| 2022 | WABI | New Algorithms for Structure Informed Genome Rearrangement. | Eden Ozery, Meirav Zehavi, Michal Ziv-Ukelson |
| 2021 | AAAI | Learning of Structurally Unambiguous Probabilistic Grammars. | Dolav Nitay, Dana Fisman, Michal Ziv-Ukelson |
| 2020 | WABI | Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees. | Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson |
| 2019 | CPM | Stringology Combats Microbiological Threats (Invited Talk). | Michal Ziv-Ukelson |
| 2019 | WABI | A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. | Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson |
| 2016 | CPM | On Almost Monge All Scores Matrices. | Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson |
| 2016 | WABI | A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands. | Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson |
| 2015 | WABI | Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns. | Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson |
| 2014 | CPM | The Worst Case Complexity of Maximum Parsimony. | Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson |
| 2014 | ECCB | Recent Results on Three Problems in Comparative Structural RNAomics. | Shay Zakov, Nimrod Milo, Tamar Pinhas, Sivan Yogev, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Dekel Tsur, Michal Ziv-Ukelson |
| 2013 | CPM | Efficient All Path Score Computations on Grid Graphs. | Ury Matarazzo, Dekel Tsur, Michal Ziv-Ukelson |
| 2012 | WABI | RNA Tree Comparisons via Unrooted Unordered Alignments. | Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson |
| 2011 | CPM | Edit Distance with Duplications and Contractions Revisited. | Tamar Pinhas, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson |
| 2011 | RECOMB | Rich Parameterization Improves RNA Structure Prediction. | Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson |
| 2010 | IWOCA | Regular Language Constrained Sequence Alignment Revisited. | Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson |
| 2010 | LATA | SA-REPC - Sequence Alignment with Regular Expression Path Constraint. | Nimrod Milo, Tamar Pinhas, Michal Ziv-Ukelson |
| 2010 | WABI | Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant's Approach. | Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson |
| 2009 | CPM | Sparse RNA Folding: Time and Space Efficient Algorithms. | Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson |
| 2008 | CPM | Fast Algorithms for Computing Tree LCS. | Shay Mozes, Dekel Tsur, Oren Weimann, Michal Ziv-Ukelson |
| 2008 | WABI | A Faster Algorithm for RNA Co-folding. | Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir |
| 2007 | CPM | Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions. | Shay Mozes, Oren Weimann, Michal Ziv-Ukelson |
| 2007 | WABI | Seeded Tree Alignment and Planar Tanglegram Layout. | Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson |
| 2006 | CPM | On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. | Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter |
| 2006 | RECOMB | A Study of Accessible Motifs and RNA Folding Complexity. | Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson |
| 2005 | CPM | On the Complexity of Sparse Exon Assembly. | Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson |
| 2005 | RECOMB | A High-Throughput Approach for Associating microRNAs with Their Activity Conditions. | Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini |
| 2005 | WABI | Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression. | Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson |
| 2004 | CPM | Two Algorithms for LCS Consecutive Suffix Alignment. | Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson |
| 2004 | CPM | Approximate Labelled Subtree Homeomorphism. | Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson |
| 2003 | CPM | Sparse LCS Common Substring Alignment. | Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson |
| 2002 | SODA | A sub-quadratic sequence alignment algorithm for unrestricted cost matrices. | Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson |
| 2000 | SODA | On the shared substring alignment problem. | Gad M. Landau, Michal Ziv-Ukelson |
| 1998 | CPM | A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length. | Michal Ziv-Ukelson, Aaron Kershenbaum |