Michal Ziv-Ukelson

83 papers A* 3B 17C 12Journal 48Unranked 3
YearRankTypeTitle / Venue / Authors
2023 J jnl
Learning of Structurally Unambiguous Probabilistic Grammars.
Log. Methods Comput. Sci.
Dana Fisman, Dolav Nitay, Michal Ziv-Ukelson
2023 J jnl
New algorithms for structure informed genome rearrangement.
Algorithms Mol. Biol.
Eden Ozeri, Meirav Zehavi, Michal Ziv-Ukelson
2022 J jnl
Learning of Structurally Unambiguous Probabilistic Grammars.
CoRR
Dana Fisman, Dolav Nitay, Michal Ziv-Ukelson
2022 C conf
New Algorithms for Structure Informed Genome Rearrangement.
WABI
Eden Ozery, Meirav Zehavi, Michal Ziv-Ukelson
2022 J jnl
Predicting the pathogenicity of bacterial genomes using widely spread protein families.
BMC Bioinform.
Shaked Naor-Hoffmann, Dina Svetlitsky, Neta Sal-Man, Yaron Orenstein, Michal Ziv-Ukelson
2021 J jnl
Approximate search for known gene clusters in new genomes using PQ-trees.
Algorithms Mol. Biol.
Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson
2021 A* conf
Learning of Structurally Unambiguous Probabilistic Grammars.
AAAI
Dolav Nitay, Dana Fisman, Michal Ziv-Ukelson
2020 J jnl
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation.
J. Comput. Biol.
Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson
2020 C conf
Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees.
WABI
Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson
2020 J jnl
Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees.
CoRR
Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson
2020 J jnl
Discovery of multi-operon colinear syntenic blocks in microbial genomes.
Bioinform.
Dina Svetlitsky, Tal Dagan, Michal Ziv-Ukelson
2020 J jnl
Learning of Structurally Unambiguous Probabilistic Grammars.
CoRR
Dolav Nitay, Dana Fisman, Michal Ziv-Ukelson
2019 C conf
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation.
WABI
Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson
2019 J jnl
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation.
CoRR
Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson
2019 J jnl
BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM.
Bioinform.
Eran Barash, Neta Sal-Man, Sivan Sabato, Michal Ziv-Ukelson
2019 J jnl
CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes.
Bioinform.
Dina Svetlitsky, Tal Dagan, Vered Chalifa-Caspi, Michal Ziv-Ukelson
2019 J jnl
Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes.
J. Comput. Biol.
Jonathan Engel, Isana Veksler-Lublinsky, Michal Ziv-Ukelson
2019 J jnl
On Almost Monge All Scores Matrices.
Algorithmica
Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson
2019 B conf
Stringology Combats Microbiological Threats (Invited Talk).
CPM
Michal Ziv-Ukelson
2018 J jnl
A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands.
J. Comput. Biol.
Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson
2018 J jnl
Dynamic all scores matrices for LCS score.
CoRR
Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson
2017 J jnl
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts.
PLoS Comput. Biol.
Ilan Y. Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, Esti Yeger Lotem
2017 J jnl
MotifNet: a web-server for network motif analysis.
Bioinform.
Ilan Y. Smoly, Eugene Lerman, Michal Ziv-Ukelson, Esti Yeger Lotem
2016 C conf
A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands.
WABI
Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson
2016 J jnl
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns.
J. Comput. Biol.
Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson
2016 B conf
On Almost Monge All Scores Matrices.
CPM
Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson
2015 C conf
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns.
WABI
Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson
2015 — conf
Learning Heuristics for Mining RNA Sequence-Structure Motifs.
GPTP
Achiya Elyasaf, Pavel Vaks, Nimrod Milo, Moshe Sipper, Michal Ziv-Ukelson
2014 J jnl
Algorithms for path-constrained sequence alignment.
J. Discrete Algorithms
Tamar Pinhas, Nimrod Milo, Gregory Kucherov, Michal Ziv-Ukelson
2014 J jnl
Efficient all path score computations on grid graphs.
Theor. Comput. Sci.
Ury Matarazzo, Dekel Tsur, Michal Ziv-Ukelson
2014 — conf
Recent Results on Three Problems in Comparative Structural RNAomics.
CMSR@ECCB
Shay Zakov, Nimrod Milo, Tamar Pinhas, Sivan Yogev, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Dekel Tsur, Michal Ziv-Ukelson
2014 B conf
The Worst Case Complexity of Maximum Parsimony.
CPM
Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson
2014 J jnl
The Worst Case Complexity of Maximum Parsimony.
J. Comput. Biol.
Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson
2013 J jnl
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks.
Bioinform.
Alexander Lan, Michal Ziv-Ukelson, Esti Yeger Lotem
2013 B conf
Efficient All Path Score Computations on Grid Graphs.
CPM
Ury Matarazzo, Dekel Tsur, Michal Ziv-Ukelson
2013 J jnl
Efficient edit distance with duplications and contractions.
Algorithms Mol. Biol.
Tamar Pinhas, Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson
2013 — conf
StemSearch: RNA search tool based on stem identification and indexing.
BIBM
Sivan Yogev, Nimrod Milo, Michal Ziv-Ukelson
2013 J jnl
Unrooted unordered homeomorphic subtree alignment of RNA trees.
Algorithms Mol. Biol.
Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson
2012 J jnl
Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV).
BMC Bioinform.
Isana Veksler-Lublinsky, Yonat Shemer-Avni, Eti Meiri, Zvi Bentwich, Klara Kedem, Michal Ziv-Ukelson
2012 C conf
RNA Tree Comparisons via Unrooted Unordered Alignments.
WABI
Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson
2011 B conf
Edit Distance with Duplications and Contractions Revisited.
CPM
Tamar Pinhas, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson
2011 J jnl
Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis.
Genet. Program. Evolvable Mach.
Kfir Wolfson, Shay Zakov, Moshe Sipper, Michal Ziv-Ukelson
2011 J jnl
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach.
Algorithms Mol. Biol.
Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson
2011 J jnl
Regular Language Constrained Sequence Alignment Revisited.
J. Comput. Biol.
Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson
2011 B conf
Rich Parameterization Improves RNA Structure Prediction.
RECOMB
Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson
2011 J jnl
Rich Parameterization Improves RNA Structure Prediction.
J. Comput. Biol.
Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson
2011 J jnl
Sparse RNA folding: Time and space efficient algorithms.
J. Discrete Algorithms
Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson
2010 J jnl
A Faster Algorithm for Simultaneous Alignment and Folding of RNA.
J. Comput. Biol.
Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir
2010 J jnl
Gene bi-targeting by viral and human miRNAs.
BMC Bioinform.
Isana Veksler-Lublinsky, Yonat Shemer-Avni, Klara Kedem, Michal Ziv-Ukelson
2010 C conf
Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant's Approach.
WABI
Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson
2010 C conf
Regular Language Constrained Sequence Alignment Revisited.
IWOCA
Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson
2010 C conf
SA-REPC - Sequence Alignment with Regular Expression Path Constraint.
LATA
Nimrod Milo, Tamar Pinhas, Michal Ziv-Ukelson
2009 J jnl
Fast algorithms for computing tree LCS.
Theor. Comput. Sci.
Shay Mozes, Dekel Tsur, Oren Weimann, Michal Ziv-Ukelson
2009 J jnl
RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.
BMC Bioinform.
Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson, Ron Unger
2009 B conf
Sparse RNA Folding: Time and Space Efficient Algorithms.
CPM
Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson
2009 J jnl
Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.
Algorithmica
Yury Lifshits, Shay Mozes, Oren Weimann, Michal Ziv-Ukelson
2008 C conf
A Faster Algorithm for RNA Co-folding.
WABI
Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir
2008 J jnl
Approximate labelled subtree homeomorphism.
J. Discrete Algorithms
Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson
2008 B conf
Fast Algorithms for Computing Tree LCS.
CPM
Shay Mozes, Dekel Tsur, Oren Weimann, Michal Ziv-Ukelson
2008 J jnl
Seeded Tree Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform.
Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson
2007 J jnl
A Structure-Based Flexible Search Method for Motifs in RNA.
J. Comput. Biol.
Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem
2007 J jnl
A Study of Accessible Motifs and RNA Folding Complexity.
J. Comput. Biol.
Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson
2007 C conf
Seeded Tree Alignment and Planar Tanglegram Layout.
WABI
Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson
2007 B conf
Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.
CPM
Shay Mozes, Oren Weimann, Michal Ziv-Ukelson
2007 J jnl
Two algorithms for LCS Consecutive Suffix Alignment.
J. Comput. Syst. Sci.
Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson
2006 J jnl
A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions.
J. Comput. Biol.
Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini
2006 B conf
A Study of Accessible Motifs and RNA Folding Complexity.
RECOMB
Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson
2006 J jnl
On the Complexity of Sparse Exon Assembly.
J. Comput. Biol.
Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson
2006 B conf
On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem.
CPM
Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter
2006 J jnl
On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem.
J. Comput. Biol.
Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter
2005 B conf
A High-Throughput Approach for Associating microRNAs with Their Activity Conditions.
RECOMB
Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini
2005 J jnl
Alignment of metabolic pathways.
Bioinform.
Ron Y. Pinter, Oleg Rokhlenko, Esti Yeger Lotem, Michal Ziv-Ukelson
2005 C conf
Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression.
WABI
Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson
2005 B conf
On the Complexity of Sparse Exon Assembly.
CPM
Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson
2004 B conf
Approximate Labelled Subtree Homeomorphism.
CPM
Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson
2004 B conf
Two Algorithms for LCS Consecutive Suffix Alignment.
CPM
Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson
2003 J jnl
A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices.
SIAM J. Comput.
Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson
2003 B conf
Sparse LCS Common Substring Alignment.
CPM
Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson
2003 J jnl
Sparse LCS Common Substring Alignment.
Inf. Process. Lett.
Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson
2002 A* conf
A sub-quadratic sequence alignment algorithm for unrestricted cost matrices.
SODA
Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson
2001 J jnl
On the Common Substring Alignment Problem.
J. Algorithms
Gad M. Landau, Michal Ziv-Ukelson
2000 A* conf
On the shared substring alignment problem.
SODA
Gad M. Landau, Michal Ziv-Ukelson
1998 B conf
A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length.
CPM
Michal Ziv-Ukelson, Aaron Kershenbaum