Tools

RNA Structure Prediction
RNA Structural Alignment
Constrained Sequence Alignment
RNA Structural Search
microRNA

Contact:

Email: Michal's email
Office: +972-8-6428042
Lab: +972-8-6477971
Fax: +972-8-6477972
More: About the group
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Michal Ziv-Ukelson

You can email me at: michaluz@cs.bgu.ac.il.
Group homepage http://www.cs.bgu.ac.il/~negevcb
Research Interests: Computational Biology, Combinatorial Pattern Matching, Algorithm Design and Analysis, Information Retrieval.

Selected Publications:

[1]
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 ]
[2]
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 ]
[3]
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 ]
[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]
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 ]
[8]
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 ]
[9]
G. Kucherov, T. Pinhas, and M. Ziv-Ukelson. Regular Language Constrained Sequence Alignment Revisited. Journal of Computational Biology (to appear), 2011. [ bib ]
[10]
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 ]
[11]
S. Zakov T. Pinhas, D. Tsur and M. Ziv-Ukelson. Edit distance with duplications and contractions revisited. In Proc. CPM 2011 (The 22nd Annual Symposium on Combinatorial Pattern Matching), 2011. [ bib ]
[12]
R. Backofen, D. Tsur, S. Zakov, and M. Ziv-Ukelson. Sparse RNA folding: Time and space efficient algorithms. Journal of Discrete Algorithms, 2010. [ bib ]
[13]
N. Milo, T. Pinhas, and M. Ziv-Ukelson. SA-REPC-Sequence Alignment with Regular Expression Path Constraint. Language and Automata Theory and Applications, pages 451-462, 2010. [ bib ]
[14]
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 ]
[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]
M. Ziv-Ukelson, I. Gat-Viks, Y. Wexler, and R. Shamir. A faster algorithm for simultaneous alignment and folding of RNA. Journal of Computational Biology, 17(8):1051-1065, 2010. [ bib ]
[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]
Y. Lifshits, S. Mozes, O. Weimann, and M. Ziv-Ukelson. Speeding up HMM decoding and training by exploiting sequence repetitions. Algorithmica, 54(3):379-399, 2009. [ bib ]
[19]
R. Backofen, D. Tsur, S. Zakov, and M. Ziv-Ukelson. Sparse RNA Folding: Time and Space Efficient Algorithms. In Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching, pages 249-262, 2009. [ bib ]
[20]
S. Mozes, D. Tsur, O. Weimann, and M. Ziv-Ukelson. Fast algorithms for computing tree LCS. Theoretical Computer Science, 410(43):4303-4314, 2009. [ bib ]
[21]
Y. Horesh, Y. Wexler, I. Lebenthal, M. Ziv-Ukelson, and R. Unger. RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry. BMC bioinformatics, 10(1):76, 2009. [ bib ]
[22]
S. Mozes, D. Tsur, O. Weimann, and M. Ziv-Ukelson. Fast algorithms for computing tree lcs. In Combinatorial Pattern Matching, pages 230-243. Springer, 2008. [ bib ]
[23]
M. Ziv-Ukelson, I. Gat-Viks, Y. Wexler, and R. Shamir. A faster algorithm for RNA co-folding. Algorithms in Bioinformatics, pages 174-185, 2008. [ bib ]
[24]
R.Y. Pinter, O. Rokhlenko, D. Tsur, and M. Ziv-Ukelson. Approximate labelled subtree homeomorphism. Journal of Discrete Algorithms, 6(3):480-496, 2008. [ bib ]
[25]
A. Loya, L. Pnueli, Y. Yosefzon, Y. Wexler, M. Ziv-Ukelson, and Y. Arava. The 3′-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein. Rna, 14(7):1352, 2008. [ bib ]
[26]
A. Lozano, R.Y. Pinter, O. Rokhlenko, G. Valiente, and M. Ziv-Ukelson. Seeded tree alignment. IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, pages 503-513, 2008. [ bib ]
[27]
Y. Wexler, C. Zilberstein, and M. Ziv-Ukelson. A study of accessible motifs and RNA folding complexity. Journal of Computational Biology, 14(6):856-872, 2007. [ bib ]
[28]
S. Mozes, O. Weimann, and M. Ziv-Ukelson. Speeding up HMM decoding and training by exploiting sequence repetitions. In Combinatorial Pattern Matching, pages 4-15. Springer, 2007. [ bib ]
[29]
A. Lozano, R. Pinter, O. Rokhlenko, G. Valiente, and M. Ziv-Ukelson. Seeded tree alignment and planar tanglegram layout. Algorithms in Bioinformatics, pages 98-110, 2007. [ bib ]
[30]
G.M. Landau, E. Myers, and M. Ziv-Ukelson. Two algorithms for LCS consecutive suffix alignment. Journal of Computer and System Sciences, 73(7):1095-1117, 2007. [ bib ]
[31]
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 ]
[32]
C. Kent, G.M. Landau, and M. Ziv-Ukelson. On the complexity of sparse exon assembly. Journal of Computational Biology, 13(5):1013-1027, 2006. [ bib ]
[33]
Y. Wexler, C. Zilberstein, and M. Ziv-Ukelson. A study of accessible motifs and rna folding complexity. In Research in Computational Molecular Biology, pages 473-487. Springer, 2006. [ bib ]
[34]
F. Swidan, M. Ziv-Ukelson, and R.Y. Pinter. On the repeat-annotated phylogenetic tree reconstruction problem. Journal of Computational Biology, 13(8):1397-1418, 2006. [ bib ]
[35]
F. Swidan, M. Ziv-Ukelson, and R. Pinter. On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. In Combinatorial Pattern Matching, pages 141-152. Springer, 2006. [ bib ]
[36]
C.B.Z. Zilberstein, M. Ziv-Ukelson, R.Y. Pinter, and Z. Yakhini. A high-throughput approach for associating microRNAs with their activity conditions. Journal of Computational Biology, 13(2):245-266, 2006. [ bib ]
[37]
C. Kent, G.M. Landau, and M. Ziv-Ukelson. On the complexity of sparse exon assembly. In Combinatorial Pattern Matching, pages 201-218. Springer, 2005. [ bib ]
[38]
C.B.Z. Zilberstein, M. Ziv-Ukelson, R.Y. Pinter, and Z. Yakhini. A high-throughput approach for associating microRNAs with their activity conditions. In Research in Computational Molecular Biology, pages 133-151. Springer, 2005. [ bib ]
[39]
C. Zilberstein and M. Ziv-Ukelson. Dynamic de-novo prediction of microRNAs associated with cell conditions: A search pruned by expression. Algorithms in Bioinformatics, pages 13-26, 2005. [ bib ]
[40]
R.Y. Pinter, O. Rokhlenko, E. Yeger-Lotem, and M. Ziv-Ukelson. Alignment of metabolic pathways. Bioinformatics, 21(16):3401, 2005. [ bib ]
[41]
G.M. Landau, E. Myers, and M. Ziv-Ukelson. Two algorithms for LCS consecutive suffix alignment. In Combinatorial Pattern Matching, pages 173-193. Springer, 2004. [ bib ]
[42]
R.Y. Pinter, O. Rokhlenko, D. Tsur, and M. Ziv-Ukelson. Approximate labelled subtree homeomorphism. In Combinatorial Pattern Matching, pages 59-73. Springer, 2004. [ bib ]
[43]
G.M. Landau, B. Schieber, and M. Ziv-Ukelson. Sparse LCS common substring alignment. In Combinatorial Pattern Matching: 14th Annual Symposium, CPM 2003, Morelia, Michoacán, Mexico, June 25-27, 2003. Proceedings, pages 1017-1017. Springer, 2003. [ bib ]
[44]
M. Crochemore, G.M. Landau, and M. Ziv-Ukelson. A subquadratic sequence alignment algorithm for unrestricted scoring matrices. SIAM Journal on Computing, 32(6):1654-1676, 2003. [ bib ]
[45]
G.M. Landau, B. Schieber, and M. Ziv-Ukelson. Sparse LCS Common Substring Alignment. Information Processing Letters, 88(6):259-270, 2003. [ bib ]
[46]
G.M. Landau and M. Ziv-Ukelson. On the Common Substring Alignment Problem* 1. Journal of Algorithms, 41(2):338-359, 2001. [ bib ]
[47]
G.M. Landau and M. Ziv-Ukelson. On the shared substring alignment problem. In PROC ANNU ACM SIAM SYMP DISCRETE ALGORITHMS, pages 804-814, 2000. [ bib ]
[48]
M. Ziv-Ukelson and A. Kershenbaum. A dictionary matching algorithm fast on the average for terms of varying length. In Combinatorial Pattern Matching, pages 34-54. Springer, 1998. [ bib ]
[49]
T. Fujisaki, HSM Beigi, CC Tappert, M. Ukelson, and CG Wolf. Online recognition of unconstrained handprinting: a stroke-based system and its evaluation. From Pixels to Features III: Frontiers in Handwriting Recognition. Elsevier Science Publishers, 1992. [ bib ]
[50]
M. Crochemore, G.M. Landau, B. Schieber, and M. Ziv-Ukelson. Re-use dynamic programming for sequence alignment: An algorithmic toolkit. String Algorithmics, 2:19-60. [ bib ]

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