Michal Ziv-Ukelson

According to our database1, Michal Ziv-Ukelson authored at least 60 papers between 1998 and 2023.

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Bibliography

2023
New algorithms for structure informed genome rearrangement.
Algorithms Mol. Biol., December, 2023

Learning of Structurally Unambiguous Probabilistic Grammars.
Log. Methods Comput. Sci., 2023

2022
Predicting the pathogenicity of bacterial genomes using widely spread protein families.
BMC Bioinform., 2022

New Algorithms for Structure Informed Genome Rearrangement.
Proceedings of the 22nd International Workshop on Algorithms in Bioinformatics, 2022

2021
Approximate search for known gene clusters in new genomes using PQ-trees.
Algorithms Mol. Biol., 2021

2020
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation.
J. Comput. Biol., 2020

Discovery of multi-operon colinear syntenic blocks in microbial genomes.
Bioinform., 2020

2019
Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes.
J. Comput. Biol., 2019

CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes.
Bioinform., 2019

BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM.
Bioinform., 2019

On Almost Monge All Scores Matrices.
Algorithmica, 2019

Stringology Combats Microbiological Threats (Invited Talk).
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.
J. Comput. Biol., 2018

Dynamic all scores matrices for LCS score.
CoRR, 2018

2017
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts.
PLoS Comput. Biol., 2017

MotifNet: a web-server for network motif analysis.
Bioinform., 2017

2016
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns.
J. Comput. Biol., 2016

A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands.
Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

2015
Learning Heuristics for Mining RNA Sequence-Structure Motifs.
Proceedings of the Genetic Programming Theory and Practice XIII [GPTP 2015]., 2015

2014
Efficient all path score computations on grid graphs.
Theor. Comput. Sci., 2014

Algorithms for path-constrained sequence alignment.
J. Discrete Algorithms, 2014

The Worst Case Complexity of Maximum Parsimony.
J. Comput. Biol., 2014

Recent Results on Three Problems in Comparative Structural RNAomics.
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.
Bioinform., 2013

Efficient edit distance with duplications and contractions.
Algorithms Mol. Biol., 2013

Unrooted unordered homeomorphic subtree alignment of RNA trees.
Algorithms Mol. Biol., 2013

StemSearch: RNA search tool based on stem identification and indexing.
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).
BMC Bioinform., 2012

RNA Tree Comparisons via Unrooted Unordered Alignments.
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

2011
Sparse RNA folding: Time and space efficient algorithms.
J. Discrete Algorithms, 2011

Rich Parameterization Improves RNA Structure Prediction.
J. Comput. Biol., 2011

Regular Language Constrained Sequence Alignment Revisited.
J. Comput. Biol., 2011

Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis.
Genet. Program. Evolvable Mach., 2011

Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach.
Algorithms Mol. Biol., 2011

Edit Distance with Duplications and Contractions Revisited.
Proceedings of the Combinatorial Pattern Matching - 22nd Annual Symposium, 2011

2010
A Faster Algorithm for Simultaneous Alignment and Folding of RNA.
J. Comput. Biol., 2010

Gene bi-targeting by viral and human miRNAs.
BMC Bioinform., 2010

SA-REPC - Sequence Alignment with Regular Expression Path Constraint.
Proceedings of the Language and Automata Theory and Applications, 2010

2009
Fast algorithms for computing tree LCS.
Theor. Comput. Sci., 2009

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.
BMC Bioinform., 2009

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.
Algorithmica, 2009

2008
Seeded Tree Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008

Approximate labelled subtree homeomorphism.
J. Discrete Algorithms, 2008

A Faster Algorithm for RNA Co-folding.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

2007
Two algorithms for LCS Consecutive Suffix Alignment.
J. Comput. Syst. Sci., 2007

A Study of Accessible Motifs and RNA Folding Complexity.
J. Comput. Biol., 2007

A Structure-Based Flexible Search Method for Motifs in RNA.
J. Comput. Biol., 2007

Seeded Tree Alignment and Planar Tanglegram Layout.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.
Proceedings of the Combinatorial Pattern Matching, 18th Annual Symposium, 2007

2006
A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions.
J. Comput. Biol., 2006

On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem.
J. Comput. Biol., 2006

On the Complexity of Sparse Exon Assembly.
J. Comput. Biol., 2006

2005
Alignment of metabolic pathways.
Bioinform., 2005

Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression.
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

2003
A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices.
SIAM J. Comput., 2003

Sparse LCS Common Substring Alignment.
Inf. Process. Lett., 2003

2002
A sub-quadratic sequence alignment algorithm for unrestricted cost matrices.
Proceedings of the Thirteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2002

2001
On the Common Substring Alignment Problem.
J. Algorithms, 2001

2000
On the shared substring alignment problem.
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.
Proceedings of the Combinatorial Pattern Matching, 9th Annual Symposium, 1998


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