Michal Ziv-Ukelson

Publication Activity (10 Years)

Years Active: 1998-2023
Publications (10 Years): 26

Top Topics

Genome Rearrangements

Escherichia Coli

Maximum Parsimony

Top Venues

J. Comput. Biol.

Publications

Eden Ozeri, Meirav Zehavi, Michal Ziv-Ukelson
New algorithms for structure informed genome rearrangement. Algorithms Mol. Biol. 18 (1) (2023)
Dana Fisman, Dolav Nitay, Michal Ziv-Ukelson
Learning of Structurally Unambiguous Probabilistic Grammars. Log. Methods Comput. Sci. 19 (1) (2023)
Eden Ozery, Meirav Zehavi, Michal Ziv-Ukelson
New Algorithms for Structure Informed Genome Rearrangement. WABI (2022)
Shaked Naor-Hoffmann, Dina Svetlitsky, Neta Sal-Man, Yaron Orenstein, Michal Ziv-Ukelson
Predicting the pathogenicity of bacterial genomes using widely spread protein families. BMC Bioinform. 23 (1) (2022)
Dana Fisman, Dolav Nitay, Michal Ziv-Ukelson
Learning of Structurally Unambiguous Probabilistic Grammars. CoRR (2022)
Dolav Nitay, Dana Fisman, Michal Ziv-Ukelson
Learning of Structurally Unambiguous Probabilistic Grammars. AAAI (2021)
Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson
Approximate search for known gene clusters in new genomes using PQ-trees. Algorithms Mol. Biol. 16 (1) (2021)
Dolav Nitay, Dana Fisman, Michal Ziv-Ukelson
Learning of Structurally Unambiguous Probabilistic Grammars. CoRR (2020)
Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. J. Comput. Biol. 27 (11) (2020)
Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson
Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees. WABI (2020)
Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson
Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees. CoRR (2020)
Dina Svetlitsky, Tal Dagan, Michal Ziv-Ukelson
Discovery of multi-operon colinear syntenic blocks in microbial genomes. Bioinform. 36 (Supplement-1) (2020)
Eran Barash, Neta Sal-Man, Sivan Sabato, Michal Ziv-Ukelson
BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM. Bioinform. 35 (12) (2019)
Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. CoRR (2019)
Jonathan Engel, Isana Veksler-Lublinsky, Michal Ziv-Ukelson
Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes. J. Comput. Biol. 26 (7) (2019)
Michal Ziv-Ukelson
Stringology Combats Microbiological Threats (Invited Talk). CPM (2019)
Dina Svetlitsky, Tal Dagan, Vered Chalifa-Caspi, Michal Ziv-Ukelson
CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes. Bioinform. 35 (10) (2019)
Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson
On Almost Monge All Scores Matrices. Algorithmica 81 (1) (2019)
Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. WABI (2019)
Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson
Dynamic all scores matrices for LCS score. CoRR (2018)
Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson
A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands. J. Comput. Biol. 25 (2) (2018)
Ilan Y. Smoly, Eugene Lerman, Michal Ziv-Ukelson, Esti Yeger Lotem
MotifNet: a web-server for network motif analysis. Bioinform. 33 (12) (2017)
Ilan Y. Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, Esti Yeger Lotem
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts. PLoS Comput. Biol. 13 (1) (2017)
Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns. J. Comput. Biol. 23 (3) (2016)
Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson
A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands. WABI (2016)
Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson
On Almost Monge All Scores Matrices. CPM (2016)
Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns. WABI (2015)
Achiya Elyasaf, Pavel Vaks, Nimrod Milo, Moshe Sipper, Michal Ziv-Ukelson
Learning Heuristics for Mining RNA Sequence-Structure Motifs. GPTP (2015)
Tamar Pinhas, Nimrod Milo, Gregory Kucherov, Michal Ziv-Ukelson
Algorithms for path-constrained sequence alignment. J. Discrete Algorithms 24 (2014)
Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson
The Worst Case Complexity of Maximum Parsimony. CPM (2014)
Shay Zakov, Nimrod Milo, Tamar Pinhas, Sivan Yogev, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Dekel Tsur, Michal Ziv-Ukelson
Recent Results on Three Problems in Comparative Structural RNAomics. CMSR@ECCB (2014)
Ury Matarazzo, Dekel Tsur, Michal Ziv-Ukelson
Efficient all path score computations on grid graphs. Theor. Comput. Sci. 525 (2014)
Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson
The Worst Case Complexity of Maximum Parsimony. J. Comput. Biol. 21 (11) (2014)
Tamar Pinhas, Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson
Efficient edit distance with duplications and contractions. Algorithms Mol. Biol. 8 (2013)
Ury Matarazzo, Dekel Tsur, Michal Ziv-Ukelson
Efficient All Path Score Computations on Grid Graphs. CPM (2013)
Alexander Lan, Michal Ziv-Ukelson, Esti Yeger Lotem
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. Bioinform. 29 (13) (2013)
Sivan Yogev, Nimrod Milo, Michal Ziv-Ukelson
StemSearch: RNA search tool based on stem identification and indexing. BIBM (2013)
Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson
Unrooted unordered homeomorphic subtree alignment of RNA trees. Algorithms Mol. Biol. 8 (2013)
Isana Veksler-Lublinsky, Yonat Shemer-Avni, Eti Meiri, Zvi Bentwich, Klara Kedem, Michal Ziv-Ukelson
Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV). BMC Bioinform. 13 (2012)
Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson
RNA Tree Comparisons via Unrooted Unordered Alignments. WABI (2012)
Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson
Rich Parameterization Improves RNA Structure Prediction. RECOMB (2011)
Tamar Pinhas, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson
Edit Distance with Duplications and Contractions Revisited. CPM (2011)
Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach. Algorithms Mol. Biol. 6 (2011)
Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson
Rich Parameterization Improves RNA Structure Prediction. J. Comput. Biol. 18 (11) (2011)
Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson
Sparse RNA folding: Time and space efficient algorithms. J. Discrete Algorithms 9 (1) (2011)
Kfir Wolfson, Shay Zakov, Moshe Sipper, Michal Ziv-Ukelson
Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis. Genet. Program. Evolvable Mach. 12 (2) (2011)
Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson
Regular Language Constrained Sequence Alignment Revisited. J. Comput. Biol. 18 (5) (2011)
Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir
A Faster Algorithm for Simultaneous Alignment and Folding of RNA. J. Comput. Biol. 17 (8) (2010)
Nimrod Milo, Tamar Pinhas, Michal Ziv-Ukelson
SA-REPC - Sequence Alignment with Regular Expression Path Constraint. LATA (2010)
Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson
Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant's Approach. WABI (2010)
Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson
Regular Language Constrained Sequence Alignment Revisited. IWOCA (2010)
Isana Veksler-Lublinsky, Yonat Shemer-Avni, Klara Kedem, Michal Ziv-Ukelson
Gene bi-targeting by viral and human miRNAs. BMC Bioinform. 11 (2010)
Yury Lifshits, Shay Mozes, Oren Weimann, Michal Ziv-Ukelson
Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions. Algorithmica 54 (3) (2009)
Shay Mozes, Dekel Tsur, Oren Weimann, Michal Ziv-Ukelson
Fast algorithms for computing tree LCS. Theor. Comput. Sci. 410 (43) (2009)
Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson, Ron Unger
RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry. BMC Bioinform. 10 (2009)
Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson
Sparse RNA Folding: Time and Space Efficient Algorithms. CPM (2009)
Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson
Seeded Tree Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (4) (2008)
Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson
Approximate labelled subtree homeomorphism. J. Discrete Algorithms 6 (3) (2008)
Shay Mozes, Dekel Tsur, Oren Weimann, Michal Ziv-Ukelson
Fast Algorithms for Computing Tree LCS. CPM (2008)
Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir
A Faster Algorithm for RNA Co-folding. WABI (2008)
Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson
Seeded Tree Alignment and Planar Tanglegram Layout. WABI (2007)
Shay Mozes, Oren Weimann, Michal Ziv-Ukelson
Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions. CPM (2007)
Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem
A Structure-Based Flexible Search Method for Motifs in RNA. J. Comput. Biol. 14 (7) (2007)
Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson
Two algorithms for LCS Consecutive Suffix Alignment. J. Comput. Syst. Sci. 73 (7) (2007)
Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson
A Study of Accessible Motifs and RNA Folding Complexity. J. Comput. Biol. 14 (6) (2007)
Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini
A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions. J. Comput. Biol. 13 (2) (2006)
Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter
On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. J. Comput. Biol. 13 (8) (2006)
Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson
On the Complexity of Sparse Exon Assembly. J. Comput. Biol. 13 (5) (2006)
Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter
On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. CPM (2006)
Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson
A Study of Accessible Motifs and RNA Folding Complexity. RECOMB (2006)
Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson
Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression. WABI (2005)
Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson
On the Complexity of Sparse Exon Assembly. CPM (2005)
Ron Y. Pinter, Oleg Rokhlenko, Esti Yeger Lotem, Michal Ziv-Ukelson
Alignment of metabolic pathways. Bioinform. 21 (16) (2005)
Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini
A High-Throughput Approach for Associating microRNAs with Their Activity Conditions. RECOMB (2005)
Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson
Approximate Labelled Subtree Homeomorphism. CPM (2004)
Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson
Two Algorithms for LCS Consecutive Suffix Alignment. CPM (2004)
Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson
A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices. SIAM J. Comput. 32 (6) (2003)
Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson
Sparse LCS Common Substring Alignment. CPM (2003)
Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson
Sparse LCS Common Substring Alignment. Inf. Process. Lett. 88 (6) (2003)
Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson
A sub-quadratic sequence alignment algorithm for unrestricted cost matrices. SODA (2002)
Gad M. Landau, Michal Ziv-Ukelson
On the Common Substring Alignment Problem. J. Algorithms 41 (2) (2001)
Gad M. Landau, Michal Ziv-Ukelson
On the shared substring alignment problem. SODA (2000)
Michal Ziv-Ukelson, Aaron Kershenbaum
A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length. CPM (1998)