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ORCIDBibTeX records: Roded Sharan
@article{DBLP:journals/ploscb/KahaneLS23,
author = {Itay Kahane and
Mark D. M. Leiserson and
Roded Sharan},
title = {A mutation-level covariate model for mutational signatures},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {6},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1011195},
doi = {10.1371/JOURNAL.PCBI.1011195},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KahaneLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/GervitsS22,
author = {Asia Gervits and
Roded Sharan},
title = {Predicting genetic interactions, cell line dependencies and drug sensitivities
with variational graph auto-encoder},
journal = {Frontiers Bioinform.},
volume = {2},
year = {2022},
url = {https://doi.org/10.3389/fbinf.2022.1025783},
doi = {10.3389/FBINF.2022.1025783},
timestamp = {Fri, 28 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fbinf/GervitsS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/NasserES22,
author = {Rami Nasser and
Yonina C. Eldar and
Roded Sharan},
title = {Deep Unfolding for Non-Negative Matrix Factorization with Application
to Mutational Signature Analysis},
journal = {J. Comput. Biol.},
volume = {29},
number = {1},
pages = {45--55},
year = {2022},
url = {https://doi.org/10.1089/cmb.2021.0438},
doi = {10.1089/CMB.2021.0438},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/NasserES22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/FranzeseFSL22,
author = {Nicholas Franzese and
Jason Fan and
Roded Sharan and
Mark D. M. Leiserson},
title = {ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity
of Mutational Signatures},
journal = {J. Comput. Biol.},
volume = {29},
number = {1},
pages = {56--73},
year = {2022},
url = {https://doi.org/10.1089/cmb.2021.0453},
doi = {10.1089/CMB.2021.0453},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/FranzeseFSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MargalitASMBCVB21,
author = {Sapir Margalit and
Yotam Abramson and
Hila Sharim and
Zohar Manber and
Surajit Bhattacharya and
Yi{-}Wen Chen and
Eric Vilain and
Hayk Barseghyan and
Ran Elkon and
Roded Sharan and
Yuval Ebenstein},
title = {Long reads capture simultaneous enhancer-promoter methylation status
for cell-type deconvolution},
journal = {Bioinform.},
volume = {37},
number = {Supplement},
pages = {327--333},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab306},
doi = {10.1093/BIOINFORMATICS/BTAB306},
timestamp = {Tue, 21 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MargalitASMBCVB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SignoriniAS21,
author = {L. F. Signorini and
T. Almozlino and
Roded Sharan},
title = {{ANAT} 3.0: a framework for elucidating functional protein subnetworks
using graph-theoretic and machine learning approaches},
journal = {{BMC} Bioinform.},
volume = {22},
number = {3},
pages = {526},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-04449-1},
doi = {10.1186/S12859-021-04449-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SignoriniAS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mlst/GiladSS21,
author = {Gal Gilad and
Itay Sason and
Roded Sharan},
title = {An automated approach for determining the number of components in
non-negative matrix factorization with application to mutational signature
learning},
journal = {Mach. Learn. Sci. Technol.},
volume = {2},
number = {1},
pages = {15013},
year = {2021},
url = {https://doi.org/10.1088/2632-2153/abc60a},
doi = {10.1088/2632-2153/ABC60A},
timestamp = {Mon, 20 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mlst/GiladSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/GiladLS21,
author = {Gal Gilad and
Mark D. M. Leiserson and
Roded Sharan},
title = {A data-driven approach for constructing mutation categories for mutational
signature analysis},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {10},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009542},
doi = {10.1371/JOURNAL.PCBI.1009542},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/GiladLS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2108-09138,
author = {Rami Nasser and
Yonina C. Eldar and
Roded Sharan},
title = {deep unfolding for non-negative matrix factorization with application
to mutational signature analysis},
journal = {CoRR},
volume = {abs/2108.09138},
year = {2021},
url = {https://arxiv.org/abs/2108.09138},
eprinttype = {arXiv},
eprint = {2108.09138},
timestamp = {Mon, 23 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2108-09138.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BrunerS20,
author = {Ariel Bruner and
Roded Sharan},
title = {A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits},
journal = {J. Comput. Biol.},
volume = {27},
number = {2},
pages = {133--143},
year = {2020},
url = {https://doi.org/10.1089/cmb.2019.0290},
doi = {10.1089/CMB.2019.0290},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/BrunerS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LeisersonPS20,
author = {Mark D. M. Leiserson and
Teresa M. Przytycka and
Roded Sharan},
title = {Session Introduction},
booktitle = {Pacific Symposium on Biocomputing 2020, Fairmont Orchid, Hawaii, USA,
January 3-7, 2020},
pages = {219--225},
year = {2020},
url = {https://psb.stanford.edu/psb-online/proceedings/psb20/Intro\_Mutational\%20Signatures.pdf},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LeisersonPS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/WojtowiczLSP20,
author = {Damian W{\'{o}}jtowicz and
Mark D. M. Leiserson and
Roded Sharan and
Teresa M. Przytycka},
title = {{DNA} Repair Footprint Uncovers Contribution of {DNA} Repair Mechanism
to MutationalSignatures},
booktitle = {Pacific Symposium on Biocomputing 2020, Fairmont Orchid, Hawaii, USA,
January 3-7, 2020},
pages = {262--273},
year = {2020},
url = {https://psb.stanford.edu/psb-online/proceedings/psb20/Wojtowicz.pdf},
timestamp = {Fri, 13 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/psb/WojtowiczLSP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SasonCLS20,
author = {Itay Sason and
Yuexi Chen and
Mark D. M. Leiserson and
Roded Sharan},
editor = {Russell Schwartz},
title = {A Mixture Model for Signature Discovery from Sparse Mutation 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 = {271--272},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-45257-5\_34},
doi = {10.1007/978-3-030-45257-5\_34},
timestamp = {Tue, 21 Apr 2020 12:14:30 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SasonCLS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RobinsonSL19,
author = {Welles Robinson and
Roded Sharan and
Mark D. M. Leiserson},
title = {Modeling clinical and molecular covariates of mutational process activity
in cancer},
journal = {Bioinform.},
volume = {35},
number = {14},
pages = {i492--i500},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz340},
doi = {10.1093/BIOINFORMATICS/BTZ340},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RobinsonSL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/BrunerS19,
author = {Ariel Bruner and
Roded Sharan},
editor = {Zhipeng Cai and
Pavel Skums and
Min Li},
title = {A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits},
booktitle = {Bioinformatics Research and Applications - 15th International Symposium,
{ISBRA} 2019, Barcelona, Spain, June 3-6, 2019, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11490},
pages = {183--195},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-20242-2\_16},
doi = {10.1007/978-3-030-20242-2\_16},
timestamp = {Thu, 20 Aug 2020 15:54:47 +0200},
biburl = {https://dblp.org/rec/conf/isbra/BrunerS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SasonWRLPS19,
author = {Itay Sason and
Damian W{\'{o}}jtowicz and
Welles Robinson and
Mark D. M. Leiserson and
Teresa M. Przytycka and
Roded Sharan},
editor = {Lenore J. Cowen},
title = {A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational
Processes in Cancer},
booktitle = {Research in Computational Molecular Biology - 23rd Annual International
Conference, {RECOMB} 2019, Washington, DC, USA, May 5-8, 2019, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11467},
pages = {243--255},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-17083-7\_15},
doi = {10.1007/978-3-030-17083-7\_15},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SasonWRLPS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PatkarS18,
author = {Sushant Patkar and
Roded Sharan},
title = {An optimization framework for network annotation},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {i502--i508},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty236},
doi = {10.1093/BIOINFORMATICS/BTY236},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PatkarS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/HartmannWSMB18,
author = {Tom Hartmann and
Nicolas Wieseke and
Roded Sharan and
Martin Middendorf and
Matthias Bernt},
title = {Genome Rearrangement with {ILP}},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {5},
pages = {1585--1593},
year = {2018},
url = {https://doi.org/10.1109/TCBB.2017.2708121},
doi = {10.1109/TCBB.2017.2708121},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/HartmannWSMB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SilverbushCYGBS18,
author = {Dana Silverbush and
Simona Cristea and
Gali Yanovich and
Tamar Geiger and
Niko Beerenwinkel and
Roded Sharan},
editor = {Benjamin J. Raphael},
title = {ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver
Modules},
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 = {283--284},
publisher = {Springer},
year = {2018},
url = {https://link.springer.com/content/pdf/bbm\%3A978-3-319-89929-9\%2F1.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/SilverbushCYGBS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SternbergS18,
author = {Barak Sternberg and
Roded Sharan},
editor = {Laxmi Parida and
Esko Ukkonen},
title = {A Dynamic Algorithm for Network Propagation},
booktitle = {18th International Workshop on Algorithms in Bioinformatics, {WABI}
2018, August 20-22, 2018, Helsinki, Finland},
series = {LIPIcs},
volume = {113},
pages = {7:1--7:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2018},
url = {https://doi.org/10.4230/LIPIcs.WABI.2018.7},
doi = {10.4230/LIPICS.WABI.2018.7},
timestamp = {Tue, 11 Feb 2020 15:52:14 +0100},
biburl = {https://dblp.org/rec/conf/wabi/SternbergS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/El-KebirRSSZZZ17,
author = {Mohammed El{-}Kebir and
Benjamin J. Raphael and
Ron Shamir and
Roded Sharan and
Simone Zaccaria and
Meirav Zehavi and
Ron Zeira},
title = {Complexity and algorithms for copy-number evolution problems},
journal = {Algorithms Mol. Biol.},
volume = {12},
number = {1},
pages = {13:1--13:11},
year = {2017},
url = {https://doi.org/10.1186/s13015-017-0103-2},
doi = {10.1186/S13015-017-0103-2},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/El-KebirRSSZZZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlmozlinoASS17,
author = {Yomtov Almozlino and
Nir Atias and
Dana Silverbush and
Roded Sharan},
title = {{ANAT} 2.0: reconstructing functional protein subnetworks},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {495},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1932-1},
doi = {10.1186/S12859-017-1932-1},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AlmozlinoASS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DaoKWMSP17,
author = {Phuong Dao and
Yoo{-}Ah Kim and
Damian W{\'{o}}jtowicz and
Sanna Madan and
Roded Sharan and
Teresa M. Przytycka},
title = {BeWith: {A} Between-Within method to discover relationships between
cancer modules via integrated analysis of mutual exclusivity, co-occurrence
and functional interactions},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {10},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005695},
doi = {10.1371/JOURNAL.PCBI.1005695},
timestamp = {Thu, 31 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DaoKWMSP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/PatkarMSH17,
author = {Sushant Patkar and
Assaf Magen and
Roded Sharan and
Sridhar Hannenhalli},
title = {A network diffusion approach to inferring sample-specific function
reveals functional changes associated with breast cancer},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {11},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005793},
doi = {10.1371/JOURNAL.PCBI.1005793},
timestamp = {Thu, 31 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/PatkarMSH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/DaoKMSP17,
author = {Phuong Dao and
Yoo{-}Ah Kim and
Sanna Madan and
Roded Sharan and
Teresa M. Przytycka},
editor = {S{\"{u}}leyman Cenk Sahinalp},
title = {BeWith: {A} Between-Within Method for Module Discovery in Cancer using
Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional
Interactions (Extended Abstract)},
booktitle = {Research in Computational Molecular Biology - 21st Annual International
Conference, {RECOMB} 2017, Hong Kong, China, May 3-7, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10229},
pages = {370--371},
year = {2017},
url = {https://link.springer.com/content/pdf/bbm\%3A978-3-319-56970-3\%2F1.pdf},
timestamp = {Sat, 30 May 2020 20:04:52 +0200},
biburl = {https://dblp.org/rec/conf/recomb/DaoKMSP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MazzaKWS16,
author = {Arnon Mazza and
Konrad Klockmeier and
Erich E. Wanker and
Roded Sharan},
title = {An integer programming framework for inferring disease complexes from
network data},
journal = {Bioinform.},
volume = {32},
number = {12},
pages = {271--277},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw263},
doi = {10.1093/BIOINFORMATICS/BTW263},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MazzaKWS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MazzaKWS16a,
author = {Arnon Mazza and
Konrad Klockmeier and
Erich E. Wanker and
Roded Sharan},
title = {An integer programming framework for inferring disease complexes from
network data},
journal = {Bioinform.},
volume = {32},
number = {24},
pages = {3855},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw692},
doi = {10.1093/BIOINFORMATICS/BTW692},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MazzaKWS16a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MazzaWRS16,
author = {Arnon Mazza and
Allon Wagner and
Eytan Ruppin and
Roded Sharan},
title = {Functional Alignment of Metabolic Networks},
journal = {J. Comput. Biol.},
volume = {23},
number = {5},
pages = {390--399},
year = {2016},
url = {https://doi.org/10.1089/cmb.2015.0203},
doi = {10.1089/CMB.2015.0203},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/MazzaWRS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/ShnapsPSS16,
author = {Ortal Shnaps and
Eyal Perry and
Dana Silverbush and
Roded Sharan},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Inference of Personalized Drug Targets via Network Propagation},
booktitle = {Biocomputing 2016: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 4-8, 2016},
pages = {156--167},
year = {2016},
url = {http://psb.stanford.edu/psb-online/proceedings/psb16/shnaps.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/ShnapsPSS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/El-KebirRSSZZZ16,
author = {Mohammed El{-}Kebir and
Benjamin J. Raphael and
Ron Shamir and
Roded Sharan and
Simone Zaccaria and
Meirav Zehavi and
Ron Zeira},
editor = {Martin C. Frith and
Christian N{\o}rgaard Storm Pedersen},
title = {Copy-Number Evolution Problems: Complexity and Algorithms},
booktitle = {Algorithms in Bioinformatics - 16th International Workshop, {WABI}
2016, Aarhus, Denmark, August 22-24, 2016. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9838},
pages = {137--149},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-43681-4\_11},
doi = {10.1007/978-3-319-43681-4\_11},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/El-KebirRSSZZZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Sharan15,
author = {Roded Sharan},
title = {Preface},
journal = {J. Comput. Biol.},
volume = {22},
number = {5},
pages = {335},
year = {2015},
url = {https://doi.org/10.1089/cmb.2015.030P},
doi = {10.1089/CMB.2015.030P},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/Sharan15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RuffaloKS15,
author = {Matthew Ruffalo and
Mehmet Koyut{\"{u}}rk and
Roded Sharan},
title = {Network-Based Integration of Disparate Omic Data To Identify "Silent
Players" in Cancer},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {12},
year = {2015},
url = {https://doi.org/10.1371/journal.pcbi.1004595},
doi = {10.1371/JOURNAL.PCBI.1004595},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RuffaloKS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/MazzaWRS15,
author = {Arnon Mazza and
Allon Wagner and
Eytan Ruppin and
Roded Sharan},
editor = {Teresa M. Przytycka},
title = {Functional Alignment of Metabolic Networks},
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 = {243--255},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-16706-0\_24},
doi = {10.1007/978-3-319-16706-0\_24},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/MazzaWRS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MazzaGFS14,
author = {Arnon Mazza and
Irit Gat{-}Viks and
Hesso Farhan and
Roded Sharan},
title = {A minimum-labeling approach for reconstructing protein networks across
multiple conditions},
journal = {Algorithms Mol. Biol.},
volume = {9},
pages = {1},
year = {2014},
url = {https://doi.org/10.1186/1748-7188-9-1},
doi = {10.1186/1748-7188-9-1},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/MazzaGFS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SilverbushS14,
author = {Dana Silverbush and
Roded Sharan},
title = {Network orientation via shortest paths},
journal = {Bioinform.},
volume = {30},
number = {10},
pages = {1449--1455},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu043},
doi = {10.1093/BIOINFORMATICS/BTU043},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SilverbushS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AtiasGLS14,
author = {Nir Atias and
Michal Gershenzon and
Katia Labazin and
Roded Sharan},
title = {Experimental design schemes for learning Boolean network models},
journal = {Bioinform.},
volume = {30},
number = {17},
pages = {445--452},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu451},
doi = {10.1093/BIOINFORMATICS/BTU451},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AtiasGLS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MazzaGS14,
author = {Arnon Mazza and
Irit Gat{-}Viks and
Roded Sharan},
title = {Elucidating Influenza Inhibition Pathways via Network Reconstruction},
journal = {J. Comput. Biol.},
volume = {21},
number = {5},
pages = {394--404},
year = {2014},
url = {https://doi.org/10.1089/cmb.2013.0147},
doi = {10.1089/CMB.2013.0147},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/MazzaGS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/recomb/2014,
editor = {Roded Sharan},
title = {Research in Computational Molecular Biology - 18th Annual International
Conference, {RECOMB} 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8394},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-05269-4},
doi = {10.1007/978-3-319-05269-4},
isbn = {978-3-319-05268-7},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/2014.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HalldorssonBS13,
author = {Bjarni V. Halld{\'{o}}rsson and
Dima Blokh and
Roded Sharan},
title = {Estimating population size via line graph reconstruction},
journal = {Algorithms Mol. Biol.},
volume = {8},
pages = {17},
year = {2013},
url = {https://doi.org/10.1186/1748-7188-8-17},
doi = {10.1186/1748-7188-8-17},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/HalldorssonBS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SharanK13,
author = {Roded Sharan and
Richard M. Karp},
title = {Reconstructing Boolean Models of Signaling},
journal = {J. Comput. Biol.},
volume = {20},
number = {3},
pages = {249--257},
year = {2013},
url = {https://doi.org/10.1089/cmb.2012.0241},
doi = {10.1089/CMB.2012.0241},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SharanK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BlokhSS13,
author = {Dima Blokh and
Danny Segev and
Roded Sharan},
title = {The Approximability of Shortest Path-Based Graph Orientations of Protein-Protein
Interaction Networks},
journal = {J. Comput. Biol.},
volume = {20},
number = {12},
pages = {945--957},
year = {2013},
url = {https://doi.org/10.1089/cmb.2013.0064},
doi = {10.1089/CMB.2013.0064},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/BlokhSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LeisersonBSR13,
author = {Mark D. M. Leiserson and
Dima Blokh and
Roded Sharan and
Benjamin J. Raphael},
title = {Simultaneous Identification of Multiple Driver Pathways in Cancer},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {5},
year = {2013},
url = {https://doi.org/10.1371/journal.pcbi.1003054},
doi = {10.1371/JOURNAL.PCBI.1003054},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LeisersonBSR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/ElberfeldSDSS13,
author = {Michael Elberfeld and
Danny Segev and
Colin R. Davidson and
Dana Silverbush and
Roded Sharan},
title = {Approximation algorithms for orienting mixed graphs},
journal = {Theor. Comput. Sci.},
volume = {483},
pages = {96--103},
year = {2013},
url = {https://doi.org/10.1016/j.tcs.2012.03.044},
doi = {10.1016/J.TCS.2012.03.044},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/ElberfeldSDSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MazzaGFS13,
author = {Arnon Mazza and
Irit Gat{-}Viks and
Hesso Farhan and
Roded Sharan},
editor = {Aaron E. Darling and
Jens Stoye},
title = {A Minimum-Labeling Approach for Reconstructing Protein Networks across
Multiple Conditions},
booktitle = {Algorithms in Bioinformatics - 13th International Workshop, {WABI}
2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8126},
pages = {33--44},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-40453-5\_4},
doi = {10.1007/978-3-642-40453-5\_4},
timestamp = {Tue, 21 Mar 2023 21:00:29 +0100},
biburl = {https://dblp.org/rec/conf/wabi/MazzaGFS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cacm/AtiasS12,
author = {Nir Atias and
Roded Sharan},
title = {Comparative analysis of protein networks: hard problems, practical
solutions},
journal = {Commun. {ACM}},
volume = {55},
number = {5},
pages = {88--97},
year = {2012},
url = {https://doi.org/10.1145/2160718.2160738},
doi = {10.1145/2160718.2160738},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cacm/AtiasS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SilberbergGKRS12,
author = {Yael Silberberg and
Assaf Gottlieb and
Martin Kupiec and
Eytan Ruppin and
Roded Sharan},
title = {Large-Scale Elucidation of Drug Response Pathways in Humans},
journal = {J. Comput. Biol.},
volume = {19},
number = {2},
pages = {163--174},
year = {2012},
url = {https://doi.org/10.1089/cmb.2011.0264},
doi = {10.1089/CMB.2011.0264},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SilberbergGKRS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/VardiRS12,
author = {Liram Vardi and
Eytan Ruppin and
Roded Sharan},
title = {A Linearized Constraint-Based Approach for Modeling Signaling Networks},
journal = {J. Comput. Biol.},
volume = {19},
number = {2},
pages = {232--240},
year = {2012},
url = {https://doi.org/10.1089/cmb.2011.0277},
doi = {10.1089/CMB.2011.0277},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/VardiRS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MaggerWRS12,
author = {Oded Magger and
Yedael Y. Waldman and
Eytan Ruppin and
Roded Sharan},
title = {Enhancing the Prioritization of Disease-Causing Genes through Tissue
Specific Protein Interaction Networks},
journal = {PLoS Comput. Biol.},
volume = {8},
number = {9},
year = {2012},
url = {https://doi.org/10.1371/journal.pcbi.1002690},
doi = {10.1371/JOURNAL.PCBI.1002690},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/MaggerWRS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/BlokhSS12,
author = {Dima Blokh and
Danny Segev and
Roded Sharan},
editor = {Juha K{\"{a}}rkk{\"{a}}inen and
Jens Stoye},
title = {Approximation Algorithms and Hardness Results for Shortest Path Based
Graph Orientations},
booktitle = {Combinatorial Pattern Matching - 23rd Annual Symposium, {CPM} 2012,
Helsinki, Finland, July 3-5, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7354},
pages = {70--82},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-31265-6\_6},
doi = {10.1007/978-3-642-31265-6\_6},
timestamp = {Tue, 21 Mar 2023 21:02:12 +0100},
biburl = {https://dblp.org/rec/conf/cpm/BlokhSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/Sharan12,
author = {Roded Sharan},
editor = {Sorin Istrail and
Ion I. Mandoiu and
Mihai Pop and
Sanguthevar Rajasekaran and
John L. Spouge},
title = {Invited: From protein networks to disease mechanisms},
booktitle = {{IEEE} 2nd International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2012, Las Vegas, NV, USA, February
23-25, 2012},
pages = {1},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/ICCABS.2012.6182624},
doi = {10.1109/ICCABS.2012.6182624},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/Sharan12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SharanK12,
author = {Roded Sharan and
Richard M. Karp},
editor = {Benny Chor},
title = {Reconstructing Boolean Models of Signaling},
booktitle = {Research in Computational Molecular Biology - 16th Annual International
Conference, {RECOMB} 2012, Barcelona, Spain, April 21-24, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7262},
pages = {261--271},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-29627-7\_28},
doi = {10.1007/978-3-642-29627-7\_28},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SharanK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/HalldorssonBS12,
author = {Bjarni V. Halld{\'{o}}rsson and
Dima Blokh and
Roded Sharan},
editor = {Benjamin J. Raphael and
Jijun Tang},
title = {Estimating Population Size via Line Graph Reconstruction},
booktitle = {Algorithms in Bioinformatics - 12th International Workshop, {WABI}
2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {69--80},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33122-0\_6},
doi = {10.1007/978-3-642-33122-0\_6},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/HalldorssonBS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/HouriS12,
author = {Shay Houri and
Roded Sharan},
editor = {Benjamin J. Raphael and
Jijun Tang},
title = {Sign Assignment Problems on Protein Networks},
booktitle = {Algorithms in Bioinformatics - 12th International Workshop, {WABI}
2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {338--345},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33122-0\_27},
doi = {10.1007/978-3-642-33122-0\_27},
timestamp = {Thu, 25 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/HouriS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GevaS11,
author = {Guy Geva and
Roded Sharan},
title = {Identification of protein complexes from co-immunoprecipitation data},
journal = {Bioinform.},
volume = {27},
number = {1},
pages = {111--117},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btq652},
doi = {10.1093/BIOINFORMATICS/BTQ652},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GevaS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GottliebMBRS11,
author = {Assaf Gottlieb and
Oded Magger and
Igor Berman and
Eytan Ruppin and
Roded Sharan},
title = {{PRINCIPLE:} a tool for associating genes with diseases via network
propagation},
journal = {Bioinform.},
volume = {27},
number = {23},
pages = {3325--3326},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr584},
doi = {10.1093/BIOINFORMATICS/BTR584},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GottliebMBRS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/im/ElberfeldBGMSSZS11,
author = {Michael Elberfeld and
Vineet Bafna and
Iftah Gamzu and
Alexander Medvedovsky and
Danny Segev and
Dana Silverbush and
Uri Zwick and
Roded Sharan},
title = {On the Approximability of Reachability-Preserving Network Orientations},
journal = {Internet Math.},
volume = {7},
number = {4},
pages = {209--232},
year = {2011},
url = {https://doi.org/10.1080/15427951.2011.604554},
doi = {10.1080/15427951.2011.604554},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/im/ElberfeldBGMSSZS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/PerlmanGARS11,
author = {Liat Perlman and
Assaf Gottlieb and
Nir Atias and
Eytan Ruppin and
Roded Sharan},
title = {Combining Drug and Gene Similarity Measures for Drug-Target Elucidation},
journal = {J. Comput. Biol.},
volume = {18},
number = {2},
pages = {133--145},
year = {2011},
url = {https://doi.org/10.1089/cmb.2010.0213},
doi = {10.1089/CMB.2010.0213},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/PerlmanGARS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/AtiasS11,
author = {Nir Atias and
Roded Sharan},
title = {An Algorithmic Framework for Predicting Side Effects of Drugs},
journal = {J. Comput. Biol.},
volume = {18},
number = {3},
pages = {207--218},
year = {2011},
url = {https://doi.org/10.1089/cmb.2010.0255},
doi = {10.1089/CMB.2010.0255},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/AtiasS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SilverbushES11,
author = {Dana Silverbush and
Michael Elberfeld and
Roded Sharan},
title = {Optimally Orienting Physical Networks},
journal = {J. Comput. Biol.},
volume = {18},
number = {11},
pages = {1437--1448},
year = {2011},
url = {https://doi.org/10.1089/cmb.2011.0163},
doi = {10.1089/CMB.2011.0163},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SilverbushES11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ShlomiBGSR11,
author = {Tomer Shlomi and
Tomer Benyamini and
Eyal Gottlieb and
Roded Sharan and
Eytan Ruppin},
title = {Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative
Adaptation in Causing the Warburg Effect},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {3},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1002018},
doi = {10.1371/JOURNAL.PCBI.1002018},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ShlomiBGSR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WolfGMSR11,
author = {Lior Wolf and
Chen Goldberg and
Nathan Manor and
Roded Sharan and
Eytan Ruppin},
title = {Gene Expression in the Rodent Brain is Associated with Its Regional
Connectivity},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {5},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1002040},
doi = {10.1371/JOURNAL.PCBI.1002040},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WolfGMSR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/ElberfeldSDSS11,
author = {Michael Elberfeld and
Danny Segev and
Colin R. Davidson and
Dana Silverbush and
Roded Sharan},
editor = {Raffaele Giancarlo and
Giovanni Manzini},
title = {Approximation Algorithms for Orienting Mixed Graphs},
booktitle = {Combinatorial Pattern Matching - 22nd Annual Symposium, {CPM} 2011,
Palermo, Italy, June 27-29, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6661},
pages = {416--428},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-21458-5\_35},
doi = {10.1007/978-3-642-21458-5\_35},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/ElberfeldSDSS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SilverbushES11,
author = {Dana Silverbush and
Michael Elberfeld and
Roded Sharan},
editor = {Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {Optimally Orienting Physical Networks},
booktitle = {Research in Computational Molecular Biology - 15th Annual International
Conference, {RECOMB} 2011, Vancouver, BC, Canada, March 28-31, 2011.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6577},
pages = {424--436},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-20036-6\_39},
doi = {10.1007/978-3-642-20036-6\_39},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SilverbushES11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sisap/Sharan11,
author = {Roded Sharan},
editor = {Alfredo Ferro},
title = {Similarity-based methods to predict drug targets, indications and
side-effects},
booktitle = {Fourth International Conference on Similarity Search and Applications,
{SISAP} 2011, Lipari Island, Italy, June 30 - July 01, 2011},
pages = {5--6},
publisher = {{ACM}},
year = {2011},
url = {https://doi.org/10.1145/1995412.1995415},
doi = {10.1145/1995412.1995415},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sisap/Sharan11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cominfsys/GrammKNSWY10,
author = {Jens Gramm and
Richard M. Karp and
William S. Noble and
Roded Sharan and
Qianfei Wang and
Nir Yosef},
title = {Prediction of Phenotype Information from Genotype Data},
journal = {Commun. Inf. Syst.},
volume = {10},
number = {2},
pages = {99--114},
year = {2010},
url = {https://doi.org/10.4310/cis.2010.v10.n2.a3},
doi = {10.4310/CIS.2010.V10.N2.A3},
timestamp = {Wed, 16 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cominfsys/GrammKNSWY10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/MongioviNGPFS10,
author = {Misael Mongiov{\`{\i}} and
Raffaele Di Natale and
Rosalba Giugno and
Alfredo Pulvirenti and
Alfredo Ferro and
Roded Sharan},
title = {Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm},
journal = {J. Bioinform. Comput. Biol.},
volume = {8},
number = {2},
pages = {199--218},
year = {2010},
url = {https://doi.org/10.1142/S021972001000477X},
doi = {10.1142/S021972001000477X},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/MongioviNGPFS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BrucknerHKSS10,
author = {Sharon Bruckner and
Falk H{\"{u}}ffner and
Richard M. Karp and
Ron Shamir and
Roded Sharan},
title = {Topology-Free Querying of Protein Interaction Networks},
journal = {J. Comput. Biol.},
volume = {17},
number = {3},
pages = {237--252},
year = {2010},
url = {https://doi.org/10.1089/cmb.2009.0170},
doi = {10.1089/CMB.2009.0170},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/BrucknerHKSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/PelegYRS10,
author = {Tal Peleg and
Nir Yosef and
Eytan Ruppin and
Roded Sharan},
title = {Network-Free Inference of Knockout Effects in Yeast},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {1},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000635},
doi = {10.1371/JOURNAL.PCBI.1000635},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/PelegYRS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/VanunuMRSS10,
author = {Oron Vanunu and
Oded Magger and
Eytan Ruppin and
Tomer Shlomi and
Roded Sharan},
title = {Associating Genes and Protein Complexes with Disease via Network Propagation},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {1},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000641},
doi = {10.1371/JOURNAL.PCBI.1000641},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/VanunuMRSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/FreilichKBGSR10,
author = {Shiri Freilich and
Anat Kreimer and
Elhanan Borenstein and
Uri Gophna and
Roded Sharan and
Eytan Ruppin},
title = {Decoupling Environment-Dependent and Independent Genetic Robustness
across Bacterial Species},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {2},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000690},
doi = {10.1371/JOURNAL.PCBI.1000690},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/FreilichKBGSR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/AtiasS10,
author = {Nir Atias and
Roded Sharan},
editor = {Bonnie Berger},
title = {An Algorithmic Framework for Predicting Side-Effects of Drugs},
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 = {1--14},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-12683-3\_1},
doi = {10.1007/978-3-642-12683-3\_1},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/AtiasS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/GamzuSS10,
author = {Iftah Gamzu and
Danny Segev and
Roded Sharan},
editor = {Vincent Moulton and
Mona Singh},
title = {Improved Orientations of Physical Networks},
booktitle = {Algorithms in Bioinformatics, 10th International Workshop, {WABI}
2010, Liverpool, UK, September 6-8, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6293},
pages = {215--225},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15294-8\_18},
doi = {10.1007/978-3-642-15294-8\_18},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/GamzuSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dm/GrammHNST09,
author = {Jens Gramm and
Tzvika Hartman and
Till Nierhoff and
Roded Sharan and
Till Tantau},
title = {On the complexity of {SNP} block partitioning under the perfect phylogeny
model},
journal = {Discret. Math.},
volume = {309},
number = {18},
pages = {5610--5617},
year = {2009},
url = {https://doi.org/10.1016/j.disc.2008.04.002},
doi = {10.1016/J.DISC.2008.04.002},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dm/GrammHNST09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KarniSS09,
author = {Shaul Karni and
Hermona Soreq and
Roded Sharan},
title = {A Network-Based Method for Predicting Disease-Causing Genes},
journal = {J. Comput. Biol.},
volume = {16},
number = {2},
pages = {181--189},
year = {2009},
url = {https://doi.org/10.1089/cmb.2008.05TT},
doi = {10.1089/CMB.2008.05TT},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/KarniSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KalaevBS09,
author = {Maxim Kalaev and
Vineet Bafna and
Roded Sharan},
title = {Fast and Accurate Alignment of Multiple Protein Networks},
journal = {J. Comput. Biol.},
volume = {16},
number = {8},
pages = {989--999},
year = {2009},
url = {https://doi.org/10.1089/cmb.2009.0136},
doi = {10.1089/CMB.2009.0136},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/KalaevBS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BrucknerHKSS09,
author = {Sharon Bruckner and
Falk H{\"{u}}ffner and
Richard M. Karp and
Ron Shamir and
Roded Sharan},
title = {Torque: topology-free querying of protein interaction networks},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Web-Server-Issue},
pages = {106--108},
year = {2009},
url = {https://doi.org/10.1093/nar/gkp474},
doi = {10.1093/NAR/GKP474},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/BrucknerHKSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BrucknerHKSS09,
author = {Sharon Bruckner and
Falk H{\"{u}}ffner and
Richard M. Karp and
Ron Shamir and
Roded Sharan},
editor = {Serafim Batzoglou},
title = {Topology-Free Querying of Protein Interaction Networks},
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 = {74--89},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02008-7\_6},
doi = {10.1007/978-3-642-02008-7\_6},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BrucknerHKSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KalaevSIS08,
author = {Maxim Kalaev and
Michael E. Smoot and
Trey Ideker and
Roded Sharan},
title = {NetworkBLAST: comparative analysis of protein networks},
journal = {Bioinform.},
volume = {24},
number = {4},
pages = {594--596},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btm630},
doi = {10.1093/BIOINFORMATICS/BTM630},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KalaevSIS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/DrorSSNWS08,
author = {Oranit Dror and
Dina Schneidman{-}Duhovny and
Alexandra Shulman{-}Peleg and
Ruth Nussinov and
Haim J. Wolfson and
Roded Sharan},
title = {Structural similarity of genetically interacting proteins},
journal = {{BMC} Syst. Biol.},
volume = {2},
pages = {69},
year = {2008},
url = {https://doi.org/10.1186/1752-0509-2-69},
doi = {10.1186/1752-0509-2-69},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcsb/DrorSSNWS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DostSGRBS08,
author = {Banu Dost and
Tomer Shlomi and
Nitin Gupta and
Eytan Ruppin and
Vineet Bafna and
Roded Sharan},
title = {QNet: {A} Tool for Querying Protein Interaction Networks},
journal = {J. Comput. Biol.},
volume = {15},
number = {7},
pages = {913--925},
year = {2008},
url = {https://doi.org/10.1089/cmb.2007.0172},
doi = {10.1089/CMB.2007.0172},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/DostSGRBS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/YosefSN08,
author = {Nir Yosef and
Roded Sharan and
William Stafford Noble},
title = {Improved network-based identification of protein orthologs},
booktitle = {ECCB'08 Proceedings, Seventh European Conference on Computational
Biology, 22-26 September 2008, Cagliari, Italy},
pages = {200--206},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn277},
doi = {10.1093/BIOINFORMATICS/BTN277},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/YosefSN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/VanunuS08,
author = {Oron Vanunu and
Roded Sharan},
editor = {Andreas Beyer and
Michael Schroeder},
title = {A Propagation-based Algorithm for Inferring Gene-Disease Assocations},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 2008,
September 9-12, 2008, Dresden, Germany},
series = {{LNI}},
volume = {{P-136}},
pages = {54--63},
publisher = {{GI}},
year = {2008},
url = {https://dl.gi.de/handle/20.500.12116/21221},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/VanunuS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/KalaevBS08,
author = {Maxim Kalaev and
Vineet Bafna and
Roded Sharan},
editor = {Martin Vingron and
Limsoon Wong},
title = {Fast and Accurate Alignment of Multiple Protein Networks},
booktitle = {Research in Computational Molecular Biology, 12th Annual International
Conference, {RECOMB} 2008, Singapore, March 30 - April 2, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4955},
pages = {246--256},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-78839-3\_21},
doi = {10.1007/978-3-540-78839-3\_21},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/KalaevBS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MedvedovskyBZS08,
author = {Alexander Medvedovsky and
Vineet Bafna and
Uri Zwick and
Roded Sharan},
editor = {Keith A. Crandall and
Jens Lagergren},
title = {An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and
Its Applications to Orienting Protein Networks},
booktitle = {Algorithms in Bioinformatics, 8th International Workshop, {WABI} 2008,
Karlsruhe, Germany, September 15-19, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5251},
pages = {222--232},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87361-7\_19},
doi = {10.1007/978-3-540-87361-7\_19},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/MedvedovskyBZS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/sp/08/YosefRS08,
author = {Nir Yosef and
Eytan Ruppin and
Roded Sharan},
editor = {Anna R. Panchenko and
Teresa M. Przytycka},
title = {Cross-Species Analysis of Protein-protein Interaction Networks},
booktitle = {Protein-protein Interactions and Networks: Identification, Computer
Analysis, and Prediction},
series = {Computational Biology},
volume = {9},
pages = {163--185},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-1-84800-125-1\_9},
doi = {10.1007/978-1-84800-125-1\_9},
timestamp = {Thu, 28 May 2020 13:10:24 +0200},
biburl = {https://dblp.org/rec/books/sp/08/YosefRS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YosefYTKBRS07,
author = {Nir Yosef and
Zohar Yakhini and
Anya Tsalenko and
Vessela N. Kristensen and
Anne{-}Lise B{\o}rresen{-}Dale and
Eytan Ruppin and
Roded Sharan},
title = {A supervised approach for identifying discriminating genotype patterns
and its application to breast cancer data},
journal = {Bioinform.},
volume = {23},
number = {2},
pages = {91--98},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl298},
doi = {10.1093/BIOINFORMATICS/BTL298},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YosefYTKBRS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HirshS07,
author = {Eitan Hirsh and
Roded Sharan},
title = {Identification of conserved protein complexes based on a model of
protein network evolution},
journal = {Bioinform.},
volume = {23},
number = {2},
pages = {170--176},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl295},
doi = {10.1093/BIOINFORMATICS/BTL295},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HirshS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RokhlenkoSSRP07,
author = {Oleg Rokhlenko and
Tomer Shlomi and
Roded Sharan and
Eytan Ruppin and
Ron Y. Pinter},
title = {Constraint-based functional similarity of metabolic genes: going beyond
network topology},
journal = {Bioinform.},
volume = {23},
number = {16},
pages = {2139--2146},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm319},
doi = {10.1093/BIOINFORMATICS/BTM319},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RokhlenkoSSRP07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MayrosePERSFBRSGMP07,
author = {Itay Mayrose and
Osnat Penn and
Elana Erez and
Nimrod D. Rubinstein and
Tomer Shlomi and
Natalia Tarnovitski Freund and
Erez M. Bublil and
Eytan Ruppin and
Roded Sharan and
Jonathan M. Gershoni and
Eric Martz and
Tal Pupko},
title = {Pepitope: epitope mapping from affinity-selected peptides},
journal = {Bioinform.},
volume = {23},
number = {23},
pages = {3244--3246},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm493},
doi = {10.1093/BIOINFORMATICS/BTM493},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MayrosePERSFBRSGMP07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/GrammNST07,
author = {Jens Gramm and
Till Nierhoff and
Roded Sharan and
Till Tantau},
title = {Haplotyping with missing data via perfect path phylogenies},
journal = {Discret. Appl. Math.},
volume = {155},
number = {6-7},
pages = {788--805},
year = {2007},
url = {https://doi.org/10.1016/j.dam.2005.09.020},
doi = {10.1016/J.DAM.2005.09.020},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/GrammNST07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/XingJS07,
author = {Eric P. Xing and
Michael I. Jordan and
Roded Sharan},
title = {Bayesian Haplotype Inference via the Dirichlet Process},
journal = {J. Comput. Biol.},
volume = {14},
number = {3},
pages = {267--284},
year = {2007},
url = {https://doi.org/10.1089/cmb.2006.0102},
doi = {10.1089/CMB.2006.0102},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/XingJS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/OurfaliSIRS07,
author = {Oved Ourfali and
Tomer Shlomi and
Trey Ideker and
Eytan Ruppin and
Roded Sharan},
title = {{SPINE:} a framework for signaling-regulatory pathway inference from
cause-effect experiments},
booktitle = {Proceedings 15th International Conference on Intelligent Systems for
Molecular Biology {(ISMB)} {\&} 6th European Conference on Computational
Biology (ECCB), Vienna, Austria, July 21-25, 2007},
pages = {359--366},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm170},
doi = {10.1093/BIOINFORMATICS/BTM170},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/OurfaliSIRS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/DostSGRBS07,
author = {Banu Dost and
Tomer Shlomi and
Nitin Gupta and
Eytan Ruppin and
Vineet Bafna and
Roded Sharan},
editor = {Terence P. Speed and
Haiyan Huang},
title = {QNet: {A} Tool for Querying Protein Interaction Networks},
booktitle = {Research in Computational Molecular Biology, 11th Annual International
Conference, {RECOMB} 2007, Oakland, CA, USA, April 21-25, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4453},
pages = {1--15},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-71681-5\_1},
doi = {10.1007/978-3-540-71681-5\_1},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/DostSGRBS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShlomiSRS06,
author = {Tomer Shlomi and
Daniel Segal and
Eytan Ruppin and
Roded Sharan},
title = {QPath: a method for querying pathways in a protein-protein interaction
network},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {199},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-199},
doi = {10.1186/1471-2105-7-199},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShlomiSRS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SuthramSRSI06,
author = {Silpa Suthram and
Tomer Shlomi and
Eytan Ruppin and
Roded Sharan and
Trey Ideker},
title = {A direct comparison of protein interaction confidence assignment schemes},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {360},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-360},
doi = {10.1186/1471-2105-7-360},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SuthramSRSI06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/TsalenkoSKEBBY06,
author = {Anya Tsalenko and
Roded Sharan and
Vessela N. Kristensen and
Hege Edvardsen and
Anne{-}Lise B{\o}rresen{-}Dale and
Amir Ben{-}Dor and
Zohar Yakhini},
title = {Analysis of Snp-expression Association Matrices},
journal = {J. Bioinform. Comput. Biol.},
volume = {4},
number = {2},
pages = {259--274},
year = {2006},
url = {https://doi.org/10.1142/S0219720006001953},
doi = {10.1142/S0219720006001953},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/TsalenkoSKEBBY06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/EskinSH06,
author = {Eleazar Eskin and
Roded Sharan and
Eran Halperin},
title = {A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions},
journal = {J. Bioinform. Comput. Biol.},
volume = {4},
number = {3},
pages = {639--648},
year = {2006},
url = {https://doi.org/10.1142/S0219720006002272},
doi = {10.1142/S0219720006002272},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/EskinSH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ScottIKS06,
author = {Jacob Scott and
Trey Ideker and
Richard M. Karp and
Roded Sharan},
title = {Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction
Networks},
journal = {J. Comput. Biol.},
volume = {13},
number = {2},
pages = {133--144},
year = {2006},
url = {https://doi.org/10.1089/cmb.2006.13.133},
doi = {10.1089/CMB.2006.13.133},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/ScottIKS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamdm/Gat-ViksKSS06,
author = {Irit Gat{-}Viks and
Richard M. Karp and
Ron Shamir and
Roded Sharan},
title = {Reconstructing Chain Functions in Genetic Networks},
journal = {{SIAM} J. Discret. Math.},
volume = {20},
number = {3},
pages = {727--740},
year = {2006},
url = {https://doi.org/10.1137/S089548010444376X},
doi = {10.1137/S089548010444376X},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamdm/Gat-ViksKSS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SharanHI06,
author = {Roded Sharan and
Bjarni V. Halld{\'{o}}rsson and
Sorin Istrail},
title = {Islands of Tractability for Parsimony Haplotyping},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {3},
number = {3},
pages = {303--311},
year = {2006},
url = {https://doi.org/10.1109/TCBB.2006.40},
doi = {10.1109/TCBB.2006.40},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/SharanHI06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/ZhangBASB06,
author = {Shaojie Zhang and
Ilya Borovok and
Yair Aharonowitz and
Roded Sharan and
Vineet Bafna},
title = {A sequence-based filtering method for ncRNA identification and its
application to searching for riboswitch elements},
booktitle = {Proceedings 14th International Conference on Intelligent Systems for
Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006},
pages = {557--565},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl232},
doi = {10.1093/BIOINFORMATICS/BTL232},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/ZhangBASB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/GrammHNST06,
author = {Jens Gramm and
Tzvika Hartman and
Till Nierhoff and
Roded Sharan and
Till Tantau},
editor = {Philipp Bucher and
Bernard M. E. Moret},
title = {On the Complexity of {SNP} Block Partitioning Under the Perfect Phylogeny
Model},
booktitle = {Algorithms in Bioinformatics, 6th International Workshop, {WABI} 2006,
Zurich, Switzerland, September 11-13, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4175},
pages = {92--102},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11851561\_9},
doi = {10.1007/11851561\_9},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/GrammHNST06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/RokhlenkoSSRP06,
author = {Oleg Rokhlenko and
Tomer Shlomi and
Roded Sharan and
Eytan Ruppin and
Ron Y. Pinter},
editor = {Philipp Bucher and
Bernard M. E. Moret},
title = {Flux-Based \emph{vs.} Topology-Based Similarity of Metabolic Genes},
booktitle = {Algorithms in Bioinformatics, 6th International Workshop, {WABI} 2006,
Zurich, Switzerland, September 11-13, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4175},
pages = {274--285},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11851561\_26},
doi = {10.1007/11851561\_26},
timestamp = {Thu, 25 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/RokhlenkoSSRP06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShamirMTLSSSE05,
author = {Ron Shamir and
Adi Maron{-}Katz and
Amos Tanay and
Chaim Linhart and
Israel Steinfeld and
Roded Sharan and
Yosef Shiloh and
Ran Elkon},
title = {\emph{EXPANDER }- an integrative program suite for microarray data
analysis},
journal = {{BMC} Bioinform.},
volume = {6},
pages = {232},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-232},
doi = {10.1186/1471-2105-6-232},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShamirMTLSSSE05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SharanGYB05,
author = {Roded Sharan and
Jens Gramm and
Zohar Yakhini and
Amir Ben{-}Dor},
title = {Multiplexing Schemes for Generic {SNP} Genotyping Assays},
journal = {J. Comput. Biol.},
volume = {12},
number = {5},
pages = {514--533},
year = {2005},
url = {https://doi.org/10.1089/cmb.2005.12.514},
doi = {10.1089/CMB.2005.12.514},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/SharanGYB05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SegalS05,
author = {Eran Segal and
Roded Sharan},
title = {A Discriminative Model for Identifying Spatial cis-Regulatory Modules},
journal = {J. Comput. Biol.},
volume = {12},
number = {6},
pages = {822--834},
year = {2005},
url = {https://doi.org/10.1089/cmb.2005.12.822},
doi = {10.1089/CMB.2005.12.822},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SegalS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SharanIKSK05,
author = {Roded Sharan and
Trey Ideker and
Brian P. Kelley and
Ron Shamir and
Richard M. Karp},
title = {Identification of Protein Complexes by Comparative Analysis of Yeast
and Bacterial Protein Interaction Data},
journal = {J. Comput. Biol.},
volume = {12},
number = {6},
pages = {835--846},
year = {2005},
url = {https://doi.org/10.1089/cmb.2005.12.835},
doi = {10.1089/CMB.2005.12.835},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/SharanIKSK05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcss/HartmanS05,
author = {Tzvika Hartman and
Roded Sharan},
title = {A 1.5-approximation algorithm for sorting by transpositions and transreversals},
journal = {J. Comput. Syst. Sci.},
volume = {70},
number = {3},
pages = {300--320},
year = {2005},
url = {https://doi.org/10.1016/j.jcss.2004.12.006},
doi = {10.1016/J.JCSS.2004.12.006},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcss/HartmanS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/SharanHI05,
author = {Roded Sharan and
Bjarni V. Halld{\'{o}}rsson and
Sorin Istrail},
title = {Islands of Tractability for Parsimony Haplotyping},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference, {CSB} 2005, Stanford, CA, USA, August 8-11,
2005},
pages = {65--72},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSB.2005.37},
doi = {10.1109/CSB.2005.37},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/SharanHI05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/TsalenkoSEKBBY05,
author = {Anya Tsalenko and
Roded Sharan and
Hege Edvardsen and
Vessela N. Kristensen and
Anne{-}Lise B{\o}rresen{-}Dale and
Amir Ben{-}Dor and
Zohar Yakhini},
title = {Analysis of SNP-Expression Association Matrices},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference, {CSB} 2005, Stanford, CA, USA, August 8-11,
2005},
pages = {135--143},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSB.2005.14},
doi = {10.1109/CSB.2005.14},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/TsalenkoSEKBBY05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/SharanM05,
author = {Roded Sharan and
Eugene W. Myers},
title = {A motif-based framework for recognizing sequence families},
booktitle = {Proceedings Thirteenth International Conference on Intelligent Systems
for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005},
pages = {387--393},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti1002},
doi = {10.1093/BIOINFORMATICS/BTI1002},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/SharanM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ScottIKS05,
author = {Jacob Scott and
Trey Ideker and
Richard M. Karp and
Roded Sharan},
editor = {Satoru Miyano and
Jill P. Mesirov and
Simon Kasif and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction
Networks},
booktitle = {Research in Computational Molecular Biology, 9th Annual International
Conference, {RECOMB} 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3500},
pages = {1--13},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11415770\_1},
doi = {10.1007/11415770\_1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ScottIKS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SuthramSRSI05,
author = {Silpa Suthram and
Tomer Shlomi and
Eytan Ruppin and
Roded Sharan and
Trey Ideker},
editor = {Eleazar Eskin and
Trey Ideker and
Benjamin J. Raphael and
Christopher T. Workman},
title = {Comparison of Protein-Protein Interaction Confidence Assignment Schemes},
booktitle = {Systems Biology and Regulatory Genomics, Joint Annual {RECOMB} 2005
Satellite Workshops on Systems Biology and on Regulatory Genomics,
San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4023},
pages = {39--50},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/978-3-540-48540-7\_4},
doi = {10.1007/978-3-540-48540-7\_4},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SuthramSRSI05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/ShamirS04,
author = {Ron Shamir and
Roded Sharan},
title = {A fully dynamic algorithm for modular decomposition and recognition
of cographs},
journal = {Discret. Appl. Math.},
volume = {136},
number = {2-3},
pages = {329--340},
year = {2004},
url = {https://doi.org/10.1016/S0166-218X(03)00448-7},
doi = {10.1016/S0166-218X(03)00448-7},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/ShamirS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/ShamirST04,
author = {Ron Shamir and
Roded Sharan and
Dekel Tsur},
title = {Cluster graph modification problems},
journal = {Discret. Appl. Math.},
volume = {144},
number = {1-2},
pages = {173--182},
year = {2004},
url = {https://doi.org/10.1016/j.dam.2004.01.007},
doi = {10.1016/J.DAM.2004.01.007},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/ShamirST04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/informs/KimmelSS04,
author = {Gad Kimmel and
Roded Sharan and
Ron Shamir},
title = {Computational Problems in Noisy {SNP} and Haplotype Analysis: Block
Scores, Block Identification, and Population Stratification},
journal = {{INFORMS} J. Comput.},
volume = {16},
number = {4},
pages = {360--370},
year = {2004},
url = {https://doi.org/10.1287/ijoc.1040.0088},
doi = {10.1287/IJOC.1040.0088},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/informs/KimmelSS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Ben-DorHKSSY04,
author = {Amir Ben{-}Dor and
Tzvika Hartman and
Richard M. Karp and
Benno Schwikowski and
Roded Sharan and
Zohar Yakhini},
title = {Towards Optimally Multiplexed Applications of Universal Arrays},
journal = {J. Comput. Biol.},
volume = {11},
number = {2/3},
pages = {476--492},
year = {2004},
url = {https://doi.org/10.1089/1066527041410373},
doi = {10.1089/1066527041410373},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/Ben-DorHKSSY04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KelleyYLSSI04,
author = {Brian P. Kelley and
Bingbing Yuan and
Fran Lewitter and
Roded Sharan and
Brent R. Stockwell and
Trey Ideker},
title = {PathBLAST: a tool for alignment of protein interaction networks},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Web-Server-Issue},
pages = {83--88},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh411},
doi = {10.1093/NAR/GKH411},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KelleyYLSSI04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SharanBLO04,
author = {Roded Sharan and
Asa Ben{-}Hur and
Gabriela G. Loots and
Ivan Ovcharenko},
title = {{CREME:} Cis-Regulatory Module Explorer for the human genome},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Web-Server-Issue},
pages = {253--256},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh385},
doi = {10.1093/NAR/GKH385},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SharanBLO04.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/icml/XingSJ04,
author = {Eric P. Xing and
Roded Sharan and
Michael I. Jordan},
editor = {Carla E. Brodley},
title = {Bayesian haplo-type inference via the dirichlet process},
booktitle = {Machine Learning, Proceedings of the Twenty-first International Conference
{(ICML} 2004), Banff, Alberta, Canada, July 4-8, 2004},
series = {{ACM} International Conference Proceeding Series},
volume = {69},
publisher = {{ACM}},
year = {2004},
url = {https://doi.org/10.1145/1015330.1015423},
doi = {10.1145/1015330.1015423},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icml/XingSJ04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/SharanBY04,
author = {Roded Sharan and
Amir Ben{-}Dor and
Zohar Yakhini},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany A. Jung and
Teri E. Klein},
title = {Multiplexing Schemes for Generic {SNP} Genotyping Assays},
booktitle = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA,
6-10 January 2004},
pages = {140--151},
publisher = {World Scientific},
year = {2004},
url = {http://psb.stanford.edu/psb-online/proceedings/psb04/sharan.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/SharanBY04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/Gat-ViksSKS04,
author = {Irit Gat{-}Viks and
Ron Shamir and
Richard M. Karp and
Roded Sharan},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany A. Jung and
Teri E. Klein},
title = {Reconstructing Chain Functions in Genetic Networks},
booktitle = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA,
6-10 January 2004},
pages = {498--509},
publisher = {World Scientific},
year = {2004},
url = {http://psb.stanford.edu/psb-online/proceedings/psb04/gat-viks.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/Gat-ViksSKS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SegalS04,
author = {Eran Segal and
Roded Sharan},
editor = {Philip E. Bourne and
Dan Gusfield},
title = {A discriminative model for identifying spatial cis-regulatory modules},
booktitle = {Proceedings of the Eighth Annual International Conference on Computational
Molecular Biology, 2004, San Diego, California, USA, March 27-31,
2004},
pages = {141--149},
publisher = {{ACM}},
year = {2004},
url = {https://doi.org/10.1145/974614.974634},
doi = {10.1145/974614.974634},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SegalS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SharanIKSK04,
author = {Roded Sharan and
Trey Ideker and
Brian P. Kelley and
Ron Shamir and
Richard M. Karp},
editor = {Philip E. Bourne and
Dan Gusfield},
title = {Identification of protein complexes by comparative analysis of yeast
and bacterial protein interaction data},
booktitle = {Proceedings of the Eighth Annual International Conference on Computational
Molecular Biology, 2004, San Diego, California, USA, March 27-31,
2004},
pages = {282--289},
publisher = {{ACM}},
year = {2004},
url = {https://doi.org/10.1145/974614.974652},
doi = {10.1145/974614.974652},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SharanIKSK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/HartmanS04,
author = {Tzvika Hartman and
Roded Sharan},
editor = {Inge Jonassen and
Junhyong Kim},
title = {A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals},
booktitle = {Algorithms in Bioinformatics, 4th International Workshop, {WABI} 2004,
Bergen, Norway, September 17-21, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3240},
pages = {50--61},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30219-3\_5},
doi = {10.1007/978-3-540-30219-3\_5},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/HartmanS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SharanMS03,
author = {Roded Sharan and
Adi Maron{-}Katz and
Ron Shamir},
title = {{CLICK} and {EXPANDER:} a system for clustering and visualizing gene
expression data},
journal = {Bioinform.},
volume = {19},
number = {14},
pages = {1787--1799},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg232},
doi = {10.1093/BIOINFORMATICS/BTG232},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SharanMS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Gat-ViksSS03,
author = {Irit Gat{-}Viks and
Roded Sharan and
Ron Shamir},
title = {Scoring clustering solutions by their biological relevance},
journal = {Bioinform.},
volume = {19},
number = {18},
pages = {2381--2389},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg330},
doi = {10.1093/BIOINFORMATICS/BTG330},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Gat-ViksSS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/SharanOBK03,
author = {Roded Sharan and
Ivan Ovcharenko and
Asa Ben{-}Hur and
Richard M. Karp},
title = {{CREME:} a framework for identifying cis-regulatory modules in human-mouse
conserved segments},
booktitle = {Proceedings of the Eleventh International Conference on Intelligent
Systems for Molecular Biology, June 29 - July 3, 2003, Brisbane, Australia},
pages = {283--291},
year = {2003},
url = {http://bioinformatics.oupjournals.org/cgi/content/abstract/19/suppl\_1/i283?etoc},
timestamp = {Tue, 15 Jul 2003 14:30:05 +0200},
biburl = {https://dblp.org/rec/conf/ismb/SharanOBK03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/Ben-DorHSSY03,
author = {Amir Ben{-}Dor and
Tzvika Hartman and
Benno Schwikowski and
Roded Sharan and
Zohar Yakhini},
editor = {Martin Vingron and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman and
Webb Miller},
title = {Towards optimally multiplexed applications of universal {DNA} tag
systems},
booktitle = {Proceedings of the Sventh Annual International Conference on Computational
Biology, {RECOMB} 2003, Berlin, Germany, April 10-13, 2003},
pages = {48--56},
publisher = {{ACM}},
year = {2003},
url = {https://doi.org/10.1145/640075.640081},
doi = {10.1145/640075.640081},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/Ben-DorHSSY03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/KimmelSS03,
author = {Gad Kimmel and
Roded Sharan and
Ron Shamir},
editor = {Gary Benson and
Roderic D. M. Page},
title = {Identifying Blocks and Sub-populations in Noisy {SNP} Data},
booktitle = {Algorithms in Bioinformatics, Third International Workshop, {WABI}
2003, Budapest, Hungary, September 15-20, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2812},
pages = {303--319},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/978-3-540-39763-2\_23},
doi = {10.1007/978-3-540-39763-2\_23},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/KimmelSS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/il/Sharan02,
author = {Roded Sharan},
title = {Graph modification problems and their applications to genomic research},
school = {Tel Aviv University, Israel},
year = {2002},
url = {https://tau.primo.exlibrisgroup.com/permalink/972TAU\_INST/bai57q/alma9932953599904146},
timestamp = {Fri, 03 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/phd/il/Sharan02.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}
}
@inproceedings{DBLP:conf/ismb/TanaySS02,
author = {Amos Tanay and
Roded Sharan and
Ron Shamir},
title = {Discovering statistically significant biclusters in gene expression
data},
booktitle = {Proceedings of the Tenth International Conference on Intelligent Systems
for Molecular Biology, August 3-7, 2002, Edmonton, Alberta, Canada},
pages = {136--144},
year = {2002},
timestamp = {Wed, 29 Jun 2011 14:55:41 +0200},
biburl = {https://dblp.org/rec/conf/ismb/TanaySS02.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/wg/ShamirST02,
author = {Ron Shamir and
Roded Sharan and
Dekel Tsur},
editor = {Ludek Kucera},
title = {Cluster Graph Modification Problems},
booktitle = {Graph-Theoretic Concepts in Computer Science, 28th International Workshop,
{WG} 2002, Cesky Krumlov, Czech Republic, June 13-15, 2002, Revised
Papers},
series = {Lecture Notes in Computer Science},
volume = {2573},
pages = {379--390},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-36379-3\_33},
doi = {10.1007/3-540-36379-3\_33},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wg/ShamirST02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/NatanzonSS01,
author = {Assaf Natanzon and
Ron Shamir and
Roded Sharan},
title = {Complexity classification of some edge modification problems},
journal = {Discret. Appl. Math.},
volume = {113},
number = {1},
pages = {109--128},
year = {2001},
url = {https://doi.org/10.1016/S0166-218X(00)00391-7},
doi = {10.1016/S0166-218X(00)00391-7},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/NatanzonSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamcomp/HellSS01,
author = {Pavol Hell and
Ron Shamir and
Roded Sharan},
title = {A Fully Dynamic Algorithm for Recognizing and Representing Proper
Interval Graphs},
journal = {{SIAM} J. Comput.},
volume = {31},
number = {1},
pages = {289--305},
year = {2001},
url = {https://doi.org/10.1137/S0097539700372216},
doi = {10.1137/S0097539700372216},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/siamcomp/HellSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/PupkoSHSG01,
author = {Tal Pupko and
Roded Sharan and
Masami Hasegawa and
Ron Shamir and
Dan Graur},
editor = {Olivier Gascuel and
Bernard M. E. Moret},
title = {A Chemical-Distance-Based Test for Positive Darwinian Selection},
booktitle = {Algorithms in Bioinformatics, First International Workshop, {WABI}
2001, Aarhus, Denmark, August 28-31, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2149},
pages = {142--155},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44696-6\_11},
doi = {10.1007/3-540-44696-6\_11},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/PupkoSHSG01.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/siamcomp/NatanzonSS00,
author = {Assaf Natanzon and
Ron Shamir and
Roded Sharan},
title = {A Polynomial Approximation Algorithm for the Minimum Fill-In Problem},
journal = {{SIAM} J. Comput.},
volume = {30},
number = {4},
pages = {1067--1079},
year = {2000},
url = {https://doi.org/10.1137/S0097539798336073},
doi = {10.1137/S0097539798336073},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/siamcomp/NatanzonSS00.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/SharanS00,
author = {Roded Sharan 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 = {Center {CLICK:} {A} Clustering Algorithm with Applications to Gene
Expression Analysis},
booktitle = {Proceedings of the Eighth International Conference on Intelligent
Systems for Molecular Biology, August 19-23, 2000, La Jolla / San
Diego, CA, {USA}},
pages = {307--316},
publisher = {{AAAI}},
year = {2000},
url = {http://www.aaai.org/Library/ISMB/2000/ismb00-032.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/SharanS00.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/esa/HellSS99,
author = {Pavol Hell and
Ron Shamir and
Roded Sharan},
editor = {Jaroslav Nesetril},
title = {A Fully Dynamic Algorithm for Recognizing and Representing Proper
Interval Graphs},
booktitle = {Algorithms - {ESA} '99, 7th Annual European Symposium, Prague, Czech
Republic, July 16-18, 1999, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1643},
pages = {527--539},
publisher = {Springer},
year = {1999},
url = {https://doi.org/10.1007/3-540-48481-7\_46},
doi = {10.1007/3-540-48481-7\_46},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/esa/HellSS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wg/NatanzonSS99,
author = {Assaf Natanzon and
Ron Shamir and
Roded Sharan},
editor = {Peter Widmayer and
Gabriele Neyer and
Stephan J. Eidenbenz},
title = {Complexity Classification of Some Edge Modification Problems},
booktitle = {Graph-Theoretic Concepts in Computer Science, 25th International Workshop,
{WG} '99, Ascona, Switzerland, June 17-19, 1999, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1665},
pages = {65--77},
publisher = {Springer},
year = {1999},
url = {https://doi.org/10.1007/3-540-46784-X\_8},
doi = {10.1007/3-540-46784-X\_8},
timestamp = {Wed, 11 Sep 2019 13:15:53 +0200},
biburl = {https://dblp.org/rec/conf/wg/NatanzonSS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stoc/NatanzonSS98,
author = {Assaf Natanzon and
Ron Shamir and
Roded Sharan},
editor = {Jeffrey Scott Vitter},
title = {A Polynomial Approximation Algorithm for the Minimum Fill-In Problem},
booktitle = {Proceedings of the Thirtieth Annual {ACM} Symposium on the Theory
of Computing, Dallas, Texas, USA, May 23-26, 1998},
pages = {41--47},
publisher = {{ACM}},
year = {1998},
url = {https://doi.org/10.1145/276698.276710},
doi = {10.1145/276698.276710},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/stoc/NatanzonSS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/istcs/SharanW96,
author = {Roded Sharan and
Avi Wigderson},
title = {A New \emph{NC}Algorithm for Perfect Matching in Bipartite Cubic Graphs},
booktitle = {Fourth Israel Symposium on Theory of Computing and Systems, {ISTCS}
1996, Jerusalem, Israel, June 10-12, 1996, Proceedings},
pages = {202--207},
publisher = {{IEEE} Computer Society},
year = {1996},
timestamp = {Tue, 31 May 2016 15:27:26 +0200},
biburl = {https://dblp.org/rec/conf/istcs/SharanW96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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