| 2025 | RECOMB | Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach. | Yoav Dvir, Sagi Snir |
| 2024 | RECOMB | Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency. | Meir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia |
| 2023 | WABI | Inferring Temporally Consistent Migration Histories. | Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir |
| 2018 | RECOMB | Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees. | Thomas Dencker, Chris-Andr Leimeister, Michael Gerth, Christoph Bleidorn, Sagi Snir, Burkhard Morgenstern |
| 2014 | RECOMB | Gene-Gene Interactions Detection Using a Two-Stage Model. | Zhanyong Wang, Jae Hoon Sul, Sagi Snir, Jos Antonio Lozano, Eleazar Eskin |
| 2014 | SODA | On the compatibility of quartet trees. | Noga Alon, Sagi Snir, Raphael Yuster |
| 2014 | WABI | Pacemaker Partition Identification. | Sagi Snir |
| 2012 | RECOMB | Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis. | Sebastien Roch, Sagi Snir |
| 2010 | SODA | Reconstructing Approximate Phylogenetic Trees from Quartet Samples. | Sagi Snir, Raphael Yuster |
| 2008 | SODA | Fast and reliable reconstruction of phylogenetic trees with very short edges. | Ilan Gronau, Shlomo Moran, Sagi Snir |
| 2008 | WABI | Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. | Sagi Snir, Tamir Tuller |
| 2007 | COCOON | Connected Coloring Completion for General Graphs: Algorithms and Complexity. | Benny Chor, Michael R. Fellows, Mark A. Ragan, Igor Razgon, Frances A. Rosamond, Sagi Snir |
| 2006 | RECOMB | Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. | Sagi Snir, Lior Pachter |
| 2005 | CIBCB | The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space. | Eleazar Eskin, Sagi Snir |
| 2005 | WABI | Using Semi-definite Programming to Enhance Supertree Resolvability. | Shlomo Moran, Satish Rao, Sagi Snir |
| 2005 | WADS | Convex Recolorings of Strings and Trees: Definitions, Hardness Results and Algorithms. | Shlomo Moran, Sagi Snir |
| 2003 | RECOMB | Maximum likelihood on four taxa phylogenetic trees: analytic solutions. | Benny Chor, Amit Khetan, Sagi Snir |
| 2002 | WABI | Restricting SBH Ambiguity via Restriction Enzymes. | Steven Skiena, Sagi Snir |