Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. - Todd Wylie; John C. Martin; Michael Dante; Makedonka Dautova Mitreva; Sandra W. Clifton; Asif T. Chinwalla; Robert H. Waterston; Richard K. Wilson; James P. McCarter (Nucleic Acids Res., 2004)

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)

Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. - John C. Martin; Sahar Abubucker; Todd Wylie; Yong Yin; Zhengyuan Wang; Makedonka Dautova Mitreva (Nucleic Acids Res., 2009)

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)