Timeline

Alexis Criscuolo

Head of Structure

16 Oct 2025

project

PARADIGM – Personalised phAge therapy against gRam-negAtive multiDrug resIstant orGanisMs

01 Aug 2025

publication

Expanding species diversity in the monotypic genera Thalassoporum and Tumidithrix (Pseudanabaenales, Cyanobacteriota) with the description of Thalassoporum mexicanum sp. nov. and Tumidithrix helvetica sp. nov.

24 May 2025

publication

Microevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans

01 Feb 2025

publication

Insight on the heterocyte patterning and the proheterocyte division in the toxic cyanobacterium Kaarinaea lacus gen. nov., sp. nov., and its genomic potential for natural products.

01 Feb 2025

publication

Pseudoalteromonas holothuriae sp. nov., isolated from the sea cucumber Holothuria forskali.

08 Jan 2025

team

CRBIP Project Management Office (CRBIP-PMO)

02 Jan 2025

project

ECDC – Temporary Strain Collection for Multidrug-Resistant Bacteria

24 Dec 2024

publication

Description of Cohnella rhizoplanae sp. nov., isolated from the root surface of soybean (Glycine max).

06 Dec 2024

publication

Comment on: Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis Division II strain: an unexpected finding

28 Sep 2023

publication

Increasing Prevalence of Artemisinin-Resistant HRP2-Negative Malaria in Eritrea

20 Jun 2023

publication

Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays

01 Apr 2023

publication

Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov., isolated from the rhizosphere of Zea mays

01 Nov 2022

publication

Neobacillus rhizosphaerae sp. nov., isolated from the rhizosphere, and reclassification of Bacillus dielmonensis as Neobacillus dielmonensis comb. nov.

08 Oct 2022

publication

Viral origin of eukaryotic type IIA DNA topoisomerases

01 Oct 2022

publication

Sutcliffiella rhizosphaerae sp. nov. isolated from roots

23 Sep 2022

publication

Neonatal acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae in the community of a low-income country (NeoLIC): protocol for a household cohort study in Moramanga, Madagascar.

18 Sep 2022

publication

Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root

11 Jul 2022

software

BIGSdb-Pasteur

01 Jul 2022

publication

Bacillus rhizoplanae sp. nov. from maize roots.

14 Jun 2022

publication

A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains

09 May 2022

software

ROCK

08 May 2022

publication

ROCK: digital normalization of whole genome sequencing data

01 May 2022

publication

Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere.

26 Mar 2022

publication

In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.

01 Dec 2021

publication

Leucobacter soli sp. nov., from soil amended with humic acid.

30 Nov 2021

course

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

01 Nov 2021

publication

Devosia equisanguinis sp. nov., isolated from horse blood.

01 Oct 2021

publication

Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays.

15 Sep 2021

publication

Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae.

05 Sep 2021

tool

fq2dna

05 Sep 2021

tool

fqCleanER

01 Aug 2021

publication

Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study.

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.

12 Jun 2021

software

JolyTree

01 Jun 2021

publication

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

01 Apr 2021

publication

Pseudomonas carbonaria sp. nov., isolated from charcoal.

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.

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.

01 Dec 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.

30 Nov 2020

publication

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

20 Nov 2020

project

NeoLIC

10 Nov 2020

publication

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

14 Oct 2020

publication

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

09 Oct 2020

publication

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

24 Sep 2020

course

Bioinformatics program for PhD students 2020-2021

01 Sep 2020

publication

Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher.

03 Aug 2020

publication

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

31 Jul 2020

center

Biological Resource Center of Institut Pasteur (CRBIP)

12 Mar 2020

course

Introduction to Molecular Phylogenetics – ENS Paris

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.

01 Mar 2020

publication

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

09 Nov 2019

course

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

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].

03 Oct 2019

publication

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

02 Aug 2019

publication

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

01 Aug 2019

publication

The speciation and hybridization history of the genus Salmonella.

08 Jul 2019

publication

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

01 Jul 2019

publication

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

10 Jun 2019

publication

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

04 Jun 2019

course

Introduction à la phylogénie moléculaire

01 Jun 2019

publication

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

01 May 2019

publication

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

26 Apr 2019

publication

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

08 Apr 2019

publication

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

08 Apr 2019

publication

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

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

09 Mar 2019

tool

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

01 Mar 2019

publication

Two Clostridium perfringens Type E Isolates in France

25 Feb 2019

publication

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

28 Jan 2019

project

Genomic studies of grouped cases involving rare yeast species

25 Jan 2019

publication

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

01 Jun 2018

publication

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

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.

05 Apr 2018

publication

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

28 Mar 2018

team

Expertise group: GIPhy – Genome Informatics and Phylogenetics

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.

23 Oct 2017

course

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

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.

01 Sep 2017

publication

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

04 Jul 2017

news

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

24 May 2017

news

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

24 May 2017

publication

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

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.

06 Apr 2017

publication

Molecular characterization of Chlamydia pneumoniae associated to atherosclerosis

01 Feb 2017

publication

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

10 Oct 2016

news

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

10 Oct 2016

publication

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

31 Aug 2016

publication

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

27 Jul 2016

publication

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

02 Jul 2016

publication

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

06 Jun 2016

team

Mutualized Platform for Microbiology

01 Mar 2016

publication

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity.

22 Feb 2016

publication

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

01 Feb 2016

news

Listeria: identification of hypervirulent strains with placental and cerebral tropism

15 Oct 2015

publication

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

05 Oct 2015

software

AlienTrimmer

15 Sep 2015

software

BMGE: Block Mapping and Gathering with Entropy

07 Sep 2015

project

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

31 Aug 2015

project

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

31 Aug 2015

publication

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

22 Jul 2015

project

Bioinformatics of genome sequencing applied to epidemiological surveillance of infectious agents

16 Jul 2015

team

Evolutionary Biology of the Microbial Cell

11 May 2015

team

Microbial Evolutionary Genomics

01 Nov 2014

publication

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

26 Sep 2014

publication

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

01 Sep 2014

publication

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

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

13 Mar 2014

publication

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

01 Aug 2013

publication

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

06 Jan 2013

publication

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

08 Sep 2011

publication

morePhyML: improving the phylogenetic tree space exploration with PhyML 3

07 Jun 2011

publication

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

13 Jul 2010

publication

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

15 Jun 2010

publication

SuperTriplets: a triplet-based supertree approach to phylogenomics

01 Apr 2010

publication

Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections

24 Mar 2009

publication

Phylogenetic inference with weighted codon evolutionary distances

26 Mar 2008

publication

Fast NJ-like algorithms to deal with incomplete distance matrices

01 Oct 2007

publication

PhySIC: a veto supertree method with desirable properties

01 Oct 2006

publication

A little guide for advanced search:

PARADIGM – Personalised phAge therapy against gRam-negAtive multiDrug resIstant orGanisMs

Expanding species diversity in the monotypic genera Thalassoporum and Tumidithrix (Pseudanabaenales, Cyanobacteriota) with the description of Thalassoporum mexicanum sp. nov. and Tumidithrix helvetica sp. nov.

Microevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans

Insight on the heterocyte patterning and the proheterocyte division in the toxic cyanobacterium Kaarinaea lacus gen. nov., sp. nov., and its genomic potential for natural products.

Pseudoalteromonas holothuriae sp. nov., isolated from the sea cucumber Holothuria forskali.

CRBIP Project Management Office (CRBIP-PMO)

ECDC – Temporary Strain Collection for Multidrug-Resistant Bacteria

Description of Cohnella rhizoplanae sp. nov., isolated from the root surface of soybean (Glycine max).

Comment on: Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis Division II strain: an unexpected finding

Increasing Prevalence of Artemisinin-Resistant HRP2-Negative Malaria in Eritrea

Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays

Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov., isolated from the rhizosphere of Zea mays

Neobacillus rhizosphaerae sp. nov., isolated from the rhizosphere, and reclassification of Bacillus dielmonensis as Neobacillus dielmonensis comb. nov.

Viral origin of eukaryotic type IIA DNA topoisomerases

Sutcliffiella rhizosphaerae sp. nov. isolated from roots

Neonatal acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae in the community of a low-income country (NeoLIC): protocol for a household cohort study in Moramanga, Madagascar.

Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root

BIGSdb-Pasteur

Bacillus rhizoplanae sp. nov. from maize roots.

A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains

ROCK

ROCK: digital normalization of whole genome sequencing data

Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere.

In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.

Leucobacter soli sp. nov., from soil amended with humic acid.

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

Devosia equisanguinis sp. nov., isolated from horse blood.

Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays.

Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae.

fq2dna

fqCleanER

Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study.

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.

JolyTree

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

Pseudomonas carbonaria sp. nov., isolated from charcoal.

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.

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.

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

NeoLIC

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

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

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

Bioinformatics program for PhD students 2020-2021

Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher.

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

Biological Resource Center of Institut Pasteur (CRBIP)

Introduction to Molecular Phylogenetics – ENS Paris

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

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

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

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].

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

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

The speciation and hybridization history of the genus Salmonella.

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

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

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

Introduction à la phylogénie moléculaire

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

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

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

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

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

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

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

Two Clostridium perfringens Type E Isolates in France

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

Genomic studies of grouped cases involving rare yeast species

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

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

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

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

Expertise group: GIPhy – Genome Informatics and Phylogenetics

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.

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

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.

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

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