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[1]
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Roni Zoller, Meirav Zehavi, and Ziv-Ukelson.Michal.
A new paradigm for identifying reconciliation-scenario altering
mutations conferring environmental adaptation.
WABI, 2019.
[ bib ]
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[2]
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Jonathan Engel, Isana Veksler-Lublinsky, and Michal Ziv-Ukelson.
Constrained gene block discovery and its application to prokaryotic
genomes.
Journal of Computational Biology, 2019.
[ bib ]
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[3]
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Dina Svetlitsky, Tal Dagan, Vered Chalifa-Caspi, and Michal Ziv-Ukelson.
CSBFinder: Discovery of colinear syntenic blocks across thousands
of prokaryotic genomes.
Bioinformatics, 2018.
[ bib ]
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[4]
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Eran Barash, Neta Sal-Man, Sivan Sabato, and Michal Ziv-Ukelson.
Bacpacs—bacterial pathogenicity classification via sparse-svm.
Bioinformatics, 2018.
[ bib ]
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[5]
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Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, and Michal Ziv-Ukelson.
A biclique approach to reference anchored gene blocks and its
applications to pathogenicity islands.
Journal of Computational Biology, 25(2):214-235, 2018.
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DOI |
Link ]
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[6]
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Amir Carmel, Dekel Tsur, and Michal Ziv-Ukelson.
On almost monge all score matrices.
Algorithmica, 2018.
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DOI |
Link ]
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[7]
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Ilan Y. Smoly, Eugene Lerman, Michal Ziv-Ukelson, and Esti Yeger Lotem.
Motifnet: a web-server for network motif analysis.
Bioinformatics, 33(12):1907-1909, 2017.
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DOI |
Link ]
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[8]
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Ilan Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, and Esti
Yeger-Lotem.
An asymmetrically balanced organization of kinases versus
phosphatases across eukaryotes determines their distinct impacts.
PLoS computational biology, 13(1):e1005221, 2017.
[ bib ]
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[9]
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D. Hermelin A. Benshahar, V. Caspi and M. Ziv-Ukelson.
A biclique approach to reference anchored gene blocks and its
applications to pathogenicity islands.
In Proc. WABI 2016(The 16th International Workshop on Algorithms
in Bioinformatics). Springer, 2016.
[ bib ]
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[10]
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D. Tsur A. Carmel and M. Ziv-Ukelson.
On almost monge all scores matrices.
In Proc. CPM 2016(The 27th Annual Symposium on Combinatorial
Pattern Matching). Springer, 2016.
[ bib ]
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[11]
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Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, and Michal
Ziv-Ukelson.
Algorithms for regular tree grammar network search and their
application to mining human-viral infection patterns.
Journal of Computational Biology, 23(3):165-179, 2016.
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DOI |
Link ]
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[12]
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Achiya Elyasaf, Pavel Vaks, Nimrod Milo, Moshe Sipper, and Michal Ziv-Ukelson.
Learning heuristics for mining rna sequence-structure motifs.
In Genetic Programming Theory and Practice XIII, pages 21-38.
Springer, 2016.
[ bib ]
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[13]
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I. Y. Smoly, A. Carmel, Y. Shemer-Avni, E Yeger-Lotem, and M. Ziv-Ukelson.
Algorithms for regular tree grammar network search and their
application to mining human-viral infection patterns.
Proc The 15th Workshop on Algorithms in Bioinformatics, 2015.
[ bib ]
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[14]
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Amir Carmel, Noa Musa-Lempel, Dekel Tsur, and Michal Ziv-Ukelson.
The worst case complexity of maximum parsimony.
Journal of Computational Biology, 21(11):799-808, 2014.
[ bib ]
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[15]
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Shay Zakov, Nimrod Milo, Tamar Pinhas, Sivan Yogev, Erez Katzenelson, Eitan
Bachmat, Yefim Dinitz, Dekel Tsur, and Michal Ziv-Ukelson.
Recent results on three problems in comparative structural
RNAomics.
In Proceedings of 1st workshop on Computational Methods for
Structural RNAs (CMSR'14), pages 57-58. McGill University, 2014.
[ bib ]
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[16]
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Amir Carmel, Noa Musa-Lempel, Dekel Tsur, and Michal Ziv-Ukelson.
The worst case complexity of maximum parsimony.
In Proc. CPM 2014 (The 25th Annual Symposium on Combinatorial
Pattern Matching). Springer, 2014.
[ bib ]
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[17]
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Nimrod Milo, Sivan Yogev, and Michal Ziv-Ukelson.
Stemsearch: Rna search tool based on stem identification and
indexing.
Methods, 69(3):326-334, 2014.
[ bib ]
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[18]
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Tamar Pinhas, Nimrod Milo, Gregory Kucherov, and Michal Ziv-Ukelson.
Algorithms for path-constrained sequence alignment.
Journal of Discrete Algorithms, 24:48-58, 2014.
[ bib ]
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[19]
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A. Lan, M. Ziv-Ukelson, and E. Yeger-Lotem.
A context-sensitive framework for the analysis of human signalling
pathways in molecular interaction networks.
Bioinformatics, 29:i210-i216, 2013.
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[20]
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A. Lan, M. Ziv-Ukelson, and E. Yeger-Lotem.
A context-sensitive framework for the analysis of human signalling
pathways in molecular interaction networks.
In 21th Annual International Conference on Intelligent Systems
for Molecular Biology (ISMB-2013). Springer, 2013.
[ bib ]
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[21]
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Ury Matarazzo, Dekel Tsur, and Michal Ziv-Ukelson.
Efficient all path score computations on grid graphs.
In Combinatorial Pattern Matching, pages 211-222. Springer,
2013.
[ bib ]
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[22]
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Ury Matarazzo, Dekel Tsur, and Michal Ziv-Ukelson.
Efficient all path score computations on grid graphs.
In Theoretical Computer Science, volume 525, pages 138-149,
2013.
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[23]
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Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, and
Michal Ziv-Ukelson.
Unrooted unordered homeomorphic subtree alignment of rna trees.
Algorithms for Molecular Biology, 8(1):13, 2013.
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DOI |
Link ]
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[24]
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Tamar Pinhas, Shay Zakov, Dekel Tsur, and Michal Ziv-Ukelson.
Efficient edit distance with duplications and contractions.
Algorithms for Molecular Biology, 8(1):27, 2013.
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[25]
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Sivan Yogev, Nimrod Milo, and Michal Ziv-Ukelson.
Stemsearch: RNA search tool based on stem identification and
indexing.
In Bioinformatics and Biomedicine (BIBM), 2013 IEEE
International Conference on, pages 145-152. IEEE, 2013.
[ bib ]
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[26]
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Sivan Yogev, Nimrod Milo, and Michal Ziv-Ukelson.
Rna search tool based on stem identification and indexing.
In Proc. IEEE International Conference on Bioinformatics and
Biomedicine (BIBM 2013). IEEE, 2013.
[ bib ]
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[27]
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M.K. Meshesha, I. Veksler-Lublinsky, O. Isakov, I. Reichenstein, N. Shomron,
K. Kedem, M. Ziv-Ukelson, Z. Bentwich, and Y.S. Avni.
The microRNA transcriptome of human cytomegalovirus (HCMV).
The Open Virology Journal, 6:38, 2012.
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[28]
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N. Milo, S. Zakov, E. Katzenelson, E. Bachmat, Y. Dinitz, and M. Ziv-Ukelson.
RNA Tree Comparisons via Unrooted Unordered Alignments.
Algorithms in Bioinformatics, pages 135-148, 2012.
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Link ]
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[29]
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I. Veksler-Lublinsky, Y. Shemer-Avni, E. Meiri, Z. Bentwich, K. Kedem, and
M. Ziv-Ukelson.
Finding quasi-modules of human and viral miRNAs: a case study of
human cytomegalovirus (HCMV).
BMC bioinformatics, 13(1):322, 2012.
[ bib ]
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[30]
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G. Kucherov, T. Pinhas, and M. Ziv-Ukelson.
Regular language constrained sequence alignment revisited.
Journal of Computational Biology, 18(5):771-781, 2011.
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[31]
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T. Pinhas, D. Tsur, S. Zakov, and M. Ziv-Ukelson.
Edit distance with duplications and contractions revisited.
In Combinatorial Pattern Matching, pages 441-454. Springer,
2011.
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Link |
Supplementary Material ]
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[32]
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T. Tuller, I. Veksler-Lublinsky, N. Gazit, M. Kupiec, E. Ruppin, and
M. Ziv-Ukelson.
Composite effects of gene determinants on the translation speed and
density of ribosomes.
Genome biology, 12(11):R110, 2011.
[ bib ]
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[33]
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Shay Zakov, Yoav Goldberg, Michael Elhadad, and Michal Ziv-Ukelson.
Rich parameterization improves RNA structure prediction.
In RECOMB 2011: Proceedings of the 15th Annual International
Conference on Research in Computational Molecular Biology, 2011.
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Link ]
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[34]
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Shay Zakov, Dekel Tsur, and Michal Ziv-Ukelson.
Reducing the worst case running times of a family of RNAand CFG
problems, using valiant's approach.
Algorithms for Molecular Biology, 6(1):20, 2011.
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DOI |
Link ]
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[35]
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R. Backofen, D. Tsur, S. Zakov, and M. Ziv-Ukelson.
Sparse RNA folding: Time and space efficient algorithms.
Journal of Discrete Algorithms, 2010.
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Link ]
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[36]
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G. Kucherov, T. Pinhas, and M. Ziv-Ukelson.
Regular Expression Constrained Sequence Alignment Revisited.
Proceedings of the 21st International Workshop on Combinatorial
Algorithms, 2010.
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Link ]
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[37]
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N. Milo, T. Pinhas, and M. Ziv-Ukelson.
SA-REPC-Sequence Alignment With Regular Expression Path
Constraints.
Language and Automata Theory and Applications, pages 451-462,
2010.
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Link ]
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[38]
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I. Veksler-Lublinsky, Y. Shemer-Avni, K. Kedem, and M. Ziv-Ukelson.
Gene bi-targeting by viral and human miRNAs.
BMC bioinformatics, 11(1):249, 2010.
[ bib |
Link ]
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[39]
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K. Wolfson, S. Zakov, M. Sipper, and M. Ziv-Ukelson.
Have your spaghetti and eat it too: evolutionary algorithmics and
post-evolutionary analysis.
Genetic Programming and Evolvable Machines, pages 1-40, 2010.
[ bib |
Link ]
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[40]
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S. Yogev, N. Milo, and M. Ziv-Ukelson.
StemSearch : RNA Search Tool Based on Stem Indexing.
EMBO workshop: RNA control of cell dynamics, 2010.
Poster presentation.
[ bib ]
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[41]
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S. Zakov, D. Tsur, and M. Ziv-Ukelson.
Reducing the Worst Case Running Times of a Family of RNA and CFG
Problems, Using Valiant’s Approach.
Algorithms in Bioinformatics, pages 65-77, 2010.
[ bib |
Link ]
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[42]
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I. Veksler-Lublinsky, M. Ziv-Ukelson, D. Barash, and K. Kedem.
A structure-based flexible search method for motifs in RNA.
Journal of Computational Biology, 14(7):908-926, 2007.
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Link ]
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