A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length. - Michal Ziv-Ukelson; Aaron Kershenbaum (CPM, 1998)

On the shared substring alignment problem. - Gad M. Landau; Michal Ziv-Ukelson (SODA, 2000)

On the Common Substring Alignment Problem. - Gad M. Landau; Michal Ziv-Ukelson (J. Algorithms, 2001)

A sub-quadratic sequence alignment algorithm for unrestricted cost matrices. - Maxime Crochemore; Gad M. Landau; Michal Ziv-Ukelson (SODA, 2002)

Sparse LCS Common Substring Alignment. - Gad M. Landau; Baruch Schieber; Michal Ziv-Ukelson (Inf. Process. Lett., 2003)

A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices. - Maxime Crochemore; Gad M. Landau; Michal Ziv-Ukelson (SIAM J. Comput., 2003)

Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression. - Chaya Ben-Zaken Zilberstein; Michal Ziv-Ukelson (WABI, 2005)

Alignment of metabolic pathways. - Ron Y. Pinter; Oleg Rokhlenko; Esti Yeger Lotem; Michal Ziv-Ukelson (Bioinform., 2005)

On the Complexity of Sparse Exon Assembly. - Carmel Kent; Gad M. Landau; Michal Ziv-Ukelson (J. Comput. Biol., 2006)

On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. - Firas Swidan; Michal Ziv-Ukelson; Ron Y. Pinter (J. Comput. Biol., 2006)

A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions. - Chaya Ben-Zaken Zilberstein; Michal Ziv-Ukelson; Ron Y. Pinter; Zohar Yakhini (J. Comput. Biol., 2006)

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions. - Shay Mozes; Oren Weimann; Michal Ziv-Ukelson (CPM, 2007)

Seeded Tree Alignment and Planar Tanglegram Layout. - Antoni Lozano; Ron Y. Pinter; Oleg Rokhlenko; Gabriel Valiente; Michal Ziv-Ukelson (WABI, 2007)

A Structure-Based Flexible Search Method for Motifs in RNA. - Isana Veksler-Lublinsky; Michal Ziv-Ukelson; Danny Barash; Klara Kedem (J. Comput. Biol., 2007)

A Study of Accessible Motifs and RNA Folding Complexity. - Ydo Wexler; Chaya Ben-Zaken Zilberstein; Michal Ziv-Ukelson (J. Comput. Biol., 2007)

Two algorithms for LCS Consecutive Suffix Alignment. - Gad M. Landau; Eugene W. Myers; Michal Ziv-Ukelson (J. Comput. Syst. Sci., 2007)

A Faster Algorithm for RNA Co-folding. - Michal Ziv-Ukelson; Irit Gat-Viks; Ydo Wexler; Ron Shamir (WABI, 2008)

Approximate labelled subtree homeomorphism. - Ron Y. Pinter; Oleg Rokhlenko; Dekel Tsur; Michal Ziv-Ukelson (J. Discrete Algorithms, 2008)

Seeded Tree Alignment. - Antoni Lozano; Ron Y. Pinter; Oleg Rokhlenko; Gabriel Valiente; Michal Ziv-Ukelson (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions. - Yury Lifshits; Shay Mozes; Oren Weimann; Michal Ziv-Ukelson (Algorithmica, 2009)

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry. - Yair Horesh; Ydo Wexler; Ilana Lebenthal; Michal Ziv-Ukelson; Ron Unger (BMC Bioinform., 2009)

Fast algorithms for computing tree LCS. - Shay Mozes; Dekel Tsur; Oren Weimann; Michal Ziv-Ukelson (Theor. Comput. Sci., 2009)

SA-REPC - Sequence Alignment with Regular Expression Path Constraint. - Nimrod Milo; Tamar Pinhas; Michal Ziv-Ukelson (LATA, 2010)

Gene bi-targeting by viral and human miRNAs. - Isana Veksler-Lublinsky; Yonat Shemer-Avni; Klara Kedem; Michal Ziv-Ukelson (BMC Bioinform., 2010)

A Faster Algorithm for Simultaneous Alignment and Folding of RNA. - Michal Ziv-Ukelson; Irit Gat-Viks; Ydo Wexler; Ron Shamir (J. Comput. Biol., 2010)

Edit Distance with Duplications and Contractions Revisited. - Tamar Pinhas; Dekel Tsur; Shay Zakov; Michal Ziv-Ukelson (CPM, 2011)

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 (Algorithms Mol. Biol., 2011)

Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis. - Kfir Wolfson; Shay Zakov; Moshe Sipper; Michal Ziv-Ukelson (Genet. Program. Evolvable Mach., 2011)

Regular Language Constrained Sequence Alignment Revisited. - Gregory Kucherov; Tamar Pinhas; Michal Ziv-Ukelson (J. Comput. Biol., 2011)

Rich Parameterization Improves RNA Structure Prediction. - Shay Zakov; Yoav Goldberg; Michael Elhadad; Michal Ziv-Ukelson (J. Comput. Biol., 2011)

Sparse RNA folding: Time and space efficient algorithms. - Rolf Backofen; Dekel Tsur; Shay Zakov; Michal Ziv-Ukelson (J. Discrete Algorithms, 2011)

RNA Tree Comparisons via Unrooted Unordered Alignments. - Nimrod Milo; Shay Zakov; Erez Katzenelson; Eitan Bachmat; Yefim Dinitz; Michal Ziv-Ukelson (WABI, 2012)

Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV). - Isana Veksler-Lublinsky; Yonat Shemer-Avni; Eti Meiri; Zvi Bentwich; Klara Kedem; Michal Ziv-Ukelson (BMC Bioinform., 2012)

StemSearch: RNA search tool based on stem identification and indexing. - Sivan Yogev; Nimrod Milo; Michal Ziv-Ukelson (BIBM, 2013)

Unrooted unordered homeomorphic subtree alignment of RNA trees. - Nimrod Milo; Shay Zakov; Erez Katzenelson; Eitan Bachmat; Yefim Dinitz; Michal Ziv-Ukelson (Algorithms Mol. Biol., 2013)

Efficient edit distance with duplications and contractions. - Tamar Pinhas; Shay Zakov; Dekel Tsur; Michal Ziv-Ukelson (Algorithms Mol. Biol., 2013)

A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. - Alexander Lan; Michal Ziv-Ukelson; Esti Yeger Lotem (Bioinform., 2013)

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 (CMSR@ECCB, 2014)

The Worst Case Complexity of Maximum Parsimony. - Amir Carmel; Noa Musa-Lempel; Dekel Tsur; Michal Ziv-Ukelson (J. Comput. Biol., 2014)

Algorithms for path-constrained sequence alignment. - Tamar Pinhas; Nimrod Milo; Gregory Kucherov; Michal Ziv-Ukelson (J. Discrete Algorithms, 2014)

Efficient all path score computations on grid graphs. - Ury Matarazzo; Dekel Tsur; Michal Ziv-Ukelson (Theor. Comput. Sci., 2014)

Learning Heuristics for Mining RNA Sequence-Structure Motifs. - Achiya Elyasaf; Pavel Vaks; Nimrod Milo; Moshe Sipper; Michal Ziv-Ukelson (GPTP, 2015)

A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands. - Arnon Benshahar; Vered Chalifa-Caspi; Danny Hermelin; Michal Ziv-Ukelson (WABI, 2016)

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 (J. Comput. Biol., 2016)

MotifNet: a web-server for network motif analysis. - Ilan Y. Smoly; Eugene Lerman; Michal Ziv-Ukelson; Esti Yeger Lotem (Bioinform., 2017)

An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts. - Ilan Y. Smoly; Netta Shemesh; Michal Ziv-Ukelson; Anat Ben-Zvi; Esti Yeger Lotem (PLoS Comput. Biol., 2017)

Dynamic all scores matrices for LCS score. - Amir Carmel; Dekel Tsur; Michal Ziv-Ukelson (CoRR, 2018)

A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands. - Arnon Benshahar; Vered Chalifa-Caspi; Danny Hermelin; Michal Ziv-Ukelson (J. Comput. Biol., 2018)

Stringology Combats Microbiological Threats (Invited Talk). - Michal Ziv-Ukelson (CPM, 2019)

On Almost Monge All Scores Matrices. - Amir Carmel; Dekel Tsur; Michal Ziv-Ukelson (Algorithmica, 2019)

BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM. - Eran Barash; Neta Sal-Man; Sivan Sabato; Michal Ziv-Ukelson (Bioinform., 2019)

CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes. - Dina Svetlitsky; Tal Dagan; Vered Chalifa-Caspi; Michal Ziv-Ukelson (Bioinform., 2019)

Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes. - Jonathan Engel; Isana Veksler-Lublinsky; Michal Ziv-Ukelson (J. Comput. Biol., 2019)

Discovery of multi-operon colinear syntenic blocks in microbial genomes. - Dina Svetlitsky; Tal Dagan; Michal Ziv-Ukelson (Bioinform., 2020)

A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. - Roni Zoller; Meirav Zehavi; Michal Ziv-Ukelson (J. Comput. Biol., 2020)

Approximate search for known gene clusters in new genomes using PQ-trees. - Galia R. Zimerman; Dina Svetlitsky; Meirav Zehavi; Michal Ziv-Ukelson (Algorithms Mol. Biol., 2021)

New Algorithms for Structure Informed Genome Rearrangement. - Eden Ozery; Meirav Zehavi; Michal Ziv-Ukelson (WABI, 2022)

Predicting the pathogenicity of bacterial genomes using widely spread protein families. - Shaked Naor-Hoffmann; Dina Svetlitsky; Neta Sal-Man; Yaron Orenstein; Michal Ziv-Ukelson (BMC Bioinform., 2022)

Learning of Structurally Unambiguous Probabilistic Grammars. - Dana Fisman; Dolav Nitay; Michal Ziv-Ukelson (Log. Methods Comput. Sci., 2023)

New algorithms for structure informed genome rearrangement. - Eden Ozeri; Meirav Zehavi; Michal Ziv-Ukelson (Algorithms Mol. Biol., 2023)