AVIS: AJAX viewer of interactive signaling networks. - Seth I. Berger; Ravi Iyengar; Avi Ma'ayan (Bioinform., 2007)

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. - Seth I. Berger; Jeremy M. Posner; Avi Ma'ayan (BMC Bioinform., 2007)

Network analyses in systems pharmacology. - Seth I. Berger; Ravi Iyengar (Bioinform., 2009)

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. - Avi Ma'ayan; Sherry L. Jenkins; Ryan L. Webb; Seth I. Berger; Sudarshan P. Purushothaman; Noura S. Abul-Husn; Jeremy M. Posner; Tony Flores; Ravi Iyengar (BMC Syst. Biol., 2009)

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. - Alexander Lachmann; Huilei Xu; Jayanth Krishnan; Seth I. Berger; Amin R. Mazloom; Avi Ma'ayan (Bioinform., 2010)