Guillaume Fertin

Anthony Labarre

Theor. Comput. Sci., 2025

The Exact Subset MultiCover problem.

[BibT_eX]

[DOI]

Emile Benoist

Theor. Comput. Sci., 2025

2024

Assignment of orthologous genes in unbalanced genomes using cycle packing of adjacency graphs.

[BibT_eX]

[DOI]

Gabriel Siqueira

J. Heuristics, December, 2024

The Maximum Zero-Sum Partition problem.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2024

Best of Both Worlds: Solving the Cyclic Bandwidth Problem by Combining Pre-existing Knowledge and Constraint Programming Techniques.

[BibT_eX]

[DOI]

Claudia Vasconcellos-Gaete

Éric Monfroy

Proceedings of the Computational Science - ICCS 2024, 2024

2023

Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides.

[BibT_eX]

[DOI]

Mélisande Blein-Nicolas

BMC Bioinform., December, 2023

Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information.

[BibT_eX]

[DOI]

J. Comput. Biol., August, 2023

Approximation algorithms for sorting by k-cuts on signed permutations.

[BibT_eX]

[DOI]

J. Comb. Optim., 2023

Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions.

[BibT_eX]

[DOI]

Gabriel Siqueira

Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

2022

Sorting by k-Cuts on Signed Permutations.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics - 19th International Conference, 2022

Transposition Distance Considering Intergenic Regions for Unbalanced Genomes.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 18th International Symposium, 2022

Permutation Pattern Matching for Doubly Partially Ordered Patterns.

[BibT_eX]

[DOI]

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

2021

The Maximum Colorful Arborescence problem: How (computationally) hard can it be?

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2021

Sorting Permutations by Intergenic Operations.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Sorting Signed Permutations by Intergenic Reversals.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Decomposing subcubic graphs into claws, paths or triangles.

[BibT_eX]

[DOI]

J. Graph Theory, 2021

Evaluation of open search methods based on theoretical mass spectra comparison.

[BibT_eX]

[DOI]

BMC Bioinform., 2021

Sorting by Multi-Cut Rearrangements.

[BibT_eX]

[DOI]

Algorithms, 2021

Improved Lower Bounds for the Cyclic Bandwidth Problem.

[BibT_eX]

[DOI]

Hugues Déprés

Éric Monfroy

Proceedings of the Computational Science - ICCS 2021, 2021

2020

Graph Motif Problems Parameterized by Dual.

[BibT_eX]

[DOI]

J. Graph Algorithms Appl., 2020

Sorting by Genome Rearrangements on Both Gene Order and Intergenic Sizes.

[BibT_eX]

[DOI]

Klairton Lima Brito

Ulisses Dias

J. Comput. Biol., 2020

A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions.

[BibT_eX]

[DOI]

Proceedings of the Algorithms for Computational Biology, 2020

2019

Super short operations on both gene order and intergenic sizes.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2019

Unshuffling Permutations: Trivial Bijections and Compositions.

[BibT_eX]

[DOI]

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

Sorting by Reversals, Transpositions, and Indels on Both Gene Order and Intergenic Sizes.

[BibT_eX]

[DOI]

Klairton Lima Brito

Ulisses Dias

Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

Finding a Small Number of Colourful Components.

[BibT_eX]

[DOI]

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

Mass Spectra Interpretation and the Interest of SpecFit for Identifying Uncommon Modifications.

[BibT_eX]

[DOI]

Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2019

2018

Sorting permutations and binary strings by length-weighted rearrangements.

[BibT_eX]

[DOI]

Carla Negri Lintzmayer

Theor. Comput. Sci., 2018

Editorial.

[BibT_eX]

[DOI]

Giancarlo Mauri

Theor. Comput. Sci., 2018

The S-labeling problem: An algorithmic tour.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2018

Optimal odd gossiping.

[BibT_eX]

[DOI]

Joseph G. Peters

Discret. Appl. Math., 2018

Prefix and suffix reversals on strings.

[BibT_eX]

[DOI]

Loïc Jankowiak

Discret. Appl. Math., 2018

Matching algorithms for assigning orthologs after genome duplication events.

[BibT_eX]

[DOI]

Falk Hüffner

Manuel Sorge

Comput. Biol. Chem., 2018

Sorting signed circular permutations by super short operations.

[BibT_eX]

[DOI]

Ulisses Dias

Algorithms Mol. Biol., 2018

Super Short Reversals on Both Gene Order and Intergenic Sizes.

[BibT_eX]

[DOI]

Proceedings of the Advances in Bioinformatics and Computational Biology, 2018

On the Maximum Colorful Arborescence Problem and Color Hierarchy Graph Structure.

[BibT_eX]

[DOI]

Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018

2017

Sorting permutations by prefix and suffix rearrangements.

[BibT_eX]

[DOI]

Carla Negri Lintzmayer

J. Bioinform. Comput. Biol., 2017

Odd gossiping.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2017

The Maximum Colorful Arborescence problem parameterized by the structure of its color hierarchy graph.

[BibT_eX]

[DOI]

CoRR, 2017

Algorithms for computing the double cut and join distance on both gene order and intergenic sizes.

[BibT_eX]

[DOI]

Eric Tannier

Algorithms Mol. Biol., 2017

Algorithmic Aspects of the Maximum Colorful Arborescence Problem.

[BibT_eX]

[DOI]

Proceedings of the Theory and Applications of Models of Computation, 2017

Beyond Adjacency Maximization: Scaffold Filling for New String Distances.

[BibT_eX]

[DOI]

Proceedings of the 28th Annual Symposium on Combinatorial Pattern Matching, 2017

2016

(Prefix) reversal distance for (signed) strings with few blocks or small alphabets.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2016

Genome rearrangements with indels in intergenes restrict the scenario space.

[BibT_eX]

[DOI]

Eric Tannier

BMC Bioinform., 2016

Genome Rearrangements on Both Gene Order and Intergenic Regions.

[BibT_eX]

[DOI]

Eric Tannier

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

SpecTrees: An Efficient Without a Priori Data Structure for MS/MS Spectra Identification.

[BibT_eX]

[DOI]

Matthieu David

Dominique Tessier

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

Decomposing Cubic Graphs into Connected Subgraphs of Size Three.

[BibT_eX]

[DOI]

Proceedings of the Computing and Combinatorics - 22nd International Conference, 2016

2015

Approximation algorithms for sorting by length-weighted prefix and suffix operations.

[BibT_eX]

[DOI]

Carla Negri Lintzmayer

Theor. Comput. Sci., 2015

Towards an algorithmic guide to Spiral Galaxies.

[BibT_eX]

[DOI]

Shahrad Jamshidi

Theor. Comput. Sci., 2015

Pancake Flipping is hard.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., 2015

Some algorithmic results for [2]-sumset covers.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2015

Path-driven orientation of mixed graphs.

[BibT_eX]

[DOI]

Hafedh Mohamed-Babou

Discret. Appl. Math., 2015

Finding Supported Paths in Heterogeneous Networks.

[BibT_eX]

[DOI]

Hafedh Mohamed-Babou

Algorithms, 2015

Algorithmic Aspects of the S-Labeling Problem.

[BibT_eX]

[DOI]

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

Obtaining a Triangular Matrix by Independent Row-Column Permutations.

[BibT_eX]

[DOI]

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

2014

Reversal Distances for Strings with Few Blocks or Small Alphabets.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 25th Annual Symposium, 2014

DExTaR: Detection of exact tandem repeats based on the de Bruijn graph.

[BibT_eX]

[DOI]

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2013

Finding approximate and constrained motifs in graphs.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2013

Revisiting the Minimum Breakpoint Linearization Problem.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2013

Maximal strip recovery problem with gaps: Hardness and approximation algorithms.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2013

A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

2012

Tractability and approximability of maximal strip recovery.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2012

Sorting by Transpositions Is Difficult.

[BibT_eX]

[DOI]

SIAM J. Discret. Math., 2012

Algorithms for Subnetwork Mining in Heterogeneous Networks.

[BibT_eX]

[DOI]

Hafedh Mohamed-Babou

Proceedings of the Experimental Algorithms - 11th International Symposium, 2012

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

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

Proper Alignment of MS/MS Spectra from Unsequenced Species.

[BibT_eX]

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2010

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]

Romeo Rizzi

J. Discrete Algorithms, 2009

On the S-Labeling problem.

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 2009

Comparison of Spectra in Unsequenced Species.

[BibT_eX]

[DOI]

Proceedings of the Advances in Bioinformatics and Computational Biology, 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

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

Comparing Bacterial Genomes by Searching Their Common Intervals.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics and Computational Biology, 2009

Combinatorics of Genome Rearrangements.

[BibT_eX]

[DOI]

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

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

Acyclic coloring of graphs of maximum degree five: Nine colors are enough.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2008

On the Approximability of Comparing Genomes with Duplicates.

[BibT_eX]

[DOI]

Sébastien Angibaud

Proceedings of the WALCOM: Algorithms and Computation, Second International Workshop, 2008

2007

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

[BibT_eX]

[DOI]

Guillaume Blin

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

L(p, q) labeling of d-dimensional grids.

[BibT_eX]

[DOI]

Discret. Math., 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

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

Extending the Hardness of RNA Secondary Structure Comparison.

[BibT_eX]

[DOI]

Proceedings of the Combinatorics, 2007

Common Structured Patterns in Linear Graphs: Approximation and Combinatorics.

[BibT_eX]

[DOI]

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

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

Edge-disjoint spanners in Cartesian products of graphs.

[BibT_eX]

[DOI]

Discret. Math., 2005

Genes Order and Phylogenetic Reconstruction: Application to <i>gamma</i>-Proteobacteria.

[BibT_eX]

[DOI]

Guillaume Blin

Cédric Chauve

Proceedings of the Comparative Genomics, 2005

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

[BibT_eX]

[DOI]

Romeo Rizzi

Proceedings of the Mathematical Foundations of Computer Science 2005, 2005

2004

On maximal instances for the original syntenic distance.

[BibT_eX]

[DOI]

Cédric Chauve

Theor. Comput. Sci., 2004

Star coloring of graphs.

[BibT_eX]

[DOI]

Bruce A. Reed

J. Graph Theory, 2004

A survey on Knödel graphs.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2004

No-Hole L(p, 0) Labelling of Cycles, Grids and Hypercubes.

[BibT_eX]

[DOI]

Ondrej Sýkora

Proceedings of the Structural Information and Communication Complexity, 2004

New Results for the 2-Interval Pattern Problem.

[BibT_eX]

[DOI]

Guillaume Blin

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

2003

On the oriented chromatic number of grids.

[BibT_eX]

[DOI]

Arup Roychowdhury

Inf. Process. Lett., 2003

Acyclic and k-distance coloring of the grid.

[BibT_eX]

[DOI]

Emmanuel Godard

Inf. Process. Lett., 2003

Factor <i>d</i>-domatic colorings of graphs.

[BibT_eX]

[DOI]

Discret. Math., 2003

Vertex Labeling and Routing in Recursive Clique-Trees, a New Family of Small-World Scale-Free Graphs.

[BibT_eX]

Francesc Comellas

Proceedings of the SIROCCO 10: Proceedings of the 10th Internaltional Colloquium on Structural Information Complexity, 2003

2002

Minimum feedback vertex set and acyclic coloring.

[BibT_eX]

[DOI]

Emmanuel Godard

Inf. Process. Lett., 2002

2001

Neighborhood Communications in Networks.

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 2001

Routing permutations and 2-1 routing requests in the hypercube.

[BibT_eX]

[DOI]

Olivier Baudon

Ivan Havel

Discret. Appl. Math., 2001

k-Neighborhood Broadcasting.

[BibT_eX]

Proceedings of the SIROCCO 8, 2001

2000

On the structure of minimum broadcast digraphs.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2000

Compounding of gossip graphs.

[BibT_eX]

[DOI]

Roger Labahn

Networks, 2000

Hierarchical broadcast and gossip networks.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2000

Recognizing Recursive Circulant Graphs (Extended Abstract).

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 2000

A study of minimum gossip graphs.

[BibT_eX]

[DOI]

Discret. Math., 2000

Diameter of the Knödel Graph.

[BibT_eX]

[DOI]

Proceedings of the Graph-Theoretic Concepts in Computer Science, 2000

1999

Routing Permutations in the Hypercube.

[BibT_eX]

[DOI]

Olivier Baudon

Ivan Havel

Proceedings of the Graph-Theoretic Concepts in Computer Science, 1999

Trade-Offs for Add Gossiping.

[BibT_eX]

Proceedings of the SIROCCO'99, 1999

1998

Families of Graphs Having Broadcasting and Gossiping Properties.

[BibT_eX]

[DOI]