Timeline

Alexis Criscuolo
Head of Structure
15 Sep 2021
publication

Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae.

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05 Sep 2021
tool

fq2dna

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05 Sep 2021
tool

fqCleanER

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17 Jul 2021
publication

Peptoniphilus nemausensis sp. nov. A new Gram-positive anaerobic coccus isolated from human clinical samples, an emendated description of the genus Peptoniphilus and an evaluation of the taxonomic status of Peptoniphilus species with not validly published names.

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01 Jun 2021
publication

Author Correction: Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda.

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01 Apr 2021
publication

Pseudomonas carbonaria sp. nov., isolated from charcoal.

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01 Apr 2021
publication

Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter.

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16 Mar 2021
publication

Jeotgalicoccus meleagridis sp. nov. isolated from bioaerosol from emissions of a turkey fattening plant and reclassification of Jeotgalicoccus halophilus Liu et al. 2011 as a later heterotypic synonym of Jeotgalicoccus aerolatus Martin et al. 2011.

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30 Nov 2020
publication

Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s.

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20 Nov 2020
project

NeoLIC

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10 Nov 2020
publication

On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference

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14 Oct 2020
publication

Halomonas lysinitropha sp. nov., a novel halophilic bacterium isolated from a hypersaline wetland.

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14 Oct 2020
publication

Flavobacterium salmonis sp. nov. isolated from Atlantic salmon (Salmo salar) and formal proposal to reclassify Flavobacterium spartansii as a later heterotypic synonym of Flavobacterium tructae.

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09 Oct 2020
publication

Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum.

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24 Sep 2020
course

Bioinformatics program for PhD students 2020-2021

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01 Sep 2020
publication

Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher.

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03 Aug 2020
publication

Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda.

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12 Mar 2020
course

Introduction to Molecular Phylogenetics – ENS Paris

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01 Mar 2020
publication

Serratia vespertilionis (García-Fraile et al. 2015) is a later heterotypic synonym of Serratia ficaria (Grimont et al. 1981).

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01 Mar 2020
publication

Arthrobacter ulcerisalmonis sp. nov., isolated from an ulcer of a farmed Atlantic salmon (Salmo salar), and emended description of the genus Arthrobacter sensu lato.

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09 Nov 2019
course

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

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05 Oct 2019
publication

Erratum to “Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.” [Res Microbiol 170 (3) (2019) 165-170]

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03 Oct 2019
publication

Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization

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02 Aug 2019
publication

The population structure of Clostridium tetani deduced from its pan-genome

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01 Aug 2019
publication

The speciation and hybridization history of the genus Salmonella.

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08 Jul 2019
publication

Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences

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01 Jul 2019
publication

Xinfangfangia humi sp. nov., isolated from soil amended with humic acid.

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01 Jul 2019
publication

Xinfangfangia humi sp. nov., isolated from soil amended with humic acid.

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12 Jun 2019
software

JolyTree

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10 Jun 2019
publication

A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

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04 Jun 2019
course

Introduction à la phylogénie moléculaire

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01 Jun 2019
publication

Pigmentiphaga humi sp. nov., isolated from soil amended with humic acid.

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01 Jun 2019
publication

Paracoccus haematequi sp. nov., isolated from horse blood.

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01 May 2019
publication

Filibacter tadaridae sp. nov., isolated from within a guano pile from a colony of Mexican free-tailed bats Tadarida brasiliensis.

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26 Apr 2019
publication

Carriage of a Single Strain of Nontoxigenic Corynebacterium diphtheriae bv. Belfanti (Corynebacterium belfantii) in Four Patients with Cystic Fibrosis

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08 Apr 2019
publication

Paracoccus haematequi sp. nov., isolated from horse blood.

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08 Apr 2019
publication

Pigmentiphaga humi sp. nov., isolated from soil amended with humic acid

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21 Mar 2019
publication

Whole-Genome Sequences of a Cluster of 14 Unidentified Related sp. Strains from Human Clinical Samples and Type Strains of 3 Validated Species

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20 Mar 2019
publication

Filibacter tadaridae sp. nov., isolated from within a guano pile from a colony of Mexican free-tailed bats Tadarida brasiliensis.

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09 Mar 2019
tool

RΕQ: assessing branch supports oƒ a distance-based phylogenetic tree with the rate oƒ elementary quartets

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01 Mar 2019
publication

Two Clostridium perfringens Type E Isolates in France

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25 Feb 2019
publication

Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov

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28 Jan 2019
project

Genomic studies of grouped cases involving rare yeast species

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25 Jan 2019
publication

Meat and Fish as Sources of Extended-Spectrum β-Lactamase-Producing Escherichia coli, Cambodia

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01 Jun 2018
publication

Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough

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24 Apr 2018
publication

Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing.

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05 Apr 2018
publication

Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753).

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28 Mar 2018
team

Expertise group: GIPhy – Genome Informatics and Phylogenetics

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01 Jan 2018
publication

Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov.

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23 Oct 2017
course

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

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01 Oct 2017
publication

Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group.

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01 Sep 2017
publication

Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter.

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04 Jul 2017
news

Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes

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24 May 2017
news

Emerging diseases: a highly mutant strain of the Elizabethkingia bacterium caused an outbreak in Wisconsin

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24 May 2017
publication

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.

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18 May 2017
publication

Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation.

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06 Apr 2017
publication

Molecular characterization of Chlamydia pneumoniae associated to atherosclerosis

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01 Feb 2017
publication

Characterization of Clostridium Baratii Type F Strains Responsible for an Outbreak of Botulism Linked to Beef Meat Consumption in France

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10 Oct 2016
news

A population biology study of Listeria ushers in a new era in listeriosis surveillance

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10 Oct 2016
publication

Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.

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31 Aug 2016
publication

Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes

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27 Jul 2016
publication

Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

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02 Jul 2016
publication

Species- and Strain-Specific Adaptation of the HSP70 Super Family in Pathogenic Trypanosomatids

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06 Jun 2016
team

Mutualized Platform for Microbiology

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01 Mar 2016
publication

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity.

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22 Feb 2016
publication

topIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB

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01 Feb 2016
news

Listeria: identification of hypervirulent strains with placental and cerebral tropism

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15 Oct 2015
publication

Whole genome sequencing to investigate an outbreak of mucormycosis in a burn unit

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05 Oct 2015
software

AlienTrimmer

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15 Sep 2015
software

BMGE: Block Mapping and Gathering with Entropy

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07 Sep 2015
project

ANR TransLeish – Discovery of druggable protein kinases in the protozoan parasite Leishmania donovani using hit compounds identified by phenotypic screening

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31 Aug 2015
project

Genomic taxonomy of bacterial strains: universal nomenclatures for epidemiology and population biology

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31 Aug 2015
publication

Épidémie de mucormycose dans un centre de traitement des brûlés : des biomarqueurs diagnostiques au séquençage complets des souches

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22 Jul 2015
project

Bioinformatics of genome sequencing applied to epidemiological surveillance of infectious agents

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16 Jul 2015
team

Evolutionary Biology of the Microbial Cell

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26 Jun 2015
team

Bioinformatics and Biostatistics HUB

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11 May 2015
team

Microbial Evolutionary Genomics

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01 Nov 2014
publication

Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups

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26 Sep 2014
publication

Development of a multiplex PCR assay for identification of Klebsiella pneumoniae hypervirulent clones of capsular serotype K2

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13 May 2014
publication

AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries

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13 Mar 2014
publication

Draft Genome Sequence of Campylobacter coli Strain IPSID-1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease.

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20 Feb 2014
publication

Campylobacter coli cultured from the stools of a patient with immunoproliferative small intestinal disease

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01 Aug 2013
publication

AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads

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06 Jan 2013
publication

Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

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08 Sep 2011
publication

morePhyML: improving the phylogenetic tree space exploration with PhyML 3

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07 Jun 2011
publication

Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria

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13 Jul 2010
publication

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

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15 Jun 2010
publication

SuperTriplets: a triplet-based supertree approach to phylogenomics

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01 Apr 2010
publication

Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections

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24 Mar 2009
publication

Phylogenetic inference with weighted codon evolutionary distances

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26 Mar 2008
publication

Fast NJ-like algorithms to deal with incomplete distance matrices

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01 Oct 2007
publication

PhySIC: a veto supertree method with desirable properties

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01 Oct 2006
publication

SDM: a fast distance-based approach for (super) tree building in phylogenomics

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