ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels. - Brian D. Halligan; Victor Ruotti; Weihong Jin; Scott Laffoon; Simon N. Twigger; Edward A. Dratz (Nucleic Acids Res., 2004)

DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. - Brian D. Halligan; Victor Ruotti; Simon N. Twigger; Andrew S. Greene (Nucleic Acids Res., 2005)

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. - You Jung Kim; Nikhil Teletia; Victor Ruotti; Christopher A. Maher; Arul M. Chinnaiyan; Ron M. Stewart; James A. Thomson; Jignesh M. Patel (Bioinform., 2009)

RNA-Seq gene expression estimation with read mapping uncertainty. - Bo Li 015; Victor Ruotti; Ron M. Stewart; James A. Thomson; Colin N. Dewey (Bioinform., 2010)

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. - Ning Leng; John A. Dawson; James A. Thomson; Victor Ruotti; Anna I. Rissman; Bart M. G. Smits; Jill D. Haag; Michael N. Gould; Ron M. Stewart; Christina Kendziorski (Bioinform., 2013)