Itsik Pe'er

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 27

Top Topics

Protein Structure Prediction

Decision Tree Algorithm

Sequential Monte Carlo Methods

Top Venues

J. Comput. Biol.

Publications

Hanming Yang, Antonio Khalil Moretti, Sebastian Macaluso, Philippe Chlenski, Christian A. Naesseth, Itsik Pe'er
Variational Pseudo Marginal Methods for Jet Reconstruction in Particle Physics. CoRR (2024)
Philippe Chlenski, Ethan Turok, Antonio Khalil Moretti, Itsik Pe'er
Fast Hyperboloid Decision Tree Algorithms. ICLR (2024)
George I. Austin, Itsik Pe'er, Tal Korem
Distributional bias compromises leave-one-out cross-validation. CoRR (2024)
Philippe Chlenski, Quentin Chu, Itsik Pe'er
Mixed-Curvature Decision Trees and Random Forests. CoRR (2024)
Philippe Chlenski, Ethan Turok, Antonio Khalil Moretti, Itsik Pe'er
Fast hyperboloid decision tree algorithms. CoRR (2023)
Itsik Pe'er
Special Issue: RECOMB 2022, Part 1. J. Comput. Biol. 29 (11) (2022)
Adele Myers, Saiteja Utpala, Shubham Talbar, Sophia Sanborn, Christian Shewmake, Claire Donnat, Johan Mathe, Umberto Lupo, Rishi Sonthalia, Xinyue Cui, Tom Szwagier, Arthur Pignet, Andri Bergsson, Søren Hauberg, Dmitriy Nielsen, Stefan Sommer, David Klindt, Erik Hermansen, Melvin Vaupel, Benjamin Dunn, Jeffrey Xiong, Noga Aharony, Itsik Pe'er, Felix Ambellan, Martin Hanik, Esfandiar Nava Yazdani, Christoph von Tycowicz, Nina Miolane
ICLR 2022 Challenge for Computational Geometry and Topology: Design and Results. CoRR (2022)
Itsik Pe'er
Special Issue: RECOMB 2022, Part 2. J. Comput. Biol. 29 (12) (2022)
Adele Myers, Saiteja Utpala, Shubham Talbar, Sophia Sanborn, Christian Shewmake, Claire Donnat, Johan Mathe, Rishi Sonthalia, Xinyue Cui, Tom Szwagier, Arthur Pignet, Andri Bergsson, Søren Hauberg, Dmitriy Nielsen, Stefan Sommer, David A. Klindt, Erik Hermansen, Melvin Vaupel, Benjamin A. Dunn, Jeffrey Xiong, Noga Aharony, Itsik Pe'er, Felix Ambellan, Martin Hanik, Esfandiar Nava-Yazdani, Christoph von Tycowicz, Nina Miolane
ICLR 2022 Challenge for Computational Geometry & Topology: Design and Results. TAG-ML (2022)
Ghada Almashaqbeh, Ran Canetti, Yaniv Erlich, Jonathan Gershoni, Tal Malkin, Itsik Pe'er, Anna Roitburd-Berman, Eran Tromer
Unclonable Polymers and Their Cryptographic Applications. IACR Cryptol. ePrint Arch. 2022 (2022)
Ghada Almashaqbeh, Ran Canetti, Yaniv Erlich, Jonathan Gershoni, Tal Malkin, Itsik Pe'er, Anna Roitburd-Berman, Eran Tromer
Unclonable Polymers and Their Cryptographic Applications. EUROCRYPT (1) (2022)
Md Shariful Islam Bhuyan, Itsik Pe'er, M. Sohel Rahman
SICaRiO: short indel call filtering with boosting. Briefings Bioinform. 22 (4) (2021)
Antonio Khalil Moretti, Liyi Zhang, Christian A. Naesseth, Hadiah Venner, David M. Blei, Itsik Pe'er
Variational Combinatorial Sequential Monte Carlo Methods for Bayesian Phylogenetic Inference. CoRR (2021)
Yining Liu, Sachin Kadyan, Itsik Pe'er
A Recovery Algorithm and Pooling Designs for One-Stage Noisy Group Testing Under the Probabilistic Framework. AlCoB (2021)
Antonio Khalil Moretti, Liyi Zhang, Christian A. Naesseth, Hadiah Venner, David M. Blei, Itsik Pe'er
variational combinatorial sequential monte carlo methods for bayesian phylogenetic inference. UAI (2021)
Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu, Iddo Drori, Itsik Pe'er
Variational Objectives for Markovian Dynamics with Backward Simulation. ECAI (2020)
Tyler A. Joseph, Amey P. Pasarkar, Itsik Pe'er
Efficient and Accurate Inference of Microbial Trajectories from Longitudinal Count Data. RECOMB (2020)
Tyler A. Joseph, Liat Shenhav, João B. Xavier, Eran Halperin, Itsik Pe'er
Compositional Lotka-Volterra describes microbial dynamics in the simplex. PLoS Comput. Biol. 16 (5) (2020)
Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe'er, Raul Rabadan
arcasHLA: high-resolution HLA typing from RNAseq. Bioinform. 36 (1) (2020)
Iddo Drori, Darshan Thaker, Arjun Srivatsa, Daniel Jeong, Yueqi Wang, Linyong Nan, Fan Wu, Dimitri Leggas, Jinhao Lei, Weiyi Lu, Weilong Fu, Yuan Gao, Sashank Karri, Anand Kannan, Antonio Khalil Moretti, Mohammed AlQuraishi, Chen Keasar, Itsik Pe'er
Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations. CoRR (2019)
Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu, Itsik Pe'er
Smoothing Nonlinear Variational Objectives with Sequential Monte Carlo. DGS@ICLR (2019)
Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu, Iddo Drori, Itsik Pe'er
Particle Smoothing Variational Objectives. CoRR (2019)
Antonio Khalil Moretti, Andrew Stirn, Gabriel Marks, Itsik Pe'er
Autoencoding Topographic Factors. J. Comput. Biol. 26 (6) (2019)
Tyler A. Joseph, Itsik Pe'er
Inference of Population Structure from Ancient DNA. RECOMB (2018)
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, Chinmay Joshi, Sonam Goenka, Chen Keasar, Itsik Pe'er
High Quality Prediction of Protein Q8 Secondary Structure by Diverse Neural Network Architectures. CoRR (2018)
Avinash Bukkittu, Baihan Lin, Trung Vu, Itsik Pe'er
Parkinson's Disease Digital Biomarker Discovery with Optimized Transitions and Inferred Markov Emissions. CoRR (2017)
Shuo Yang, Shai Carmi, Itsik Pe'er
Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. J. Comput. Biol. 23 (6) (2016)
Shuo Yang, Shai Carmi, Itsik Pe'er
Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. RECOMB (2015)
Angad Pal Singh, Samreen Zafer, Itsik Pe'er
MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association Studies. Pacific Symposium on Biocomputing (2013)
Pier Francesco Palamara, Itsik Pe'er
Inference of historical migration rates via haplotype sharing. Bioinform. 29 (13) (2013)
Yufeng Shen, Yiwei Gu, Itsik Pe'er
Poster: A Hidden Markov Model for Copy Number Variant prediction from Whole genome resequencing data. ICCABS (2011)
Arthi Ramachandran, Mariann Micsinai, Itsik Pe'er
CONDEX: Copy number detection in exome sequences. BIBM Workshops (2011)
Yufeng Shen, Yiwei Gu, Itsik Pe'er
A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data. BMC Bioinform. 12 (S-6) (2011)
Manu N. Setty, Alexander Gusev, Itsik Pe'er
HLA Type Inference via Haplotypes Identical by Descent. J. Comput. Biol. 18 (3) (2011)
Yufeng Shen, Ruijie Song, Itsik Pe'er
Workshop: Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association. ICCABS (2011)
Yufeng Shen, Ruijie Song, Itsik Pe'er
Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association. Bioinform. 27 (14) (2011)
Yufeng Shen, Yee Him Cheung, Shuang Wang, Itsik Pe'er
A parametric Bayesian method to test the association of rare variants. BIBM Workshops (2011)
Ninad Dewal, Matthew L. Freedman, Thomas LaFramboise, Itsik Pe'er
Power to detect selective allelic amplification in genome-wide scans of tumor data. Bioinform. 26 (4) (2010)
Manu N. Setty, Alexander Gusev, Itsik Pe'er
HLA Type Inference via Haplotypes Identical by Descent. RECOMB (2010)
Snehit Prabhu, Itsik Pe'er
Overlapping Pools for High Throughput Targeted Resequencing. RECOMB (2009)
Julia Stoyanovich, Itsik Pe'er
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. Bioinform. 24 (3) (2008)
Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er
Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (1) (2008)
Itsik Pe'er, Tal Pupko, Ron Shamir, Roded Sharan
Incomplete Directed Perfect Phylogeny. SIAM J. Comput. 33 (3) (2004)
Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er
Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs. CPM (2004)
Itsik Pe'er, Jacques S. Beckmann
Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples. RECOMB (2003)
Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko
A Structural EM Algorithm for Phylogenetic Inference. J. Comput. Biol. 9 (2) (2002)
Itsik Pe'er, Ron Shamir, Roded Sharan
On the Generality of Phylogenies from Incomplete Directed Characters. SWAT (2002)
Tal Pupko, Itsik Pe'er, Masami Hasegawa, Dan Graur, Nir Friedman
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. Bioinform. 18 (8) (2002)
Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan
On the Complexity of Positional Sequencing by Hybridization. J. Comput. Biol. 8 (4) (2002)
Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko
A structural EM algorithm for phylogenetic inference. RECOMB (2001)
Piotr Berman, Amir Ben-Dor, Itsik Pe'er, Roded Sharan, Ron Shamir
On the Complexity of Positional Sequencing by Hybridization Electron. Colloquium Comput. Complex. 8 (54) (2001)
Richard M. Karp, Itsik Pe'er, Ron Shamir
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. J. Comput. Biol. 7 (5) (2000)
Itsik Pe'er, Ron Shamir
Spectrum Alignment: Efficient Resequencing by Hybridization. ISMB (2000)
Itsik Pe'er, Ron Shamir, Roded Sharan
Incomplete Directed Perfect Phylogeny. CPM (2000)
Richard M. Karp, Itsik Pe'er, Ron Shamir
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. ISMB (1999)
Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan
On the Complexity of Positional Sequencing by Hybridization. CPM (1999)
Itsik Pe'er, Ron Shamir
The median problems for breakpoints are NP-complete Electron. Colloquium Comput. Complex. 5 (71) (1998)
Itsik Pe'er, Ron Shamir
Satisfiability Problems on Intervals and Unit Intervals. Theor. Comput. Sci. 175 (2) (1997)
Itsik Pe'er, Ron Shamir
Realizing Interval Graphs with Size and Distance Constraints. SIAM J. Discret. Math. 10 (4) (1997)
Itsik Pe'er, Ron Shamir
Interval Graphs with Side (and Size) Constraints. ESA (1995)