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  • 2022

    New Algorithms for Structure Informed Genome Rearrangement

    Ozery, E., Zehavi, M. & Ziv-Ukelson, M., 1 Sep 2022, 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022. Boucher, C. & Rahmann, S. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 11. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 242).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • 2021

    Learning of Structurally Unambiguous Probabilistic Grammars

    Nitay, D., Fisman, D. & Ziv-Ukelson, M., 18 May 2021, 35th AAAI Conference on Artificial Intelligence, AAAI 2021. Association for the Advancement of Artificial Intelligence, Vol. 35. p. 9170-9178 9 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    5 Scopus citations
    28 Downloads (Pure)
  • 2020

    Approximate search for known gene clusters in new genomes using PQ-trees

    Zimerman, G. R., Svetlitsky, D., Zehavi, M. & Ziv-Ukelson, M., 1 Aug 2020, 20th International Workshop on Algorithms in Bioinformatics, WABI 2020. Kingsford, C. & Pisanti, N. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 1. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 172).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    1 Scopus citations
  • 2019

    A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation

    Zoller, R., Zehavi, M. & Ziv-Ukelson, M., 1 Sep 2019, 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. Huber, K. T. & Gusfield, D. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, p. 9:1-9:13 9. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 143).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • 2016

    A biclique approach to reference anchored gene blocks and its applications to pathogenicity Islands

    Benshahar, A., Chalifa-Caspi, V., Hermelin, D. & Ziv-Ukelson, M., 1 Jan 2016, Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Frith, M. & Pedersen, C. N. S. (eds.). Springer Verlag, p. 14-26 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9838 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • On almost Monge all scores matrices

    Carmel, A., Tsur, D. & Ziv-Ukelson, M., 1 Jun 2016, 27th Annual Symposium on Combinatorial Pattern Matching, CPM 2016. Grossi, R. & Lewenstein, M. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, p. 17.1-17.12 (Leibniz International Proceedings in Informatics, LIPIcs; vol. 54).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • 2015

    Algorithms for regular tree grammar network search and their application to mining human-viral infection patterns

    Smoly, I., Carmel, A., Shemer-Avni, Y., Yeger-Lotem, E. & Ziv-Ukelson, M., 1 Jan 2015, Algorithms in Bioinformatics - 15th International Workshop, WABI 2015, Proceedings. Pop, M. & Touzet, H. (eds.). Springer Verlag, p. 53-65 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9289).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • 2014

    The worst case complexity of maximum parsimony

    Carmel, A., Musa-Lempel, N., Tsur, D. & Ziv-Ukelson, M., 1 Jan 2014, Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings. Springer Verlag, p. 79-88 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8486 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    1 Scopus citations
  • 2013

    Efficient all path score computations on grid graphs

    Matarazzo, U., Tsur, D. & Ziv-Ukelson, M., 24 Sep 2013, Combinatorial Pattern Matching - 24th Annual Symposium, CPM 2013, Proceedings. p. 211-222 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7922 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • StemSearch: RNA Search Tool Based on Stem Identification and Indexing

    Yogev, S., Milo, N. & Ziv-Ukelson, M., 1 Dec 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 145-152 8 p. 6732478

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • 2012

    RNA tree comparisons via unrooted unordered alignments

    Milo, N., Zakov, S., Katzenelson, E., Bachmat, E., Dinitz, Y. & Ziv-Ukelson, M., 1 Oct 2012, Algorithms in Bioinformatics - 12th International Workshop, WABI 2012, Proceedings. p. 135-148 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7534 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • 2011

    Edit distance with duplications and contractions revisited

    Pinhas, T., Tsur, D., Zakov, S. & Ziv-Ukelson, M., 13 Jul 2011, Combinatorial Pattern Matching - 22nd Annual Symposium, CPM 2011, Proceedings. p. 441-454 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6661 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    8 Scopus citations
  • Regular language constrained sequence alignment revisited

    Kucherov, G., Pinhas, T. & Ziv-Ukelson, M., 4 Apr 2011, Combinatorial Algorithms - 21st International Workshop, IWOCA 2010, Revised Selected Papers. p. 404-415 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6460 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • Rich Parameterization Improves RNA Structure Prediction

    Zakov, S., Goldberg, Y., Elhadad, M. & Ziv-Ukelson, M., 1 Jan 2011, Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Bafna, V. & Sahinalp, S. C. (eds.). Springer Verlag, p. 546-562 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6577 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    14 Scopus citations
  • 2010

    Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach

    Zakov, S., Tsur, D. & Ziv-Ukelson, M., 10 Nov 2010, Algorithms in Bioinformatics - 10th International Workshop, WABI 2010, Proceedings. p. 65-77 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6293 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    10 Scopus citations
  • SA-REPC - Sequence alignment with regular expression path constraint

    Milo, N., Pinhas, T. & Ziv-Ukelson, M., 25 Jun 2010, Language and Automata Theory and Applications - 4th International Conference, LATA 2010, Proceedings. p. 451-462 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6031 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    1 Scopus citations
  • 2009

    Sparse RNA folding: Time and space efficient algorithms

    Backofen, R., Tsur, D., Zakov, S. & Ziv-Ukelson, M., 9 Nov 2009, Combinatorial Pattern Matching - 20th Annual Symposium, CPM 2009, Proceedings. p. 249-262 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5577 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    23 Scopus citations
  • 2008

    A faster algorithm for RNA co-folding

    Ziv-Ukelson, M., Gat-Viks, I., Wexler, Y. & Shamir, R., 28 Nov 2008, Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings. p. 174-185 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5251 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    25 Scopus citations
  • Fast algorithms for computing tree LCS

    Mozes, S., Tsur, D., Weimann, O. & Ziv-Ukelson, M., 1 Jul 2008, Combinatorial Pattern Matching - 19th Annual Symposium, CPM 2008, Proceedings. p. 230-243 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5029 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    1 Scopus citations
  • 2007

    Seeded tree alignment and planar tanglegram layout

    Lozano, A., Pinter, R. Y., Rokhlenko, O., Valiente, G. & Ziv-Ukelson, M., 1 Jan 2007, Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. Springer Verlag, p. 98-110 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4645 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    16 Scopus citations
  • Speeding up HMM decoding and training by exploiting sequence repetitions

    Mozes, S., Weimann, O. & Ziv-Ukelson, M., 1 Jan 2007, Combinatorial Pattern Matching - 18th Annual Symposium, CPM 2007, Proceedings. Springer Verlag, p. 4-15 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4580 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    17 Scopus citations
  • 2006

    A study of accessible motifs and RNA folding complexity

    Wexler, Y., Zilberstein, C. & Ziv-Ukelson, M., 14 Jul 2006, Research in Computational Molecular Biology - 10th Annual International Conference, RECOMB 2006, Proceedings. p. 473-487 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3909 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    7 Scopus citations
  • On the repeat-annotated phylogenetic tree reconstruction problem

    Swidan, F., Ziv-Ukelson, M. & Pinter, R. Y., 1 Jan 2006, Combinatorial Pattern Matching - 17th Annual Symposium, CPM 2006, Proceedings. Springer Verlag, p. 141-152 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4009 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    1 Scopus citations
  • 2005

    Dynamic De-novo prediction of microRNAs associated with cell conditions: A search pruned by expression

    Zilberstein, C. B. Z. & Ziv-Ukelson, M., 1 Dec 2005, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). p. 13-26 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3692 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • Re-Use Dynamic Programming for Sequence Alignment: An Algorithmic Toolkit

    Crochemore, M., Landau, G., Schieber, B. & Ziv-Ukelson, M., 1 Jan 2005, London Stringology Day. p. 1-26

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

  • 2004

    Two Algorithms for LCS Consecutive Suffix Alignment

    Landau, G. M., Myers, E. & Ziv-Ukelson, M., 1 Jan 2004, Combinatorial Pattern Matching: Proceedings of the 15th Annual Symposium, CPM 2004. Sahinalp, S. C., Muthukrishnan, S. & Dogrusoz, U. (eds.). Springer Verlag, p. 173-193 21 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3109).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    14 Scopus citations
  • 2002

    A sub-quadratic sequence alignment algorithm for unrestricted cost matrices

    Crochemore, M., Landau, G. M. & Ziv-Ukelson, M., 1 Jan 2002, Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2002. Association for Computing Machinery, p. 679-688 10 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms; vol. 06-08-January-2002).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    45 Scopus citations
  • 1998

    A dictionary matching algorithm fast on the average for terms of varying length

    Ziv-Ukelson, M. & Kershenbaum, A., 1 Jan 1998, Combinatorial Pattern Matching - 9th Annual Symposium, CPM 1998, Proceedings. Springer Verlag, p. 34-54 21 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1448 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review