Cédric Chauve

Orcid: 0000-0001-9837-1878

Affiliations:
  • Simon Fraser University, Department of Mathematics
  • Université du Québec à Montréal, Computer Science Department


According to our database1, Cédric Chauve authored at least 102 papers between 2000 and 2024.

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Bibliography

2024
A Vector Representation for Phylogenetic Trees.
CoRR, 2024

2023
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.
Bioinform., 2023

2022
A Mixed Integer Linear Programming Algorithm for Plasmid Binning.
Proceedings of the Comparative Genomics - 19th International Conference, 2022

2021
Small parsimony for natural genomes in the DCJ-indel model.
J. Bioinform. Comput. Biol., 2021

Refined Upper Bounds on the Size of the Condensed Neighbourhood of Sequences.
Proceedings of the Prague Stringology Conference 2021, 2021

2020
Breakpoint distance and PQ-trees.
Inf. Comput., 2020

The distance and median problems in the single-cut-or-join model with single-gene duplications.
Algorithms Mol. Biol., 2020

A Graph-Theoretic Barcode Ordering Model for Linked-Reads.
Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals.
Proceedings of the Algorithms for Computational Biology, 2020

2019
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.
CoRR, 2019

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework.
BMC Bioinform., 2019

Alignment-free clustering of UMI tagged DNA molecules.
Bioinform., 2019

HyAsP, a greedy tool for plasmids identification.
Bioinform., 2019

Exponentially Few RNA Structures are Designable.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Gene Tree Construction and Correction Using SuperTree and Reconciliation.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Counting, Generating, Analyzing and Sampling Tree Alignments.
Int. J. Found. Comput. Sci., 2018

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.
BMC Genom., 2018

flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry.
Bioinform., 2018

PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

The Rooted SCJ Median with Single Gene Duplications.
Proceedings of the Comparative Genomics - 16th International Conference, 2018

Detecting Introgression in Anopheles Mosquito Genomes Using a Reconciliation-Based Approach.
Proceedings of the Comparative Genomics - 16th International Conference, 2018

2017
Algorithms and Complexity Results for Genome Mapping Problems.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017

Constructing a Consensus Phylogeny from a Leaf-Removal Distance.
CoRR, 2017

LRCstats, a tool for evaluating long reads correction methods.
Bioinform., 2017

The BRaliBase dent - a tale of benchmark design and interpretation.
Briefings Bioinform., 2017

The gene family-free median of three.
Algorithms Mol. Biol., 2017

Constructing a Consensus Phylogeny from a Leaf-Removal Distance (Extended Abstract).
Proceedings of the String Processing and Information Retrieval, 2017

A Tractable Variant of the Single Cut or Join Distance with Duplicated Genes.
Proceedings of the Comparative Genomics - 15th International Workshop, 2017

An Exact Enumeration of Distance-Hereditary Graphs.
Proceedings of the Fourteenth Workshop on Analytic Algorithmics and Combinatorics, 2017

2016
The SCJ small parsimony problem for weighted gene adjacencies (Extended version).
CoRR, 2016

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.
Bioinform., 2016

CoLoRMap: Correcting Long Reads by Mapping short reads.
Bioinform., 2016

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.
Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

Counting, Generating and Sampling Tree Alignments.
Proceedings of the Algorithms for Computational Biology - Third International Conference, 2016

2015
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.
BMC Bioinform., December, 2015

Chaining Sequence/Structure Seeds for Computing RNA Similarity.
J. Comput. Biol., 2015

Joint Inference of Genome Structure and Content in Heterogeneous Tumour Samples.
CoRR, 2015

An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment.
CoRR, 2015

Chaining fragments in sequences: to sweep or not.
CoRR, 2015

Chaining Fragments in Sequences: to Sweep or Not (Extended Abstract).
Proceedings of the String Processing and Information Retrieval, 2015

Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples.
Proceedings of the Research in Computational Molecular Biology, 2015

Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

2014
Polytomy refinement for the correction of dubious duplications in gene trees.
Bioinform., 2014

2013
FPSAC: fast phylogenetic scaffolding of ancient contigs.
Bioinform., 2013

Hypergraph Covering Problems Motivated by Genome Assembly Questions.
Proceedings of the Combinatorial Algorithms - 24th International Workshop, 2013

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later.
Proceedings of the Models and Algorithms for Genome Evolution, 2013

The Potential of Family-Free Genome Comparison.
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.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Efficient chaining of seeds in ordered trees.
J. Discrete Algorithms, 2012

A tight bound on the length of odd cycles in the incompatibility graph of a non-C1P matrix.
Inf. Process. Lett., 2012

Hardness results on the gapped consecutive-ones property problem.
Discret. Appl. Math., 2012

Average-case analysis of perfect sorting by reversals (Journal Version)
CoRR, 2012

Linearization of ancestral multichromosomal genomes.
BMC Bioinform., 2012

ANGES: reconstructing ANcestral GEnomeS maps.
Bioinform., 2012

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.
Adv. Bioinformatics, 2012

2011
A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes.
Theor. Comput. Sci., 2011

A 2-Approximation for the Minimum Duplication Speciation Problem.
J. Comput. Biol., 2011

Average-Case Analysis of Perfect Sorting by Reversals.
Discret. Math. Algorithms Appl., 2011

Tractability results for the Double-Cut-and-Join circular median problem
CoRR, 2011

Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes.
BMC Bioinform., 2011

Reconstructing the architecture of the ancestral amniote genome.
Bioinform., 2011

Mapping ancestral genomes with massive gene loss: A matrix sandwich problem.
Bioinform., 2011

Tractability Results for the Consecutive-Ones Property with Multiplicity.
Proceedings of the Combinatorial Pattern Matching - 22nd Annual Symposium, 2011

2010
Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction.
J. Comput. Biol., 2010

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II.
J. Comput. Biol., 2010

An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model.
Proceedings of the Comparative Genomics - International Workshop, 2010

Breakpoint Distance and PQ-Trees.
Proceedings of the Combinatorial Pattern Matching, 21st Annual Symposium, 2010

2009
Space of Gene/Species Trees Reconciliations and Parsimonious Models.
J. Comput. Biol., 2009

Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes.
J. Comput. Biol., 2009

On the Gapped Consecutive-Ones Property.
Electron. Notes Discret. Math., 2009

Hardness Results for the Gapped Consecutive-Ones Property
CoRR, 2009

A 3-approximation algorithm for computing a parsimonious first speciation in the gene duplication model
CoRR, 2009

New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees.
Proceedings of the Research in Computational Molecular Biology, 2009

Prediction of Contiguous Regions in the Amniote Ancestral Genome.
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.
SIAM J. Discret. Math., 2008

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes.
PLoS Comput. Biol., 2008

Gene Family Evolution by Duplication, Speciation, and Loss.
J. Comput. Biol., 2008

A more efficient algorithm for perfect sorting by reversals.
Inf. Process. Lett., 2008

Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations.
Proceedings of the Comparative Genomics, International Workshop, 2008

Perfect DCJ Rearrangement.
Proceedings of the Comparative Genomics, International Workshop, 2008

2007
Comparing Genomes with Duplications: A Computational Complexity Point of View.
IEEE ACM Trans. Comput. Biol. Bioinform., 2007

Perfect Sorting by Reversals Is Not Always Difficult.
IEEE ACM Trans. Comput. Biol. Bioinform., 2007

FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring.
Genom. Proteom. Bioinform., 2007

Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract).
Proceedings of the Comparative Genomics, RECOMB 2007 International Workshop, 2007

Exploring Genome Rearrangements using Virtual Hybridization.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006
Inferring Positional Homologs with Common Intervals of Sequences.
Proceedings of the Comparative Genomics, 2006

Genomes Containing Duplicates Are Hard to Compare.
Proceedings of the Computational Science, 2006

2005
An Edit Distance Between RNA Stem-Loops.
Proceedings of the String Processing and Information Retrieval, 2005

Genes Order and Phylogenetic Reconstruction: Application to <i>gamma</i>-Proteobacteria.
Proceedings of the Comparative Genomics, 2005

Computing Common Intervals of <i>K</i> Permutations, with Applications to Modular Decomposition of Graphs.
Proceedings of the Algorithms, 2005

2004
On maximal instances for the original syntenic distance.
Theor. Comput. Sci., 2004

Reconstructing Ancestral Gene Orders Using Conserved Intervals.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Conservation of Combinatorial Structures in Evolution Scenarios.
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.
Theor. Comput. Sci., 2003

A Bijection Between Planar Constellations and Some Colored Lagrangian Trees.
Discret. Math. Theor. Comput. Sci., 2003

2002
Tree pattern matching with a more general notion of occurrence of the pattern.
Inf. Process. Lett., 2002

A geometric version of the Robinson-Schensted correspondence for skew oscillating tableaux.
Discret. Math., 2002

Tree Pattern Matching for Linear Static Terms.
Proceedings of the String Processing and Information Retrieval, 2002

2001
Enumerating Alternating Trees.
J. Comb. Theory A, 2001

2000
Structures arborescentes : problèmes algorithmiques et combinatoires. (Tree-like structures: algorithmics and combinatorial problems).
PhD thesis, 2000


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