PROXIMO - a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS). - Sebastien K. Gerega; Kevin M. Downard (Bioinform., 2006)

ETISEQ - an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics. - Jason W. H. Wong; Alexander B. Schwahn; Kevin M. Downard (BMC Bioinform., 2009)

FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data. - Jason W. H. Wong; Alexander B. Schwahn; Kevin M. Downard (BMC Bioinform., 2010)

FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry. - Aaron T. L. Lun; Jason W. H. Wong; Kevin M. Downard (BMC Bioinform., 2012)