N,Title,Authors,Journal,Date,Team,Url
1,"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/
2,"First Description of a Yersinia pseudotuberculosis Clonal Outbreak in France, Confirmed Using a New Core Genome Multilocus Sequence Typing Method.","Savin C, Le Guern AS, Chereau F, Guglielmini J, Heuzé G, Demeure C, Pizarro-Cerdá J, ","Microbiology spectrum",'2022-07-06,"Yersinia, Bioinformatics and Biostatistics HUB, Expertise group : PAGE – Protein And Gene Evolution",https://research.pasteur.fr/en/publication/first-description-of-a-yersinia-pseudotuberculosis-clonal-outbreak-in-france-confirmed-using-a-new-core-genome-multilocus-sequence-typing-method/
3,"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/
4,"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/
5,"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/
6,"Phylogenetic analysis of Harmonin homology domains.","Colcombet-Cazenave B, Druart K, Bonnet C, Petit C, Spérandio O, Guglielmini J, Wolff N, ","BMC bioinformatics",'2021-04-14,"Signalling and Molecular interactions, Channel Receptors, Chemoinformatics and proteochemometrics, Structural Bioinformatics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Expertise group : PAGE – Protein And Gene Evolution",https://research.pasteur.fr/en/publication/phylogenetic-analysis-of-harmonin-homology-domains/
7,"High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones.","Jamet A, Guglielmini J, Brancotte B, Coureuil M, Euphrasie D, Meyer J, Roux J, Barnier JP, Bille E, Ferroni A, Magny JF, Bôle-Feysot C, Charbit A, Nassif X, Brisse S, ","Journal of clinical microbiology",'2021-02-18,"Biodiversity and Epidemiology of Bacterial Pathogens, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Expertise group : PAGE – Protein And Gene Evolution",https://research.pasteur.fr/en/publication/high-resolution-typing-of-staphylococcus-epidermidis-based-on-cgmlst-to-investigate-the-hospital-spread-of-multidrug-resistant-clones/
8,"Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy.","Woo AC, Gaia M, Guglielmini J, Da Cunha V, Forterre P, ","Frontiers in microbiology",'2021-01-01,"Expertise group : PAGE – Protein And Gene Evolution, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/phylogeny-of-the-varidnaviria-morphogenesis-module-congruence-and-incongruence-with-the-tree-of-life-and-viral-taxonomy/
9,"Diversity and evolution of B-family DNA polymerases","Kazlauskas D, Krupovic M, Guglielmini J, Forterre P, Venclovas Č","Nucleic acids research",'2020-10-09,"Expertise group : PAGE – Protein And Gene Evolution, Bioinformatics and Biostatistics HUB, Archaeal Virology",https://research.pasteur.fr/en/publication/diversity-and-evolution-of-b-family-dna-polymerases/
10,"Reply to Ku and Sun: Ancestors of modern giant and large eukaryotic dsDNA viruses infected proto-eukaryotes","Guglielmini J, Woo AC, Krupovic M, Forterre P, Gaia M","Proceedings of the National Academy of Sciences of the United States of America",'2020-01-28,"Expertise group: GIPhy – Genome Informatics and Phylogenetics, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/reply-to-ku-and-sun-ancestors-of-modern-giant-and-large-eukaryotic-dsdna-viruses-infected-proto-eukaryotes/
11,"Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations.","Baidaliuk A, Lequime S, Moltini-Conclois I, Dabo S, Dickson LB, Prot M, Duong V, Dussart P, Boyer S, Shi C, Matthijnssens J, Guglielmini J, Gloria-Soria A, Simon-Lorière E, Lambrechts L, ","Virus evolution",'2020-01-01,"Insect-Virus Interactions, Evolutionary genomics of RNA viruses, Bioinformatics and Biostatistics HUB, Expertise group : PAGE – Protein And Gene Evolution",https://research.pasteur.fr/en/publication/novel-genome-sequences-of-cell-fusing-agent-virus-allow-comparison-of-virus-phylogeny-with-the-genetic-structure-of-populations/
12,"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/
13,"Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes","Guglielmini J, Woo AC, Krupovic M, Forterre P, Gaia M","Proceedings of the National Academy of Sciences of the United States of America",'2019-09-10,"Expertise group : PAGE – Protein And Gene Evolution, Bioinformatics and Biostatistics HUB, Archaeal Virology",https://research.pasteur.fr/en/publication/diversification-of-giant-and-large-eukaryotic-dsdna-viruses-predated-the-origin-of-modern-eukaryotes/
14,"Role of a patatin-like phospholipase in Plasmodium falciparum gametogenesis and malaria transmission.","Singh P, Alaganan A, More KR, Lorthiois A, Thiberge S, Gorgette O, Guillotte Blisnick M, Guglielmini J, Aguilera SS, Touqui L, Singh S, Chitnis CE, ","Proceedings of the National Academy of Sciences of the United States of America",'2019-08-27,"Center for the Production and Infection of Anopheles, Ultrastructural BioImaging, Malaria Infection & Immunity, Malaria Parasite Biology and Vaccines, Expertise group : PAGE – Protein And Gene Evolution, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/role-of-a-patatin-like-phospholipase-in-gametogenesis-and-malaria-transmission/
15,"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/
16,"Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance.","Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M, ","PLoS neglected tropical diseases",'2019-04-01,"Expertise group : PAGE – Protein And Gene Evolution, Mutualized Platform for Microbiology, Bioinformatics and Biostatistics HUB, Biodiversity and Epidemiology of Bacterial Pathogens, Biology of Spirochetes, Clinical Investigation Platform ICAReB-Clin",https://research.pasteur.fr/en/publication/genus-wide-leptospira-core-genome-multilocus-sequence-typing-for-strain-taxonomy-and-global-surveillance/
17,"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/
18,"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/
19,"Identification of protein secretion systems in bacterial genomes","Sophie S. Abby, Jean Cury, Julien Guglielmini, Bertrand Néron, Marie Touchon & Eduardo P. C. Rocha","Scientific Reports",'2016-03-16,"Microbial Evolutionary Genomics, Archived: Center of Informatics for Biology",https://research.pasteur.fr/en/publication/identification-of-protein-secretion-systems-in-bacterial-genomes/
20,"Genome Analysis of Kingella kingae Strain KWG1 Reveals How a β-Lactamase Gene Inserted in the Chromosome of This Species","Bidet P, Basmaci R, Guglielmini J, Doit C, Jost C, Birgy A, Bonacorsi S","Antimicrobial agents and chemotherapy",'2016-01-29,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/genome-analysis-of-kingella-kingae-strain-kwg1-reveals-how-a-%ce%b2-lactamase-gene-inserted-in-the-chromosome-of-this-species/
21,"Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations","Xue H, Cordero OX, Camas FM, Trimble W, Meyer F, Guglielmini J, Rocha EP, Polz MF",mBio,'2015-05-05,"Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/eco-evolutionary-dynamics-of-episomes-among-ecologically-cohesive-bacterial-populations/
22,"A systematic and functional classification of Streptococcus pyogenes that serves as a new tool for molecular typing and vaccine development","Sanderson-Smith M, De Oliveira DM, Guglielmini J, McMillan DJ, Vu T, Holien JK, Henningham A, Steer AC, Bessen DE, Dale JB, Curtis N, Beall BW, Walker MJ, Parker MW, Carapetis JR, Van Melderen L, Sriprakash KS, Smeesters PR, ","The Journal of infectious diseases",'2014-05-05,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/a-systematic-and-functional-classification-of-streptococcus-pyogenes-that-serves-as-a-new-tool-for-molecular-typing-and-vaccine-development/
23,"Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion","Guglielmini J, Néron B, Abby SS, Garcillán-Barcia MP, de la Cruz F, Rocha EP","Nucleic acids research",'2014-03-12,"Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB, Archived: Web Integration and Software Development group, Archived: Center of Informatics for Biology",https://research.pasteur.fr/en/publication/key-components-of-the-eight-classes-of-type-iv-secretion-systems-involved-in-bacterial-conjugation-or-protein-secretion/
24,"Updated model of group A Streptococcus M proteins based on a comprehensive worldwide study","McMillan DJ, Drèze PA, Vu T, Bessen DE, Guglielmini J, Steer AC, Carapetis JR, Van Melderen L, Sriprakash KS, Smeesters PR","Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases",'2013-03-07,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/updated-model-of-group-a-streptococcus-m-proteins-based-on-a-comprehensive-worldwide-study/
25,"Evolution of conjugation and type IV secretion systems","Guglielmini J, de la Cruz F, Rocha EP","Molecular biology and evolution",'2012-09-13,"Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/evolution-of-conjugation-and-type-iv-secretion-systems/
26,"Bacterial toxin-antitoxin systems: Translation inhibitors everywhere","Guglielmini J, Van Melderen L","Mobile genetic elements",'2011-11-01,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/bacterial-toxin-antitoxin-systems-translation-inhibitors-everywhere/
27,"The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation","Guglielmini J, Quintais L, Garcillán-Barcia MP, de la Cruz F, Rocha EP","PLoS genetics",'2011-08-18,"Microbial Evolutionary Genomics, Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/the-repertoire-of-ice-in-prokaryotes-underscores-the-unity-diversity-and-ubiquity-of-conjugation/
28,"Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families","Leplae R, Geeraerts D, Hallez R, Guglielmini J, Drèze P, Van Melderen L","Nucleic acids research",'2011-03-21,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/diversity-of-bacterial-type-ii-toxin-antitoxin-systems-a-comprehensive-search-and-functional-analysis-of-novel-families/
29,"Evolutionary history of hepatitis C virus genotype 5a in France, a multicenter ANRS study","Henquell C, Guglielmini J, Verbeeck J, Mahul A, Thibault V, Lebray P, Laperche S, Trimoulet P, Foucher J, Le Guillou-Guillemette H, Fouchard-Hubert I, Legrand-Abravanel F, Métivier S, Gaudy C, D'Alteroche L, Rosenberg AR, Podevin P, Plantier JC, Riachi G, Saoudin H, Coppere H, André E, Gournay J, Feray C, Vallet S, Nousbaum JB, Baazia Y, Roulot D, Alain S, Loustaud-Ratti V, Schvoerer E, Habersetzer F, Pérez-Serra RJ, Gourari S, Mirand A, Odent-Malaure H, Garraud O, Izopet J, Bommelaer G, Peigue-Lafeuille H, van Ranst M, Abergel A, Bailly JL","Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases",'2011-01-18,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/evolutionary-history-of-hepatitis-c-virus-genotype-5a-in-france-a-multicenter-anrs-study/
30,"Phylogenomics of unusual histone H2A Variants in Bdelloid rotifers","Van Doninck K, Mandigo ML, Hur JH, Wang P, Guglielmini J, Milinkovitch MC, Lane WS, Meselson M","PLoS genetics",'2009-03-06,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/phylogenomics-of-unusual-histone-h2a-variants-in-bdelloid-rotifers/
31,"The decay of the chromosomally encoded ccdO157 toxin-antitoxin system in the Escherichia coli species","Mine N, Guglielmini J, Wilbaux M, Van Melderen L",Genetics,'2009-02-02,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/the-decay-of-the-chromosomally-encoded-ccdo157-toxin-antitoxin-system-in-the-escherichia-coli-species/
32,"Automated discovery and phylogenetic analysis of new toxin-antitoxin systems","Guglielmini J, Szpirer C, Milinkovitch MC","BMC microbiology",'2008-06-25,"Bioinformatics and Biostatistics HUB",https://research.pasteur.fr/en/publication/automated-discovery-and-phylogenetic-analysis-of-new-toxin-antitoxin-systems/