Computational expansion of genetic networks. - Amos Tanay; Ron Shamir (ISMB (Supplement of Bioinformatics), 2001)

Minreg: Inferring an active regulator set. - Dana Pe'er; Aviv Regev; Amos Tanay (ISMB, 2002)

Discovering statistically significant biclusters in gene expression data. - Amos Tanay; Roded Sharan; Ron Shamir (ISMB, 2002)

Modeling transcription programs: inferring binding site activity and dose-response model optimization. - Amos Tanay; Ron Shamir (RECOMB, 2003)

Modeling and Analysis of Heterogeneous Regulation in Biological Networks. - Irit Gat-Viks; Amos Tanay; Ron Shamir (Regulatory Genomics, 2004)

Multilevel Modeling and Inference of Transcription Regulation. - Amos Tanay; Ron Shamir (J. Comput. Biol., 2004)

The Factor Graph Network Model for Biological Systems. - Irit Gat-Viks; Amos Tanay; Daniela Raijman; Ron Shamir (RECOMB, 2005)

EXPANDER - an integrative program suite for microarray data analysis. - Ron Shamir; Adi Maron-Katz; Amos Tanay; Chaim Linhart; Israel Steinfeld; Roded Sharan; Yosef Shiloh; Ran Elkon (BMC Bioinform., 2005)

Computational analysis of transcriptional programs: function and evolution - Amos Tanay (2005)

A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks. - Irit Gat-Viks; Amos Tanay; Daniela Raijman; Ron Shamir (J. Comput. Biol., 2006)

MinReg: A Scalable Algorithm for Learning Parsimonious Regulatory Networks in Yeast and Mammals. - Dana Pe'er; Amos Tanay; Aviv Regev (J. Mach. Learn. Res., 2006)

Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites. - Daniela Raijman; Ron Shamir; Amos Tanay (PLoS Comput. Biol., 2008)

Spatial Clustering of Multivariate Genomic and Epigenomic Information. - Rami Jaschek; Amos Tanay (RECOMB, 2009)

Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast. - Ephraim Kenigsberg; Amir Bar; Eran Segal; Amos Tanay (PLoS Comput. Biol., 2010)

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks. - Pedro Olivares-Chauvet; Zohar Mukamel; Aviezer Lifshitz; Omer Schwartzman; Noa Oded Elkayam; Yaniv Lubling; Gintaras Deikus; Robert P. Sebra; Amos Tanay (Nat., 2016)