Michal Ziv-Ukelson

Algorithms Mol. Biol., December, 2023

Learning of Structurally Unambiguous Probabilistic Grammars.

[BibT_eX]

[DOI]

Dana Fisman

Dolav Nitay

Log. Methods Comput. Sci., 2023

2022

Predicting the pathogenicity of bacterial genomes using widely spread protein families.

[BibT_eX]

[DOI]

BMC Bioinform., 2022

New Algorithms for Structure Informed Genome Rearrangement.

[BibT_eX]

[DOI]

Eden Ozery

Meirav Zehavi

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

2021

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

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2021

2020

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

[BibT_eX]

[DOI]

Roni Zoller

Meirav Zehavi

J. Comput. Biol., 2020

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

[BibT_eX]

[DOI]

Dina Svetlitsky

Tal Dagan

Bioinform., 2020

2019

Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes.

[BibT_eX]

[DOI]

Jonathan Engel

J. Comput. Biol., 2019

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

[BibT_eX]

[DOI]

Bioinform., 2019

BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM.

[BibT_eX]

[DOI]

Bioinform., 2019

On Almost Monge All Scores Matrices.

[BibT_eX]

[DOI]

Amir Carmel

Algorithmica, 2019

Stringology Combats Microbiological Threats (Invited Talk).

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

J. Comput. Biol., 2018

Dynamic all scores matrices for LCS score.

[BibT_eX]

[DOI]

Amir Carmel

CoRR, 2018

2017

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

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2017

MotifNet: a web-server for network motif analysis.

[BibT_eX]

[DOI]

Bioinform., 2017

2016

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

[BibT_eX]

[DOI]

J. Comput. Biol., 2016

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

[BibT_eX]

[DOI]

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

2014

Efficient all path score computations on grid graphs.

[BibT_eX]

[DOI]

Ury Matarazzo

Theor. Comput. Sci., 2014

Algorithms for path-constrained sequence alignment.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2014

The Worst Case Complexity of Maximum Parsimony.

[BibT_eX]

[DOI]

J. Comput. Biol., 2014

Recent Results on Three Problems in Comparative Structural RNAomics.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Alexander Lan

Esti Yeger Lotem

Bioinform., 2013

Efficient edit distance with duplications and contractions.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2013

Unrooted unordered homeomorphic subtree alignment of RNA trees.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2013

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

[BibT_eX]

[DOI]

Sivan Yogev

Nimrod Milo

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).

[BibT_eX]

[DOI]

BMC Bioinform., 2012

RNA Tree Comparisons via Unrooted Unordered Alignments.

[BibT_eX]

[DOI]

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

2011

Sparse RNA folding: Time and space efficient algorithms.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2011

Rich Parameterization Improves RNA Structure Prediction.

[BibT_eX]

[DOI]

J. Comput. Biol., 2011

Regular Language Constrained Sequence Alignment Revisited.

[BibT_eX]

[DOI]

Gregory Kucherov

Tamar Pinhas

J. Comput. Biol., 2011

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

[BibT_eX]

[DOI]

Genet. Program. Evolvable Mach., 2011

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

[BibT_eX]

[DOI]

Shay Zakov

Algorithms Mol. Biol., 2011

Edit Distance with Duplications and Contractions Revisited.

[BibT_eX]

[DOI]

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

2010

A Faster Algorithm for Simultaneous Alignment and Folding of RNA.

[BibT_eX]

[DOI]

J. Comput. Biol., 2010

Gene bi-targeting by viral and human miRNAs.

[BibT_eX]

[DOI]

Yonat Shemer-Avni

Klara Kedem

BMC Bioinform., 2010

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

[BibT_eX]

[DOI]

Nimrod Milo

Tamar Pinhas

Proceedings of the Language and Automata Theory and Applications, 2010

2009

Fast algorithms for computing tree LCS.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2009

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

[BibT_eX]

[DOI]

BMC Bioinform., 2009

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.

[BibT_eX]

[DOI]

Algorithmica, 2009

2008

Seeded Tree Alignment.

[BibT_eX]

[DOI]

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

Approximate labelled subtree homeomorphism.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2008

A Faster Algorithm for RNA Co-folding.

[BibT_eX]

[DOI]

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

2007

Two algorithms for LCS Consecutive Suffix Alignment.

[BibT_eX]

[DOI]

Eugene W. Myers

Chaya Ben-Zaken Zilberstein

J. Comput. Syst. Sci., 2007

A Study of Accessible Motifs and RNA Folding Complexity.

[BibT_eX]

[DOI]

Ydo Wexler

J. Comput. Biol., 2007

A Structure-Based Flexible Search Method for Motifs in RNA.

[BibT_eX]

[DOI]

Danny Barash

Klara Kedem

J. Comput. Biol., 2007

Seeded Tree Alignment and Planar Tanglegram Layout.

[BibT_eX]

[DOI]

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

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.

[BibT_eX]

[DOI]

Shay Mozes

Oren Weimann

Chaya Ben-Zaken Zilberstein

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

2006

A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions.

[BibT_eX]

[DOI]

Ron Y. Pinter

Zohar Yakhini

J. Comput. Biol., 2006

On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem.

[BibT_eX]

[DOI]

Firas Swidan

Ron Y. Pinter

J. Comput. Biol., 2006

On the Complexity of Sparse Exon Assembly.

[BibT_eX]

[DOI]

Carmel Kent

Chaya Ben-Zaken Zilberstein

J. Comput. Biol., 2006

2005

Alignment of metabolic pathways.

[BibT_eX]

[DOI]

Bioinform., 2005

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

[BibT_eX]

[DOI]

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

2003

A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices.

[BibT_eX]

[DOI]

Maxime Crochemore

SIAM J. Comput., 2003

Sparse LCS Common Substring Alignment.

[BibT_eX]

[DOI]

Baruch Schieber

Inf. Process. Lett., 2003

2002

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

[BibT_eX]

[DOI]

Maxime Crochemore

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

2001

On the Common Substring Alignment Problem.

[BibT_eX]

[DOI]

J. Algorithms, 2001

2000

On the shared substring alignment problem.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]