Interval Graphs with Side (and Size) Constraints. - Itsik Pe'er; Ron Shamir (ESA, 1995)

Realizing Interval Graphs with Size and Distance Constraints. - Itsik Pe'er; Ron Shamir (SIAM J. Discret. Math., 1997)

Satisfiability Problems on Intervals and Unit Intervals. - Itsik Pe'er; Ron Shamir (Theor. Comput. Sci., 1997)

The median problems for breakpoints are NP-complete - Itsik Pe'er; Ron Shamir (Electron. Colloquium Comput. Complex., 1998)

Incomplete Directed Perfect Phylogeny. - Itsik Pe'er; Ron Shamir; Roded Sharan (CPM, 2000)

Spectrum Alignment: Efficient Resequencing by Hybridization. - Itsik Pe'er; Ron Shamir (ISMB, 2000)

An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. - Richard M. Karp; Itsik Pe'er; Ron Shamir (J. Comput. Biol., 2000)

On the Complexity of Positional Sequencing by Hybridization - Piotr Berman; Amir Ben-Dor; Itsik Pe'er; Roded Sharan; Ron Shamir (Electron. Colloquium Comput. Complex., 2001)

On the Generality of Phylogenies from Incomplete Directed Characters. - Itsik Pe'er; Ron Shamir; Roded Sharan (SWAT, 2002)

A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. - Tal Pupko; Itsik Pe'er; Masami Hasegawa; Dan Graur; Nir Friedman (Bioinform., 2002)

On the Complexity of Positional Sequencing by Hybridization. - Amir Ben-Dor; Itsik Pe'er; Ron Shamir; Roded Sharan (J. Comput. Biol., 2002)

A Structural EM Algorithm for Phylogenetic Inference. - Nir Friedman; Matan Ninio; Itsik Pe'er; Tal Pupko (J. Comput. Biol., 2002)

Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples. - Itsik Pe'er; Jacques S. Beckmann (RECOMB, 2003)

Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs. - Tamar Barzuza; Jacques S. Beckmann; Ron Shamir; Itsik Pe'er (CPM, 2004)

Incomplete Directed Perfect Phylogeny. - Itsik Pe'er; Tal Pupko; Ron Shamir; Roded Sharan (SIAM J. Comput., 2004)

MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. - Julia Stoyanovich; Itsik Pe'er (Bioinform., 2008)

Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele. - Tamar Barzuza; Jacques S. Beckmann; Ron Shamir; Itsik Pe'er (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Overlapping Pools for High Throughput Targeted Resequencing. - Snehit Prabhu; Itsik Pe'er (RECOMB, 2009)

Power to detect selective allelic amplification in genome-wide scans of tumor data. - Ninad Dewal; Matthew L. Freedman; Thomas LaFramboise; Itsik Pe'er (Bioinform., 2010)

CONDEX: Copy number detection in exome sequences. - Arthi Ramachandran; Mariann Micsinai; Itsik Pe'er (BIBM Workshops, 2011)

A parametric Bayesian method to test the association of rare variants. - Yufeng Shen; Yee Him Cheung; Shuang Wang; Itsik Pe'er (BIBM Workshops, 2011)

Poster: A Hidden Markov Model for Copy Number Variant prediction from Whole genome resequencing data. - Yufeng Shen; Yiwei Gu; Itsik Pe'er (ICCABS, 2011)

Workshop: Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association. - Yufeng Shen; Ruijie Song; Itsik Pe'er (ICCABS, 2011)

Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association. - Yufeng Shen; Ruijie Song; Itsik Pe'er (Bioinform., 2011)

A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data. - Yufeng Shen; Yiwei Gu; Itsik Pe'er (BMC Bioinform., 2011)

HLA Type Inference via Haplotypes Identical by Descent. - Manu N. Setty; Alexander Gusev; Itsik Pe'er (J. Comput. Biol., 2011)

MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association Studies. - Angad Pal Singh; Samreen Zafer; Itsik Pe'er (Pacific Symposium on Biocomputing, 2013)

Inference of historical migration rates via haplotype sharing. - Pier Francesco Palamara; Itsik Pe'er (Bioinform., 2013)

Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. - Shuo Yang; Shai Carmi; Itsik Pe'er (J. Comput. Biol., 2016)

Parkinson's Disease Digital Biomarker Discovery with Optimized Transitions and Inferred Markov Emissions. - Avinash Bukkittu; Baihan Lin; Trung Vu; Itsik Pe'er (CoRR, 2017)

Inference of Population Structure from Ancient DNA. - Tyler A. Joseph; Itsik Pe'er (RECOMB, 2018)

High Quality Prediction of Protein Q8 Secondary Structure by Diverse Neural Network Architectures. - Iddo Drori; Isht Dwivedi; Pranav Shrestha; Jeffrey Wan; Yueqi Wang; Yunchu He; Anthony Mazza; Hugh Krogh-Freeman; Dimitri Leggas; Kendal Sandridge; Linyong Nan; Kaveri A. Thakoor; et al. (CoRR, 2018)

Smoothing Nonlinear Variational Objectives with Sequential Monte Carlo. - Antonio Khalil Moretti; Zizhao Wang; Luhuan Wu; Itsik Pe'er (DGS@ICLR, 2019)

Particle Smoothing Variational Objectives. - Antonio Khalil Moretti; Zizhao Wang; Luhuan Wu; Iddo Drori; Itsik Pe'er (CoRR, 2019)

Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations. - Iddo Drori; Darshan Thaker; Arjun Srivatsa; Daniel Jeong; Yueqi Wang; Linyong Nan; Fan Wu; Dimitri Leggas; Jinhao Lei; Weiyi Lu; Weilong Fu; Yuan Gao; et al. (CoRR, 2019)

Autoencoding Topographic Factors. - Antonio Khalil Moretti; Andrew Stirn; Gabriel Marks; Itsik Pe'er (J. Comput. Biol., 2019)

Variational Objectives for Markovian Dynamics with Backward Simulation. - Antonio Khalil Moretti; Zizhao Wang; Luhuan Wu; Iddo Drori; Itsik Pe'er (ECAI, 2020)

Efficient and Accurate Inference of Microbial Trajectories from Longitudinal Count Data. - Tyler A. Joseph; Amey P. Pasarkar; Itsik Pe'er (RECOMB, 2020)

arcasHLA: high-resolution HLA typing from RNAseq. - Rose Orenbuch; Ioan Filip; Devon Comito; Jeffrey Shaman; Itsik Pe'er; Raul Rabadan (Bioinform., 2020)

Compositional Lotka-Volterra describes microbial dynamics in the simplex. - Tyler A. Joseph; Liat Shenhav; João B. Xavier; Eran Halperin; Itsik Pe'er (PLoS Comput. Biol., 2020)

A Recovery Algorithm and Pooling Designs for One-Stage Noisy Group Testing Under the Probabilistic Framework. - Yining Liu; Sachin Kadyan; Itsik Pe'er (AlCoB, 2021)

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 (UAI, 2021)

SICaRiO: short indel call filtering with boosting. - Md Shariful Islam Bhuyan; Itsik Pe'er; M. Sohel Rahman (Briefings Bioinform., 2021)

ICLR 2022 Challenge for Computational Geometry & Topology: Design and Results. - Adele Myers; Saiteja Utpala; Shubham Talbar; Sophia Sanborn; Christian Shewmake; Claire Donnat; Johan Mathe; Rishi Sonthalia; Xinyue Cui; Tom Szwagier; Arthur Pignet; Andri Bergsson; et al. (TAG-ML, 2022)

ICLR 2022 Challenge for Computational Geometry and Topology: Design and Results. - Adele Myers; Saiteja Utpala; Shubham Talbar; Sophia Sanborn; Christian Shewmake; Claire Donnat; Johan Mathe; Umberto Lupo; Rishi Sonthalia; Xinyue Cui; Tom Szwagier; Arthur Pignet; et al. (CoRR, 2022)

Unclonable Polymers and Their Cryptographic Applications. - Ghada Almashaqbeh; Ran Canetti; Yaniv Erlich; Jonathan Gershoni; Tal Malkin; Itsik Pe'er; Anna Roitburd-Berman; Eran Tromer (IACR Cryptol. ePrint Arch., 2022)

Special Issue: RECOMB 2022, Part 1. - Itsik Pe'er (J. Comput. Biol., 2022)

Special Issue: RECOMB 2022, Part 2. - Itsik Pe'er (J. Comput. Biol., 2022)

Fast Hyperboloid Decision Tree Algorithms. - Philippe Chlenski; Ethan Turok; Antonio Khalil Moretti; Itsik Pe'er (ICLR, 2024)

Distributional bias compromises leave-one-out cross-validation. - George I. Austin; Itsik Pe'er; Tal Korem (CoRR, 2024)

Mixed-curvature decision trees and random forests. - Philippe Chlenski; Quentin Chu; Raiyan R. Khan; Antonio Khalil Moretti; Itsik Pe'er (CoRR, 2024)

Variational Pseudo Marginal Methods for Jet Reconstruction in Particle Physics. - Hanming Yang; Antonio Khalil Moretti; Sebastian Macaluso; Philippe Chlenski; Christian A. Naesseth; Itsik Pe'er (Trans. Mach. Learn. Res., 2024)

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 (AISTATS, 2025)

Hyperbolic Genome Embeddings. - Raiyan R. Khan; Philippe Chlenski; Itsik Pe'er (ICLR, 2025)

Manify: A Python Library for Learning Non-Euclidean Representations. - Philippe Chlenski; Kaizhu Du; Dylan Satow; Itsik Pe'er (CoRR, 2025)

Even Faster Hyperbolic Random Forests: A Beltrami-Klein Wrapper Approach. - Philippe Chlenski; Itsik Pe'er (CoRR, 2025)