SpecAlign - processing and alignment of mass spectra datasets. - Jason W. H. Wong; Gerard Cagney; Hugh M. Cartwright (Bioinform., 2005)

msmsEval: tandem mass spectral quality assignment for high-throughput proteomics. - Jason W. H. Wong; Matthew J. Sullivan; Hugh M. Cartwright; Gerard Cagney (BMC Bioinform., 2007)

Experimental Methods for Protein Interaction Identification and Characterization. - Peter Uetz; Björn Titz; Gerard Cagney (Protein-protein Interactions and Networks, 2008)

Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments. - Jason W. H. Wong; Matthew J. Sullivan; Gerard Cagney (Briefings Bioinform., 2008)

Optimal stepwise experimental design for pairwise functional interaction studies. - Fergal P. Casey; Gerard Cagney; Nevan J. Krogan; Denis C. Shields (Bioinform., 2008)

Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. - Derek Greene; Gerard Cagney; Nevan J. Krogan; Padraig Cunningham (Bioinform., 2008)

An Overview of Label-Free Quantitation Methods in Proteomics by Mass Spectrometry. - Jason W. H. Wong; Gerard Cagney (Proteome Bioinformatics, 2010)

Missing value imputation for epistatic MAPs. - Colm J. Ryan; Derek Greene; Gerard Cagney; Padraig Cunningham (BMC Bioinform., 2010)

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs. - Fergal P. Casey; Nevan J. Krogan; Denis C. Shields; Gerard Cagney (BMC Syst. Biol., 2011)

Improved functional overview of protein complexes using inferred epistatic relationships. - Colm J. Ryan; Derek Greene; Aude Guénolé; Haico van Attikum; Nevan J. Krogan; Pádraig Cunningham; Gerard Cagney (BMC Syst. Biol., 2011)

Global landscape of HIV-human protein complexes. - Stefanie Jäger; Peter Cimermancic; Natali Gulbahce; Jeffrey R. Johnson; Kathryn E. McGovern; Starlynn C. Clarke; Michael Shales; Gaelle Mercenne; Lars Pache; Kathy Li; Hilda Hernandez; Gwendolyn M. Jang; et al. (Nat., 2012)