nancy J. Cox; Rodney S. Daniels; C. Palani Gunasekaran; Aeron C. Hurt; Anne Kelso; Alexander Klimov; Nicola S. Lewis; et al. (Nat., 2015)

STAMS: STRING-assisted module search for genome wide association studies and application to autism. - Sara Hillenmeyer; Lea K. Davis; Eric R. Gamazon; Edwin H. Cook Jr.; Nancy J. Cox; Russ B. Altman (Bioinform., 2016)

Consistency in large pharmacogenomic studies. - Paul Geeleher; Eric R. Gamazon; Cathal Seoighe; Nancy J. Cox; Rong Stephanie Huang (Nat., 2016)

The impact of rare variation on gene expression across tissues. - Xin Li 130; Yungil Kim; Emily K. Tsang; Joe R. Davis; Farhan N. Damani; Colby Chiang; Gaelen T. Hess; Zachary Zappala; Benjamin J. Strober; Alexandra J. Scott; Amy Li; Andrea Ganna; et al. (Nat., 2017)

De novo pattern discovery enables robust assessment of functional consequences of non-coding variants. - Hai Yang 002; Rui Chen 021; Quan Wang 004; Qiang Wei; Ying Ji 002; Guangze Zheng 002; Xue Zhong; Nancy J. Cox; Bingshan Li (Bioinform., 2019)

PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records. - Neil S. Zheng; QiPing Feng; Vern Eric Kerchberger; Juan Zhao 003; Todd L. Edwards; Nancy J. Cox; C. Michael Stein; Dan M. Roden; Joshua C. Denny; Wei-Qi Wei (J. Am. Medical Informatics Assoc., 2020)

Implications of Clinical Bias When Building Electronic Algorithms for Medical Record Phenotyping: Lessons from Type 2 Diabetes Mellitus. - Annika B. Faucon; Megan Shuey; Lea K. Davis; Nancy J. Cox (AMIA, 2021)

DDIWAS: High-throughput electronic health record-based screening of drug-drug interactions. - Patrick Wu; Scott D. Nelson; Juan Zhao 003; Cosby A. Stone Jr.; QiPing Feng; Qingxia Chen; Eric A. Larson; Bingshan Li; Nancy J. Cox; C. Michael Stein; Elizabeth Phillips; Dan M. Roden; et al. (J. Am. Medical Informatics Assoc., 2021)

A retrospective approach to evaluating potential adverse outcomes associated with delay of procedures for cardiovascular and cancer-related diagnoses in the context of COVID-19. - Neil S. Zheng; Jeremy L. Warner; Travis J. Osterman; Quinn Stanton Wells; Xiao-Ou Shu; Stephen A. Deppen; Seth J. Karp; Shon Dwyer; QiPing Feng; Nancy J. Cox; Josh F. Peterson; C. Michael Stein; et al. (J. Biomed. Informatics, 2021)

The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. - Gengjie Jia; Yu Li 006; Xue Zhong; Kanix Wang; Milton Pividori; Rabab Alomairy; Aniello Esposito; Hatem Ltaief; Chikashi Terao; Masato Akiyama; Koichi Matsuda; David E. Keyes; et al. (Nat. Comput. Sci., 2023)

Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. - Gengjie Jia; Yu Li 006; Xue Zhong; Kanix Wang; Milton Pividori; Rabab Alomairy; Aniello Esposito; Hatem Ltaief; Chikashi Terao; Masato Akiyama; Koichi Matsuda; David E. Keyes; et al. (Nat. Comput. Sci., 2023)

Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs. - Nick Strayer; Siwei Zhang; Lydia Yao; Tess Vessels; Cosmin Adrian Bejan; Ryan S. Hsi; Jana K. Shirey-Rice; Justin M. Balko; Douglas B. Johnson; Elizabeth J. Phillips; Alex Bick; Todd L. Edwards; et al. (Bioinform., 2023)

FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. - Hufeng Zhou; Theodore Arapoglou; Xihao Li; Zilin Li; Xiuwen Zheng 001; Jill Moore; Abhijith Asok; Sushant Kumar; Elizabeth E. Blue; Steven Buyske; Nancy J. Cox; Adam Felsenfeld; et al. (Nucleic Acids Res., 2023)