Cédric Chauve

ORCID

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 41

Top Venues

CoRR

Bioinform.

IEEE ACM Trans. Comput. Biol. Bioinform.

RECOMB-CG

University of Bordeaux, France (PHD)

Education History

University of Bordeaux, France

PHD

Publications

Cédric Chauve, Caroline Colijn, Louxin Zhang
A Vector Representation for Phylogenetic Trees. CoRR (2024)
Aniket C. Mane, Mahsa Faizrahnemoon, Tomás Vinar, Brona Brejová, Cédric Chauve
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning. Bioinform. 39 (Supplement-1) (2023)
Aniket C. Mane, Mahsa Faizrahnemoon, Cédric Chauve
A Mixed Integer Linear Programming Algorithm for Plasmid Binning. RECOMB-CG (2022)
Cédric Chauve, Marni Mishna, France Paquet-Nadeau
Refined Upper Bounds on the Size of the Condensed Neighbourhood of Sequences. Stringology (2021)
Daniel Doerr, Cédric Chauve
Small Parsimony for Natural Genomes in the DCJ-Indel Model. CoRR (2021)
Daniel Doerr, Cédric Chauve
Small parsimony for natural genomes in the DCJ-indel model. J. Bioinform. Comput. Biol. 19 (6) (2021)
Aniket C. Mane, Manuel Lafond, Pedro Cipriano Feijão, Cédric Chauve
The distance and median problems in the single-cut-or-join model with single-gene duplications. Algorithms Mol. Biol. 15 (1) (2020)
Haitao Jiang, Hong Liu, Cédric Chauve, Binhai Zhu
Breakpoint distance and PQ-trees. Inf. Comput. 275 (2020)
Mohsen Katebi, Pedro Feijão, Julius Booth, Mehrdad Mansouri, Sean La, Alex Sweeten, Reza Miraskarshahi, Matthew Nguyen, Johnathan Wong, William Hsiao, Cédric Chauve, Leonid Chindelevitch
PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals. AlCoB (2020)
Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi
A Graph-Theoretic Barcode Ordering Model for Linked-Reads. WABI (2020)
Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach
Alignment-free clustering of UMI tagged DNA molecules. Bioinform. 35 (11) (2019)
Nina Luhmann, Manuel Lafond, Annelyse Thévenin, Aïda Ouangraoua, Roland Wittler, Cédric Chauve
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (4) (2019)
Robert Müller, Cédric Chauve
HyAsP, a greedy tool for plasmids identification. Bioinform. 35 (21) (2019)
Guo Liang Gan, Elijah Willie, Cédric Chauve, Leonid Chindelevitch
Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework. BMC Bioinform. (20) (2019)
Hua-Ting Yao, Cédric Chauve, Mireille Régnier, Yann Ponty
Exponentially Few RNA Structures are Designable. BCB (2019)
Cédric Chauve, Yann Ponty, Michael Wallner
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models. CoRR (2019)
Mehrdad Mansouri, Julian Booth, Margaryta Vityaz, Cédric Chauve, Leonid Chindelevitch
PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats. WABI (2018)
Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
Aniket C. Mane, Manuel Lafond, Pedro Feijão, Cédric Chauve
The Rooted SCJ Median with Single Gene Duplications. RECOMB-CG (2018)
Manuel Lafond, Cédric Chauve, Nadia El-Mabrouk, Aïda Ouangraoua
Gene Tree Construction and Correction Using SuperTree and Reconciliation. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (5) (2018)
Cédric Chauve, Julien Courtiel, Yann Ponty
Counting, Generating, Analyzing and Sampling Tree Alignments. Int. J. Found. Comput. Sci. 29 (5) (2018)
Cédric Chauve, Jingxue Feng, Liangliang Wang
Detecting Introgression in Anopheles Mosquito Genomes Using a Reconciliation-Based Approach. RECOMB-CG (2018)
Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cédric Chauve, Sèverine Bérard
Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes. BMC Genom. 19 (S2) (2018)
Markus Lux, Ryan Remy Brinkman, Cédric Chauve, Adam Laing, Anna Lorenc, Lucie Abeler-Dörner, Barbara Hammer
flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry. Bioinform. 34 (13) (2018)
Ashok Rajaraman, João Paulo Pereira Zanetti, Ján Manuch, Cédric Chauve
Algorithms and Complexity Results for Genome Mapping Problems. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (2) (2017)
Sean La, Ehsan Haghshenas, Cédric Chauve
LRCstats, a tool for evaluating long reads correction methods. Bioinform. 33 (22) (2017)
Benedikt Löwes, Cédric Chauve, Yann Ponty, Robert Giegerich
The BRaliBase dent - a tale of benchmark design and interpretation. Briefings Bioinform. 18 (2) (2017)
Cédric Chauve, Mark Jones, Manuel Lafond, Céline Scornavacca, Mathias Weller
Constructing a Consensus Phylogeny from a Leaf-Removal Distance (Extended Abstract). SPIRE (2017)
Daniel Doerr, Metin Balaban, Pedro Feijão, Cédric Chauve
The gene family-free median of three. Algorithms Mol. Biol. 12 (1) (2017)
Cédric Chauve, Éric Fusy, Jérémie O. Lumbroso
An Exact Enumeration of Distance-Hereditary Graphs. ANALCO (2017)
Cédric Chauve, Mark Jones, Manuel Lafond, Céline Scornavacca, Mathias Weller
Constructing a Consensus Phylogeny from a Leaf-Removal Distance. CoRR (2017)
Pedro Feijão, Aniket C. Mane, Cédric Chauve
A Tractable Variant of the Single Cut or Join Distance with Duplicated Genes. RECOMB-CG (2017)
Cédric Chauve, Julien Courtiel, Yann Ponty
Counting, Generating and Sampling Tree Alignments. AlCoB (2016)
Nina Luhmann, Annelyse Thévenin, Aïda Ouangraoua, Roland Wittler, Cédric Chauve
The SCJ small parsimony problem for weighted gene adjacencies (Extended version). CoRR (2016)
Daniel Doerr, Pedro Feijão, Metin Balaban, Cédric Chauve
The gene family-free median of three. CoRR (2016)
Nina Luhmann, Annelyse Thévenin, Aïda Ouangraoua, Roland Wittler, Cédric Chauve
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. ISBRA (2016)
Daniel Doerr, Pedro Feijão, Metin Balaban, Cédric Chauve
The Gene Family-Free Median of Three. WABI (2016)
Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve
CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinform. 32 (17) (2016)
Cédric Chauve, Éric Fusy, Jérémie O. Lumbroso
An Exact Enumeration of Distance-Hereditary Graphs. CoRR (2016)
Manuel Lafond, Cédric Chauve, Nadia El-Mabrouk, Aïda Ouangraoua
Gene Tree Construction and Correction using SuperTree and Reconciliation. CoRR (2016)
Edwin Jacox, Cédric Chauve, Gergely J. Szöllosi, Yann Ponty, Céline Scornavacca
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinform. 32 (13) (2016)
Laetitia Bourgeade, Cédric Chauve, Julien Allali
Chaining Sequence/Structure Seeds for Computing RNA Similarity. J. Comput. Biol. 22 (3) (2015)
Julien Allali, Cédric Chauve, Laetitia Bourgeade
Chaining Fragments in Sequences: to Sweep or Not (Extended Abstract). SPIRE (2015)
Julien Allali, Laetitia Bourgeade, Cédric Chauve
Chaining fragments in sequences: to sweep or not. CoRR (2015)
Ashok Rajaraman, Cédric Chauve, Yann Ponty
Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material. ISBRA (2015)
Andrew W. McPherson, Andrew Roth, Gavin Ha, Sohrab P. Shah, Cédric Chauve, Süleyman Cenk Sahinalp
Joint Inference of Genome Structure and Content in Heterogeneous Tumour Samples. CoRR (2015)
Andrew W. McPherson, Andrew Roth, Cédric Chauve, Süleyman Cenk Sahinalp
Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. RECOMB (2015)
Cédric Chauve, Julien Courtiel, Yann Ponty
An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment. CoRR (2015)
Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinform. 16 (S19) (2015)
Laetitia Bourgeade, Julien Allali, Cédric Chauve
Chaining Sequence/Structure Seeds for Computing RNA Similarity. CMSR@ECCB (2014)
Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. BSB (2014)
Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti
Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach. BSB (2014)
Manuel Lafond, Cédric Chauve, Riccardo Dondi, Nadia El-Mabrouk
Polytomy refinement for the correction of dubious duplications in gene trees. Bioinform. 30 (17) (2014)
Ashok Rajaraman, Eric Tannier, Cédric Chauve
FPSAC: fast phylogenetic scaffolding of ancient contigs. Bioinform. 29 (23) (2013)
Ján Manuch, Murray Patterson, Roland Wittler, Cédric Chauve, Eric Tannier
Linearization of ancestral multichromosomal genomes. CTW (2013)
Cédric Chauve, Murray Patterson, Ashok Rajaraman
Hypergraph covering problems motivated by genome assembly questions. CoRR (2013)
Cédric Chauve, Murray Patterson, Ashok Rajaraman
Hypergraph Covering Problems Motivated by Genome Assembly Questions. IWOCA (2013)
Julien Allali, Cédric Chauve, Pascal Ferraro, Anne-Laure Gaillard
Efficient chaining of seeds in ordered trees. J. Discrete Algorithms 14 (2012)
Ján Manuch, Murray Patterson, Roland Wittler, Cédric Chauve, Eric Tannier
Linearization of ancestral multichromosomal genomes. BMC Bioinform. 13 (S-19) (2012)
Bradley R. Jones, Ashok Rajaraman, Eric Tannier, Cédric Chauve
ANGES: reconstructing ANcestral GEnomeS maps. Bioinform. 28 (18) (2012)
Jean-Philippe Doyon, Sylvie Hamel, Cédric Chauve
An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (1) (2012)
Mehrnoush Malekesmaeili, Cédric Chauve, Tamon Stephen
A tight bound on the length of odd cycles in the incompatibility graph of a non-C1P matrix. Inf. Process. Lett. 112 (20) (2012)
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
BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. Adv. Bioinformatics 2012 (2012)
Mathilde Bouvel, Cédric Chauve, Marni Mishna, Dominique Rossin
Average-case analysis of perfect sorting by reversals (Journal Version) CoRR (2012)
Ján Manuch, Murray Patterson, Cédric Chauve
Hardness results on the gapped consecutive-ones property problem. Discret. Appl. Math. 160 (18) (2012)
Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve
A 2-Approximation for the Minimum Duplication Speciation Problem. J. Comput. Biol. 18 (9) (2011)
Haris Gavranovic, Cédric Chauve, Jérôme Salse, Eric Tannier
Mapping ancestral genomes with massive gene loss: A matrix sandwich problem. Bioinform. 27 (13) (2011)
Mathilde Bouvel, Cédric Chauve, Marni Mishna, Dominique Rossin
Average-Case Analysis of Perfect Sorting by Reversals. Discret. Math. Algorithms Appl. 3 (3) (2011)
Ahmad Mahmoody-Ghaidary, Cédric Chauve, Ladislav Stacho
Tractability results for the Double-Cut-and-Join circular median problem CoRR (2011)
Mehrnoush Malekesmaeili, Cédric Chauve, Tamon Stephen
A tight bound on the length of odd cycles in the incompatibility graph of a non-C1P matrix CoRR (2011)
Roland Wittler, Cédric Chauve
Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. BMC Bioinform. 12 (S-9) (2011)
Aïda Ouangraoua, Valentin Guignon, Sylvie Hamel, Cédric Chauve
A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes. Theor. Comput. Sci. 412 (8-10) (2011)
Cédric Chauve, Ján Manuch, Murray Patterson, Roland Wittler
Tractability Results for the Consecutive-Ones Property with Multiplicity. CPM (2011)
Aïda Ouangraoua, Eric Tannier, Cédric Chauve
Reconstructing the architecture of the ancestral amniote genome. Bioinform. 27 (19) (2011)
Cédric Chauve, Utz-Uwe Haus, Tamon Stephen, Vivija P. You
Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction. J. Comput. Biol. 17 (9) (2010)
Julien Allali, Cédric Chauve, Pascal Ferraro, Anne-Laure Gaillard
Efficient Chaining of Seeds in Ordered Trees. IWOCA (2010)
Haitao Jiang, Cédric Chauve, Binhai Zhu
Breakpoint Distance and PQ-Trees. CPM (2010)
Aïda Ouangraoua, Krister M. Swenson, Cédric Chauve
An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. RECOMB-CG (2010)
Cédric Chauve, Haris Gavranovic, Aïda Ouangraoua, Eric Tannier
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II. J. Comput. Biol. 17 (9) (2010)
Cédric Chauve, Aïda Ouangraoua
A 3-approximation algorithm for computing a parsimonious first speciation in the gene duplication model CoRR (2009)
Cédric Chauve, Ján Manuch, Murray Patterson
Hardness Results for the Gapped Consecutive-Ones Property CoRR (2009)
Cédric Chauve, Ján Manuch, Murray Patterson
On the Gapped Consecutive-Ones Property. Electron. Notes Discret. Math. 34 (2009)
Cédric Chauve, Utz-Uwe Haus, Tamon Stephen, Vivija P. You
Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction. RECOMB-CG (2009)
Sèverine Bérard, Annie Chateau, Cédric Chauve, Christophe Paul, Eric Tannier
Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes. J. Comput. Biol. 16 (10) (2009)
Cédric Chauve, Nadia El-Mabrouk
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. RECOMB (2009)
Aïda Ouangraoua, Frédéric Boyer, Andrew W. McPherson, Eric Tannier, Cédric Chauve
Prediction of Contiguous Regions in the Amniote Ancestral Genome. ISBRA (2009)
Mathilde Bouvel, Cédric Chauve, Marni Mishna, Dominique Rossin
Average-case analysis of perfect sorting by reversals CoRR (2009)
Mathilde Bouvel, Cédric Chauve, Marni Mishna, Dominique Rossin
Average-Case Analysis of Perfect Sorting by Reversals. CPM (2009)
Cédric Chauve, Utz-Uwe Haus, Tamon Stephen, Vivija P. You
Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction. CoRR (2009)
Jean-Philippe Doyon, Cédric Chauve, Sylvie Hamel
Space of Gene/Species Trees Reconciliations and Parsimonious Models. J. Comput. Biol. 16 (10) (2009)
Anne Bergeron, Cédric Chauve, Fabien de Montgolfier, Mathieu Raffinot
Computing Common Intervals of K Permutations, with Applications to Modular Decomposition of Graphs. SIAM J. Discret. Math. 22 (3) (2008)
Cédric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk
Gene Family Evolution by Duplication, Speciation, and Loss. J. Comput. Biol. 15 (8) (2008)
Sèverine Bérard, Annie Chateau, Cédric Chauve, Christophe Paul, Eric Tannier
Perfect DCJ Rearrangement. RECOMB-CG (2008)
Sèverine Bérard, Cédric Chauve, Christophe Paul
A more efficient algorithm for perfect sorting by reversals. Inf. Process. Lett. 106 (3) (2008)
Jean-Philippe Doyon, Cédric Chauve, Sylvie Hamel
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations. RECOMB-CG (2008)
Cédric Chauve, Eric Tannier
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes. PLoS Comput. Biol. 4 (11) (2008)
Guylaine Poisson, Cédric Chauve, Xin Chen, Anne Bergeron
FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring. Genom. Proteom. Bioinform. 5 (2) (2007)
Sèverine Bérard, Anne Bergeron, Cédric Chauve, Christophe Paul
Perfect Sorting by Reversals Is Not Always Difficult. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (1) (2007)
Cédric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk
Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract). RECOMB-CG (2007)
Guillaume Blin, Cédric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
Comparing Genomes with Duplications: A Computational Complexity Point of View. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (4) (2007)

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Publication Activity (10 Years)

Top Topics

Top Venues

Cédric Chauve