Stéphane Vialette

Theor. Comput. Sci., May, 2023

On shuffled-square-free words.

[BibT_eX]

[DOI]

Vincent Jugé

Virginia Ardévol Martínez

Theor. Comput. Sci., 2023

Quasi-kernels in split graphs.

[BibT_eX]

[DOI]

CoRR, 2023

Parity Permutation Pattern Matching.

[BibT_eX]

[DOI]

Virginia Ardévol Martínez

Proceedings of the WALCOM: Algorithms and Computation, 2023

Recognizing Unit Multiple Intervals Is Hard.

[BibT_eX]

[DOI]

Proceedings of the 34th International Symposium on Algorithms and Computation, 2023

2022

Algorithmic Aspects of Small Quasi-Kernels.

[BibT_eX]

[DOI]

Proceedings of the Graph-Theoretic Concepts in Computer Science, 2022

The Maximum Zero-Sum Partition Problem.

[BibT_eX]

[DOI]

Proceedings of the New Trends in Computer Technologies and Applications, 2022

Permutation Pattern Matching for Doubly Partially Ordered Patterns.

[BibT_eX]

[DOI]

Proceedings of the 33rd Annual Symposium on Combinatorial Pattern Matching, 2022

2021

Efficient, robust and effective rank aggregation for massive biological datasets.

[BibT_eX]

[DOI]

Future Gener. Comput. Syst., 2021

Algorithmic aspects of quasi-kernels.

[BibT_eX]

[DOI]

CoRR, 2021

Disorders and Permutations.

[BibT_eX]

[DOI]

Samuele Giraudo

Proceedings of the 32nd Annual Symposium on Combinatorial Pattern Matching, 2021

2020

Recognizing binary shuffle squares is NP-hard.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2020

The Clever Shopper Problem.

[BibT_eX]

[DOI]

Theory Comput. Syst., 2020

Sorting with forbidden intermediates.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2020

2019

Unshuffling Permutations: Trivial Bijections and Compositions.

[BibT_eX]

[DOI]

Proceedings of the Theory and Applications of Models of Computation, 2019

Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data.

[BibT_eX]

[DOI]

Proceedings of the 15th International Conference on eScience, 2019

Finding a Small Number of Colourful Components.

[BibT_eX]

[DOI]

Proceedings of the 30th Annual Symposium on Combinatorial Pattern Matching, 2019

2018

Algorithmic and algebraic aspects of unshuffling permutations.

[BibT_eX]

[DOI]

Samuele Giraudo

Theor. Comput. Sci., 2018

Solving the tree containment problem in linear time for nearly stable phylogenetic networks.

[BibT_eX]

[DOI]

Andreas D. M. Gunawan

Anthony Labarre

Louxin Zhang

Discret. Appl. Math., 2018

The S-labeling problem: An algorithmic tour.

[BibT_eX]

[DOI]

Irena Rusu

Discret. Appl. Math., 2018

Pattern Matching for k-Track Permutations.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Algorithms - 29th International Workshop, 2018

The Clever Shopper Problem.

[BibT_eX]

[DOI]

Proceedings of the Computer Science - Theory and Applications, 2018

2016

Two-Interval Pattern Problems.

[BibT_eX]

[DOI]

Encyclopedia of Algorithms, 2016

Permutation Pattern matching in (213, 231)-avoiding permutations.

[BibT_eX]

[DOI]

Both Emerite Neou

Discret. Math. Theor. Comput. Sci., 2016

Pattern Matching for Separable Permutations.

[BibT_eX]

[DOI]

Both Emerite Neou

Proceedings of the String Processing and Information Retrieval, 2016

Unshuffling Permutations.

[BibT_eX]

[DOI]

Samuele Giraudo

Proceedings of the LATIN 2016: Theoretical Informatics, 2016

2015

Some algorithmic results for [2]-sumset covers.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2015

Pattern matching in $(213, 231)$-avoiding permutations.

[BibT_eX]

[DOI]

Both Emerite Neou

CoRR, 2015

Locating a Tree in a Phylogenetic Network in Quadratic Time.

[BibT_eX]

[DOI]

Andreas D. M. Gunawan

Anthony Labarre

Louxin Zhang

Proceedings of the Research in Computational Molecular Biology, 2015

Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time.

[BibT_eX]

[DOI]

Andreas D. M. Gunawan

Anthony Labarre

Louxin Zhang

Proceedings of the Combinatorial Algorithms - 26th International Workshop, 2015

Algorithmic Aspects of the S-Labeling Problem.

[BibT_eX]

[DOI]

Irena Rusu

Proceedings of the Combinatorial Algorithms - 26th International Workshop, 2015

Obtaining a Triangular Matrix by Independent Row-Column Permutations.

[BibT_eX]

[DOI]

Irena Rusu

Proceedings of the Algorithms and Computation - 26th International Symposium, 2015

2014

Towards Unlocking the Full Potential of Multileaf Collimators.

[BibT_eX]

[DOI]

Proceedings of the SOFSEM 2014: Theory and Practice of Computer Science, 2014

2013

Finding approximate and constrained motifs in graphs.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2013

On the combinatorics of suffix arrays.

[BibT_eX]

[DOI]

Gregory Kucherov

Lilla Tóthmérész

Inf. Process. Lett., 2013

Minimum Mosaic Inference of a Set of Recombinants.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2013

Single and Multiple Consecutive Permutation Motif Search.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Computation - 24th International Symposium, 2013

On Recognizing Words That Are Squares for the Shuffle Product.

[BibT_eX]

[DOI]

Proceedings of the Computer Science - Theory and Applications, 2013

Flexible RNA design under structure and sequence constraints using formal languages.

[BibT_eX]

[DOI]

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

A Faster Algorithm for Finding Minimum Tucker Submatrices.

[BibT_eX]

[DOI]

Theory Comput. Syst., 2012

The Longest Common Subsequence Problem with Crossing-Free Arc-Annotated Sequences.

[BibT_eX]

[DOI]

Minghui Jiang

Proceedings of the String Processing and Information Retrieval, 2012

Algorithmic Aspects of the Intersection and Overlap Numbers of a Graph.

[BibT_eX]

[DOI]

Danny Hermelin

Proceedings of the Algorithms and Computation - 23rd International Symposium, 2012

Hardness of Longest Common Subsequence for Sequences with Bounded Run-Lengths.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

2011

Approximation of RNA multiple structural alignment.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2011

Complexity issues in vertex-colored graph pattern matching.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2011

Upper and lower bounds for finding connected motifs in vertex-colored graphs.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., 2011

A Polynomial-Time Algorithm for Finding a Minimal Conflicting Set Containing a Given Row.

[BibT_eX]

[DOI]

Proceedings of the Computer Science - Theory and Applications, 2011

Algorithmic Aspects of Heterogeneous Biological Networks Comparison.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Optimization and Applications, 2011

2010

Finding common structured patterns in linear graphs.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2010

Complexity issues in color-preserving graph embeddings.

[BibT_eX]

[DOI]

Gaëlle Brevier

Theor. Comput. Sci., 2010

Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Comparing RNA Structures with Biologically Relevant Operations Cannot Be Done without Strong Combinatorial Restrictions.

[BibT_eX]

[DOI]

Sylvie Hamel

Proceedings of the WALCOM: Algorithms and Computation, 4th International Workshop, 2010

GraMoFoNe: a Cytoscape Plugin for Querying Motifs without Topology in Protein-Protein Interactions Networks.

[BibT_eX]

Proceedings of the ISCA 2nd International Conference on Bioinformatics and Computational Biology, 2010

Algorithmic Contributions to Computational Molecular Biology.

[BibT_eX]

[DOI]

, 2010

2009

On the parameterized complexity of multiple-interval graph problems.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2009

On the Approximability of Comparing Genomes with Duplicates.

[BibT_eX]

[DOI]

J. Graph Algorithms Appl., 2009

Finding occurrences of protein complexes in protein-protein interaction graphs.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2009

RECOMB-Comparative Genomics Special Issue.

[BibT_eX]

Craig E. Nelson

J. Comput. Biol., 2009

On the S-Labeling problem.

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 2009

The ExemplarBreakpointDistancefor Non-trivial Genomes Cannot Be Approximated.

[BibT_eX]

[DOI]

Proceedings of the WALCOM: Algorithms and Computation, Third International Workshop, 2009

Pseudo Boolean Programming for Partially Ordered Genomes.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics, International Workshop, 2009

Querying Protein-Protein Interaction Networks.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications, 5th International Symposium, 2009

Pattern Matching for 321-Avoiding Permutations.

[BibT_eX]

[DOI]

Sylvain Guillemot

Proceedings of the Algorithms and Computation, 20th International Symposium, 2009

Maximum Motif Problem in Vertex-Colored Graphs.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 20th Annual Symposium, 2009

On Finding Small 2-Generating Sets.

[BibT_eX]

[DOI]

Isabelle Fagnot

Proceedings of the Computing and Combinatorics, 15th Annual International Conference, 2009

Combinatorics of Genome Rearrangements.

[BibT_eX]

[DOI]

Computational molecular biology, MIT Press, ISBN: 978-0-262-06282-4, 2009

2008

Two-Interval Pattern Problems.

[BibT_eX]

[DOI]

Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Approximating the 2-interval pattern problem.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2008

Bounded list injective homomorphism for comparative analysis of protein-protein interaction graphs.

[BibT_eX]

[DOI]

Isabelle Fagnot

Gaëlle Lelandais

J. Discrete Algorithms, 2008

Fixed-parameter algorithms for protein similarity search under mRNA structure constraints.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2008

Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between Two Genomes with Duplicate Genes.

[BibT_eX]

[DOI]

J. Comput. Biol., 2008

The Minimum Substring Cover problem.

[BibT_eX]

[DOI]

Inf. Comput., 2008

Comparing RNA structures using a full set of biologically relevant edit operations is intractable

[BibT_eX]

[DOI]

Sylvie Hamel

CoRR, 2008

2007

Extracting constrained 2-interval subsets in 2-interval sets.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2007

Exemplar Longest Common Subsequence.

[BibT_eX]

[DOI]

Paola Bonizzoni

Gianluca Della Vedova

IEEE ACM Trans. Comput. Biol. Bioinform., 2007

Comparing Genomes with Duplications: A Computational Complexity Point of View.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2007

A Pseudo-Boolean Framework for Computing Rearrangement Distances between Genomes with Duplicates.

[BibT_eX]

[DOI]

J. Comput. Biol., 2007

Longest Common Separable Pattern between Permutations

[BibT_eX]

[DOI]

Mathilde Bouvel

Dominique Rossin

CoRR, 2007

Comparing RNA Structures: Towards an Intermediate Model Between the Editand the LapcsProblems.

[BibT_eX]

[DOI]

Proceedings of the Advances in Bioinformatics and Computational Biology, 2007

On Restrictions of Balanced 2-Interval Graphs.

[BibT_eX]

[DOI]

Proceedings of the Graph-Theoretic Concepts in Computer Science, 2007

A Pseudo-boolean Programming Approach for Computing the Breakpoint Distance Between Two Genomes with Duplicate Genes.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics, RECOMB 2007 International Workshop, 2007

Weak pattern matching in colored graphs: Minimizing the number of connected components.

[BibT_eX]

Proceedings of the Theoretical Computer Science, 10th Italian Conference, 2007

Sharp Tractability Borderlines for Finding Connected Motifs in Vertex-Colored Graphs.

[BibT_eX]

[DOI]

Proceedings of the Automata, Languages and Programming, 34th International Colloquium, 2007

Pattern Matching in Protein-Protein Interaction Graphs.

[BibT_eX]

[DOI]

Gaëlle Brevier

Proceedings of the Fundamentals of Computation Theory, 16th International Symposium, 2007

Common Structured Patterns in Linear Graphs: Approximation and Combinatorics.

[BibT_eX]

[DOI]

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

Longest Common Separable Pattern Among Permutations.

[BibT_eX]

[DOI]

Mathilde Bouvel

Dominique Rossin

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

2006

Packing of (0, 1)-matrices.

[BibT_eX]

[DOI]

RAIRO Theor. Informatics Appl., 2006

Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms.

[BibT_eX]

[DOI]

Bioinform., 2006

How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics, 2006

Genomes Containing Duplicates Are Hard to Compare.

[BibT_eX]

[DOI]

Proceedings of the Computational Science, 2006

Exemplar Longest Common Subsequence.

[BibT_eX]

[DOI]

Paola Bonizzoni

Gianluca Della Vedova

Proceedings of the Computational Science, 2006

2005

What Makes the Arc-Preserving Subsequence Problem Hard?

[BibT_eX]

[DOI]

Trans. Comp. Sys. Biology, 2005

Finding Exact and Maximum Occurrences of Protein Complexes in Protein-Protein Interaction Graphs.

[BibT_eX]

[DOI]

Proceedings of the Mathematical Foundations of Computer Science 2005, 2005

Approximating the 2-Interval Pattern Problem.

[BibT_eX]

[DOI]

Proceedings of the Algorithms, 2005

2004

On the computational complexity of 2-interval pattern matching problems.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2004

yMGV: a cross-species expression data mining tool.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2004

MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states.

[BibT_eX]

[DOI]

BMC Bioinform., 2004

New Results for the 2-Interval Pattern Problem.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 2004

2002

Pattern Matching Problems over 2-Interval Sets.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002

2001

Aspects algorithmiques de la prédiction des structures secondaires d'ARN.

[BibT_eX]

[DOI]