| 2025 | AISTATS | Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetics in Hyperbolic Space. | Alex Chen, Philippe Chlenski, Kenneth Munyuza, Antonio Khalil Moretti, Christian A. Naesseth, Itsik Pe'er |
| 2025 | ICLR | Hyperbolic Genome Embeddings. | Raiyan R. Khan, Philippe Chlenski, Itsik Pe'er |
| 2025 | ICML | Mixed-curvature decision trees and random forests. | Philippe Chlenski, Quentin Chu, Raiyan R. Khan, Kaizhu Du, Antonio Khalil Moretti, Itsik Pe'er |
| 2024 | ICLR | Fast Hyperboloid Decision Tree Algorithms. | Philippe Chlenski, Ethan Turok, Antonio Khalil Moretti, Itsik Pe'er |
| 2022 | EuroCrypt | Unclonable Polymers and Their Cryptographic Applications. | Ghada Almashaqbeh, Ran Canetti, Yaniv Erlich, Jonathan Gershoni, Tal Malkin, Itsik Pe'er, Anna Roitburd-Berman, Eran Tromer |
| 2021 | UAI | variational combinatorial sequential monte carlo methods for bayesian phylogenetic inference. | Antonio Khalil Moretti, Liyi Zhang, Christian A. Naesseth, Hadiah Venner, David M. Blei, Itsik Pe'er |
| 2020 | ECAI | Variational Objectives for Markovian Dynamics with Backward Simulation. | Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu, Iddo Drori, Itsik Pe'er |
| 2020 | RECOMB | Efficient and Accurate Inference of Microbial Trajectories from Longitudinal Count Data. | Tyler A. Joseph, Amey P. Pasarkar, Itsik Pe'er |
| 2019 | ICLR | Smoothing Nonlinear Variational Objectives with Sequential Monte Carlo. | Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu, Itsik Pe'er |
| 2018 | RECOMB | Inference of Population Structure from Ancient DNA. | Tyler A. Joseph, Itsik Pe'er |
| 2015 | RECOMB | Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. | Shuo Yang, Shai Carmi, Itsik Pe'er |
| 2013 | PSB | MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association Studies. | Angad Pal Singh, Samreen Zafer, Itsik Pe'er |
| 2010 | RECOMB | HLA Type Inference via Haplotypes Identical by Descent. | Manu N. Setty, Alexander Gusev, Itsik Pe'er |
| 2009 | RECOMB | Overlapping Pools for High Throughput Targeted Resequencing. | Snehit Prabhu, Itsik Pe'er |
| 2004 | CPM | Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs. | Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er |
| 2003 | RECOMB | Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples. | Itsik Pe'er, Jacques S. Beckmann |
| 2001 | RECOMB | A structural EM algorithm for phylogenetic inference. | Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko |
| 2000 | CPM | Incomplete Directed Perfect Phylogeny. | Itsik Pe'er, Ron Shamir, Roded Sharan |
| 2000 | ISMB | Spectrum Alignment: Efficient Resequencing by Hybridization. | Itsik Pe'er, Ron Shamir |
| 1999 | CPM | On the Complexity of Positional Sequencing by Hybridization. | Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan |
| 1999 | ISMB | An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. | Richard M. Karp, Itsik Pe'er, Ron Shamir |
| 1995 | ESA | Interval Graphs with Side (and Size) Constraints. | Itsik Pe'er, Ron Shamir |