N,Title,Authors,Journal,Date,Team,Url
1,"Increasing Prevalence of Artemisinin-Resistant HRP2-Negative Malaria in Eritrea","Selam Mihreteab, Lucien Platon, Araia Berhane, Barbara Stokes, Marian Warsame, Pascal Campagne, Alexis Criscuolo, Laurence Ma, Nathalie Petiot, Cécile Doderer-Lang, Eric Legrand, Kurt Ward, Assefash Zehaie Kassahun, Pascal Ringwald, David Fidock, Didier Ménard","New England Journal of Medicine",'2023-09-28,"Malaria Parasite Biology and Vaccines, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, U1201 – Genetic and molecular basis of host-parasite interactions, Biomics",https://research.pasteur.fr/en/publication/increasing-prevalence-of-artemisinin-resistant-hrp2-negative-malaria-in-eritrea/
2,"Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays","Kämpfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A, McInroy JA, Glaeser SP","Antonie van Leeuwenhoek",'2023-06-20,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/paenibacillus-plantiphilus-sp-nov-from-the-plant-environment-of-zea-mays/
3,"Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov., isolated from the rhizosphere of Zea mays","Kämpfer P, Lipski A, McInroy JA, Clermont D, Lamothe L, Glaeser SP, Criscuolo A, ","International journal of systematic and evolutionary microbiology",'2023-04-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/paenibacillus-auburnensis-sp-nov-and-paenibacillus-pseudetheri-sp-nov-isolated-from-the-rhizosphere-of-zea-mays/
4,"Neobacillus rhizosphaerae sp. nov., isolated from the rhizosphere, and reclassification of Bacillus dielmonensis as Neobacillus dielmonensis comb. nov.","Kämpfer P, Glaeser SP, McInroy JA, Clermont D, Lipski A, Criscuolo A","International Journal of Systematic and Evolutionary Microbiology",'2022-11-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/neobacillus-rhizosphaerae-sp-nov-isolated-from-the-rhizosphere-and-reclassification-of-bacillus-dielmonensis-as-neobacillus-dielmonensis-comb-nov/
5,"Viral origin of eukaryotic type IIA DNA topoisomerases"," Julien Guglielmini, Morgan Gaia, Violette Da Cunha, Alexis Criscuolo, Mart Krupovic, Patrick Forterre","Virus Evolution",'2022-10-08,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Archaeal Virology, Expertise group : PAGE – Protein And Gene Evolution",https://research.pasteur.fr/en/publication/viral-origin-of-eukaryotic-type-iia-dna-topoisomerases/
6,"Sutcliffiella rhizosphaerae sp. nov. isolated from roots","Kämpfer P, Glaeser SP, Lipski A, McInroy JA, Clermont D, Criscuolo A","International journal of systematic and evolutionary microbiology",'2022-10-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/sutcliffiella-rhizosphaerae-sp-nov-isolated-from-roots/
7,"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.","Harimanana A, Rakotondrasoa A, Rivoarilala LO, Criscuolo A, Opatowski L, Rakotomanana EFN, Herindrainy P, Collard JM, Crucitti T, Huynh BT, , ","BMJ open",'2022-09-23,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Epidemiology and Modelling of Antibacterial Evasion (EMAE)",https://research.pasteur.fr/en/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/
8,"Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root","Peter Kämpfer, André Lipski, Lucie Lamothe, Dominique Clermont, Alexis Criscuolo, John A. McInroy, Stefanie P. Glaeser ","Archives of Microbiology volume",'2022-09-18,"Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP), Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/publication/paenibacillus-allorhizoplanae-sp-nov-from-the-rhizoplane-of-a-zea-mays-root/
9,"Bacillus rhizoplanae sp. nov. from maize roots.","Kämpfer P, Lipski A, McInroy JA, Clermont D, Criscuolo A, Glaeser SP, ","International journal of systematic and evolutionary microbiology",'2022-07-01,"Mutualized Platform for Microbiology, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/bacillus-rhizoplanae-sp-nov-from-maize-roots/
10,"A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains","Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S","Molecular biology and evolution",'2022-06-14,"Biodiversity and Epidemiology of Bacterial Pathogens, Bioinformatics and Biostatistics HUB, Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/publication/a-dual-barcoding-approach-to-bacterial-strain-nomenclature-genomic-taxonomy-of-klebsiella-pneumoniae-strains/
11,"ROCK: digital normalization of whole genome sequencing data","Legrand V, Kergrohen T, Joly N, Criscuolo A","Journal of Open Source Software",'2022-05-08,"HPC Core Facility, Bioinformatics and Biostatistics HUB, Mutualized Platform for Microbiology, Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/publication/rock-digital-normalization-of-whole-genome-sequencing-data/
12,"Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere.","Kämpfer P, Glaeser SP, Busse HJ, McInroy JA, Clermont D, Criscuolo A, ","International journal of systematic and evolutionary microbiology",'2022-05-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/pseudoneobacillus-rhizosphaerae-gen-nov-sp-nov-isolated-from-maize-root-rhizosphere/
13,"In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.","Palma F, Mangone I, Janowicz A, Moura A, Chiaverini A, Torresi M, Garofolo G, Criscuolo A, Brisse S, Di Pasquale A, Cammà C, Radomski N, ","BMC genomics",'2022-03-26,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Biodiversity and Epidemiology of Bacterial Pathogens",https://research.pasteur.fr/en/publication/in-vitro-and-in-silico-parameters-for-precise-cgmlst-typing-of-listeria-monocytogenes/
14,"Viral origin of eukaryotic type IIA DNA topoisomerases.","Guglielmini J, Gaia M, Da Cunha V, Criscuolo A, Krupovic M, Forterre P","Virus evolution",'2022-01-01,"Bioinformatics and Biostatistics HUB, Archaeal Virology, UMR6047 – Integrative and Molecular Microbiology",https://research.pasteur.fr/en/publication/viral-origin-of-eukaryotic-type-iia-dna-topoisomerases-2/
15,"Leucobacter soli sp. nov., from soil amended with humic acid.","Kämpfer P, McInroy JA, Clermont D, Neumann-Schaal M, Criscuolo A, Busse HJ, Glaeser SP, ","International journal of systematic and evolutionary microbiology",'2021-12-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/leucobacter-soli-sp-nov-from-soil-amended-with-humic-acid/
16,"Devosia equisanguinis sp. nov., isolated from horse blood.","Kämpfer P, Busse HJ, Clermont D, Criscuolo A, Glaeser SP, ","International journal of systematic and evolutionary microbiology",'2021-11-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/devosia-equisanguinis-sp-nov-isolated-from-horse-blood/
17,"Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays.","Kämpfer P, Busse HJ, McInroy JA, Clermont D, Criscuolo A, Glaeser SP, ","International journal of systematic and evolutionary microbiology",'2021-10-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/paenibacillus-allorhizosphaerae-sp-nov-from-soil-of-the-rhizosphere-of-zea-mays/
18,"Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae.","Guglielmini J, Hennart M, Badell E, Toubiana J, Criscuolo A, Brisse S, ","Journal of clinical microbiology",'2021-09-15,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Biodiversity and Epidemiology of Bacterial Pathogens",https://research.pasteur.fr/en/publication/genomic-epidemiology-and-strain-taxonomy-of-corynebacterium-diphtheriae/
19,"Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study.","Badell E, Alharazi A, Criscuolo A, Almoayed KAA, Lefrancq N, Bouchez V, Guglielmini J, Hennart M, Carmi-Leroy A, Zidane N, Pascal-Perrigault M, Lebreton M, Martini H, Salje H, Toubiana J, Dureab F, Dhabaan G, Brisse S","The Lancet. Microbe",'2021-08-01,"Biodiversity and Epidemiology of Bacterial Pathogens, Bioinformatics and Biostatistics HUB, Mathematical Modelling Of Infectious Diseases, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology",https://research.pasteur.fr/en/publication/ongoing-diphtheria-outbreak-in-yemen-a-cross-sectional-and-genomic-epidemiology-study/
20,"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.","Aujoulat F, Mazuet C, Criscuolo A, Popoff MR, Enault C, Diancourt L, Jumas-Bilak E, Lavigne JP, Marchandin H","Systematic and applied microbiology",'2021-07-17,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/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-sta/
21,"Author Correction: Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda.","Uwimana A, Legrand E, Stokes BH, Ndikumana JM, Warsame M, Umulisa N, Ngamije D, Munyaneza T, Mazarati JB, Munguti K, Campagne P, Criscuolo A, Ariey F, Murindahabi M, Ringwald P, Fidock DA, Mbituyumuremyi A, Menard D, ","Nature medicine",'2021-06-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/author-correction-emergence-and-clonal-expansion-of-in-vitro-artemisinin-resistant-plasmodium-falciparum-kelch13-r561h-mutant-parasites-in-rwanda/
22,"Pseudomonas carbonaria sp. nov., isolated from charcoal.","Kämpfer P, Glaeser SP, McInroy JA, Clermont D, Criscuolo A, Busse HJ, ","International journal of systematic and evolutionary microbiology",'2021-04-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/pseudomonas-carbonaria-sp-nov-isolated-from-charcoal/
23,"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.","Schumann P, Kalensee F, Cao J, Criscuolo A, Clermont D, Köhler JM, Meier-Kolthoff JP, Neumann-Schaal M, Tindall BJ, Pukall R, ","International journal of systematic and evolutionary microbiology",'2021-04-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/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-rua/
24,"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.","Kämpfer P, Busse HJ, Glaeser SP, Clermont D, Criscuolo A, Mietke H, ","International journal of systematic and evolutionary microbiology",'2021-03-16,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/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/
25,"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.","Kämpfer P, Irgang R, Glaeser SP, Busse HJ, Criscuolo A, Clermont D, Avendaño-Herrera R, ","International journal of systematic and evolutionary microbiology",'2020-12-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/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/
26,"Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s.","Mühle E, Abry C, Leclerc P, Goly GM, Criscuolo A, Busse HJ, Kämpfer P, Bernardet JF, Clermont D, Chesneau O, ","International journal of systematic and evolutionary microbiology",'2020-11-30,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/flavobacterium-bizetiae-sp-nov-isolated-from-diseased-freshwater-fish-in-canada-at-the-end-of-the-1970s/
27,"On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference","Criscuolo A",F1000Research,'2020-11-10,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/on-the-transformation-of-minhash-based-uncorrected-distances-into-proper-evolutionary-distances-for-phylogenetic-inference/
28,"Halomonas lysinitropha sp. nov., a novel halophilic bacterium isolated from a hypersaline wetland.","Ramezani M, Pourmohyadini M, Nikou MM, Makzum S, Schumann P, Clermont D, Criscuolo A, Amoozegar MA, Kämpfer P, Spröer C, ","International journal of systematic and evolutionary microbiology",'2020-10-14,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/halomonas-lysinitropha-sp-nov-a-novel-halophilic-bacterium-isolated-from-a-hypersaline-wetland/
29,"Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum.","Kämpfer P, Glaeser SP, McInroy JA, Xu J, Busse HJ, Clermont D, Criscuolo A, ","International journal of systematic and evolutionary microbiology",'2020-10-09,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/flavobacterium-panici-sp-nov-isolated-from-the-rhizosphere-of-the-switchgrass-panicum-virgatum/
30,"Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher.","Menu E, Criscuolo A, Desnos-Ollivier M, Cassagne C, D'Incan E, Furst S, Ranque S, Berger P, Dromer F, ","Emerging infectious diseases",'2020-09-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Archived: Molecular Mycology",https://research.pasteur.fr/en/publication/saprochaete-clavata-outbreak-infecting-cancer-center-through-dishwasher/
31,"Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda.","Uwimana A, Legrand E, Stokes BH, Ndikumana JM, Warsame M, Umulisa N, Ngamije D, Munyaneza T, Mazarati JB, Munguti K, Campagne P, Criscuolo A, Ariey F, Murindahabi M, Ringwald P, Fidock DA, Mbituyumuremyi A, Menard D, ","Nature medicine",'2020-08-03,"Archived: Malaria Genetics and Resistance, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/emergence-and-clonal-expansion-of-in-vitro-artemisinin-resistant-plasmodium-falciparum-kelch13-r561h-mutant-parasites-in-rwanda/
32,"Arthrobacter ulcerisalmonis sp. nov., isolated from an ulcer of a farmed Atlantic salmon (Salmo salar), and emended description of the genus Arthrobacter sensu lato.","Kämpfer P, Busse HJ, Schumann P, Criscuolo A, Clermont D, Irgang R, Poblete-Morales M, Glaeser SP, Avendaño-Herrera R, ","International journal of systematic and evolutionary microbiology",'2020-03-01,"Collection of the Institut Pasteur (CIP), Bioinformatics and Biostatistics HUB, Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/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/
33,"Serratia vespertilionis (García-Fraile et al. 2015) is a later heterotypic synonym of Serratia ficaria (Grimont et al. 1981).","García-Fraile P, Spröer C, Chesneau O, Criscuolo A, Lang E, Clermont D, ","International journal of systematic and evolutionary microbiology",'2020-03-01,"Collection of the Institut Pasteur (CIP), Bioinformatics and Biostatistics HUB, Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/publication/serratia-vespertilionis-garcia-fraile-et-al-2015-is-a-later-heterotypic-synonym-of-serratia-ficaria-grimont-et-al-1981-is-a-later-heterotypic-synonym-of-serratia-ficaria-grimont-et-al-1981/
34,"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].","Rodrigues C, Passet V, Rakotondrasoa A, Diallo TA, Criscuolo A, Brisse S, ","Research in microbiology",'2019-10-05,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Biodiversity and Epidemiology of Bacterial Pathogens",https://research.pasteur.fr/en/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/
35,"Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization","Savin C, Criscuolo A, Guglielmini J, Le Guern AS, Carniel E, Pizarro-Cerdá J, Brisse S","Microbial genomics",'2019-10-03,"Yersinia, Bioinformatics and Biostatistics HUB, Biodiversity and Epidemiology of Bacterial Pathogens, Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/publication/genus-wide-core-genome-multilocus-sequence-typing-for-species-identification-and-strain-characterization/
36,"The population structure of Clostridium tetani deduced from its pan-genome","Chapeton-Montes D, Plourde L, Bouchier C, Ma L, Diancourt L, Criscuolo A, Popoff MR, Brüggemann H","Scientific reports",'2019-08-02,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/the-population-structure-of-clostridium-tetani-deduced-from-its-pan-genome/
37,"The speciation and hybridization history of the genus Salmonella.","Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J, Parkhill J, Thomson NR, Weill FX, Falush D, Brisse S, ","Microbial genomics",'2019-08-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Biodiversity and Epidemiology of Bacterial Pathogens, Enteric Bacterial Pathogens",https://research.pasteur.fr/en/publication/the-speciation-and-hybridization-history-of-the-genus-salmonella/
38,"Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences","Bigot T, Guglielmini J, Criscuolo A","Data in Brief",'2019-07-08,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/simulation-data-for-the-estimation-of-numerical-constants-for-approximating-pairwise-evolutionary-distances-between-amino-acid-sequences/
39,"Xinfangfangia humi sp. nov., isolated from soil amended with humic acid.","Kämpfer P, Busse HJ, McInroy JA, Criscuolo A, Clermont D, Glaeser SP, ","International journal of systematic and evolutionary microbiology",'2019-07-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/xinfangfangia-humi-sp-nov-isolated-from-soil-amended-with-humic-acid/
40,"A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies","Alexis Criscuolo","Research Ideas and Outcomes",'2019-06-10,"Bioinformatics and Biostatistics HUB, Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/publication/a-fast-alignment-free-bioinformatics-procedure-to-infer-accurate-distance-based-phylogenetic-trees-from-genome-assemblies/
41,"Paracoccus haematequi sp. nov., isolated from horse blood.","Kämpfer P, Busse HJ, Galatis H, Criscuolo A, Clermont D, Bizet C, Glaeser SP, ","International journal of systematic and evolutionary microbiology",'2019-06-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/paracoccus-haematequi-sp-nov-isolated-from-horse-blood/
42,"Pigmentiphaga humi sp. nov., isolated from soil amended with humic acid.","Kämpfer P, Busse HJ, Criscuolo A, Bizet C, Clermont D, McInroy JA, Glaeser SP, ","International journal of systematic and evolutionary microbiology",'2019-06-01,"Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/pigmentiphaga-humi-sp-nov-isolated-from-soil-amended-with-humic-acid-2/
43,"Filibacter tadaridae sp. nov., isolated from within a guano pile from a colony of Mexican free-tailed bats Tadarida brasiliensis.","Kämpfer P, Bizet C, Clermont D, Criscuolo A, Kloepper LN, Duncan MB, McInroy JA, Kloepper JW, Schumann P, Glaeser SP, ","International journal of systematic and evolutionary microbiology",'2019-05-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/filibacter-tadaridae-sp-nov-isolated-from-within-a-guano-pile-from-a-colony-of-mexican-free-tailed-bats-tadarida-brasiliensis/
44,"Carriage of a Single Strain of Nontoxigenic Corynebacterium diphtheriae bv. Belfanti (Corynebacterium belfantii) in Four Patients with Cystic Fibrosis","Pivot D, Fanton A, Badell-Ocando E, Benouachkou M, Astruc K, Huet F, Amoureux L, Neuwirth C, Criscuolo A, Aho S, Toubiana J, Brisse S","Journal of clinical microbiology",'2019-04-26,"Biodiversity and Epidemiology of Bacterial Pathogens, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/carriage-of-a-single-strain-of-non-toxigenic-biovar-belfanti-in-four-patients-with-cystic-fibrosis/
45,"Pigmentiphaga humi sp. nov., isolated from soil amended with humic acid","Kämpfer P, Busse HJ, Criscuolo A, Bizet C, Clermont D, McInroy JA, Glaeser SP","International journal of systematic and evolutionary microbiology",'2019-04-08,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/pigmentiphaga-humi-sp-nov-isolated-from-soil-amended-with-humic-acid/
46,"Paracoccus haematequi sp. nov., isolated from horse blood.","Kämpfer P, Busse HJ, Galatis H, Criscuolo A, Clermont D, Bizet C, Glaeser SP.",,'2019-04-08,"Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/paracoccus-haematequi-sp-nov-isolated-from-horse-blood-2/
47,"Whole-Genome Sequences of a Cluster of 14 Unidentified Related sp. Strains from Human Clinical Samples and Type Strains of 3 Validated Species","Aujoulat F, Popoff MR, Diancourt L, Criscuolo A, Jean-Pierre H, Jumas-Bilak E, Marchandin H","Microbiology resource announcements",'2019-03-21,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/whole-genome-sequences-of-a-cluster-of-14-unidentified-related-sp-strains-from-human-clinical-samples-and-type-strains-of-3-validated-species/
48,"Filibacter tadaridae sp. nov., isolated from within a guano pile from a colony of Mexican free-tailed bats Tadarida brasiliensis.","Kämpfer P, Bizet C, Clermont D, Criscuolo A, Kloepper LN, Duncan MB, McInroy JA, Kloepper JW, Schumann P, Glaeser SP.",,'2019-03-20,"Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/filibacter-tadaridae-sp-nov-isolated-from-within-a-guano-pile-from-a-colony-of-mexican-free-tailed-bats-tadarida-brasiliensis-2/
49,"Two Clostridium perfringens Type E Isolates in France","Diancourt L, Sautereau J, Criscuolo A, Popoff MR",Toxins,'2019-03-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/two-type-e-isolates-in-france/
50,"Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.","Rodrigues C, Passet V, Rakotondrasoa A, Diallo TA, Criscuolo A, Brisse S, ","Research in microbiology",'2019-02-25,"Biodiversity and Epidemiology of Bacterial Pathogens, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/description-of-klebsiella-africanensis-sp-nov-klebsiella-variicola-subsp-tropicalensis-subsp-nov-and-klebsiella-variicola-subsp-variicola-subsp-nov/
51,"Meat and Fish as Sources of Extended-Spectrum β-Lactamase-Producing Escherichia coli, Cambodia","Nadimpalli M, Vuthy Y, de Lauzanne A, Fabre L, Criscuolo A, Gouali M, Huynh BT, Naas T, Phe T, Borand L, Jacobs J, Kerléguer A, Piola P, Guillemot D, Le Hello S, Delarocque-Astagneau E","Emerging infectious diseases",'2019-01-25,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Epidemiology and Modelling of Antibacterial Evasion (EMAE), Anthropology and Ecology of Disease Emergence, Epidemiology of Emerging Diseases",https://research.pasteur.fr/en/publication/meat-and-fish-as-sources-of-extended-spectrum-%ce%b2-lactamase-producing-escherichia-coli-cambodia/
52,"Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough","Bouchez V, Guglielmini J, Dazas M, Landier A, Toubiana J, Guillot S, Criscuolo A, Brisse S","Emerging infectious diseases",'2018-06-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Biodiversity and Epidemiology of Bacterial Pathogens",https://research.pasteur.fr/en/publication/genomic-sequencing-of-bordetella-pertussis-for-epidemiology-and-global-surveillance-of-whooping-cough/
53,"Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing.","Garcia-Hermoso D, Criscuolo A, Lee SC, Legrand M, Chaouat M, Denis B, Lafaurie M, Rouveau M, Soler C, Schaal JV, Mimoun M, Mebazaa A, Heitman J, Dromer F, Brisse S, Bretagne S, Alanio A, ",mBio,'2018-04-24,"Archived: Molecular Mycology, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Biodiversity and Epidemiology of Bacterial Pathogens",https://research.pasteur.fr/en/publication/outbreak-of-invasive-wound-mucormycosis-in-a-burn-unit-due-to-multiple-strains-of-mucor-circinelloides-f-circinelloides-resolved-by-whole-genome-sequencing/
54,"Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753).","Criscuolo A, Chesneau O, Clermont D, Bizet C, ","Genome announcements",'2018-04-05,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP), Centre de Ressources Biologiques de l’Institut Pasteur (CRBIP)",https://research.pasteur.fr/en/publication/draft-genome-sequence-of-the-fish-pathogen-flavobacterium-columnare-genomovar-iii-strain-ph-97028-cip-109753/
55,"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.","Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Graziano J, Emery B, Bell M, Loparev V, Juieng P, Gartin J, Bizet C, Clermont D, Criscuolo A, Brisse S, McQuiston JR, ","Antonie van Leeuwenhoek",'2018-01-01,"Mutualized Platform for Microbiology, Biodiversity and Epidemiology of Bacterial Pathogens, Microbial Evolutionary Genomics, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP), Centre de Ressources Biologiques de l’Institut Pasteur (CRBIP)",https://research.pasteur.fr/en/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-bruunian/
56,"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.","Christo-Foroux E, Vallaeys T, Loux V, Dassa E, Deutscher J, Wandersman C, Livernois A, Hot C, Criscuolo A, Dauga C, Clermont D, Chesneau O, ","Systematic and applied microbiology",'2017-10-01,"Mutualized Platform for Microbiology, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/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/
57,"Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter.","Hurtado-Ortiz R, Nazimoudine A, Criscuolo A, Hugon P, Mornico D, Brisse S, Bizet C, Clermont D, ","International journal of systematic and evolutionary microbiology",'2017-09-01,"Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Microbial Evolutionary Genomics, Centre de Ressources Biologiques de l’Institut Pasteur (CRBIP), Expertise group: GIPhy – Genome Informatics and Phylogenetics, Expertise group : SysBio – System Bioinformatics, Collection of the Institut Pasteur (CIP)",https://research.pasteur.fr/en/publication/psychrobacter-pasteurii-and-psychrobacter-piechaudii-sp-nov-two-novel-species-within-the-genus-psychrobacter/
58,"Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.","Perrin A, Larsonneur E, Nicholson AC, Edwards DJ, Gundlach KM, Whitney AM, Gulvik CA, Bell ME, Rendueles O, Cury J, Hugon P, Clermont D, Enouf V, Loparev V, Juieng P, Monson T, Warshauer D, Elbadawi LI, Walters MS, Crist MB, Noble-Wang J, Borlaug G, Rocha EPC, Criscuolo A, Touchon M, Davis JP, Holt KE, McQuiston JR, Brisse S, ","Nature communications",'2017-05-24,"Mutualized Platform for Microbiology, Biodiversity and Epidemiology of Bacterial Pathogens, Microbial Evolutionary Genomics, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Collection of the Institut Pasteur (CIP), Centre de Ressources Biologiques de l’Institut Pasteur (CRBIP)",https://research.pasteur.fr/en/publication/evolutionary-dynamics-and-genomic-features-of-the-elizabethkingia-anophelis-2015-to-2016-wisconsin-outbreak-strain-2/
59,"Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation.","Lago M, Monteil V, Douche T, Guglielmini J, Criscuolo A, Maufrais C, Matondo M, Norel F, ","Scientific reports",'2017-05-18,"Archived: Membrane and metabolism in quiescent Salmonella, Biochemistry of Macromolecular Interactions, Mass Spectrometry for Biology, Proteomics, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB, Expertise group: Genomics",https://research.pasteur.fr/en/publication/proteome-remodelling-by-the-stress-sigma-factor-rpos%cf%83s-in-salmonella-identification-of-small-proteins-and-evidence-for-post-transcriptional-regulation/
60,"Molecular characterization of Chlamydia pneumoniae associated to atherosclerosis","Yazouli LE, Criscuolo A, Hejaji H, Bouaaza M, Elmdaghri N, Alami AA, Amraoui A, Dakka N, Radouani F","Pathogens and disease",'2017-04-06,"Mutualized Platform for Microbiology, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/molecular-characterization-of-chlamydia-pneumoniae-associated-to-atherosclerosis/
61,"Characterization of Clostridium Baratii Type F Strains Responsible for an Outbreak of Botulism Linked to Beef Meat Consumption in France","Mazuet C, Legeay C, Sautereau J, Bouchier C, Criscuolo A, Bouvet P, Trehard H, Jourdan Da Silva N, Popoff M","PLOS Currents Outbreaks",'2017-02-01,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/characterization-of-clostridium-baratii-type-f-strains-responsible-for-an-outbreak-of-botulism-linked-to-beef-meat-consumption-in-france/
62,"Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.","Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A, Tarr C, Björkman JT, Dallman T, Reimer A, Enouf V, Larsonneur E, Carleton H, Bracq-Dieye H, Katz LS, Jones L, Touchon M, Tourdjman M, Walker M, Stroika S, Cantinelli T, Chenal-Francisque V, Kucerova Z, Rocha EP, Nadon C, Grant K, Nielsen EM, Pot B, Gerner-Smidt P, Lecuit M, Brisse S, ","Nature microbiology",'2016-10-10,"Biology of infection, Microbial Evolutionary Genomics, Mutualized Platform for Microbiology, Biodiversity and Epidemiology of Bacterial Pathogens, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/whole-genome-based-population-biology-and-epidemiological-surveillance-of-listeria-monocytogenes/
63,"Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes.","Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, Céline Brochier-Armanet, Christophe Beloin, Simonetta Gribaldo",eLife,'2016-08-31,"Mutualized Platform for Microbiology, Evolutionary Biology of the Microbial Cell, Archived: Molecular Biology of Gene in Extremophiles, Microbial Individuality and Infection, Pathogenesis of Bacterial Anaerobes, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/phylogenomic-analysis-supports-the-ancestral-presence-of-lps-outer-membranes-in-the-firmicutes/
64,"Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis","Breurec S, Criscuolo A, Diancourt L, Rendueles O, Vandenbogaert M, Passet V, Caro V, Rocha EP, Touchon M, Brisse S","Scientific reports",'2016-07-27,"Mutualized Platform for Microbiology, Archived: Group: Sylvain Brisse, Microbial Evolutionary Genomics, Archived: Molecular Prevention and Therapy of Human Diseases, Biodiversity and Epidemiology of Bacterial Pathogens, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/genomic-epidemiology-and-global-diversity-of-the-emerging-bacterial-pathogen-elizabethkingia-anophelis/
65,"Species- and Strain-Specific Adaptation of the HSP70 Super Family in Pathogenic Trypanosomatids.","Drini S, Criscuolo A, Lechat P, Imamura H, Skalický T, Rachidi N, Lukeš J, Dujardin JC, Späth GF, ","Genome biology and evolution",'2016-07-02,"Bioinformatics and Biostatistics HUB, Expertise group: GIPhy – Genome Informatics and Phylogenetics, Molecular Parasitology and Signaling, Signalling and host-parasite interactions",https://research.pasteur.fr/en/publication/species-and-strain-specific-adaptation-of-the-hsp70-super-family-in-pathogenic-trypanosomatids/
66,"Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity.","Maury MM, Tsai YH, Charlier C, Touchon M, Chenal-Francisque V, Leclercq A, Criscuolo A, Gaultier C, Roussel S, Brisabois A, Disson O, Rocha EPC, Brisse S, Lecuit M, ","Nature genetics",'2016-03-01,"Biology of infection, Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB, Archived: Group: Sylvain Brisse, Archived: Molecular Prevention and Therapy of Human Diseases, Biodiversity and Epidemiology of Bacterial Pathogens, Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/publication/uncovering-listeria-monocytogenes-hypervirulence-by-harnessing-its-biodiversity/
67,"topIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB","Dahmane N, Gadelle D, Delmas S, Criscuolo A, Eberhard S, Desnoues N, Collin S, Zhang H, Pommier Y, Forterre P, Sezonov G","Nucleic acids research",'2016-02-22,"Bioinformatics and Biostatistics HUB, Expertise group: GIPhy – Genome Informatics and Phylogenetics",https://research.pasteur.fr/en/publication/topib-a-phylogenetic-hallmark-gene-of-thaumarchaeota-encodes-a-functional-eukaryote-like-topoisomerase-ib/
68,"Whole genome sequencing to investigate an outbreak of mucormycosis in a burn unit","Alanio A, Garcia-Hermoso D, Criscuolo A, Legrand M, Chaouat M, Denis B, Lafaurie M, Rouveau M, Soler C, Mimoun M, Mebazaa A, Dromer F, Brisse S, Bretagne S",Mycoses,'2015-10-15,,https://research.pasteur.fr/en/publication/whole-genome-sequencing-to-investigate-an-outbreak-of-mucormycosis-in-a-burn-unit/
69,"Épidémie de mucormycose dans un centre de traitement des brûlés : des biomarqueurs diagnostiques au séquençage complets des souches","D Garcia-Hermoso, A Criscuolo, M Legrande, M Chaouat, B Denis, M Lafaurie, M Rouveau, C Soler, M Mimoun, A Mebazaa, F Dromer, S Brisse, S Bretagne, A Alanio","Journal of Medical Mycology",'2015-08-31,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/epidemie-de-mucormycose-dans-un-centre-de-traitement-des-brules-des-biomarqueurs-diagnostiques-au-sequencage-complets-des-souches/
70,"Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups","Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S","Emerging infectious diseases",'2014-11-01,"Microbial Evolutionary Genomics, Archived: Group: Sylvain Brisse, Bioinformatics and Biostatistics HUB, Enteric Bacterial Pathogens, Biodiversity and Epidemiology of Bacterial Pathogens",https://research.pasteur.fr/en/publication/genomic-definition-of-hypervirulent-and-multidrug-resistant-klebsiella-pneumoniae-clonal-groups/
71,"Development of a multiplex PCR assay for identification of Klebsiella pneumoniae hypervirulent clones of capsular serotype K2","Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Nicolas-Chanoine MH, Decré D, Brisse S","Journal of medical microbiology",'2014-09-26,"Archived: Group: Sylvain Brisse, Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/development-of-a-multiplex-pcr-assay-for-identification-of-klebsiella-pneumoniae-hypervirulent-clones-of-capsular-serotype-k2/
72,"Campylobacter coli cultured from the stools of a patient with immunoproliferative small intestinal disease.","Coeuret S, de La Blanchardière A, Saguet-Rysanek V, Chèze S, Tavernier M, Arsène D, Criscuolo A, Brisse S, Vergnaud M, Verdon R, Lecuit M, ","Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases",'2014-09-01,"Microbial Evolutionary Genomics, Archived: Group: Sylvain Brisse, Bioinformatics and Biostatistics HUB, Biology of infection",https://research.pasteur.fr/en/publication/campylobacter-coli-cultured-from-the-stools-of-a-patient-with-immunoproliferative-small-intestinal-disease/
73,"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","Criscuolo A, Brisse S","Frontiers in genetics",'2014-05-13,"Archived: Group: Sylvain Brisse, Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/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-next/
74,"Draft Genome Sequence of Campylobacter coli Strain IPSID-1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease.","Criscuolo A, de la Blanchardière A, Coeuret S, Passet V, Saguet-Rysanek V, Vergnaud M, Verdon R, Leclercq A, Lecuit M, Brisse S, ","Genome announcements",'2014-03-13,"Archived: Group: Sylvain Brisse, Microbial Evolutionary Genomics, Biology of infection, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/draft-genome-sequence-of-campylobacter-coli-strain-ipsid-1-isolated-from-a-patient-with-immunoproliferative-small-intestinal-disease/
75,"AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads","Criscuolo A, Brisse S",Genomics,'2013-08-01,"Archived: Group: Sylvain Brisse, Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/alientrimmer-a-tool-to-quickly-and-accurately-trim-off-multiple-short-contaminant-sequences-from-high-throughput-sequencing-reads/
76,"Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis","Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Médigue C, Parkhill J, Cruveiller S, Brosch R","Nature genetics",'2013-01-06,"Biomics, Archived: Genomics, Archived: Group: Sylvain Brisse, Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB, Archived: Immune Regulation and Vaccinology, Archived: Experimental neuropathology, Integrated Mycobacterial Pathogenomics",https://research.pasteur.fr/en/publication/genomic-analysis-of-smooth-tubercle-bacilli-provides-insights-into-ancestry-and-pathoadaptation-of-mycobacterium-tuberculosis/
77,"morePhyML: improving the phylogenetic tree space exploration with PhyML 3","Criscuolo A","Molecular phylogenetics and evolution",'2011-09-08,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/morephyml-improving-the-phylogenetic-tree-space-exploration-with-phyml-3/
78,"Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria","Criscuolo A, Gribaldo S","Molecular biology and evolution",'2011-06-07,"Evolutionary Biology of the Microbial Cell, Archived: Molecular Biology of Gene in Extremophiles, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/large-scale-phylogenomic-analyses-indicate-a-deep-origin-of-primary-plastids-within-cyanobacteria/
79,"BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments","Criscuolo A, Gribaldo S","BMC evolutionary biology",'2010-07-13,"Evolutionary Biology of the Microbial Cell, Archived: Molecular Biology of Gene in Extremophiles, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/bmge-block-mapping-and-gathering-with-entropy-a-new-software-for-selection-of-phylogenetic-informative-regions-from-multiple-sequence-alignments/
80,"SuperTriplets: a triplet-based supertree approach to phylogenomics","Ranwez V, Criscuolo A, Douzery EJ","Bioinformatics (Oxford, England)",'2010-06-15,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/supertriplets-a-triplet-based-supertree-approach-to-phylogenomics/
81,"Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections","Debarbieux L, Leduc D, Maura D, Morello E, Criscuolo A, Grossi O, Balloy V, Touqui L","The Journal of infectious diseases",'2010-04-01,"Bacteriophage, bacterium, host, Archived: Molecular Biology of Gene in Extremophiles, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/bacteriophages-can-treat-and-prevent-pseudomonas-aeruginosa-lung-infections/
82,"Phylogenetic inference with weighted codon evolutionary distances","Criscuolo A, Michel CJ","Journal of molecular evolution",'2009-03-24,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/phylogenetic-inference-with-weighted-codon-evolutionary-distances/
83,"Fast NJ-like algorithms to deal with incomplete distance matrices","Criscuolo A, Gascuel O","BMC bioinformatics",'2008-03-26,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/fast-nj-like-algorithms-to-deal-with-incomplete-distance-matrices/
84,"PhySIC: a veto supertree method with desirable properties","Ranwez V, Berry V, Criscuolo A, Fabre PH, Guillemot S, Scornavacca C, Douzery EJ","Systematic biology",'2007-10-01,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/physic-a-veto-supertree-method-with-desirable-properties/
85,"SDM: a fast distance-based approach for (super) tree building in phylogenomics","Criscuolo A, Berry V, Douzery EJ, Gascuel O","Systematic biology",'2006-10-01,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/sdm-a-fast-distance-based-approach-for-super-tree-building-in-phylogenomics/