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)

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)

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. - Beifang Niu; Kai Ye 001; Qunyuan Zhang; Charles Lu 002; Mingchao Xie; Michael D. McLellan; Michael C. Wendl; Li Ding (Bioinform., 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)

BreakPoint Surveyor: a pipeline for structural variant visualization. - Matthew A. Wyczalkowski; Kristine M. Wylie; Song Cao; Michael D. McLellan; Jennifer Flynn; Mo Huang; Kai Ye 001; Xian Fan; Ken Chen 001; Michael C. Wendl; Li Ding (Bioinform., 2017)