| 2017 | RECOMB | Generation and Comparative Genomics of Synthetic Dengue Viruses. | Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Shimshi Atar, Tahel Altman, Justin Julander, Tamir Tuller |
| 2011 | RECOMB | A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract). | Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller |
| 2009 | RECOMB | Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples. | Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin |
| 2008 | RECOMB | Discovering Local Patterns of Co-evolution. | Yifat Felder, Tamir Tuller |
| 2008 | WABI | Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. | Sagi Snir, Tamir Tuller |
| 2007 | WABI | Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. | Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller |
| 2006 | RECOMB | Biological Networks: Comparison, Conservation, and Evolutionary Trees. | Benny Chor, Tamir Tuller |
| 2005 | ISMB | Maximum likelihood of evolutionary trees: hardness and approximation. | Benny Chor, Tamir Tuller |
| 2005 | RECOMB | Information Theoretic Approaches to Whole Genome Phylogenies. | David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor |
| 2005 | RECOMB | Maximum Likelihood of Evolutionary Trees Is Hard. | Benny Chor, Tamir Tuller |
| 2005 | WABI | Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds. | Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor |
| 2004 | WABI | Adding Hidden Nodes to Gene Networks (Extended Abstract). | Benny Chor, Tamir Tuller |