The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database. - John S. Garavelli; Zhenglin Hou; Nagarajan Pattabiraman; Robert M. Stephens (Nucleic Acids Res., 2001)

RTCGD: retroviral tagged cancer gene database. - Keiko Akagi; Takeshi Suzuki; Robert M. Stephens; Nancy A. Jenkins; Neal G. Copeland (Nucleic Acids Res., 2004)

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). - Barry Zeeberg; Haiying Qin; Sudarshan Narasimhan; Margot Sunshine; Hong Cao; David W. Kane; Mark Reimers; Robert M. Stephens; David Bryant; Stanley K. Burt; Eldad Elnekave; Danielle M. Hari; et al. (BMC Bioinform., 2005)

Transcriptomic response to differentiation induction. - G. W. Patton; Robert M. Stephens; I. A. Sidorov; X. Xiao; Richard A. Lempicki; Dimiter S. Dimitrov; Robert H. Shoemaker; G. Tudor (BMC Bioinform., 2006)

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. - Ming Yi; Jay D. Horton; Jonathan C. Cohen; Helen H. Hobbs; Robert M. Stephens (BMC Bioinform., 2006)

botXminer: mining biomedical literature with a new web-based application. - Uma Mudunuri; Robert M. Stephens; David Bruining; David Liu; Frank J. Lebeda (Nucleic Acids Res., 2006)

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. - Brad T. Sherman; Da Wei Huang; Qina Tan; Yongjian Guo; Stephan Bour; David Liu; Robert M. Stephens; Michael W. Baseler; H. Clifford Lane; Richard A. Lempicki (BMC Bioinform., 2007)

DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. - Da Wei Huang; Brad T. Sherman; Qina Tan; Joseph Kir; David Liu; David Bryant; Yongjian Guo; Robert M. Stephens; Michael W. Baseler; H. Clifford Lane; Richard A. Lempicki (Nucleic Acids Res., 2007)

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. - Yuelin Zhu; Sean R. Davis; Robert M. Stephens; Paul S. Meltzer; Yidong Chen 002 (Bioinform., 2008)

Pathway Analysis: Pathway Signatures and Classification. - Ming Yi; Robert M. Stephens (Statistics and Informatics in Molecular Cancer Research, 2009)

bioDBnet: the biological database network. - Uma Mudunuri; Anney Che; Ming Yi; Robert M. Stephens (Bioinform., 2009)

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis. - Ming Yi; Uma Mudunuri; Anney Che; Robert M. Stephens (BMC Bioinform., 2009)

IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding. - Regina Z. Cer; Uma Mudunuri; Robert M. Stephens; Frank J. Lebeda (Nucleic Acids Res., 2009)

MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains. - Keiko Akagi; Robert M. Stephens; Jingfeng Li; Evgenji Evdokimov; Michael R. Kuehn; Natalia Volfovsky; David E. Symer (Nucleic Acids Res., 2010)

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. - Regina Z. Cer; Kevin H. Bruce; Uma Mudunuri; Ming Yi; Natalia Volfovsky; Brian T. Luke; Albino Bacolla; Jack R. Collins; Robert M. Stephens (Nucleic Acids Res., 2011)

DAVID-WS: a stateful web service to facilitate gene/protein list analysis. - Xiaoli Jiao; Brad T. Sherman; Da Wei Huang; Robert M. Stephens; Michael W. Baseler; H. Clifford Lane; Richard A. Lempicki (Bioinform., 2012)

SRAdb: query and use public next-generation sequencing data from within R. - Yuelin Zhu; Robert M. Stephens; Paul S. Meltzer; Sean R. Davis (BMC Bioinform., 2013)

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools. - Regina Z. Cer; Duncan E. Donohue; Uma Mudunuri; Nuri A. Temiz; Michael A. Loss; Nathan J. Starner; Goran N. Halusa; Natalia Volfovsky; Ming Yi; Brian T. Luke; Albino Bacolla; Jack R. Collins; et al. (Nucleic Acids Res., 2013)

AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations. - Hue Vuong; Robert M. Stephens; Natalia Volfovsky (Bioinform., 2014)

Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. - Ma Liang; Castle Raley; Xin Zheng; Geetha Kutty; Emile Gogineni; Brad T. Sherman; Qiang Sun; Xiongfong Chen; Thomas Skelly; Kristine Jones; Robert M. Stephens; Bin Zhou; et al. (BioData Min., 2016)