Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. - Amin R. Mazloom; Ruth Dannenfelser; Neil R. Clark; Arsen V. Grigoryan; Kathryn M. Linder; Timothy Cardozo; Julia C. Bond; Aislyn D. W. Boran; Ravi Iyengar; Anna Malovannaya; Rainer B. Lanz; Avi Ma'ayan (PLoS Comput. Biol., 2011)

Genes2FANs: connecting genes through functional association networks. - Ruth Dannenfelser; Neil R. Clark; Avi Ma'ayan (BMC Bioinform., 2012)

Sets2Networks: network inference from repeated observations of sets. - Neil R. Clark; Ruth Dannenfelser; Christopher M. Tan; Michael E. Komosinski; Avi Ma'ayan (BMC Syst. Biol., 2012)

ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. - Yan Kou; Edward Y. Chen; Neil R. Clark; Qiaonan Duan; Christopher M. Tan; Avi Ma'ayan (CD-ARES, 2013)

Network2Canvas: network visualization on a canvas with enrichment analysis. - Christopher M. Tan; Edward Y. Chen; Ruth Dannenfelser; Neil R. Clark; Avi Ma'ayan (Bioinform., 2013)

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. - Edward Y. Chen; Christopher M. Tan; Yan Kou; Qiaonan Duan; Zichen Wang 002; Gabriela Vaz Meirelles; Neil R. Clark; Avi Ma'ayan (BMC Bioinform., 2013)

The characteristic direction: a geometrical approach to identify differentially expressed genes. - Neil R. Clark; Kevin S. Hu; Axel S. Feldmann; Yan Kou; Edward Y. Chen; Qiaonan Duan; Avi Ma'ayan (BMC Bioinform., 2014)

Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. - Neil R. Clark; Maciej Szymkiewicz; Zichen Wang 002; Caroline D. Monteiro; Matthew R. Jones; Avi Ma'ayan (BIBM, 2015)

Dynamics of the discovery process of protein-protein interactions from low content studies. - Zichen Wang 002; Neil R. Clark; Avi Ma'ayan (BMC Syst. Biol., 2015)

Drug-induced adverse events prediction with the LINCS L1000 data. - Zichen Wang 002; Neil R. Clark; Avi Ma'ayan (Bioinform., 2016)

Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations. - Avi Ma'ayan; Neil R. Clark (CoRR, 2016)

Cell-specific prediction and application of drug-induced gene expression . - Rachel Hodos; Ping Zhang 016; Hao-Chih Lee; Qiaonan Duan; Zichen Wang 002; Neil R. Clark; Avi Ma'ayan; Fei Wang 001; Brian A. Kidd; Jianying Hu; David A. Sontag; Joel Dudley (PSB, 2018)