Michal Ziv-Ukelson's Research Group

Selected Publications

[1]

Roni Zoller, Meirav Zehavi, and Ziv-Ukelson.Michal. A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation. WABI, 2019. [ bib ]

[2]

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 ]

[3]

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 ]

[4]

Eran Barash, Neta Sal-Man, Sivan Sabato, and Michal Ziv-Ukelson. Bacpacs—bacterial pathogenicity classification via sparse-svm. Bioinformatics, 2018. [ bib ]

[5]

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. [ bib | DOI | Link ]

[6]

Amir Carmel, Dekel Tsur, and Michal Ziv-Ukelson. On almost monge all score matrices. Algorithmica, 2018. [ bib | DOI | Link ]

[7]

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. [ bib | DOI | Link ]

[8]

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 ]

[9]

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 ]

[10]

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 ]

[11]

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. [ bib | DOI | Link ]

[12]

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 ]

[13]

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 ]

[14]

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 ]

[15]

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 ]

[16]

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 ]

[17]

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 ]

[18]

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 ]

[19]

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. [ bib ]

[20]

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 ]

[21]

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 ]

[22]

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. [ bib ]

[23]

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. [ bib | DOI | Link ]

[24]

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. [ bib ]

[25]

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 ]

[26]

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 ]

[27]

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. [ bib ]

[28]

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. [ bib | Link ]

[29]

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 ]

[30]

G. Kucherov, T. Pinhas, and M. Ziv-Ukelson. Regular language constrained sequence alignment revisited. Journal of Computational Biology, 18(5):771-781, 2011. [ bib ]

[31]

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. [ bib | Link | Supplementary Material ]

[32]

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 ]

[33]

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. [ bib | Link ]

[34]

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. [ bib | DOI | Link ]

[35]

R. Backofen, D. Tsur, S. Zakov, and M. Ziv-Ukelson. Sparse RNA folding: Time and space efficient algorithms. Journal of Discrete Algorithms, 2010. [ bib | Link ]

[36]

G. Kucherov, T. Pinhas, and M. Ziv-Ukelson. Regular Expression Constrained Sequence Alignment Revisited. Proceedings of the 21st International Workshop on Combinatorial Algorithms, 2010. [ bib | Link ]

[37]

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. [ bib | Link ]

[38]

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 ]

[39]

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 ]

[40]

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 ]

[41]

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 ]

[42]

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. [ bib | Link ]

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