THOR: targeted high-throughput ortholog reconstructor. - Matthew N. Bainbridge; René L. Warren; An He; Mikhail Bilenky; Gordon Robertson; Steven J. M. Jones (Bioinform., 2007)

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. - Anthony P. Fejes; Gordon Robertson; Mikhail Bilenky; Richard Varhol; Matthew N. Bainbridge; Steven J. M. Jones (Bioinform., 2008)

Enabling Atlas2 personal genome analysis on the cloud. - Uday S. Evani; Danny Challis; Jin Yu 003; Andrew R. Jackson; Sameer Paithankar; Matthew N. Bainbridge; Cristian Coarfa; Aleksandar Milosavljevic; Fuli Yu (GENSiPS, 2011)

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. - Jeffrey G. Reid; Andrew Carroll; Narayanan Veeraraghavan; Mahmoud Dahdouli; Andreas Sundquist; Adam C. English; Matthew N. Bainbridge; Simon White; William J. Salerno; Christian Buhay; Fuli Yu; Donna M. Muzny; et al. (BMC Bioinform., 2014)

SV-STAT accurately detects structural variation via alignment to reference-based assemblies. - Caleb F. Davis; Deborah I. Ritter; David A. Wheeler; Hongmei Wang; Yan Ding; Shannon P. Dugan; Matthew N. Bainbridge; Donna M. Muzny; Pulivarthi H. Rao; Tsz-Kwong Man; Sharon E. Plon; Richard A. Gibbs; et al. (Source Code Biol. Medicine, 2016)

A machine learning decision support tool optimizes WGS utilization in a neonatal intensive care unit. - Edwin F. Juarez; Bennet Peterson; Erica Sanford Kobayashi; Sheldon Gilmer; Laura E. Tobin; Brandan Schultz; Jerica Lenberg; Jeanne Carroll; Shiyu Bai-Tong; Nathaly M. Sweeney; Curtis Beebe; Lawrence Stewart; et al. (npj Digit. Medicine, 2025)