@article{svetlitsky2018csbfinder,
title = {{CSBF}inder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes},
author = {Svetlitsky, Dina and Dagan, Tal and Chalifa-Caspi, Vered and Ziv-Ukelson, Michal},
journal = {Bioinformatics},
year = {2018}
}
@article{ZollerRSAM,
title = {A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation},
author = {Zoller, Roni and Zehavi, Meirav and Ziv-Ukelson.Michal},
journal = {WABI},
year = {2019}
}
@article{engel2019constrained,
title = {Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes},
author = {Engel, Jonathan and Veksler-Lublinsky, Isana and Ziv-Ukelson, Michal},
journal = {Journal of Computational Biology},
year = {2019},
publisher = {Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New~…}
}
@article{barash2018bacpacs,
title = {BacPaCS—Bacterial Pathogenicity Classification via Sparse-SVM},
author = {Barash, Eran and Sal-Man, Neta and Sabato, Sivan and Ziv-Ukelson, Michal},
journal = {Bioinformatics},
year = {2018},
publisher = {Bioinformatics}
}
@article{DBLP:journals/jcb/BENSHAHAR2018,
author = {Arnon Benshahar and
Vered Chalifa-Caspi and
Danny Hermelin and
Michal Ziv{-}Ukelson},
title = {A Biclique Approach to Reference Anchored Gene Blocks and its Applications to Pathogenicity Islands},
journal = {Journal of Computational Biology},
volume = {25},
number = {2},
pages = {214--235},
year = {2018},
url = {https://doi.org/10.1089/cmb.2017.0108},
doi = {10.1089/cmb.2017.0108}
}
@article{CarmelAlgorithmical,
title = {On Almost Monge All Score Matrices},
author = {Carmel, Amir and Tsur, Dekel and Ziv-Ukelson, Michal },
journal = {Algorithmica},
url = {https://doi.org/10.1007/s00453-018-0432-7},
doi = {https://doi.org/10.1007/s0045},
year = {2018},
publisher = {Public Library of Science}
}
@article{DBLP:journals/bioinformatics/SmolyLZL17,
author = {Ilan Y. Smoly and
Eugene Lerman and
Michal Ziv{-}Ukelson and
Esti Yeger Lotem},
title = {MotifNet: a web-server for network motif analysis},
journal = {Bioinformatics},
volume = {33},
number = {12},
pages = {1907--1909},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx056},
doi = {10.1093/bioinformatics/btx056},
timestamp = {Wed, 29 Nov 2017 15:52:47 +0100},
biburl = {http://dblp.org/rec/bib/journals/bioinformatics/SmolyLZL17},
bibsource = {dblp computer science bibliography, http://dblp.org}
}
@article{smoly2017asymmetrically,
title = {An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts},
author = {Smoly, Ilan and Shemesh, Netta and Ziv-Ukelson, Michal and Ben-Zvi, Anat and Yeger-Lotem, Esti},
journal = {PLoS computational biology},
volume = {13},
number = {1},
pages = {e1005221},
year = {2017},
publisher = {Public Library of Science}
}
@inproceedings{WABI2016,
title = {A Biclique Approach to Reference Anchored Gene Blocks and its Applications to Pathogenicity Islands},
author = {A. Benshahar, V. Caspi, D. Hermelin and M. Ziv-Ukelson},
booktitle = {Proc. WABI 2016(The 16th International Workshop on Algorithms in Bioinformatics)},
title = {Algorithms in Bioinformatics},
year = {2016},
organization = {Springer}
}
@inproceedings{CPM2016,
title = {On Almost Monge All Scores Matrices},
author = {A. Carmel, D. Tsur and M. Ziv-Ukelson},
booktitle = {Proc. CPM 2016(The 27th Annual Symposium on Combinatorial Pattern Matching)},
year = {2016},
organization = {Springer}
}
@article{DBLP:journals/jcb/SmolyCSYZ16,
author = {Ilan Y. Smoly and
Amir Carmel and
Yonat Shemer{-}Avni and
Esti Yeger Lotem and
Michal Ziv{-}Ukelson},
title = {Algorithms for Regular Tree Grammar Network Search and Their Application
to Mining Human-viral Infection Patterns},
journal = {Journal of Computational Biology},
volume = {23},
number = {3},
pages = {165--179},
year = {2016},
url = {http://dx.doi.org/10.1089/cmb.2015.0168},
doi = {10.1089/cmb.2015.0168},
timestamp = {Thu, 31 Mar 2016 15:38:14 +0200},
biburl = {http://dblp.uni-trier.de/rec/bib/journals/jcb/SmolyCSYZ16},
bibsource = {dblp computer science bibliography, http://dblp.org}
}
@incollection{elyasaf2016learning,
title = {Learning heuristics for mining RNA sequence-structure motifs},
author = {Elyasaf, Achiya and Vaks, Pavel and Milo, Nimrod and Sipper, Moshe and Ziv-Ukelson, Michal},
booktitle = {Genetic Programming Theory and Practice XIII},
pages = {21--38},
year = {2016},
publisher = {Springer}
}
@article{MZBDM,
title = {Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns},
author = {Smoly, I. Y. and Carmel, A. and Shemer-Avni, Y. and Yeger-Lotem, E and Ziv-Ukelson, M.},
journal = {Proc The 15th Workshop on Algorithms in Bioinformatics},
year = {2015},
publisher = {Lecture Notes in Computer Science, LNBI 9289, pp:53-65, Atlanta, Georgia, USA}
}
@article{carmel2014worst,
title = {The worst case complexity of Maximum Parsimony},
author = {Carmel, Amir and Musa-Lempel, Noa and Tsur, Dekel and Ziv-Ukelson, Michal},
journal = {Journal of Computational Biology},
volume = {21},
number = {11},
pages = {799--808},
year = {2014},
publisher = {Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}
@inproceedings{zakov2014recent,
title = {Recent Results on Three Problems in Comparative Structural {RNA}omics},
author = {Zakov, Shay and Milo, Nimrod and Pinhas, Tamar and Yogev, Sivan and Katzenelson, Erez and Bachmat, Eitan and Dinitz, Yefim and Tsur, Dekel and Ziv-Ukelson, Michal},
booktitle = {Proceedings of 1st workshop on Computational Methods for Structural {RNA}s (CMSR'14)},
pages = {57--58},
year = {2014},
organization = {McGill University}
}
@article{backofen2010sparse,
title = {{Sparse {RNA} folding: Time and space efficient algorithms}},
author = {Backofen, R. and Tsur, D. and Zakov, S. and Ziv-Ukelson, M.},
journal = {Journal of Discrete Algorithms},
year = {2010},
issn = {1570-8667},
publisher = {Elsevier},
url = {http://linkinghub.elsevier.com/retrieve/pii/S157086671000033X}
}
@inproceedings{CPM2014,
title = {The Worst Case Complexity of Maximum Parsimony},
author = {Carmel, Amir and Musa-Lempel, Noa and Tsur, Dekel and Ziv-Ukelson, Michal},
booktitle = {Proc. CPM 2014 (The 25th Annual Symposium on Combinatorial Pattern Matching)},
year = {2014},
organization = {Springer}
}
@article{kucherov2011regular,
title = {Regular language constrained sequence alignment revisited},
author = {Kucherov, G. and Pinhas, T. and Ziv-Ukelson, M.},
journal = {Journal of Computational Biology},
year = {2011},
number = {5},
pages = {771--781},
volume = {18},
publisher = {Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}
@article{kucherov2010re,
title = {{Regular Expression Constrained Sequence Alignment Revisited}},
author = {Kucherov, G. and Pinhas, T. and Ziv-Ukelson, M.},
journal = {Proceedings of the 21st International Workshop on Combinatorial Algorithms},
year = {2010},
publisher = {Springer-Verlag},
url = {http://www.cs.bgu.ac.il/~matuskat/kucherov2010iwoca.pdf}
}
@article{LanBioinformatics2013,
title = {A Context-Sensitive Framework for the Analysis of Human Signalling Pathways in Molecular Interaction Networks},
author = {Lan, A. and Ziv-Ukelson, M. and Yeger-Lotem, E.},
journal = {Bioinformatics},
year = {2013},
pages = {i210--i216},
volume = {29}
}
@inproceedings{LanISMB2013,
title = {A Context-Sensitive Framework for the Analysis of Human Signalling Pathways in Molecular Interaction Networks},
author = {Lan, A. and Ziv-Ukelson, M. and Yeger-Lotem, E.},
booktitle = {21th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB-2013)},
year = {2013},
organization = {Springer}
}
@inproceedings{matarazzo2013efficient,
title = {Efficient All Path Score Computations on Grid Graphs},
author = {Matarazzo, Ury and Tsur, Dekel and Ziv-Ukelson, Michal},
booktitle = {Combinatorial Pattern Matching},
year = {2013},
organization = {Springer},
pages = {211--222}
}
@inproceedings{matarazzo2013efficientTCS,
title = {Efficient All Path Score Computations on Grid Graphs},
author = {Matarazzo, Ury and Tsur, Dekel and Ziv-Ukelson, Michal},
booktitle = {Theoretical Computer Science},
year = {2013},
pages = {138--149},
volume = {525}
}
@article{meshesha2012microrna,
title = {The micro{RNA} Transcriptome of Human Cytomegalovirus ({HCMV})},
author = {Meshesha, M.K. and Veksler-Lublinsky, I. and Isakov, O. and Reichenstein, I. and Shomron, N. and Kedem, K. and Ziv-Ukelson, M. and Bentwich, Z. and Avni, Y.S.},
journal = {The Open Virology Journal},
year = {2012},
pages = {38},
volume = {6},
publisher = {Bentham Science Publishers}
}
@article{milo2010sa,
title = {{{SA-REPC}--Sequence Alignment With Regular Expression Path Constraints}},
author = {Milo, N. and Pinhas, T. and Ziv-Ukelson, M.},
journal = {Language and Automata Theory and Applications},
year = {2010},
pages = {451--462},
publisher = {Springer},
url = {http://www.springerlink.com/content/71gk3583723h5811}
}
@article{milo2014stemsearch,
title = {StemSearch: RNA search tool based on stem identification and indexing},
author = {Milo, Nimrod and Yogev, Sivan and Ziv-Ukelson, Michal},
journal = {Methods},
year = {2014},
number = {3},
pages = {326--334},
volume = {69},
publisher = {Elsevier}
}
@article{milo2013AMB,
title = {Unrooted unordered homeomorphic subtree alignment of RNA trees},
author = {Milo, Nimrod and Zakov, Shay and Katzenelson, Erez and Bachmat, Eitan and Dinitz, Yefim and Ziv-Ukelson, Michal},
journal = {Algorithms for Molecular Biology},
year = {2013},
number = {1},
pages = {13},
volume = {8},
doi = {10.1186/1748-7188-8-13},
issn = {1748-7188},
url = {http://www.almob.org/content/pdf/1748-7188-8-13.pdf}
}
@article{milo2012rna,
title = {{{RNA} Tree Comparisons via Unrooted Unordered Alignments}},
author = {Milo, N. and Zakov, S. and Katzenelson, E. and Bachmat, E. and Dinitz, Y. and Ziv-Ukelson, M.},
journal = {Algorithms in Bioinformatics},
year = {2012},
pages = {135--148},
publisher = {Springer},
url = {http://www.springerlink.com/content/2n7152748231l874/}
}
@article{pinhas2014algorithms,
title = {Algorithms for path-constrained sequence alignment},
author = {Pinhas, Tamar and Milo, Nimrod and Kucherov, Gregory and Ziv-Ukelson, Michal},
journal = {Journal of Discrete Algorithms},
year = {2014},
pages = {48--58},
volume = {24},
publisher = {Elsevier}
}
@inproceedings{pinhas2011edit,
title = {Edit Distance with Duplications and Contractions Revisited},
author = {Pinhas, T. and Tsur, D. and Zakov, S. and Ziv-Ukelson, M.},
booktitle = {Combinatorial Pattern Matching},
year = {2011},
organization = {Springer},
pages = {441--454},
ps = {http://www.cs.bgu.ac.il/~matuskat/minisatellites-cpm2011-supp.pdf},
url = {http://www.cs.bgu.ac.il/~matuskat/minisatellites-cpm2011.pdf}
}
@article{pinhas2013efficient,
title = {Efficient edit distance with duplications and contractions},
author = {Pinhas, Tamar and Zakov, Shay and Tsur, Dekel and Ziv-Ukelson, Michal},
journal = {Algorithms for Molecular Biology},
year = {2013},
number = {1},
pages = {27},
volume = {8},
publisher = {BioMed Central Ltd}
}
@article{tuller2011composite,
title = {Composite effects of gene determinants on the translation speed and density of ribosomes},
author = {Tuller, T. and Veksler-Lublinsky, I. and Gazit, N. and Kupiec, M. and Ruppin, E. and Ziv-Ukelson, M.},
journal = {Genome biology},
year = {2011},
number = {11},
pages = {R110},
volume = {12},
publisher = {BioMed Central Ltd}
}
@article{veksler2010gene,
title = {{Gene bi-targeting by viral and human mi{RNA}s}},
author = {Veksler-Lublinsky, I. and Shemer-Avni, Y. and Kedem, K. and Ziv-Ukelson, M.},
journal = {BMC bioinformatics},
year = {2010},
number = {1},
pages = {249},
volume = {11},
issn = {1471-2105},
publisher = {BioMed Central Ltd},
url = {http://www.biomedcentral.com/1471-2105/11/249/abstract/}
}
@article{veksler2012finding,
title = {Finding quasi-modules of human and viral mi{RNA}s: a case study of human cytomegalovirus ({HCMV})},
author = {Veksler-Lublinsky, I. and Shemer-Avni, Y. and Meiri, E. and Bentwich, Z. and Kedem, K. and Ziv-Ukelson, M.},
journal = {BMC bioinformatics},
year = {2012},
number = {1},
pages = {322},
volume = {13},
publisher = {BioMed Central Ltd}
}
@article{veksler2007structure,
title = {{A structure-based flexible search method for motifs in {RNA}}},
author = {Veksler-Lublinsky, I. and Ziv-Ukelson, M. and Barash, D. and Kedem, K.},
journal = {Journal of Computational Biology},
year = {2007},
number = {7},
pages = {908--926},
volume = {14},
issn = {1066-5277},
publisher = {Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA},
url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2007.0061}
}
@article{wolfsonhave,
title = {{Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis}},
author = {Wolfson, K. and Zakov, S. and Sipper, M. and Ziv-Ukelson, M.},
journal = {Genetic Programming and Evolvable Machines},
year = {2010},
pages = {1--40},
issn = {1389-2576},
publisher = {Springer},
url = {http://www.springerlink.com/index/JG7217823027K847.pdf}
}
@inproceedings{yogev2013stemsearch,
title = {StemSearch: {RNA} search tool based on stem identification and indexing},
author = {Yogev, Sivan and Milo, Nimrod and Ziv-Ukelson, Michal},
booktitle = {Bioinformatics and Biomedicine (BIBM), 2013 IEEE International Conference on},
year = {2013},
organization = {IEEE},
pages = {145--152}
}
@misc{stemsearchposter2010,
title = {{StemSearch : RNA Search Tool Based on Stem Indexing}},
author = {Yogev, S. and Milo, N. and Ziv-Ukelson, M.},
howpublished = {EMBO workshop: RNA control of cell dynamics},
note = {Poster presentation},
year = {2010}
}
@inproceedings{StemSearch2013,
title = {RNA Search Tool Based on Stem Identification and Indexing},
author = {Yogev, Sivan and Milo, Nimrod and Ziv-Ukelson, Michal},
booktitle = {Proc. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013)},
year = {2013},
organization = {IEEE}
}
@inproceedings{ContextFold,
title = {Rich Parameterization Improves {RNA} Structure Prediction},
author = {Shay Zakov and Yoav Goldberg and Michael Elhadad and Michal
Ziv-Ukelson},
booktitle = {RECOMB 2011: Proceedings of the 15th Annual
International Conference on Research in Computational Molecular
Biology},
year = {2011},
location = {Vancouver, Canada},
url = {http://www.cs.bgu.ac.il/~negevcb/contextfold/}
}
@article{21851589,
title = {Reducing the worst case running times of a family of {RNA}and {CFG} problems, using Valiant's approach},
author = {Zakov, Shay and Tsur, Dekel and Ziv-Ukelson, Michal},
journal = {Algorithms for Molecular Biology},
year = {2011},
number = {1},
pages = {20},
volume = {6},
doi = {10.1186/1748-7188-6-20},
issn = {1748-7188},
pubmedid = {21851589},
url = {http://www.almob.org/content/6/1/20}
}
@article{zakov2010reducing,
title = {{Reducing the Worst Case Running Times of a Family of {RNA} and {CFG} Problems, Using Valiant’s Approach}},
author = {Zakov, S. and Tsur, D. and Ziv-Ukelson, M.},
journal = {Algorithms in Bioinformatics},
year = {2010},
pages = {65--77},
publisher = {Springer},
url = {http://www.cs.bgu.ac.il/~dekelts/publications/vmt.pdf}
}
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