| 2016 | RECOMB | Revealing the Genetic Basis of Immune Traits in the Absence of Experimental Immunophenotyping. | Yael Steuerman, Irit Gat-Viks |
| 2015 | RECOMB | A Novel Probabilistic Methodology for eQTL Analysis of Signaling Networks. | Roni Wilentzik, Irit Gat-Viks |
| 2013 | WABI | A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions. | Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan |
| 2011 | RECOMB | Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast. | Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir |
| 2008 | WABI | A Faster Algorithm for RNA Co-folding. | Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir |
| 2005 | RECOMB | The Factor Graph Network Model for Biological Systems. | Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir |
| 2004 | PSB | Reconstructing Chain Functions in Genetic Networks. | Irit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan |
| 2004 | RECOMB | Modeling and Analysis of Heterogeneous Regulation in Biological Networks. | Irit Gat-Viks, Amos Tanay, Ron Shamir |
| 2003 | ISMB | Chain functions and scoring functions in genetic networks. | Irit Gat-Viks, Ron Shamir |