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List of works by Cedric Chauve

A 2-approximation for the minimum duplication speciation problem

scientific article

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes

scientific article (publication date: November 2008)

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

ANGES: reconstructing ANcestral GEnomeS maps

scientific article

Algorithms and Complexity Results for Genome Mapping Problems

scientific article published on 11 February 2016

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

article

Alignment-free Clustering of UMI Tagged DNA Molecules

article

An Edit Distance Between RNA Stem-Loops

An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework

scientific article

Ancestral gene synteny reconstruction improves extant species scaffolding

scientific article published on 2 October 2015

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

article

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

scientific article (publication date: 2012)

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis

scientific article published on 25 April 2018

Biochemical clustering of monomeric GTPases of the Ras superfamily.

scientific article published on 6 April 2005

Branch-and-bound approach for parsimonious inference of a species tree from a set of gene family trees

scientific article published in January 2011

Chaining sequence/structure seeds for computing RNA similarity

scientific article published on March 2015

CoLoRMap: Correcting Long Reads by Mapping short reads

scientific article

Comparative Methods for Reconstructing Ancient Genome Organization.

scientific article published in January 2018

Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes.

scientific article published on 8 July 2017

Comparing genomes with duplications: a computational complexity point of view

scientific article published in October 2007

Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes

scientific article published in October 2009

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

scientific article

Correction to: ReMixT: clone-specific genomic structure estimation in cancer

scientific article published on 6 October 2017

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

scientific article published on 15 February 2020

Counting, Generating and Sampling Tree Alignments

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

scientific article published on 8 April 2017

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

scientific article published on 17 December 2019

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

scientific article published on 16 December 2015

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

scientific article published on 02 January 2020

FPSAC: fast phylogenetic scaffolding of ancient contigs.

scientific article

FragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring

scientific article published on May 2007

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing

scientific article published in 2022

Gene Tree Construction and Correction using SuperTree and Reconciliation

scientific article

Gene family evolution by duplication, speciation, and loss

scientific article published in October 2008

HASLR: Fast Hybrid Assembly of Long Reads

scientific article published on 25 July 2020

HyAsP, a greedy tool for plasmids identification

scientific article published on 01 November 2019

Identification, expression, and evolutionary analyses of plant lipocalins

scientific article

LRCstats, a tool for evaluating long reads correction methods.

scientific article published on 2 August 2017

Leveraging evolutionary relationships to improve Anopheles genome assemblies

Linearization of ancestral multichromosomal genomes

scientific article

Mapping ancestral genomes with massive gene loss: a matrix sandwich problem ⬇️

scientific article published on July 2011

MentaLiST - A fast MLST caller for large MLST schemes

scientific article published on 10 January 2018

MentaLiST - A fast MLST caller for large MLST schemes

article

Minimal conflicting sets for the consecutive ones property in ancestral genome reconstruction

scientific article published in September 2010

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

scientific article published on 27 November 2014

Perfect sorting by reversals is not always difficult

scientific article published in January 2007

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

scientific article published on 9 May 2018

Polytomy refinement for the correction of dubious duplications in gene trees

scientific article published on September 2014

ReMixT: clone-specific genomic structure estimation in cancer.

scientific article published on 27 July 2017

Reconstructing the architecture of the ancestral amniote genome

scientific article

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

scientific article published on 15 March 2018

Space of gene/species trees reconciliations and parsimonious models

scientific article published in October 2009

The BRaliBase dent-a tale of benchmark design and interpretation

scientific article published on 16 March 2016

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

scholarly article published 31 July 2018

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies

scientific article published in 2018

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

scientific article published on 04 May 2020

The gene family-free median of three

scientific article

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

scientific article published in 2003

Yeast ancestral genome reconstructions: the possibilities of computational methods II.

scientific article

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony

scientific article published on 26 February 2016

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

scientific article published on 15 February 2018

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