Cédric Chauve

According to our database, Cédric Chauve authored at least 103 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Plaseval: a framework for comparing and evaluating plasmid detection tools.

Aniket C. Mane, Haley Sanderson, Aaron P. White, Rahat Zaheer, Robert Beiko, Cédric Chauve

BMC Bioinform., December, 2024

A Vector Representation for Phylogenetic Trees.

Cédric Chauve, Caroline Colijn, Louxin Zhang

CoRR, 2024

2023

PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.

Aniket C. Mane, Mahsa Faizrahnemoon, Tomás Vinar, Brona Brejová, Cédric Chauve

Bioinform., 2023

2022

A Mixed Integer Linear Programming Algorithm for Plasmid Binning.

Aniket C. Mane, Mahsa Faizrahnemoon, Cédric Chauve

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

2021

Small parsimony for natural genomes in the DCJ-indel model.

Daniel Doerr, Cédric Chauve

J. Bioinform. Comput. Biol., 2021

Refined Upper Bounds on the Size of the Condensed Neighbourhood of Sequences.

Cédric Chauve, Marni Mishna, France Paquet-Nadeau

Proceedings of the Prague Stringology Conference 2021, 2021

2020

Breakpoint distance and PQ-trees.

Haitao Jiang, Hong Liu, Cédric Chauve, Binhai Zhu

Inf. Comput., 2020

The distance and median problems in the single-cut-or-join model with single-gene duplications.

Aniket C. Mane, Manuel Lafond, Pedro Cipriano Feijão, Cédric Chauve

Algorithms Mol. Biol., 2020

A Graph-Theoretic Barcode Ordering Model for Linked-Reads.

Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi

Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals.

Mohsen Katebi, Pedro Feijão, Julius Booth, Mehrdad Mansouri, Sean La, Alex Sweeten, Reza Miraskarshahi, Matthew Nguyen, Johnathan Wong, William Hsiao, Cédric Chauve, Leonid Chindelevitch

Proceedings of the Algorithms for Computational Biology, 2020

2019

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.

Nina Luhmann, Manuel Lafond, Annelyse Thévenin, Aïda Ouangraoua, Roland Wittler, Cédric Chauve

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.

Cédric Chauve, Yann Ponty, Michael Wallner

CoRR, 2019

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework.

Guo Liang Gan, Elijah Willie, Cédric Chauve, Leonid Chindelevitch

BMC Bioinform., 2019

Alignment-free clustering of UMI tagged DNA molecules.

Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach

Bioinform., 2019

HyAsP, a greedy tool for plasmids identification.

Robert Müller, Cédric Chauve

Bioinform., 2019

Exponentially Few RNA Structures are Designable.

Hua-Ting Yao, Cédric Chauve, Mireille Régnier, Yann Ponty

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.

Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Gene Tree Construction and Correction Using SuperTree and Reconciliation.

Manuel Lafond, Cédric Chauve, Nadia El-Mabrouk, Aïda Ouangraoua

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Counting, Generating, Analyzing and Sampling Tree Alignments.

Cédric Chauve, Julien Courtiel, Yann Ponty

Int. J. Found. Comput. Sci., 2018

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cédric Chauve, Sèverine Bérard

BMC Genom., 2018

flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry.

Markus Lux, Ryan Remy Brinkman, Cédric Chauve, Adam Laing, Anna Lorenc, Lucie Abeler-Dörner, Barbara Hammer

Bioinform., 2018

PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats.

Mehrdad Mansouri, Julian Booth, Margaryta Vityaz, Cédric Chauve, Leonid Chindelevitch

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

The Rooted SCJ Median with Single Gene Duplications.

Aniket C. Mane, Manuel Lafond, Pedro Feijão, Cédric Chauve

Proceedings of the Comparative Genomics - 16th International Conference, 2018

Detecting Introgression in Anopheles Mosquito Genomes Using a Reconciliation-Based Approach.

Cédric Chauve, Jingxue Feng, Liangliang Wang

Proceedings of the Comparative Genomics - 16th International Conference, 2018

2017

Algorithms and Complexity Results for Genome Mapping Problems.

Ashok Rajaraman, João Paulo Pereira Zanetti, Ján Manuch, Cédric Chauve

IEEE ACM Trans. Comput. Biol. Bioinform., 2017

Constructing a Consensus Phylogeny from a Leaf-Removal Distance.

Cédric Chauve, Mark Jones, Manuel Lafond, Céline Scornavacca, Mathias Weller

CoRR, 2017

LRCstats, a tool for evaluating long reads correction methods.

Sean La, Ehsan Haghshenas, Cédric Chauve

Bioinform., 2017

The BRaliBase dent - a tale of benchmark design and interpretation.

Benedikt Löwes, Cédric Chauve, Yann Ponty, Robert Giegerich

Briefings Bioinform., 2017

The gene family-free median of three.

Daniel Doerr, Metin Balaban, Pedro Feijão, Cédric Chauve

Algorithms Mol. Biol., 2017

Constructing a Consensus Phylogeny from a Leaf-Removal Distance (Extended Abstract).

Cédric Chauve, Mark Jones, Manuel Lafond, Céline Scornavacca, Mathias Weller

Proceedings of the String Processing and Information Retrieval, 2017

A Tractable Variant of the Single Cut or Join Distance with Duplicated Genes.

Pedro Feijão, Aniket C. Mane, Cédric Chauve

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

An Exact Enumeration of Distance-Hereditary Graphs.

Cédric Chauve, Éric Fusy, Jérémie O. Lumbroso

Proceedings of the Fourteenth Workshop on Analytic Algorithmics and Combinatorics, 2017

2016

The SCJ small parsimony problem for weighted gene adjacencies (Extended version).

Nina Luhmann, Annelyse Thévenin, Aïda Ouangraoua, Roland Wittler, Cédric Chauve

CoRR, 2016

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.

Edwin Jacox, Cédric Chauve, Gergely J. Szöllosi, Yann Ponty, Céline Scornavacca

Bioinform., 2016

CoLoRMap: Correcting Long Reads by Mapping short reads.

Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve

Bioinform., 2016

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.

Nina Luhmann, Annelyse Thévenin, Aïda Ouangraoua, Roland Wittler, Cédric Chauve

Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

Counting, Generating and Sampling Tree Alignments.

Cédric Chauve, Julien Courtiel, Yann Ponty

Proceedings of the Algorithms for Computational Biology - Third International Conference, 2016

2015

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.

Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti

BMC Bioinform., December, 2015

Chaining Sequence/Structure Seeds for Computing RNA Similarity.

Laetitia Bourgeade, Cédric Chauve, Julien Allali

J. Comput. Biol., 2015

Joint Inference of Genome Structure and Content in Heterogeneous Tumour Samples.

Andrew W. McPherson, Andrew Roth, Gavin Ha, Sohrab P. Shah, Cédric Chauve, Süleyman Cenk Sahinalp

CoRR, 2015

An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment.

Cédric Chauve, Julien Courtiel, Yann Ponty

CoRR, 2015

Chaining fragments in sequences: to sweep or not.

Julien Allali, Laetitia Bourgeade, Cédric Chauve

CoRR, 2015

Chaining Fragments in Sequences: to Sweep or Not (Extended Abstract).

Julien Allali, Cédric Chauve, Laetitia Bourgeade

Proceedings of the String Processing and Information Retrieval, 2015

Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples.

Andrew W. McPherson, Andrew Roth, Cédric Chauve, Süleyman Cenk Sahinalp

Proceedings of the Research in Computational Molecular Biology, 2015

Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material.

Ashok Rajaraman, Cédric Chauve, Yann Ponty

Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

2014

Polytomy refinement for the correction of dubious duplications in gene trees.

Manuel Lafond, Cédric Chauve, Riccardo Dondi, Nadia El-Mabrouk

Bioinform., 2014

2013

FPSAC: fast phylogenetic scaffolding of ancient contigs.

Ashok Rajaraman, Eric Tannier, Cédric Chauve

Bioinform., 2013

Hypergraph Covering Problems Motivated by Genome Assembly Questions.

Cédric Chauve, Murray Patterson, Ashok Rajaraman

Proceedings of the Combinatorial Algorithms - 24th International Workshop, 2013

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later.

Cédric Chauve, Nadia El-Mabrouk, Laurent Guéguen, Magali Semeria, Eric Tannier

Proceedings of the Models and Algorithms for Genome Evolution, 2013

The Potential of Family-Free Genome Comparison.

Marília D. V. Braga, Cédric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler

Proceedings of the Models and Algorithms for Genome Evolution, 2013

2012

An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework.

Jean-Philippe Doyon, Sylvie Hamel, Cédric Chauve

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Efficient chaining of seeds in ordered trees.

Julien Allali, Cédric Chauve, Pascal Ferraro, Anne-Laure Gaillard

J. Discrete Algorithms, 2012

A tight bound on the length of odd cycles in the incompatibility graph of a non-C1P matrix.

Mehrnoush Malekesmaeili, Cédric Chauve, Tamon Stephen

Inf. Process. Lett., 2012

Hardness results on the gapped consecutive-ones property problem.

Ján Manuch, Murray Patterson, Cédric Chauve

Discret. Appl. Math., 2012

Average-case analysis of perfect sorting by reversals (Journal Version)

Mathilde Bouvel, Cédric Chauve, Marni Mishna, Dominique Rossin

CoRR, 2012

Linearization of ancestral multichromosomal genomes.

Ján Manuch, Murray Patterson, Roland Wittler, Cédric Chauve, Eric Tannier

BMC Bioinform., 2012

ANGES: reconstructing ANcestral GEnomeS maps.

Bradley R. Jones, Ashok Rajaraman, Eric Tannier, Cédric Chauve

Bioinform., 2012

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.

Julien Allali, Cédric Saule, Cédric Chauve, Yves D'Aubenton-Carafa, Alain Denise, Christine Drevet, Pascal Ferraro, Daniel Gautheret, Claire Herrbach, Fabrice Leclerc, Antoine de Monte, Aïda Ouangraoua, Marie-France Sagot, Michel Termier, Claude Thermes, Hélène Touzet

Adv. Bioinformatics, 2012

2011

A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes.

Aïda Ouangraoua, Valentin Guignon, Sylvie Hamel, Cédric Chauve

Theor. Comput. Sci., 2011

A 2-Approximation for the Minimum Duplication Speciation Problem.

Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve

J. Comput. Biol., 2011

Average-Case Analysis of Perfect Sorting by Reversals.

Mathilde Bouvel, Cédric Chauve, Marni Mishna, Dominique Rossin

Discret. Math. Algorithms Appl., 2011

Tractability results for the Double-Cut-and-Join circular median problem

Ahmad Mahmoody-Ghaidary, Cédric Chauve, Ladislav Stacho

CoRR, 2011

Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes.

Roland Wittler, Cédric Chauve

BMC Bioinform., 2011

Reconstructing the architecture of the ancestral amniote genome.

Aïda Ouangraoua, Eric Tannier, Cédric Chauve

Bioinform., 2011

Mapping ancestral genomes with massive gene loss: A matrix sandwich problem.

Haris Gavranovic, Cédric Chauve, Jérôme Salse, Eric Tannier

Bioinform., 2011

Tractability Results for the Consecutive-Ones Property with Multiplicity.

Cédric Chauve, Ján Manuch, Murray Patterson, Roland Wittler

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

2010

Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction.

Cédric Chauve, Utz-Uwe Haus, Tamon Stephen, Vivija P. You

J. Comput. Biol., 2010

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II.

Cédric Chauve, Haris Gavranovic, Aïda Ouangraoua, Eric Tannier

J. Comput. Biol., 2010

An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model.

Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve

Proceedings of the Comparative Genomics - International Workshop, 2010

Breakpoint Distance and PQ-Trees.

Haitao Jiang, Cédric Chauve, Binhai Zhu

Proceedings of the Combinatorial Pattern Matching, 21st Annual Symposium, 2010

2009

Space of Gene/Species Trees Reconciliations and Parsimonious Models.

Jean-Philippe Doyon, Cédric Chauve, Sylvie Hamel

J. Comput. Biol., 2009

Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes.

Sèverine Bérard, Annie Chateau, Cédric Chauve, Christophe Paul, Eric Tannier

J. Comput. Biol., 2009

On the Gapped Consecutive-Ones Property.

Cédric Chauve, Ján Manuch, Murray Patterson

Electron. Notes Discret. Math., 2009

Hardness Results for the Gapped Consecutive-Ones Property

Cédric Chauve, Ján Manuch, Murray Patterson

CoRR, 2009

A 3-approximation algorithm for computing a parsimonious first speciation in the gene duplication model

Cédric Chauve, Aïda Ouangraoua

CoRR, 2009

New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees.

Cédric Chauve, Nadia El-Mabrouk

Proceedings of the Research in Computational Molecular Biology, 2009

Prediction of Contiguous Regions in the Amniote Ancestral Genome.

Aïda Ouangraoua, Frédéric Boyer, Andrew W. McPherson, Eric Tannier, Cédric Chauve

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

2008

Computing Common Intervals of K Permutations, with Applications to Modular Decomposition of Graphs.

Anne Bergeron, Cédric Chauve, Fabien de Montgolfier, Mathieu Raffinot

SIAM J. Discret. Math., 2008

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes.

Cédric Chauve, Eric Tannier

PLoS Comput. Biol., 2008

Gene Family Evolution by Duplication, Speciation, and Loss.

Cédric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk

J. Comput. Biol., 2008

A more efficient algorithm for perfect sorting by reversals.

Sèverine Bérard, Cédric Chauve, Christophe Paul

Inf. Process. Lett., 2008

Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations.

Jean-Philippe Doyon, Cédric Chauve, Sylvie Hamel

Proceedings of the Comparative Genomics, International Workshop, 2008

Perfect DCJ Rearrangement.

Sèverine Bérard, Annie Chateau, Cédric Chauve, Christophe Paul, Eric Tannier

Proceedings of the Comparative Genomics, International Workshop, 2008

2007

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

Guillaume Blin, Cédric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette

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

Perfect Sorting by Reversals Is Not Always Difficult.

Sèverine Bérard, Anne Bergeron, Cédric Chauve, Christophe Paul

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

FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring.

Guylaine Poisson, Cédric Chauve, Xin Chen, Anne Bergeron

Genom. Proteom. Bioinform., 2007

Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract).

Cédric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk

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

Exploring Genome Rearrangements using Virtual Hybridization.

Mahdi Belcaid, Anne Bergeron, Annie Chateau, Cédric Chauve, Yannick Gingras, Guylaine Poisson, M. Vendette

Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006

Inferring Positional Homologs with Common Intervals of Sequences.

Guillaume Blin, Annie Chateau, Cédric Chauve, Yannick Gingras

Proceedings of the Comparative Genomics, 2006

Genomes Containing Duplicates Are Hard to Compare.

Cédric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette

Proceedings of the Computational Science, 2006

2005

An Edit Distance Between RNA Stem-Loops.

Valentin Guignon, Cédric Chauve, Sylvie Hamel

Proceedings of the String Processing and Information Retrieval, 2005

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

Guillaume Blin, Cédric Chauve, Guillaume Fertin

Proceedings of the Comparative Genomics, 2005

Computing Common Intervals of <i>K</i> Permutations, with Applications to Modular Decomposition of Graphs.

Anne Bergeron, Cédric Chauve, Fabien de Montgolfier, Mathieu Raffinot

Proceedings of the Algorithms, 2005

2004

On maximal instances for the original syntenic distance.

Cédric Chauve, Guillaume Fertin

Theor. Comput. Sci., 2004

Reconstructing Ancestral Gene Orders Using Conserved Intervals.

Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cédric Chauve

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Conservation of Combinatorial Structures in Evolution Scenarios.

Sèverine Bérard, Anne Bergeron, Cédric Chauve

Proceedings of the Comparative Genomics, 2004

2003

Two bijective proofs for the arborescent form of the Good-Lagrange formula and some applications to colored rooted trees and cacti.

Michel Bousquet, Cédric Chauve, Gilbert Labelle, Pierre Leroux

Theor. Comput. Sci., 2003

A Bijection Between Planar Constellations and Some Colored Lagrangian Trees.

Cédric Chauve

Discret. Math. Theor. Comput. Sci., 2003

2002

Tree pattern matching with a more general notion of occurrence of the pattern.

Cédric Chauve

Inf. Process. Lett., 2002

A geometric version of the Robinson-Schensted correspondence for skew oscillating tableaux.

Cédric Chauve, Serge Dulucq

Discret. Math., 2002

Tree Pattern Matching for Linear Static Terms.

Cédric Chauve

Proceedings of the String Processing and Information Retrieval, 2002

2001

Enumerating Alternating Trees.

Cédric Chauve, Serge Dulucq, Andrew Rechnitzer

J. Comb. Theory A, 2001

2000

Structures arborescentes : problèmes algorithmiques et combinatoires. (Tree-like structures: algorithmics and combinatorial problems).

Cédric Chauve

PhD thesis, 2000