GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks. - James Vlasblom; Samuel Wu; Shuye Pu; Mark Superina; Gina Liu; Chris Orsi; Shoshana J. Wodak (Bioinform., 2006)

Local coherence in genetic interaction patterns reveals prevalent functional versatility. - Shuye Pu; Karen Ronen; James Vlasblom; Jack Greenblatt; Shoshana J. Wodak (Bioinform., 2008)

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. - James Vlasblom; Shoshana J. Wodak (BMC Bioinform., 2009)

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. - Brian Turner; Sabry Razick; Andrei L. Turinsky; James Vlasblom; Edgard K. Crowdy; Emerson Cho; Kyle Morrison; Ian M. Donaldson; Shoshana J. Wodak (Database J. Biol. Databases Curation, 2010)

OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. - Yanqi Hao; Anna Merkoulovitch; James Vlasblom; Shuye Pu; Andrei L. Turinsky; Denitza Roudeva; Brian Turner; Jack Greenblatt; Shoshana J. Wodak (Bioinform., 2011)

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. - James Vlasblom; Khalid Zuberi; Harold Rodriguez; Roland Arnold; Alla Gagarinova; Viktor Deineko; Ashwani Kumar; Elisa Leung; Kamran Rizzolo; Bahram Samanfar; Luke Chang; Sadhna Phanse; et al. (Bioinform., 2015)