Michal Ziv-Ukelson

发表

Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson, 2003, CPM.

Re-Use Dynamic Programming for Sequence Alignment: An Algorithmic Toolkit

Gad M. Landau, Maxime Crochemore, Baruch Schieber, 2005 .

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..

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.

Seeded Tree Alignment and Planar Tanglegram Layout

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

SA-REPC - Sequence Alignment with Regular Expression Path Constraint

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

Algorithms for path-constrained sequence alignment

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

Recent Results on Three Problems in Comparative Structural RNAomics

Michal Ziv-Ukelson, Eitan Bachmat, Nimrod Milo, 2014, CMSR@ECCB.

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

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

Regular Language Constrained Sequence Alignment Revisited

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

Rich Parameterization Improves RNA Structure Prediction

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

Fast algorithms for computing tree LCS

Michal Ziv-Ukelson, Dekel Tsur, Oren Weimann, 2009, Theor. Comput. Sci..

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..

Efficient All Path Score Computations on Grid Graphs

Michal Ziv-Ukelson, Dekel Tsur, Ury Matarazzo, 2013, CPM.

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.

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions

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

Seeded Tree Alignment

Ron Y. Pinter, Michal Ziv-Ukelson, Gabriel Valiente, 2008, IEEE ACM Trans. Comput. Biol. Bioinform..

Dynamic all scores matrices for LCS score pdf

Michal Ziv-Ukelson, Dekel Tsur, Amir Carmel, 2018, ArXiv.

A sub-quadratic sequence alignment algorithm for unrestricted cost matrices

Gad M. Landau, Maxime Crochemore, Michal Ziv-Ukelson, 2002, SODA '02.

Alignment of metabolic pathways

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

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..

Efficient edit distance with duplications and contractions

Michal Ziv-Ukelson, Dekel Tsur, Tamar Pinhas, 2012, Algorithms for Molecular Biology.

BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM

Michal Ziv-Ukelson, Sivan Sabato, Eran Barash, 2019, Bioinform..

Efficient all path score computations on grid graphs

Michal Ziv-Ukelson, Dekel Tsur, Ury Matarazzo, 2014, Theor. Comput. Sci..

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, WABI.

On Almost Monge All Scores Matrices

Michal Ziv-Ukelson, Dekel Tsur, Amir Carmel, 2016, CPM.

Discovery of multi-operon colinear syntenic blocks in microbial genomes

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

Learning Heuristics for Mining RNA Sequence-Structure Motifs

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

Learning of Structurally Unambiguous Probabilistic Grammars pdf

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

Two Algorithms for LCS Consecutive Suffix Alignment

Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson, 2004, CPM.

On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem

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

A Structure-Based Flexible Search Method for Motifs in RNA

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

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.

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

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

On the Complexity of Sparse Exon Assembly

Gad M. Landau, Michal Ziv-Ukelson, Carmel Kent, 2005, CPM.

Sparse LCS Common Substring Alignment

Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson, 2003, Inf. Process. Lett..

Regular Language Constrained Sequence Alignment Revisited

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

A Faster Algorithm for RNA Co-folding

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

Approximate Labelled Subtree Homeomorphism

Ron Y. Pinter, Michal Ziv-Ukelson, Dekel Tsur, 2004, CPM.

On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem

Ron Y. Pinter, Michal Ziv-Ukelson, Firas Swidan, 2006, CPM.

Rich Parameterization Improves RNA Structure Prediction

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

On the Common Substring Alignment Problem

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

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions

Michal Ziv-Ukelson, Oren Weimann, Shay Mozes, 2007, CPM.

Gene bi-targeting by viral and human miRNAs

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

RNA Tree Comparisons via Unrooted Unordered Alignments

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

Stringology Combats Microbiological Threats (Invited Talk)

Michal Ziv-Ukelson, 2019, CPM.

Fast Algorithms for Computing Tree LCS

Michal Ziv-Ukelson, Dekel Tsur, Oren Weimann, 2008, CPM.

Approximate labelled subtree homeomorphism

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

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 Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices

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

Edit Distance with Duplications and Contractions Revisited

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

Sparse RNA folding: Time and space efficient algorithms

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

A Study of Accessible Motifs and RNA Folding Complexity

Michal Ziv-Ukelson, Chaya Ben-Zaken Zilberstein, Ydo Wexler, 2007, J. Comput. Biol..

The Worst Case Complexity of Maximum Parsimony

Michal Ziv-Ukelson, Dekel Tsur, Amir Carmel, 2014, CPM.

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.

Two algorithms for LCS Consecutive Suffix Alignment

Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson, 2007, J. Comput. Syst. Sci..

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

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

On Almost Monge All Scores Matrices

Michal Ziv-Ukelson, Dekel Tsur, Amir Carmel, 2018, Algorithmica.

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

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

Unrooted unordered homeomorphic subtree alignment of RNA trees

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

On the Complexity of Sparse Exon Assembly

Gad M. Landau, Michal Ziv-Ukelson, Carmel Kent, 2006, J. Comput. Biol..

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.

Sparse RNA Folding: Time and Space Efficient Algorithms

Rolf Backofen, Michal Ziv-Ukelson, Dekel Tsur, 2009, CPM.

Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes

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

On the shared substring alignment problem

Gad M. Landau, Michal Ziv-Ukelson, 2000, SODA '00.

A Study of Accessible Motifs and RNA Folding Complexity

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

A Faster Algorithm for Simultaneous Alignment and Folding of RNA

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

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

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

The Worst Case Complexity of Maximum Parsimony

Michal Ziv-Ukelson, Dekel Tsur, Amir Carmel, 2014, J. Comput. Biol..

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, 2016, J. Comput. Biol..

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

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

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.

Bioimage informatics MotifNet : a webserver for network motif analysis

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

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

Michal Ziv-Ukelson, Meirav Zehavi, Galia R. Zimerman, 2021, Algorithms Mol. Biol..

Learning of Structurally Unambiguous Probabilistic Grammars

Dana Fisman, Michal Ziv-Ukelson, Dolav Nitay, 2021, AAAI.

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

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

A new tool for the alignment of metabolic pathways

Ron Y. Pinter, Michal Ziv-Ukelson, Oleg Rokhlenko, 2004 .

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

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