Graph-Theoretic Barcode Ordering Model for Linked-Reads
WABI 2020 Dufresne Y, Sun C, Marijon P, Lavenier D, Chauve C, Chikhi R Considering a set of intervals on the real line, an interval...
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Jul 1, 2020
ARIAweb: a server for automated NMR structure calculation
Nucleic Acids Res Fabrice Allain, Fabien Mareuil, Hervé Ménager, Michael Nilges, Benjamin Bardiaux. Nuclear magnetic resonance (NMR)...
Jun 30, 2020
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Bioinformatics Marchet C, Iqbal Z, Gautheret D, Salson M, Chikhi R. Motivation: In this work we present REINDEER, a novel computational...
Jun 30, 2020
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing
Brief Bioinform Lima L, Marchet C, Caboche S, da Silva C, Istace B, Aury JM, Touzet H, Chikhi R Motivation Nanopore long-read sequencing...
May 31, 2020
Yacrd and fpa: upstream tools for long-read genome assembly
Bioinformatics Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré Motivation: Genome assembly is increasingly performed on long,...
Apr 30, 2020
A Darwinian Uncertainty Principle
Systematic Biology Olivier Gascuel, Mike Steel Reconstructing ancestral characters and traits along a phylogenetic tree is central to...
Apr 20, 2020
Identification and molecular characterization of the first complete genome sequence
Scientific Reports Fernandez-Garcia MD, Simon-Loriere E, Kebe O, Sakuntabhai A, Ndiaye K Using a metagenomics approach, we have...
Apr 14, 2020
Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics
Phylogenetics in the Genomic Era Zhukova A, Gascuel O, Duchene S, Ayres D, Lemey P, Baele G Viral evolutionary analyses are confronted...
Mar 1, 2020
JASS: command line and web interface for the joint analysis of GWAS results
Nar Genomics and Bioinformatics Julienne H, Lechat P, Guillemot V, Lasry C, Yao C, Araud R, Laville V, Vilhjalmsson B, Ménager H,...
Feb 6, 2020
Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria
Nature Communications Marc Garcia-Garcera & Eduardo P. C. Rocha We test the hypothesis that the frequency and cost of extracellular...
Feb 1, 2020
Genome Assembly and Analysis of the North American Mountain Goat Species-Level Responses
G3 Genes Genomes Genetics Daria Martchenko, Rayan Chikhi, and Aaron B. A. Shafer The North American mountain goat (Oreamnos americanus)...
Jan 24, 2020
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes
Nucleic Acids Research Aude Bernheim, David Bikard, Marie Touchon, Eduardo P C Rocha Prokaryotes use CRISPR–Cas systems for adaptive...
Sep 11, 2019
Highly pathogenic avian influenza H5N8 in south-west France 2016–2017
Epidemics Alessio Andronic, Aurélie Courcoul, Anne Bronner, Axelle Scoizec, Sophie Lebouquin-Leneveu, Claire Guinat, Mathilde C.Paul,...
Aug 1, 2019
PastView: a user-friendly interface to explore ancestral scenarios
BMC Evolutionary Biology François Chevenet, Guillaume Castel, Emmanuelle Jousselin, and Olivier Gascuel. BACKGROUND: Ancestral character...
Jul 18, 2019
Diversification of the type IV filament superfamily into machines for adhesion, protein secretion
Plos Biology Rémi Denise, Sophie S. Abby, Eduardo P. C. Rocha Processes of molecular innovation require tinkering and shifting in the...
May 23, 2019
A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios
Mol Biol Evol. Ishikawa SA, Zhukova A, Iwasaki W, Gascuel O. The reconstruction of ancestral scenarios is widely used to study the...
May 22, 2019
Dynamics of a type 2 secretion system pseudopilus unraveled by complementary approaches
J Biomol NMR Bardiaux B, Cordier F, Brier S, López-Castilla A, Izadi-Pruneyre N, Nilges M. Secretion pili, bacterial fibers responsible...
Apr 28, 2019
Distribution and asymptotic behavior of the phylogenetic transfer distance
Journal of Mathematical Biology Dávila Felipe M, Domelevo Entfellner JB, Lemoine F, Truszkowski J, Gascuel O. The transfer distance (TD)...
Apr 26, 2019
NGPhylogeny.fr: new generation phylogenetic services for non-specialists
Nucleic Acids Research Frédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia,...
Mar 27, 2019
Graph analysis of fragmented long-read bacterial genome assemblies
Bioinformatics Marijon P, Chikhi R, Varré JS. Abstract MOTIVATION: Long-read genome assembly tools are expected to reconstruct bacterial...
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