PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. - Sylvain Pitre; Frank K. H. A. Dehne; Albert Chan; James Cheetham; Alex Duong; Andrew Emili; Marinella Gebbia; Jack Greenblatt; Matthew Jessulat; Nevan J. Krogan; Xuemei Luo; Ashkan Golshani (BMC Bioinform., 2006)

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)

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data. - Sourav Bandyopadhyay; Ryan M. Kelley; Nevan J. Krogan; Trey Ideker (PLoS Comput. Biol., 2008)

GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. - Marie E. Fahey; Melanie J. Bennett; Cathal Mahon; Stefanie Jäger; Lars Pache; Dhiraj Kumar; Alex Shapiro; Kanury Rao; Sumit K. Chanda; Charles S. Craik; Alan D. Frankel; Nevan J. Krogan (BMC Bioinform., 2011)

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)

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. - Jeffrey R. Johnson; Silvia D. Santos; Tasha Johnson; Ursula Pieper 001; Marta Strumillo; Omar Wagih; Andrej Sali; Nevan J. Krogan; Pedro Beltrão (PLoS Comput. Biol., 2015)

Non-degradative Ubiquitination of Protein Kinases. - K. Aurelia Ball; Jeffrey R. Johnson; Mary K. Lewinski; John Guatelli; Erik Verschueren; Nevan J. Krogan; Matthew P. Jacobson (PLoS Comput. Biol., 2016)