Michal Ziv-Ukelson

According to our database, Michal Ziv-Ukelson authored at least 60 papers between 1998 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

New algorithms for structure informed genome rearrangement.

Eden Ozeri, Meirav Zehavi, Michal Ziv-Ukelson

Algorithms Mol. Biol., December, 2023

Learning of Structurally Unambiguous Probabilistic Grammars.

Dana Fisman, Dolav Nitay, Michal Ziv-Ukelson

Log. Methods Comput. Sci., 2023

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

New Algorithms for Structure Informed Genome Rearrangement.

Eden Ozery, Meirav Zehavi, Michal Ziv-Ukelson

Proceedings of the 22nd International Workshop on Algorithms in Bioinformatics, 2022

2021

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

2020

A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation.

Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson

J. Comput. Biol., 2020

Discovery of multi-operon colinear syntenic blocks in microbial genomes.

Dina Svetlitsky, Tal Dagan, Michal Ziv-Ukelson

Bioinform., 2020

2019

Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes.

Jonathan Engel, Isana Veksler-Lublinsky, Michal Ziv-Ukelson

J. Comput. Biol., 2019

CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes.

Dina Svetlitsky, Tal Dagan, Vered Chalifa-Caspi, Michal Ziv-Ukelson

Bioinform., 2019

BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM.

Eran Barash, Neta Sal-Man, Sivan Sabato, Michal Ziv-Ukelson

Bioinform., 2019

On Almost Monge All Scores Matrices.

Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson

Algorithmica, 2019

Stringology Combats Microbiological Threats (Invited Talk).

Michal Ziv-Ukelson

Proceedings of the 30th Annual Symposium on Combinatorial Pattern Matching, 2019

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

Dynamic all scores matrices for LCS score.

Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson

CoRR, 2018

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

MotifNet: a web-server for network motif analysis.

Ilan Y. Smoly, Eugene Lerman, Michal Ziv-Ukelson, Esti Yeger Lotem

Bioinform., 2017

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

A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands.

Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

2015

Learning Heuristics for Mining RNA Sequence-Structure Motifs.

Achiya Elyasaf, Pavel Vaks, Nimrod Milo, Moshe Sipper, Michal Ziv-Ukelson

Proceedings of the Genetic Programming Theory and Practice XIII [GPTP 2015]., 2015

2014

Efficient all path score computations on grid graphs.

Ury Matarazzo, Dekel Tsur, Michal Ziv-Ukelson

Theor. Comput. Sci., 2014

Algorithms for path-constrained sequence alignment.

Tamar Pinhas, Nimrod Milo, Gregory Kucherov, Michal Ziv-Ukelson

J. Discrete Algorithms, 2014

The Worst Case Complexity of Maximum Parsimony.

Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson

J. Comput. Biol., 2014

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

Proceedings of the 1st Workshop on Computational Methods for Structural RNAs (CMSR 2014), 2014

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

Efficient edit distance with duplications and contractions.

Tamar Pinhas, Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson

Algorithms Mol. Biol., 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

StemSearch: RNA search tool based on stem identification and indexing.

Sivan Yogev, Nimrod Milo, Michal Ziv-Ukelson

Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

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

RNA Tree Comparisons via Unrooted Unordered Alignments.

Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

2011

Sparse RNA folding: Time and space efficient algorithms.

Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson

J. Discrete Algorithms, 2011

Rich Parameterization Improves RNA Structure Prediction.

Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson

J. Comput. Biol., 2011

Regular Language Constrained Sequence Alignment Revisited.

Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson

J. Comput. 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

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

Edit Distance with Duplications and Contractions Revisited.

Tamar Pinhas, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson

Proceedings of the Combinatorial Pattern Matching - 22nd Annual Symposium, 2011

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

Gene bi-targeting by viral and human miRNAs.

Isana Veksler-Lublinsky, Yonat Shemer-Avni, Klara Kedem, Michal Ziv-Ukelson

BMC Bioinform., 2010

SA-REPC - Sequence Alignment with Regular Expression Path Constraint.

Nimrod Milo, Tamar Pinhas, Michal Ziv-Ukelson

Proceedings of the Language and Automata Theory and Applications, 2010

2009

Fast algorithms for computing tree LCS.

Shay Mozes, Dekel Tsur, Oren Weimann, Michal Ziv-Ukelson

Theor. Comput. Sci., 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

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.

Yury Lifshits, Shay Mozes, Oren Weimann, Michal Ziv-Ukelson

Algorithmica, 2009

2008

Seeded Tree Alignment.

Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson

IEEE ACM Trans. Comput. Biol. Bioinform., 2008

Approximate labelled subtree homeomorphism.

Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson

J. Discrete Algorithms, 2008

A Faster Algorithm for RNA Co-folding.

Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

2007

Two algorithms for LCS Consecutive Suffix Alignment.

Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson

J. Comput. Syst. Sci., 2007

A Study of Accessible Motifs and RNA Folding Complexity.

Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson

J. Comput. Biol., 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

Seeded Tree Alignment and Planar Tanglegram Layout.

Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.

Shay Mozes, Oren Weimann, Michal Ziv-Ukelson

Proceedings of the Combinatorial Pattern Matching, 18th Annual Symposium, 2007

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

On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem.

Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter

J. Comput. Biol., 2006

On the Complexity of Sparse Exon Assembly.

Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson

J. Comput. Biol., 2006

2005

Alignment of metabolic pathways.

Ron Y. Pinter, Oleg Rokhlenko, Esti Yeger Lotem, Michal Ziv-Ukelson

Bioinform., 2005

Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression.

Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson

Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

2003

A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices.

Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson

SIAM J. Comput., 2003

Sparse LCS Common Substring Alignment.

Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson

Inf. Process. Lett., 2003

2002

A sub-quadratic sequence alignment algorithm for unrestricted cost matrices.

Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson

Proceedings of the Thirteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2002

2001

On the Common Substring Alignment Problem.

Gad M. Landau, Michal Ziv-Ukelson

J. Algorithms, 2001

2000

On the shared substring alignment problem.

Gad M. Landau, Michal Ziv-Ukelson

Proceedings of the Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms, 2000

1998

A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length.

Michal Ziv-Ukelson, Aaron Kershenbaum

Proceedings of the Combinatorial Pattern Matching, 9th Annual Symposium, 1998