Michal Ziv-Ukelson

发表

Regular Language Constrained Sequence Alignment Revisited

Michal Ziv-Ukelson, Gregory Kucherov, Tamar Pinhas, 2010, IWOCA.

Efficient edit distance with duplications and

Michal Ziv-Ukelson, Dekel Tsur, Shay Zakov, 2013 .

On the Uniqueness and Complexity of Reconstructing Repeat-Annotated Phylogenetic Trees

Michal Ziv-Ukelson, R. Pinter, Firas Swidan, 2006 .

Regular expression constrained sequence alignment revisited

G. Kucherov, Tamar Pinhas, Michal Ziv-Ukelson, 2018 .

Composite effects of gene determinants on the translation speed and density of ribosomes

Michal Ziv-Ukelson, Eytan Ruppin, Tamir Tuller, 2011, Genome Biology.

A probabilistic model for the evolution of promoters

R. Elkon, Michal Ziv-Ukelson, Chaim Linhart, 2007 .

Edit Distance with Duplications and Contractions Revisited-Supplementary Materials

Tamar Pinhas, Michal Ziv-Ukelson, Dekel Tsur, 2011 .

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

Michal Ziv-Ukelson, Nimrod Milo, Sivan Yogev, 2014, Methods.

Appendix Algorithms for Regular Tree Grammar based search and their application to mining human-viral infection patterns

Ilan Y. Smoly, Michal Ziv-Ukelson, A. Carmel, 2015 .

The 3'-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein.

Michal Ziv-Ukelson, Ydo Wexler, L. Pnueli, 2008, RNA.

Predicting the pathogenicity of bacterial genomes using widely spread protein families

Michal Ziv-Ukelson, Yaron Orenstein, N. Sal-Man, 2022, BMC Bioinformatics.

New Algorithms for Structure Informed Genome Rearrangement

Michal Ziv-Ukelson, M. Zehavi, Eden Ozery, 2022, WABI.

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

Michal Ziv-Ukelson, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, 2005, WABI.

A High-Throughput Approach for Associating microRNAs with Their Activity Conditions

Ron Y. Pinter, Michal Ziv-Ukelson, Zohar Yakhini, 2005, RECOMB.

The microRNA Transcriptome of Human Cytomegalovirus (HCMV)

K. Kedem, Michal Ziv-Ukelson, N. Shomron, 2012, The open virology journal.

Gene bi-targeting by viral and human miRNAs

Michal Ziv-Ukelson, Klara Kedem, Isana Veksler-Lublinsky, 2010, BMC Bioinformatics.

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions

Michal Ziv-Ukelson, Yury Lifshits, Oren Weimann, 2007, Algorithmica.

Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach

Michal Ziv-Ukelson, Dekel Tsur, Shay Zakov, 2010, Algorithms for Molecular Biology.

A Structure-Based Flexible Search Method for Motifs in RNA

Michal Ziv-Ukelson, Klara Kedem, Danny Barash, 2007, J. Comput. Biol..

Algorithms for path-constrained sequence alignment

Michal Ziv-Ukelson, Gregory Kucherov, Nimrod Milo, 2014, J. Discrete Algorithms.

SA-REPC - Sequence Alignment with Regular Expression Path Constraint

Michal Ziv-Ukelson, Nimrod Milo, Tamar Pinhas, 2010, LATA.

A Study of Accessible Motifs and RNA Folding Complexity

Michal Ziv-Ukelson, Chaya Ben-Zaken Zilberstein, Ydo Wexler, 2006, RECOMB.

An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts

Michal Ziv-Ukelson, Ilan Y. Smoly, Netta Shemesh, 2017, PLoS Comput. Biol..

Discovery of multi-operon colinear syntenic blocks in microbial genomes

Michal Ziv-Ukelson, Tal Dagan, Dina Svetlitsky, 2020, Bioinform..

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

Michal Ziv-Ukelson, Vered Chalifa-Caspi, Tal Dagan, 2018, Bioinform..

Learning of Structurally Unambiguous Probabilistic Grammars pdf

Dana Fisman, Michal Ziv-Ukelson, Dolav Nitay, 2020, AAAI.

Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes

Michal Ziv-Ukelson, Isana Veksler-Lublinsky, Jonathan Engel, 2019, J. Comput. Biol..

Learning Heuristics for Mining RNA Sequence-Structure Motifs

Moshe Sipper, Michal Ziv-Ukelson, Achiya Elyasaf, 2016 .

A Faster Algorithm for Simultaneous Alignment and Folding of RNA

Ron Shamir, Michal Ziv-Ukelson, Irit Gat-Viks, 2010, J. Comput. Biol..

A Faster Algorithm for RNA Co-folding

Ron Shamir, Michal Ziv-Ukelson, Irit Gat-Viks, 2008, WABI.

Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV)

K. Kedem, Michal Ziv-Ukelson, E. Meiri, 2012, BMC Bioinformatics.

Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV)

Michal Ziv-Ukelson, Klara Kedem, Isana Veksler-Lublinsky, 2012, BMC Bioinformatics.

Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis

Moshe Sipper, Michal Ziv-Ukelson, Shay Zakov, 2010, Genetic Programming and Evolvable Machines.

On the Common Substring Alignment Problem

Gad M. Landau, Michal Ziv-Ukelson, G. M. Landau, 2001, J. Algorithms.

A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices

Gad M. Landau, Maxime Crochemore, Michal Ziv-Ukelson, 2003, SIAM J. Comput..

Approximate search for known gene clusters in new genomes using PQ-trees pdf

G. R. Zimerman, Dina Svetlitsky, Meirav Zehavi, 2020, Algorithms for Molecular Biology.

Rich Parameterization Improves RNA Structure Prediction

Michal Ziv-Ukelson, Yoav Goldberg, Michael Elhadad, 2011, RECOMB.

Sparse RNA folding: Time and space efficient algorithms

Rolf Backofen, Michal Ziv-Ukelson, Dekel Tsur, 2009, J. Discrete Algorithms.

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

Michal Ziv-Ukelson, Meirav Zehavi, Roni Zoller, 2019, WABI.

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

Michal Ziv-Ukelson, Danny Hermelin, Vered Chalifa-Caspi, 2017, WABI.

A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands

Michal Ziv-Ukelson, Danny Hermelin, Vered Chalifa-Caspi, 2018, J. Comput. Biol..

Unrooted unordered homeomorphic subtree alignment of RNA trees

Michal Ziv-Ukelson, Eitan Bachmat, Nimrod Milo, 2013, Algorithms for Molecular Biology.

Approximate labelled subtree homeomorphism

Ron Y. Pinter, Michal Ziv-Ukelson, Dekel Tsur, 2004, J. Discrete Algorithms.

Alignment of metabolic pathways

Ron Y. Pinter, Michal Ziv-Ukelson, Esti Yeger Lotem, 2005, Bioinform..

StemSearch: RNA search tool based on stem identification and indexing

Michal Ziv-Ukelson, Nimrod Milo, Sivan Yogev, 2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine.

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry

Michal Ziv-Ukelson, Yair Horesh, Ron Unger, 2009, BMC Bioinformatics.

MotifNet: a web-server for network motif analysis

Ilan Y. Smoly, Esti Yeger Lotem, Michal Ziv-Ukelson, 2017, Bioinform..

Bioimage informatics MotifNet : a webserver for network motif analysis

Michal Ziv-Ukelson, Ilan Y. Smoly, Esti Yeger Lotem, 2017 .

A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks

Michal Ziv-Ukelson, Esti Yeger Lotem, Alexander Lan, 2013, Bioinform..

Regular Language Constrained Sequence Alignment Revisited

Michal Ziv-Ukelson, Gregory Kucherov, Tamar Pinhas, 2010, J. Comput. Biol..

On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem

Michal Ziv-Ukelson, R. Pinter, Firas Swidan, 2006, J. Comput. Biol..

RNA Tree Comparisons via Unrooted Unordered Alignments

Michal Ziv-Ukelson, Eitan Bachmat, Nimrod Milo, 2012, WABI.

RNA Tree Comparisons Via Unrooted Unordered Alignments ( Supplemental Materials )

Michal Ziv-Ukelson, Shay Zakov, E. Bachmat, 2012 .

Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns

Michal Ziv-Ukelson, Ilan Y. Smoly, Esti Yeger Lotem, 2015, WABI.

Rich Parameterization Improves RNA Structure Prediction

Michael Elhadad, Yoav Goldberg, Michal Ziv-Ukelson, 2011, RECOMB.

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

Michal Ziv-Ukelson, Aaron Kershenbaum, Michal Ziv-Ukelson, 1998, CPM.

Seeded Tree Alignment

A. Lozano, R.Y. Pinter, O. Rokhlenko, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Seeded Tree Alignment and Planar Tanglegram Layout

Ron Y. Pinter, Michal Ziv-Ukelson, Gabriel Valiente, 2007, WABI.

BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM

Michal Ziv-Ukelson, Sivan Sabato, Eran Barash, 2018, Bioinform..