Extending assembly of short DNA sequences to handle error. - William R. Jeck; Josephine A. Reinhardt; David A. Baltrus; Matthew T. Hickenbotham; Vincent J. Magrini; Elaine R. Mardis; Jeffery L. Dangl; Corbin D. Jones (Bioinform., 2007)

Design and implementation of a generalized laboratory data model. - Michael C. Wendl; Scott M. Smith; Craig S. Pohl; David J. Dooling; Asif T. Chinwalla; Kevin Crouse; Todd G. Hepler; Shin Leong; Lynn K. Carmichael; Mike Nhan; Benjamin J. Oberkfell; Elaine R. Mardis; et al. (BMC Bioinform., 2007)

Gallus GBrowse: a unified genomic database for the chicken. - Carl J. Schmidt; Michael Romanov; Oliver Ryder; Vincent J. Magrini; Matthew T. Hickenbotham; Jarret Glasscock; Sean McGrath 003; Elaine R. Mardis; Lincoln D. Stein (Nucleic Acids Res., 2008)

VarScan: variant detection in massively parallel sequencing of individual and pooled samples. - Daniel C. Koboldt; Ken Chen 001; Todd Wylie; David E. Larson; Michael D. McLellan; Elaine R. Mardis; George M. Weinstock; Richard K. Wilson; Li Ding (Bioinform., 2009)

Challenges of sequencing human genomes. - Daniel C. Koboldt; Li Ding; Elaine R. Mardis; Richard K. Wilson (Briefings Bioinform., 2010)

CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. - Qunyuan Zhang; Li Ding; David E. Larson; Daniel C. Koboldt; Michael D. McLellan; Ken Chen 001; Xiaoqi Shi; Aldi T. Kraja; Elaine R. Mardis; Richard K. Wilson; Ingrid B. Borecki; Michael A. Province (Bioinform., 2010)

PathScan: a tool for discerning mutational significance in groups of putative cancer genes. - Michael C. Wendl; John W. Wallis; Ling Lin; Cyriac Kandoth; Elaine R. Mardis; Richard K. Wilson; Li Ding (Bioinform., 2011)

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. - Ken Chen 001; John W. Wallis; Cyriac Kandoth; Joelle M. Kalicki-Veizer; Karen L. Mungall; Andrew J. Mungall; Steven J. M. Jones; Marco A. Marra; Timothy J. Ley; Elaine R. Mardis; Richard K. Wilson; John N. Weinstein; et al. (Bioinform., 2012)

SomaticSniper: identification of somatic point mutations in whole genome sequencing data. - David E. Larson; Christopher C. Harris; Ken Chen 001; Daniel C. Koboldt; Travis E. Abbott; David J. Dooling; Timothy J. Ley; Elaine R. Mardis; Richard K. Wilson; Li Ding (Bioinform., 2012)

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. - Christopher A. Miller 002; Brian S. White; Nathan D. Dees; Malachi Griffith; John S. Welch; Obi L. Griffith; Ravi Vij; Michael H. Tomasson; Timothy A. Graubert; Matthew J. Walter; Matthew J. Ellis; William S. Schierding; et al. (PLoS Comput. Biol., 2014)

Genome Modeling System: A Knowledge Management Platform for Genomics. - Malachi Griffith; Obi L. Griffith; Scott M. Smith; Avinash Ramu; Matthew B. Callaway; Anthony M. Brummett; Michael J. Kiwala; Adam C. Coffman; Allison A. Regier; Benjamin J. Oberkfell; Gabriel E. Sanderson; Thomas P. Mooney; et al. (PLoS Comput. Biol., 2015)

DGIdb 2.0: mining clinically relevant drug-gene interactions. - Alex H. Wagner; Adam C. Coffman; Benjamin J. Ainscough; Nicholas C. Spies; Zachary L. Skidmore; Katie M. Campbell; Kilannin Krysiak; Deng Pan; Joshua F. McMichael; James M. Eldred; Jason R. Walker; Richard K. Wilson; et al. (Nucleic Acids Res., 2016)

INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. - Jin Zhang 038; Elaine R. Mardis; Christopher A. Maher (Bioinform., 2017)

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. - Kilannin Krysiak; Arpad M. Danos; Jason Saliba; Joshua F. McMichael; Adam C. Coffman; Susanna Kiwala; Erica K. Barnell; Lana Sheta; Cameron J. Grisdale; Lynzey Kujan; Shahil Pema; Jake Lever; et al. (Nucleic Acids Res., 2023)

SNVstory: inferring genetic ancestry from genome sequencing data. - Audrey E. Bollas; Andrei Rajkovic; Defne Ceyhan; Jeffrey B. Gaither; Elaine R. Mardis; Peter White (BMC Bioinform., 2024)