Michal Ziv-Ukelson's Research Group

Selected Publications

[1]

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 ]

[2]

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 ]

[3]

Ury Matarazzo, Dekel Tsur, and Michal Ziv-Ukelson. Efficient all path score computations on grid graphs. In Theoretical Computer Science, 2013. [ bib ]

[4]

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 ]

[5]

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 ]

[6]

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 ]

[7]

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 ]

[8]

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 ]

[9]

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 ]

[10]

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

[11]

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 ]

[12]

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 ]

[13]

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 ]

[14]

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 ]

[15]

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 ]

[16]

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 ]

[17]

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 ]

[18]

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 ]

[19]

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 ]

[20]

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 ]

[21]

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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