Selected Publications

[1]
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 ]
[2]
G. Kucherov, T. Pinhas, and M. Ziv-Ukelson. Regular language constrained sequence alignment revisited. Journal of Computational Biology, 18(5):771-781, 2011. [ bib ]
[3]
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 (to appear), 09 2011. [ bib ]
[4]
Shay Zakov, Dekel Tsur, and Michal Ziv-Ukelson. Reducing the worst case running times of a family of rna and cfg problems, using valiant's approach. Algorithms for Molecular Biology, 6(1):20, 2011. [ bib | DOI | Link ]
[5]
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 ]
[6]
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 ]
[7]
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 ]
[8]
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 ]
[9]
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 ]
[10]
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 ]
[11]
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 ]
[12]
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 ]
[13]
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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