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)

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)

Finding Maximum Edge Bicliques in Convex Bipartite Graphs. - Doron Nussbaum; Shuye Pu; Jörg-Rüdiger Sack; Takeaki Uno; Hamid Zarrabi-Zadeh (Algorithmica, 2012)