1986 …2024

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  • 2021

    Improving the efficiency of de Bruijn graph construction using compact universal hitting sets

    Ben-Ari, Y., Flomin, D., Pu, L., Orenstein, Y. & Shamir, R., 18 Jan 2021, Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021. Association for Computing Machinery, Inc, (Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021).

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

    Open Access
  • 2016

    A linear-time algorithm for the copy number transformation problem

    Shamir, R., Zehavi, M. & Zeira, R., 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. 16.1-16.13 (Leibniz International Proceedings in Informatics, LIPIcs; vol. 54).

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

  • Compact universal k-mer hitting sets

    Orenstein, Y., Pellow, D., Marçais, G., Shamir, R. & Kingsford, C., 2016, Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Frith, M. & Pedersen, C. N. S. (eds.). Springer Verlag, p. 257-268 12 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

  • Copy-number evolution problems: Complexity and algorithms

    El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M. & Zeira, R., 2016, Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Frith, M. & Pedersen, C. N. S. (eds.). Springer Verlag, p. 137-149 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

  • 2015

    Sorting by cuts, joins and whole chromosome duplications

    Zeira, R. & Shamir, R., 2015, Combinatorial Pattern Matching - 26th Annual Symposium, CPM 2015, Proceedings. Vaccaro, U., Porat, E. & Cicalese, F. (eds.). Springer Verlag, p. 396-409 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9133).

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

  • 2011

    Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast

    Gat-Viks, I., Meller, R., Kupiec, M. & Shamir, R., 2011, Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Bafna, V. & Sahinalp, S. C. (eds.). Springer Verlag, p. 69 1 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

    Open Access
  • 2010

    Detecting highways of horizontal gene transfer

    Bansal, M. S., Gogarten, J. P. & Shamir, R., 2010, Comparative Genomics - International Workshop, RECOMB-CG 2010, Proceedings. p. 109-120 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6398 LNBI).

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

  • 2009

    Topology-free querying of protein interaction networks

    Bruckner, S., Hüffner, F., Karp, R. M., Shamir, R. & Sharan, R., 2009, Research in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings. p. 74-89 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5541 LNBI).

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

    Open Access
  • 2008

    A faster algorithm for RNA co-folding

    Ziv-Ukelson, M., Gat-Viks, I., Wexler, Y. & Shamir, R., 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

  • Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles

    Ulitsky, I., Karp, R. M. & Shamir, R., 2008, Research in Computational Molecular Biology - 12th Annual International Conference, RECOMB 2008, Proceedings. p. 347-359 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4955 LNBI).

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

    Open Access
  • Sorting cancer karyotypes by elementary operations

    Ozery-Flato, M. & Shamir, R., 2008, Comparative Genomics, International Workshop, RECOMB-CG 2008, Proceedings. p. 211-225 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5267 LNBI).

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

  • 2007

    Rearrangements in genomes with centromeres part I: Translocations

    Ozery-Flato, M. & Shamir, R., 2007, Research in Computational Molecular Biology - 11th Annual International Conference, RECOMB 2007, Proceedings. Springer Verlag, p. 339-353 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4453 LNBI).

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

    Open Access
  • 2006

    An O(n3/2 √log(n)) algorithm for sorting by reciprocal translocations

    Ozery-Flato, M. & Shamir, R., 2006, Combinatorial Pattern Matching - 17th Annual Symposium, CPM 2006, Proceedings. Springer Verlag, p. 258-269 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

  • Some computational challenges in today's bio-medicine

    Shamir, R., 2006, Algorithms, ESA 2006 - 14th Annual European Symposium, Proceedings. Springer Verlag, p. 3 1 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4168 LNCS).

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

  • Sorting by translocations via reversals theory

    Ozery-Flato, M. & Shamir, R., 2006, Comparative Genomics RECOMB 2006 International Workshop, RCG 2006, Proceedings. Springer Verlag, p. 87-98 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4205 LNBI).

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

  • 2004

    Computational dissection of regulatory networks using diverse high-throughput data

    Shamir, R., 2004, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. p. 2-3 2 p. (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

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

  • 2002

    Cluster graph modification problems

    Shamir, R., Sharan, R. & Tsur, D., 2002, Graph-Theoretic Concepts in Computer Science - 28th International Workshop, WG 2002, Revised Papers. Kucera, L. (ed.). Springer Verlag, p. 379-390 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2573 LNCS).

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

    Open Access
  • Improved algorithms for the random cluster graph model

    Shamir, R. & Tsur, D., 2002, Algorithm Theory - SWAT 2002 - 8th Scandinavian Workshop on Algorithm Theory, Proceedings. Penttonen, M. & Schmidt, E. M. (eds.). Springer Verlag, p. 230-239 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2368).

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

  • 2001

    A chemical-distance-based test for positive Darwinian selection

    Pupko, T., Sharan, R., Hasegawa, M., Shamir, R. & Graur, D., 2001, Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Moret, B. M. E. & Gascuel, O. (eds.). Springer Verlag, p. 142-155 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2149).

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

  • 1999

    A fully dynamic algorithm for recognizing and representing proper interval graphs

    Hell, P., Shamir, R. & Sharan, R., 1999, Algorithms - ESA 1999 - 7th Annual European Symposium, Proceedings. Nešetřil, J. (ed.). Springer Verlag, p. 527-539 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1643).

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

    Open Access
  • Complexity classification of some edge modification problems

    Natanzon, A., Shamir, R. & Sharan, R., 1999, Graph-Theoretic Concepts in Computer Science - 25th International Workshop, WG 1999, Proceedings. Widmayer, P., Neyer, G. & Eidenbenz, S. (eds.). Springer Verlag, p. 65-77 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1665).

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

    Open Access
  • On the complexity of positional sequencing by hybridization

    Ben-Dor, A., Pe’er, I., Shamir, R. & Sharan, R., 1999, Combinatorial Pattern Matching - 10th Annual Symposium, CPM 1999, Proceedings. Paterson, M. & Crochemore, M. (eds.). Springer Verlag, p. 88-100 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1645).

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

  • 1995

    Interval graphs with side (and size) constraints

    Pe’er, I. & Shamir, R., 1995, Algorithms - ESA 1995 - 3rd Annual European Symposium, Proceedings. Spirakis, P. (ed.). Springer Verlag, p. 142-154 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 979).

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

  • 1994

    Algorithms and complexity of sandwich problems in graphs

    Golumbic, M. C., Kaplan, H. & Shamir, R., 1994, Graph-Theoretic Concepts in Computer Science - 19th International Workshop, WG 1993, Proceedings. van Leeuwen, J. (ed.). Springer Verlag, p. 57-69 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 790 LNCS).

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

  • 1992

    Algorithms and complexity for reasoning about time

    Golumbic, M. C. & Shamir, R., 1992, Proceedings Tenth National Conference on Artificial Intelligence. Publ by AAAI, p. 741-747 7 p. (Proceedings Tenth National Conference on Artificial Intelligence).

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

  • Interval graphs, interval orders and the consistency of temporal events

    Golumbic, M. C. & Shamir, R., 1992, Theory of Computing and Systems - ISTCS 1992, Israel Symposium, Proceedings. Dolev, D., Rodeh, M., Galil, Z. & Galil, Z. (eds.). Springer Verlag, p. 32-42 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 601 LNCS).

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

  • 1990

    Characterization and algorithms for greedily solvable transportation problems

    Shamir, R. & Dietrich, B., 1 Jan 1990, Proceedings of the 1st Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1990. Association for Computing Machinery, p. 358-366 9 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).

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