Structures arborescentes : problèmes algorithmiques et combinatoires. (Tree-like structures: algorithmics and combinatorial problems). - Cédric Chauve (2000)

Enumerating Alternating Trees. - Cédric Chauve; Serge Dulucq; Andrew Rechnitzer (J. Comb. Theory A, 2001)

Tree Pattern Matching for Linear Static Terms. - Cédric Chauve (SPIRE, 2002)

A geometric version of the Robinson-Schensted correspondence for skew oscillating tableaux. - Cédric Chauve; Serge Dulucq (Discret. Math., 2002)

Tree pattern matching with a more general notion of occurrence of the pattern. - Cédric Chauve (Inf. Process. Lett., 2002)

A Bijection Between Planar Constellations and Some Colored Lagrangian Trees. - Cédric Chauve (Discret. Math. Theor. Comput. Sci., 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)

Conservation of Combinatorial Structures in Evolution Scenarios. - Sèverine Bérard; Anne Bergeron; Cédric Chauve (Comparative Genomics, 2004)

Reconstructing Ancestral Gene Orders Using Conserved Intervals. - Anne Bergeron; Mathieu Blanchette; Annie Chateau; Cédric Chauve (WABI, 2004)

On maximal instances for the original syntenic distance. - Cédric Chauve; Guillaume Fertin (Theor. Comput. Sci., 2004)

Computing Common Intervals of K Permutations, with Applications to Modular Decomposition of Graphs. - Anne Bergeron; Cédric Chauve; Fabien de Montgolfier; Mathieu Raffinot (ESA, 2005)

Genes Order and Phylogenetic Reconstruction: Application to gamma-Proteobacteria. - Guillaume Blin; Cédric Chauve; Guillaume Fertin (Comparative Genomics, 2005)

An Edit Distance Between RNA Stem-Loops. - Valentin Guignon; Cédric Chauve; Sylvie Hamel (SPIRE, 2005)

Genomes Containing Duplicates Are Hard to Compare. - Cédric Chauve; Guillaume Fertin; Romeo Rizzi; Stéphane Vialette (International Conference on Computational Science (2), 2006)

Inferring Positional Homologs with Common Intervals of Sequences. - Guillaume Blin; Annie Chateau; Cédric Chauve; Yannick Gingras (Comparative Genomics, 2006)

Exploring Genome Rearrangements using Virtual Hybridization. - Mahdi Belcaid; Anne Bergeron; Annie Chateau; Cédric Chauve; Yannick Gingras; Guylaine Poisson; M. Vendette (APBC, 2007)

Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract). - Cédric Chauve; Jean-Philippe Doyon; Nadia El-Mabrouk (RECOMB-CG, 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)

Perfect Sorting by Reversals Is Not Always Difficult. - Sèverine Bérard; Anne Bergeron; Cédric Chauve; Christophe Paul (IEEE ACM Trans. Comput. Biol. Bioinform., 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 DCJ Rearrangement. - Sèverine Bérard; Annie Chateau; Cédric Chauve; Christophe Paul; Eric Tannier (RECOMB-CG, 2008)

Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations. - Jean-Philippe Doyon; Cédric Chauve; Sylvie Hamel (RECOMB-CG, 2008)

A more efficient algorithm for perfect sorting by reversals. - Sèverine Bérard; Cédric Chauve; Christophe Paul (Inf. Process. Lett., 2008)

Gene Family Evolution by Duplication, Speciation, and Loss. - Cédric Chauve; Jean-Philippe Doyon; Nadia El-Mabrouk (J. Comput. Biol., 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)

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)

Prediction of Contiguous Regions in the Amniote Ancestral Genome. - Aïda Ouangraoua; Frédéric Boyer; Andrew W. McPherson; Eric Tannier; Cédric Chauve (ISBRA, 2009)

New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. - Cédric Chauve; Nadia El-Mabrouk (RECOMB, 2009)

A 3-approximation algorithm for computing a parsimonious first speciation in the gene duplication model - Cédric Chauve; Aïda Ouangraoua (CoRR, 2009)

Hardness Results for the Gapped Consecutive-Ones Property - Cédric Chauve; Ján Manuch; Murray Patterson (CoRR, 2009)

On the Gapped Consecutive-Ones Property. - Cédric Chauve; Ján Manuch; Murray Patterson (Electron. Notes Discret. Math., 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)

Space of Gene/Species Trees Reconciliations and Parsimonious Models. - Jean-Philippe Doyon; Cédric Chauve; Sylvie Hamel (J. Comput. Biol., 2009)

Breakpoint Distance and PQ-Trees. - Haitao Jiang; Cédric Chauve; Binhai Zhu (CPM, 2010)

An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. - Aïda Ouangraoua; Krister M. Swenson; Cédric Chauve (RECOMB-CG, 2010)

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II. - Cédric Chauve; Haris Gavranovic; Aïda Ouangraoua; Eric Tannier (J. Comput. Biol., 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)

Tractability Results for the Consecutive-Ones Property with Multiplicity. - Cédric Chauve; Ján Manuch; Murray Patterson; Roland Wittler (CPM, 2011)

Mapping ancestral genomes with massive gene loss: A matrix sandwich problem. - Haris Gavranovic; Cédric Chauve; Jérôme Salse; Eric Tannier (Bioinform., 2011)

Reconstructing the architecture of the ancestral amniote genome. - Aïda Ouangraoua; Eric Tannier; Cédric Chauve (Bioinform., 2011)

Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. - Roland Wittler; Cédric Chauve (BMC Bioinform., 2011)

Tractability results for the Double-Cut-and-Join circular median problem - Ahmad Mahmoody-Ghaidary; Cédric Chauve; Ladislav Stacho (CoRR, 2011)

Average-Case Analysis of Perfect Sorting by Reversals. - Mathilde Bouvel; Cédric Chauve; Marni Mishna; Dominique Rossin (Discret. Math. Algorithms Appl., 2011)

A 2-Approximation for the Minimum Duplication Speciation Problem. - Aïda Ouangraoua; Krister M. Swenson; Cédric Chauve (J. Comput. Biol., 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)

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; et al. (Adv. Bioinformatics, 2012)

ANGES: reconstructing ANcestral GEnomeS maps. - Bradley R. Jones; Ashok Rajaraman; Eric Tannier; Cédric Chauve (Bioinform., 2012)

Linearization of ancestral multichromosomal genomes. - Ján Manuch; Murray Patterson; Roland Wittler; Cédric Chauve; Eric Tannier (BMC Bioinform., 2012)

Average-case analysis of perfect sorting by reversals (Journal Version) - Mathilde Bouvel; Cédric Chauve; Marni Mishna; Dominique Rossin (CoRR, 2012)

Hardness results on the gapped consecutive-ones property problem. - Ján Manuch; Murray Patterson; Cédric Chauve (Discret. Appl. Math., 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)

Efficient chaining of seeds in ordered trees. - Julien Allali; Cédric Chauve; Pascal Ferraro; Anne-Laure Gaillard (J. Discrete Algorithms, 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)

The Potential of Family-Free Genome Comparison. - Marília D. V. Braga; Cédric Chauve; Daniel Doerr; Katharina Jahn 001; Jens Stoye; Annelyse Thévenin; Roland Wittler (Models and Algorithms for Genome Evolution, 2013)

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later. - Cédric Chauve; Nadia El-Mabrouk; Laurent Guéguen; Magali Semeria; Eric Tannier (Models and Algorithms for Genome Evolution, 2013)

Hypergraph Covering Problems Motivated by Genome Assembly Questions. - Cédric Chauve; Murray Patterson; Ashok Rajaraman (IWOCA, 2013)

FPSAC: fast phylogenetic scaffolding of ancient contigs. - Ashok Rajaraman; Eric Tannier; Cédric Chauve (Bioinform., 2013)

Polytomy refinement for the correction of dubious duplications in gene trees. - Manuel Lafond; Cédric Chauve; Riccardo Dondi; Nadia El-Mabrouk (Bioinform., 2014)

Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material. - Ashok Rajaraman; Cédric Chauve; Yann Ponty (ISBRA, 2015)

Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. - Andrew W. McPherson; Andrew Roth; Cédric Chauve; Süleyman Cenk Sahinalp (RECOMB, 2015)

Chaining Fragments in Sequences: to Sweep or Not (Extended Abstract). - Julien Allali; Cédric Chauve; Laetitia Bourgeade (SPIRE, 2015)

Chaining fragments in sequences: to sweep or not. - Julien Allali; Laetitia Bourgeade; Cédric Chauve (CoRR, 2015)

An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment. - Cédric Chauve; Julien Courtiel; Yann Ponty (CoRR, 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)

Chaining Sequence/Structure Seeds for Computing RNA Similarity. - Laetitia Bourgeade; Cédric Chauve; Julien Allali (J. Comput. Biol., 2015)

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. - Cédric Chauve; Yann Ponty; João Paulo Pereira Zanetti (BMC Bioinform., 2015)

Counting, Generating and Sampling Tree Alignments. - Cédric Chauve; Julien Courtiel; Yann Ponty (AlCoB, 2016)

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. - Nina Luhmann; Annelyse Thévenin; Aïda Ouangraoua; Roland Wittler; Cédric Chauve (ISBRA, 2016)

CoLoRMap: Correcting Long Reads by Mapping short reads. - Ehsan Haghshenas; Faraz Hach; Süleyman Cenk Sahinalp; Cédric Chauve (Bioinform., 2016)

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. - Edwin Jacox; Cédric Chauve; Gergely J. Szöllosi; Yann Ponty; Céline Scornavacca (Bioinform., 2016)

The SCJ small parsimony problem for weighted gene adjacencies (Extended version). - Nina Luhmann; Annelyse Thévenin; Aïda Ouangraoua; Roland Wittler; Cédric Chauve (CoRR, 2016)

An Exact Enumeration of Distance-Hereditary Graphs. - Cédric Chauve; Éric Fusy; Jérémie O. Lumbroso (ANALCO, 2017)

A Tractable Variant of the Single Cut or Join Distance with Duplicated Genes. - Pedro Feijão; Aniket C. Mane; Cédric Chauve (RECOMB-CG, 2017)

Constructing a Consensus Phylogeny from a Leaf-Removal Distance (Extended Abstract). - Cédric Chauve; Mark Jones 001; Manuel Lafond; Céline Scornavacca; Mathias Weller (SPIRE, 2017)

The gene family-free median of three. - Daniel Doerr; Metin Balaban; Pedro Feijão; Cédric Chauve (Algorithms Mol. Biol., 2017)

The BRaliBase dent - a tale of benchmark design and interpretation. - Benedikt Löwes; Cédric Chauve; Yann Ponty; Robert Giegerich (Briefings Bioinform., 2017)

LRCstats, a tool for evaluating long reads correction methods. - Sean La; Ehsan Haghshenas; Cédric Chauve (Bioinform., 2017)

Constructing a Consensus Phylogeny from a Leaf-Removal Distance. - Cédric Chauve; Mark Jones 001; Manuel Lafond; Céline Scornavacca; Mathias Weller (CoRR, 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)

Detecting Introgression in Anopheles Mosquito Genomes Using a Reconciliation-Based Approach. - Cédric Chauve; Jingxue Feng; Liangliang Wang (RECOMB-CG, 2018)

The Rooted SCJ Median with Single Gene Duplications. - Aniket C. Mane; Manuel Lafond; Pedro Feijão; Cédric Chauve (RECOMB-CG, 2018)

PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats. - Mehrdad Mansouri; Julian Booth; Margaryta Vityaz; Cédric Chauve; Leonid Chindelevitch (WABI, 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)

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)

Counting, Generating, Analyzing and Sampling Tree Alignments. - Cédric Chauve; Julien Courtiel; Yann Ponty (Int. J. Found. Comput. Sci., 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)

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)

Exponentially Few RNA Structures are Designable. - Hua-Ting Yao; Cédric Chauve; Mireille Régnier; Yann Ponty (BCB, 2019)

HyAsP, a greedy tool for plasmids identification. - Robert Müller 006; Cédric Chauve (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)

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)

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models. - Cédric Chauve; Yann Ponty; Michael Wallner 001 (CoRR, 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)

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 (AlCoB, 2020)

A Graph-Theoretic Barcode Ordering Model for Linked-Reads. - Yoann Dufresne; Chen Sun 014; Pierre Marijon; Dominique Lavenier; Cédric Chauve; Rayan Chikhi (WABI, 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)

Breakpoint distance and PQ-trees. - Haitao Jiang; Hong Liu; Cédric Chauve; Binhai Zhu (Inf. Comput., 2020)

Refined Upper Bounds on the Size of the Condensed Neighbourhood of Sequences. - Cédric Chauve; Marni Mishna; France Paquet-Nadeau (Stringology, 2021)

Small parsimony for natural genomes in the DCJ-indel model. - Daniel Doerr; Cédric Chauve (J. Bioinform. Comput. Biol., 2021)

A Mixed Integer Linear Programming Algorithm for Plasmid Binning. - Aniket C. Mane; Mahsa Faizrahnemoon; Cédric Chauve (RECOMB-CG, 2022)

PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning. - Aniket C. Mane; Mahsa Faizrahnemoon; Tomás Vinar; Brona Brejová; Cédric Chauve (Bioinform., 2023)

A Vector Representation for Phylogenetic Trees. - Cédric Chauve; Caroline Colijn; Louxin Zhang (CoRR, 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., 2024)

On the size of the neighborhoods of a word. - Cédric Chauve; Louxin Zhang (CoRR, 2025)