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)

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

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)

DAnCER: Disease-Annotated Chromatin Epigenetics Resource. - Andrei L. Turinsky; Brian Turner; Rosanne C. Borja; James A. Gleeson; Michael Heath; Shuye Pu; Thomas Switzer; Dong Dong; Yunchen Gong; Tuan On; Xuejian Xiong; Andrew Emili; et al. (Nucleic Acids Res., 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)