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ORCIDBibTeX records: Itsik Pe'er
@article{DBLP:journals/corr/abs-2310-13841,
author = {Philippe Chlenski and
Ethan Turok and
Antonio Khalil Moretti and
Itsik Pe'er},
title = {Fast hyperboloid decision tree algorithms},
journal = {CoRR},
volume = {abs/2310.13841},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2310.13841},
doi = {10.48550/ARXIV.2310.13841},
eprinttype = {arXiv},
eprint = {2310.13841},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2310-13841.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Peer22,
author = {Itsik Pe'er},
title = {Special Issue: {RECOMB} 2022, Part 1},
journal = {J. Comput. Biol.},
volume = {29},
number = {11},
pages = {1155},
year = {2022},
url = {https://doi.org/10.1089/cmb.2022.29075.ip},
doi = {10.1089/CMB.2022.29075.IP},
timestamp = {Mon, 02 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/Peer22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Peer22a,
author = {Itsik Pe'er},
title = {Special Issue: {RECOMB} 2022, Part 2},
journal = {J. Comput. Biol.},
volume = {29},
number = {12},
pages = {1269},
year = {2022},
url = {https://doi.org/10.1089/cmb.2022.29076.ip},
doi = {10.1089/CMB.2022.29076.IP},
timestamp = {Sat, 14 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/Peer22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eurocrypt/AlmashaqbehCEGM22,
author = {Ghada Almashaqbeh and
Ran Canetti and
Yaniv Erlich and
Jonathan Gershoni and
Tal Malkin and
Itsik Pe'er and
Anna Roitburd{-}Berman and
Eran Tromer},
editor = {Orr Dunkelman and
Stefan Dziembowski},
title = {Unclonable Polymers and Their Cryptographic Applications},
booktitle = {Advances in Cryptology - {EUROCRYPT} 2022 - 41st Annual International
Conference on the Theory and Applications of Cryptographic Techniques,
Trondheim, Norway, May 30 - June 3, 2022, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {13275},
pages = {759--789},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-06944-4\_26},
doi = {10.1007/978-3-031-06944-4\_26},
timestamp = {Tue, 31 May 2022 17:23:10 +0200},
biburl = {https://dblp.org/rec/conf/eurocrypt/AlmashaqbehCEGM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/tagml/MyersUTSSDMSCSP22,
author = {Adele Myers and
Saiteja Utpala and
Shubham Talbar and
Sophia Sanborn and
Christian Shewmake and
Claire Donnat and
Johan Mathe and
Rishi Sonthalia and
Xinyue Cui and
Tom Szwagier and
Arthur Pignet and
Andri Bergsson and
S{\o}ren Hauberg and
Dmitriy Nielsen and
Stefan Sommer and
David A. Klindt and
Erik Hermansen and
Melvin Vaupel and
Benjamin A. Dunn and
Jeffrey Xiong and
Noga Aharony and
Itsik Pe'er and
Felix Ambellan and
Martin Hanik and
Esfandiar Nava{-}Yazdani and
Christoph von Tycowicz and
Nina Miolane},
editor = {Alexander Cloninger and
Timothy Doster and
Tegan Emerson and
Manohar Kaul and
Ira Ktena and
Henry Kvinge and
Nina Miolane and
Bastian Rice and
Sarah Tymochko and
Guy Wolf},
title = {{ICLR} 2022 Challenge for Computational Geometry {\&} Topology:
Design and Results},
booktitle = {Topological, Algebraic and Geometric Learning Workshops 2022, 25-22
July 2022, Virtual},
series = {Proceedings of Machine Learning Research},
volume = {196},
pages = {269--276},
publisher = {{PMLR}},
year = {2022},
url = {https://proceedings.mlr.press/v196/myers22a.html},
timestamp = {Tue, 05 Sep 2023 17:08:45 +0200},
biburl = {https://dblp.org/rec/conf/tagml/MyersUTSSDMSCSP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/recomb/2022,
editor = {Itsik Pe'er},
title = {Research in Computational Molecular Biology - 26th Annual International
Conference, {RECOMB} 2022, San Diego, CA, USA, May 22-25, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13278},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-04749-7},
doi = {10.1007/978-3-031-04749-7},
isbn = {978-3-031-04748-0},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/2022.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2206-09048,
author = {Adele Myers and
Saiteja Utpala and
Shubham Talbar and
Sophia Sanborn and
Christian Shewmake and
Claire Donnat and
Johan Mathe and
Umberto Lupo and
Rishi Sonthalia and
Xinyue Cui and
Tom Szwagier and
Arthur Pignet and
Andri Bergsson and
S{\o}ren Hauberg and
Dmitriy Nielsen and
Stefan Sommer and
David A. Klindt and
Erik Hermansen and
Melvin Vaupel and
Benjamin A. Dunn and
Jeffrey Xiong and
Noga Aharony and
Itsik Pe'er and
Felix Ambellan and
Martin Hanik and
Esfandiar Nava{-}Yazdani and
Christoph von Tycowicz and
Nina Miolane},
title = {{ICLR} 2022 Challenge for Computational Geometry and Topology: Design
and Results},
journal = {CoRR},
volume = {abs/2206.09048},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2206.09048},
doi = {10.48550/ARXIV.2206.09048},
eprinttype = {arXiv},
eprint = {2206.09048},
timestamp = {Mon, 04 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2206-09048.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/iacr/AlmashaqbehCEGM22,
author = {Ghada Almashaqbeh and
Ran Canetti and
Yaniv Erlich and
Jonathan Gershoni and
Tal Malkin and
Itsik Pe'er and
Anna Roitburd{-}Berman and
Eran Tromer},
title = {Unclonable Polymers and Their Cryptographic Applications},
journal = {{IACR} Cryptol. ePrint Arch.},
pages = {658},
year = {2022},
url = {https://eprint.iacr.org/2022/658},
timestamp = {Mon, 20 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/iacr/AlmashaqbehCEGM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BhuyanPR21,
author = {Md Shariful Islam Bhuyan and
Itsik Pe'er and
M. Sohel Rahman},
title = {SICaRiO: short indel call filtering with boosting},
journal = {Briefings Bioinform.},
volume = {22},
number = {4},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa238},
doi = {10.1093/BIB/BBAA238},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BhuyanPR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/LiuKP21,
author = {Yining Liu and
Sachin Kadyan and
Itsik Pe'er},
editor = {Carlos Mart{\'{\i}}n{-}Vide and
Miguel A. Vega{-}Rodr{\'{\i}}guez and
Travis J. Wheeler},
title = {A Recovery Algorithm and Pooling Designs for One-Stage Noisy Group
Testing Under the Probabilistic Framework},
booktitle = {Algorithms for Computational Biology - 8th International Conference,
AlCoB 2021, Missoula, MT, USA, June 7-11, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12715},
pages = {42--53},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-74432-8\_4},
doi = {10.1007/978-3-030-74432-8\_4},
timestamp = {Tue, 15 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alcob/LiuKP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/uai/MorettiZNVBP21,
author = {Antonio Khalil Moretti and
Liyi Zhang and
Christian A. Naesseth and
Hadiah Venner and
David M. Blei and
Itsik Pe'er},
editor = {Cassio P. de Campos and
Marloes H. Maathuis and
Erik Quaeghebeur},
title = {variational combinatorial sequential monte carlo methods for bayesian
phylogenetic inference},
booktitle = {Proceedings of the Thirty-Seventh Conference on Uncertainty in Artificial
Intelligence, {UAI} 2021, Virtual Event, 27-30 July 2021},
series = {Proceedings of Machine Learning Research},
volume = {161},
pages = {971--981},
publisher = {{AUAI} Press},
year = {2021},
url = {https://proceedings.mlr.press/v161/moretti21a.html},
timestamp = {Fri, 17 Dec 2021 17:06:27 +0100},
biburl = {https://dblp.org/rec/conf/uai/MorettiZNVBP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2106-00075,
author = {Antonio Khalil Moretti and
Liyi Zhang and
Christian A. Naesseth and
Hadiah Venner and
David M. Blei and
Itsik Pe'er},
title = {Variational Combinatorial Sequential Monte Carlo Methods for Bayesian
Phylogenetic Inference},
journal = {CoRR},
volume = {abs/2106.00075},
year = {2021},
url = {https://arxiv.org/abs/2106.00075},
eprinttype = {arXiv},
eprint = {2106.00075},
timestamp = {Fri, 11 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2106-00075.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OrenbuchFCSPR20,
author = {Rose Orenbuch and
Ioan Filip and
Devon Comito and
Jeffrey Shaman and
Itsik Pe'er and
Raul Rabadan},
title = {arcasHLA: high-resolution {HLA} typing from RNAseq},
journal = {Bioinform.},
volume = {36},
number = {1},
pages = {33--40},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz474},
doi = {10.1093/BIOINFORMATICS/BTZ474},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OrenbuchFCSPR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/JosephSXHP20,
author = {Tyler A. Joseph and
Liat Shenhav and
Jo{\~{a}}o B. Xavier and
Eran Halperin and
Itsik Pe'er},
title = {Compositional Lotka-Volterra describes microbial dynamics in the simplex},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {5},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1007917},
doi = {10.1371/JOURNAL.PCBI.1007917},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/JosephSXHP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ecai/MorettiWWDP20,
author = {Antonio Khalil Moretti and
Zizhao Wang and
Luhuan Wu and
Iddo Drori and
Itsik Pe'er},
editor = {Giuseppe De Giacomo and
Alejandro Catal{\'{a}} and
Bistra Dilkina and
Michela Milano and
Sen{\'{e}}n Barro and
Alberto Bugar{\'{\i}}n and
J{\'{e}}r{\^{o}}me Lang},
title = {Variational Objectives for Markovian Dynamics with Backward Simulation},
booktitle = {{ECAI} 2020 - 24th European Conference on Artificial Intelligence,
29 August-8 September 2020, Santiago de Compostela, Spain, August
29 - September 8, 2020 - Including 10th Conference on Prestigious
Applications of Artificial Intelligence {(PAIS} 2020)},
series = {Frontiers in Artificial Intelligence and Applications},
volume = {325},
pages = {1371--1378},
publisher = {{IOS} Press},
year = {2020},
url = {https://doi.org/10.3233/FAIA200241},
doi = {10.3233/FAIA200241},
timestamp = {Fri, 09 Apr 2021 18:50:05 +0200},
biburl = {https://dblp.org/rec/conf/ecai/MorettiWWDP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/JosephPP20,
author = {Tyler A. Joseph and
Amey P. Pasarkar and
Itsik Pe'er},
editor = {Russell Schwartz},
title = {Efficient and Accurate Inference of Microbial Trajectories from Longitudinal
Count Data},
booktitle = {Research in Computational Molecular Biology - 24th Annual International
Conference, {RECOMB} 2020, Padua, Italy, May 10-13, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12074},
pages = {255--256},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-45257-5\_27},
doi = {10.1007/978-3-030-45257-5\_27},
timestamp = {Tue, 21 Apr 2020 12:14:30 +0200},
biburl = {https://dblp.org/rec/conf/recomb/JosephPP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MorettiSMP19,
author = {Antonio Khalil Moretti and
Andrew Stirn and
Gabriel Marks and
Itsik Pe'er},
title = {Autoencoding Topographic Factors},
journal = {J. Comput. Biol.},
volume = {26},
number = {6},
pages = {546--560},
year = {2019},
url = {https://doi.org/10.1089/cmb.2018.0176},
doi = {10.1089/CMB.2018.0176},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/MorettiSMP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclr/MorettiWWP19,
author = {Antonio Khalil Moretti and
Zizhao Wang and
Luhuan Wu and
Itsik Pe'er},
title = {Smoothing Nonlinear Variational Objectives with Sequential Monte Carlo},
booktitle = {Deep Generative Models for Highly Structured Data, {ICLR} 2019 Workshop,
New Orleans, Louisiana, United States, May 6, 2019},
publisher = {OpenReview.net},
year = {2019},
url = {https://openreview.net/forum?id=HJg24U8tuE},
timestamp = {Fri, 27 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iclr/MorettiWWP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1909-09734,
author = {Antonio Khalil Moretti and
Zizhao Wang and
Luhuan Wu and
Iddo Drori and
Itsik Pe'er},
title = {Particle Smoothing Variational Objectives},
journal = {CoRR},
volume = {abs/1909.09734},
year = {2019},
url = {http://arxiv.org/abs/1909.09734},
eprinttype = {arXiv},
eprint = {1909.09734},
timestamp = {Fri, 27 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1909-09734.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1911-05531,
author = {Iddo Drori and
Darshan Thaker and
Arjun Srivatsa and
Daniel Jeong and
Yueqi Wang and
Linyong Nan and
Fan Wu and
Dimitri Leggas and
Jinhao Lei and
Weiyi Lu and
Weilong Fu and
Yuan Gao and
Sashank Karri and
Anand Kannan and
Antonio Khalil Moretti and
Mohammed AlQuraishi and
Chen Keasar and
Itsik Pe'er},
title = {Accurate Protein Structure Prediction by Embeddings and Deep Learning
Representations},
journal = {CoRR},
volume = {abs/1911.05531},
year = {2019},
url = {http://arxiv.org/abs/1911.05531},
eprinttype = {arXiv},
eprint = {1911.05531},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1911-05531.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/JosephP18,
author = {Tyler A. Joseph and
Itsik Pe'er},
editor = {Benjamin J. Raphael},
title = {Inference of Population Structure from Ancient {DNA}},
booktitle = {Research in Computational Molecular Biology - 22nd Annual International
Conference, {RECOMB} 2018, Paris, France, April 21-24, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10812},
pages = {90--104},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-319-89929-9\_6},
doi = {10.1007/978-3-319-89929-9\_6},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/JosephP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1811-07143,
author = {Iddo Drori and
Isht Dwivedi and
Pranav Shrestha and
Jeffrey Wan and
Yueqi Wang and
Yunchu He and
Anthony Mazza and
Hugh Krogh{-}Freeman and
Dimitri Leggas and
Kendal Sandridge and
Linyong Nan and
Kaveri A. Thakoor and
Chinmay Joshi and
Sonam Goenka and
Chen Keasar and
Itsik Pe'er},
title = {High Quality Prediction of Protein {Q8} Secondary Structure by Diverse
Neural Network Architectures},
journal = {CoRR},
volume = {abs/1811.07143},
year = {2018},
url = {http://arxiv.org/abs/1811.07143},
eprinttype = {arXiv},
eprint = {1811.07143},
timestamp = {Sun, 25 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1811-07143.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1711-04078,
author = {Avinash Bukkittu and
Baihan Lin and
Trung Vu and
Itsik Pe'er},
title = {Parkinson's Disease Digital Biomarker Discovery with Optimized Transitions
and Inferred Markov Emissions},
journal = {CoRR},
volume = {abs/1711.04078},
year = {2017},
url = {http://arxiv.org/abs/1711.04078},
eprinttype = {arXiv},
eprint = {1711.04078},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1711-04078.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/YangCP16,
author = {Shuo Yang and
Shai Carmi and
Itsik Pe'er},
title = {Rapidly Registering Identity-by-Descent Across Ancestral Recombination
Graphs},
journal = {J. Comput. Biol.},
volume = {23},
number = {6},
pages = {495--507},
year = {2016},
url = {https://doi.org/10.1089/cmb.2016.0016},
doi = {10.1089/CMB.2016.0016},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/YangCP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/YangCP15,
author = {Shuo Yang and
Shai Carmi and
Itsik Pe'er},
editor = {Teresa M. Przytycka},
title = {Rapidly Registering Identity-by-Descent Across Ancestral Recombination
Graphs},
booktitle = {Research in Computational Molecular Biology - 19th Annual International
Conference, {RECOMB} 2015, Warsaw, Poland, April 12-15, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9029},
pages = {340--353},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-16706-0\_35},
doi = {10.1007/978-3-319-16706-0\_35},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/YangCP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PalamaraP13,
author = {Pier Francesco Palamara and
Itsik Pe'er},
title = {Inference of historical migration rates via haplotype sharing},
journal = {Bioinform.},
volume = {29},
number = {13},
pages = {180--188},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt239},
doi = {10.1093/BIOINFORMATICS/BTT239},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PalamaraP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/SinghZP13,
author = {Angad Pal Singh and
Samreen Zafer and
Itsik Pe'er},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association
Studies},
booktitle = {Biocomputing 2013: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2013},
pages = {356--367},
publisher = {World Scientific Publishing},
year = {2013},
url = {http://psb.stanford.edu/psb-online/proceedings/psb13/singh.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/SinghZP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShenSP11,
author = {Yufeng Shen and
Ruijie Song and
Itsik Pe'er},
title = {Coverage tradeoffs and power estimation in the design of whole-genome
sequencing experiments for detecting association},
journal = {Bioinform.},
volume = {27},
number = {14},
pages = {1995--1997},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr305},
doi = {10.1093/BIOINFORMATICS/BTR305},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShenSP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShenGP11,
author = {Yufeng Shen and
Yiwei Gu and
Itsik Pe'er},
title = {A Hidden Markov Model for Copy Number Variant prediction from whole
genome resequencing data},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-6}},
pages = {S4},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S6-S4},
doi = {10.1186/1471-2105-12-S6-S4},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShenGP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SettyGP11,
author = {Manu N. Setty and
Alexander Gusev and
Itsik Pe'er},
title = {{HLA} Type Inference via Haplotypes Identical by Descent},
journal = {J. Comput. Biol.},
volume = {18},
number = {3},
pages = {483--493},
year = {2011},
url = {https://doi.org/10.1089/cmb.2010.0258},
doi = {10.1089/CMB.2010.0258},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SettyGP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/RamachandranMP11,
author = {Arthi Ramachandran and
Mariann Micsinai and
Itsik Pe'er},
title = {{CONDEX:} Copy number detection in exome sequences},
booktitle = {2011 {IEEE} International Conference on Bioinformatics and Biomedicine
Workshops, {BIBMW} 2011, Atlanta, GA, USA, November 12-15, 2011},
pages = {87--93},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/BIBMW.2011.6112359},
doi = {10.1109/BIBMW.2011.6112359},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/RamachandranMP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/ShenCWP11,
author = {Yufeng Shen and
Yee Him Cheung and
Shuang Wang and
Itsik Pe'er},
title = {A parametric Bayesian method to test the association of rare variants},
booktitle = {2011 {IEEE} International Conference on Bioinformatics and Biomedicine
Workshops, {BIBMW} 2011, Atlanta, GA, USA, November 12-15, 2011},
pages = {137--143},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/BIBMW.2011.6112366},
doi = {10.1109/BIBMW.2011.6112366},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/ShenCWP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/ShenGP11,
author = {Yufeng Shen and
Yiwei Gu and
Itsik Pe'er},
editor = {Ion I. Mandoiu and
Satoru Miyano and
Teresa M. Przytycka and
Sanguthevar Rajasekaran},
title = {Poster: {A} Hidden Markov Model for Copy Number Variant prediction
from Whole genome resequencing data},
booktitle = {{IEEE} 1st International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2011, Orlando, FL, USA, February 3-5,
2011},
pages = {260},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/ICCABS.2011.5729914},
doi = {10.1109/ICCABS.2011.5729914},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/ShenGP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/ShenSP11,
author = {Yufeng Shen and
Ruijie Song and
Itsik Pe'er},
editor = {Ion I. Mandoiu and
Satoru Miyano and
Teresa M. Przytycka and
Sanguthevar Rajasekaran},
title = {Workshop: Coverage tradeoffs and power estimation in the design of
whole-genome sequencing experiments for detecting association},
booktitle = {{IEEE} 1st International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2011, Orlando, FL, USA, February 3-5,
2011},
pages = {276},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/ICCABS.2011.5729930},
doi = {10.1109/ICCABS.2011.5729930},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/ShenSP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DewalFLP10,
author = {Ninad Dewal and
Matthew L. Freedman and
Thomas LaFramboise and
Itsik Pe'er},
title = {Power to detect selective allelic amplification in genome-wide scans
of tumor data},
journal = {Bioinform.},
volume = {26},
number = {4},
pages = {518--528},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btp694},
doi = {10.1093/BIOINFORMATICS/BTP694},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DewalFLP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SettyGP10,
author = {Manu N. Setty and
Alexander Gusev and
Itsik Pe'er},
editor = {Bonnie Berger},
title = {{HLA} Type Inference via Haplotypes Identical by Descent},
booktitle = {Research in Computational Molecular Biology, 14th Annual International
Conference, {RECOMB} 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6044},
pages = {491--505},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-12683-3\_32},
doi = {10.1007/978-3-642-12683-3\_32},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SettyGP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/PrabhuP09,
author = {Snehit Prabhu and
Itsik Pe'er},
editor = {Serafim Batzoglou},
title = {Overlapping Pools for High Throughput Targeted Resequencing},
booktitle = {Research in Computational Molecular Biology, 13th Annual International
Conference, {RECOMB} 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5541},
pages = {270},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02008-7\_20},
doi = {10.1007/978-3-642-02008-7\_20},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/PrabhuP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StoyanovichP08,
author = {Julia Stoyanovich and
Itsik Pe'er},
title = {MutaGeneSys: estimating individual disease susceptibility based on
genome-wide {SNP} array data},
journal = {Bioinform.},
volume = {24},
number = {3},
pages = {440--442},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btm587},
doi = {10.1093/BIOINFORMATICS/BTM587},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StoyanovichP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/BarzuzaBSP08,
author = {Tamar Barzuza and
Jacques S. Beckmann and
Ron Shamir and
Itsik Pe'er},
title = {Computational Problems in Perfect Phylogeny Haplotyping: Typing without
Calling the Allele},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {5},
number = {1},
pages = {101--109},
year = {2008},
url = {https://doi.org/10.1109/TCBB.2007.1063},
doi = {10.1109/TCBB.2007.1063},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/BarzuzaBSP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamcomp/PeerPSS04,
author = {Itsik Pe'er and
Tal Pupko and
Ron Shamir and
Roded Sharan},
title = {Incomplete Directed Perfect Phylogeny},
journal = {{SIAM} J. Comput.},
volume = {33},
number = {3},
pages = {590--607},
year = {2004},
url = {https://doi.org/10.1137/S0097539702406510},
doi = {10.1137/S0097539702406510},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/siamcomp/PeerPSS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/BarzuzaBSP04,
author = {Tamar Barzuza and
Jacques S. Beckmann and
Ron Shamir and
Itsik Pe'er},
editor = {S{\"{u}}leyman Cenk Sahinalp and
S. Muthukrishnan and
Ugur Dogrus{\"{o}}z},
title = {Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes
and Tag SNPs},
booktitle = {Combinatorial Pattern Matching, 15th Annual Symposium, {CPM} 2004,
Istanbul,Turkey, July 5-7, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3109},
pages = {14--31},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-27801-6\_2},
doi = {10.1007/978-3-540-27801-6\_2},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/BarzuzaBSP04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/PeerB03,
author = {Itsik Pe'er and
Jacques S. Beckmann},
editor = {Martin Vingron and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman and
Webb Miller},
title = {Resolution of haplotypes and haplotype frequencies from {SNP} genotypes
of pooled samples},
booktitle = {Proceedings of the Sventh Annual International Conference on Computational
Biology, {RECOMB} 2003, Berlin, Germany, April 10-13, 2003},
pages = {237--246},
publisher = {{ACM}},
year = {2003},
url = {https://doi.org/10.1145/640075.640107},
doi = {10.1145/640075.640107},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/PeerB03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PupkoPHGF02,
author = {Tal Pupko and
Itsik Pe'er and
Masami Hasegawa and
Dan Graur and
Nir Friedman},
title = {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},
journal = {Bioinform.},
volume = {18},
number = {8},
pages = {1116--1123},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.8.1116},
doi = {10.1093/BIOINFORMATICS/18.8.1116},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PupkoPHGF02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Ben-DorPSS02,
author = {Amir Ben{-}Dor and
Itsik Pe'er and
Ron Shamir and
Roded Sharan},
title = {On the Complexity of Positional Sequencing by Hybridization},
journal = {J. Comput. Biol.},
volume = {8},
number = {4},
pages = {361--371},
year = {2002},
url = {https://doi.org/10.1089/106652701752236188},
doi = {10.1089/106652701752236188},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/Ben-DorPSS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/FriedmanNPP02,
author = {Nir Friedman and
Matan Ninio and
Itsik Pe'er and
Tal Pupko},
title = {A Structural {EM} Algorithm for Phylogenetic Inference},
journal = {J. Comput. Biol.},
volume = {9},
number = {2},
pages = {331--353},
year = {2002},
url = {https://doi.org/10.1089/10665270252935494},
doi = {10.1089/10665270252935494},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/FriedmanNPP02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swat/PeerSS02,
author = {Itsik Pe'er and
Ron Shamir and
Roded Sharan},
editor = {Martti Penttonen and
Erik Meineche Schmidt},
title = {On the Generality of Phylogenies from Incomplete Directed Characters},
booktitle = {Algorithm Theory - {SWAT} 2002, 8th Scandinavian Workshop on Algorithm
Theory, Turku, Finland, July 3-5, 2002 Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2368},
pages = {358--367},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45471-3\_37},
doi = {10.1007/3-540-45471-3\_37},
timestamp = {Tue, 14 May 2019 10:00:39 +0200},
biburl = {https://dblp.org/rec/conf/swat/PeerSS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/FriedmanNPP01,
author = {Nir Friedman and
Matan Ninio and
Itsik Pe'er and
Tal Pupko},
editor = {Thomas Lengauer},
title = {A structural {EM} algorithm for phylogenetic inference},
booktitle = {Proceedings of the Fifth Annual International Conference on Computational
Biology, {RECOMB} 2001, Montr{\'{e}}al, Qu{\'{e}}bec, Canada,
April 22-25, 2001},
pages = {132--140},
publisher = {{ACM}},
year = {2001},
url = {https://doi.org/10.1145/369133.369182},
doi = {10.1145/369133.369182},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/FriedmanNPP01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/eccc/ECCC-TR01-054,
author = {Piotr Berman and
Amir Ben{-}Dor and
Itsik Pe'er and
Roded Sharan and
Ron Shamir},
title = {On the Complexity of Positional Sequencing by Hybridization},
journal = {Electron. Colloquium Comput. Complex.},
volume = {{TR01-054}},
year = {2001},
url = {https://eccc.weizmann.ac.il/eccc-reports/2001/TR01-054/index.html},
eprinttype = {ECCC},
eprint = {TR01-054},
timestamp = {Wed, 28 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/eccc/ECCC-TR01-054.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KarpPS00,
author = {Richard M. Karp and
Itsik Pe'er and
Ron Shamir},
title = {An Algorithm Combining Discrete and Continuous Methods for Optical
Mapping},
journal = {J. Comput. Biol.},
volume = {7},
number = {5},
pages = {745--760},
year = {2000},
url = {https://doi.org/10.1089/106652701446189},
doi = {10.1089/106652701446189},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/KarpPS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/PeerSS00,
author = {Itsik Pe'er and
Ron Shamir and
Roded Sharan},
editor = {Raffaele Giancarlo and
David Sankoff},
title = {Incomplete Directed Perfect Phylogeny},
booktitle = {Combinatorial Pattern Matching, 11th Annual Symposium, {CPM} 2000,
Montreal, Canada, June 21-23, 2000, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1848},
pages = {143--153},
publisher = {Springer},
year = {2000},
url = {https://doi.org/10.1007/3-540-45123-4\_14},
doi = {10.1007/3-540-45123-4\_14},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/PeerSS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/PeerS00,
author = {Itsik Pe'er and
Ron Shamir},
editor = {Philip E. Bourne and
Michael Gribskov and
Russ B. Altman and
Nancy Jensen and
Debra A. Hope and
Thomas Lengauer and
Julie C. Mitchell and
Eric D. Scheeff and
Chris Smith and
Shawn Strande and
Helge Weissig},
title = {Spectrum Alignment: Efficient Resequencing by Hybridization},
booktitle = {Proceedings of the Eighth International Conference on Intelligent
Systems for Molecular Biology, August 19-23, 2000, La Jolla / San
Diego, CA, {USA}},
pages = {260--268},
publisher = {{AAAI}},
year = {2000},
url = {http://www.aaai.org/Library/ISMB/2000/ismb00-027.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/PeerS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/Ben-DorPSS99,
author = {Amir Ben{-}Dor and
Itsik Pe'er and
Ron Shamir and
Roded Sharan},
editor = {Maxime Crochemore and
Mike Paterson},
title = {On the Complexity of Positional Sequencing by Hybridization},
booktitle = {Combinatorial Pattern Matching, 10th Annual Symposium, {CPM} 99, Warwick
University, UK, July 22-24, 1999, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1645},
pages = {88--100},
publisher = {Springer},
year = {1999},
url = {https://doi.org/10.1007/3-540-48452-3\_7},
doi = {10.1007/3-540-48452-3\_7},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cpm/Ben-DorPSS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KarpPS99,
author = {Richard M. Karp and
Itsik Pe'er and
Ron Shamir},
editor = {Thomas Lengauer and
Reinhard Schneider and
Peer Bork and
Douglas L. Brutlag and
Janice I. Glasgow and
Hans{-}Werner Mewes and
Ralf Zimmer},
title = {An Algorithm Combining Discrete and Continuous Methods for Optical
Mapping},
booktitle = {Proceedings of the Seventh International Conference on Intelligent
Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany},
pages = {159--168},
publisher = {{AAAI}},
year = {1999},
url = {http://www.aaai.org/Library/ISMB/1999/ismb99-019.php},
timestamp = {Mon, 24 Jun 2013 09:48:15 +0200},
biburl = {https://dblp.org/rec/conf/ismb/KarpPS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/eccc/ECCC-TR98-071,
author = {Itsik Pe'er and
Ron Shamir},
title = {The median problems for breakpoints are NP-complete},
journal = {Electron. Colloquium Comput. Complex.},
volume = {{TR98-071}},
year = {1998},
url = {https://eccc.weizmann.ac.il/eccc-reports/1998/TR98-071/index.html},
eprinttype = {ECCC},
eprint = {TR98-071},
timestamp = {Wed, 28 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/eccc/ECCC-TR98-071.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamdm/PeerS97,
author = {Itsik Pe'er and
Ron Shamir},
title = {Realizing Interval Graphs with Size and Distance Constraints},
journal = {{SIAM} J. Discret. Math.},
volume = {10},
number = {4},
pages = {662--687},
year = {1997},
url = {https://doi.org/10.1137/S0895480196306373},
doi = {10.1137/S0895480196306373},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamdm/PeerS97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/PeerS97,
author = {Itsik Pe'er and
Ron Shamir},
title = {Satisfiability Problems on Intervals and Unit Intervals},
journal = {Theor. Comput. Sci.},
volume = {175},
number = {2},
pages = {349--372},
year = {1997},
url = {https://doi.org/10.1016/S0304-3975(96)00208-3},
doi = {10.1016/S0304-3975(96)00208-3},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/PeerS97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/esa/PeerS95,
author = {Itsik Pe'er and
Ron Shamir},
editor = {Paul G. Spirakis},
title = {Interval Graphs with Side (and Size) Constraints},
booktitle = {Algorithms - {ESA} '95, Third Annual European Symposium, Corfu, Greece,
September 25-27, 1995, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {979},
pages = {142--154},
publisher = {Springer},
year = {1995},
url = {https://doi.org/10.1007/3-540-60313-1\_140},
doi = {10.1007/3-540-60313-1\_140},
timestamp = {Tue, 14 May 2019 10:00:54 +0200},
biburl = {https://dblp.org/rec/conf/esa/PeerS95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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