Pierre Pontarotti

Pierre Pontarotti

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Pierre Pontarotti

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The functional convergence of antibiotic resistance in β-lactamases is not conferred by a simple convergent substitution of amino acid.

Evol Appl 2019 Oct 18;12(9):1812-1822. Epub 2019 Jul 18.

Aix-Marseille Université, IRD, APHM, Microbe, Evolution, PHylogenie, Infection, IHU -Méditerranée Infection Marseille France.

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http://dx.doi.org/10.1111/eva.12835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752183PMC
October 2019

HLAIb worldwide genetic diversity: New HLA-H alleles and haplotype structure description.

Mol Immunol 2019 Aug 8;112:40-50. Epub 2019 May 8.

Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France; Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.molimm.2019.04.017DOI Listing
August 2019

An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees.

Antimicrob Agents Chemother 2019 May 25;63(5). Epub 2019 Apr 25.

Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France

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http://dx.doi.org/10.1128/AAC.02319-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6496087PMC
May 2019

Why do arthropods secrete β-lactams?

Int J Antimicrob Agents 2019 Apr 23;53(4):370. Epub 2018 Nov 23.

Aix Marseille Université, MEPHI, IRD, IHU Méditerranée Infection, Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, Marseille, France.. Electronic address:

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http://dx.doi.org/10.1016/j.ijantimicag.2018.11.006DOI Listing
April 2019

Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes.

Front Microbiol 2018 27;9:2668. Epub 2018 Nov 27.

Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.

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https://www.frontiersin.org/article/10.3389/fmicb.2018.02668
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http://dx.doi.org/10.3389/fmicb.2018.02668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277510PMC
November 2018

Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium.

Sci Rep 2018 10 4;8(1):14817. Epub 2018 Oct 4.

Aix-Marseille-Univ., IRD, MEPHI, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France.

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http://dx.doi.org/10.1038/s41598-018-33261-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172269PMC
October 2018

In silico analysis of Schmidtea mediterranea TIR domain-containing proteins.

Dev Comp Immunol 2018 09 7;86:214-218. Epub 2018 May 7.

CNRS, 31 Chemin Joseph Aiguier, 13402, Marseille, France; CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13385, Marseille Cedex 05, France. Electronic address:

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http://dx.doi.org/10.1016/j.dci.2018.05.004DOI Listing
September 2018

A Phylogenomic Study of Draft Genome Sequences Suggests Genetic Exchanges With Giant Viruses.

Front Microbiol 2018 6;9:2098. Epub 2018 Sep 6.

Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes, Evolution, Phylogeny and Infection, and Institut Hospitalo-Universitaire - Méditerranée Infection, Aix-Marseille Université, Marseille, France.

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http://dx.doi.org/10.3389/fmicb.2018.02098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135880PMC
September 2018

Evolutionary and expression analyses reveal a pattern of ancient duplications and functional specializations in the diversification of the Downstream of Kinase (DOK) genes.

Dev Comp Immunol 2018 07 15;84:193-198. Epub 2018 Feb 15.

Centre de Recherche en Cancérologie de Marseille, Immunity and Cancer Team, Institut Paoli-Calmettes, Inserm, U1068, CNRS, UMR7258, Aix-Marseille Université UM 105, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.dci.2018.02.011DOI Listing
July 2018

Convergent evolution of the adaptive immune response in jawed vertebrates and cyclostomes: An evolutionary biology approach based study.

Dev Comp Immunol 2017 10 21;75:120-126. Epub 2017 Feb 21.

Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, équipe évolution biologique modélisation, 13453, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.dci.2017.02.011DOI Listing
October 2017

The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes.

Genome Biol Evol 2017 10;9(10):2635-2639

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM 1095, AP-HM, IHU - Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, France.

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http://dx.doi.org/10.1093/gbe/evx208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737619PMC
October 2017

Evolutionary and polymorphism analyses reveal the central role of BTN3A2 in the concerted evolution of the BTN3 gene family.

Immunogenetics 2017 06 5;69(6):379-390. Epub 2017 Apr 5.

Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, F-13009, Marseille, France.

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http://dx.doi.org/10.1007/s00251-017-0980-zDOI Listing
June 2017

The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates.

Immunogenetics 2017 06 28;69(6):391-400. Epub 2017 Apr 28.

Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, équipe évolution biologique modélisation, 13453, Marseille, France.

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http://dx.doi.org/10.1007/s00251-017-0979-5DOI Listing
June 2017

MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales.

Viruses 2017 04 7;9(4). Epub 2017 Apr 7.

Aix-Marseille Université, Ecole Centrale de Marseille, I2M UMR 7373, CNRS équipe Evolution Biologique et Modélisation, 13284 Marseille, France.

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http://dx.doi.org/10.3390/v9040072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408678PMC
April 2017

Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum.

BMC Evol Biol 2017 03 9;17(1):75. Epub 2017 Mar 9.

Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005, France.

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http://dx.doi.org/10.1186/s12862-017-0921-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343374PMC
March 2017

Compartmentalization in PVC super-phylum: evolution and impact.

Biol Direct 2016 08 9;11:38. Epub 2016 Aug 9.

Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385, Marseille Cedex 5, France.

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http://dx.doi.org/10.1186/s13062-016-0144-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977879PMC
August 2016

Origin and Evolution of Rickettsial Plasmids.

PLoS One 2016 11;11(2):e0147492. Epub 2016 Feb 11.

Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille cedex 5, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147492PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750851PMC
July 2016

Mimivirus inaugurated in the 21st century the beginning of a reclassification of viruses.

Curr Opin Microbiol 2016 06 30;31:16-24. Epub 2016 Jan 30.

IHU Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo-Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France; Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, 27 boulevard Jean Moulin, 13385 Marseille Cedex 05, France. Electronic address:

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http://dx.doi.org/10.1016/j.mib.2015.12.010DOI Listing
June 2016

Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination.

Cell 2016 Jun 9;166(1):102-14. Epub 2016 Jun 9.

State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China; Beijing University of Chinese Medicine, Dong San Huan Road, Chao-yang District, Beijing 100029, People's Republic of China. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.05.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5017859PMC
June 2016

MIMIVIRE is a defence system in mimivirus that confers resistance to virophage.

Nature 2016 Mar 29;531(7593):249-52. Epub 2016 Feb 29.

Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, Marseille, France.

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http://dx.doi.org/10.1038/nature17146DOI Listing
March 2016

Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club.

Front Microbiol 2015 4;6:722. Epub 2015 Aug 4.

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National de la Recherche Scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale U1095, Aix-Marseille University Marseille, France ; Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille Marseille, France.

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http://dx.doi.org/10.3389/fmicb.2015.00722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523831PMC
August 2015

The human gut microbiome, a taxonomic conundrum.

Syst Appl Microbiol 2015 Jun 25;38(4):276-86. Epub 2015 Mar 25.

URMITE, UM63, CNRS7278, IRD198, insermU1095, Institut Hospitalo-Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.syapm.2015.03.004DOI Listing
June 2015

Welcome to pandoraviruses at the 'Fourth TRUC' club.

Front Microbiol 2015 18;6:423. Epub 2015 May 18.

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UM63 CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Aix-Marseille University Marseille, France ; Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille Marseille, France.

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http://dx.doi.org/10.3389/fmicb.2015.00423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435241PMC
June 2015

Methods to study the occurrence and the evolution of pseudogenes through a phylogenetic approach.

Methods Mol Biol 2014 ;1167:87-99

Evolutionary Biology and Modeling Group, Aix-Marseille Université, LATP - UMR 7353, 3 Place Victor Hugo - Case 19, 13331, Marseille Cedex 3, France,

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http://dx.doi.org/10.1007/978-1-4939-0835-6_7DOI Listing
January 2015

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.

Nat Commun 2014 Dec 19;5:5896. Epub 2014 Dec 19.

1] State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China [2] Beijing University of Chinese Medicine, Dong San Huang Road, Chao-yang District, Beijing 100029, China.

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http://dx.doi.org/10.1038/ncomms6896DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284660PMC
December 2014

The proto-MHC of placozoans, a region specialized in cellular stress and ubiquitination/proteasome pathways.

J Immunol 2014 Sep 11;193(6):2891-901. Epub 2014 Aug 11.

Institut National de la Recherche Agronomique, Virologie et Immunologie Moléculaires, F-78350 Jouy-en-Josas, France;

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http://dx.doi.org/10.4049/jimmunol.1401177DOI Listing
September 2014

Mycobacteriophage-drived diversification of Mycobacterium abscessus.

Biol Direct 2014 Sep 15;9:19. Epub 2014 Sep 15.

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IRD198, IFR48, Institut Méditerranée Infection, Aix Marseille Université, Marseille, France.

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http://biologydirect.biomedcentral.com/articles/10.1186/1745
Publisher Site
http://dx.doi.org/10.1186/1745-6150-9-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172396PMC
September 2014

African relapsing Fever borreliae genomospecies revealed by comparative genomics.

Front Public Health 2014 14;2:43. Epub 2014 May 14.

URMITE, UMR63, CNRS 7278, IRD 198, INSERM 1095, Aix Marseille Université , Marseille , France.

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http://dx.doi.org/10.3389/fpubh.2014.00043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157404PMC
September 2014

DNA-dependent RNA polymerase detects hidden giant viruses in published databanks.

Genome Biol Evol 2014 Jun 13;6(7):1603-10. Epub 2014 Jun 13.

Aix-Marseille Univ., Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Marseille, FranceFondation Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France

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http://dx.doi.org/10.1093/gbe/evu128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122926PMC
June 2014

Alphaproteobacteria species as a source and target of lateral sequence transfers.

Trends Microbiol 2014 Mar 21;22(3):147-56. Epub 2014 Jan 21.

Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.tim.2013.12.006DOI Listing
March 2014

The rhizome of life: what about metazoa?

Front Cell Infect Microbiol 2012 11;2:50. Epub 2012 Apr 11.

LATP UMR-CNRS 7353, Evolution Biologique et Modélisation, Aix-Marseille Universitée Marseille, France.

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http://dx.doi.org/10.3389/fcimb.2012.00050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3417402PMC
December 2013

Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.

PLoS One 2012 30;7(11):e50875. Epub 2012 Nov 30.

Aix-Marseille Université, Centre National de la Recherche Scientifique, LATP, UMR 7353, Evolution Biologique et Modélisation, Marseille, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050875PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511272PMC
May 2013

Choosing the best ancestral character state reconstruction method.

Math Biosci 2013 Mar 28;242(1):95-109. Epub 2012 Dec 28.

LATP, UMR CNRS 7352 FR 3098 IFR 48, Evolution Biologique et Modélisation, Aix-Marseille Université, 13331 Marseille Cedex 3, France.

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http://dx.doi.org/10.1016/j.mbs.2012.12.003DOI Listing
March 2013

The genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa.

PLoS One 2012 12;7(4):e34754. Epub 2012 Apr 12.

URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034754PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325273PMC
December 2012

GLADX: an automated approach to analyze the lineage-specific loss and pseudogenization of genes.

PLoS One 2012 18;7(6):e38792. Epub 2012 Jun 18.

Aix-Marseille Université Laboratoire d'Analyse, Topologogie, Probabilités (LATP) UMR-CNRS 7353 équipe Evolution Biologique & Modélisation, Marseille, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038792PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377690PMC
December 2012

Peptidoglycan: a post-genomic analysis.

BMC Microbiol 2012 Dec 18;12:294. Epub 2012 Dec 18.

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7872 IRD 198, Méditerranée Infection, Aix-Marseille-Université, Marseille, France.

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http://dx.doi.org/10.1186/1471-2180-12-294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541169PMC
December 2012

The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response.

Immunogenetics 2012 Nov 23;64(11):781-94. Epub 2012 Sep 23.

Aix Marseille Université, Marseille, France.

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http://dx.doi.org/10.1007/s00251-012-0619-zDOI Listing
November 2012

FunGene-DB: a web-based tool for Polyporales strains authentication.

J Biotechnol 2012 Oct 2;161(3):383-6. Epub 2012 Jul 2.

INRA, UMR 1163 Biotechnologie des Champignons Filamenteux ESIL, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.

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http://dx.doi.org/10.1016/j.jbiotec.2012.06.023DOI Listing
October 2012

The chordate proteome history database.

Evol Bioinform Online 2012 1;8:437-47. Epub 2012 Aug 1.

INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix Marseille Université, ESIL Polytech, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.

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http://dx.doi.org/10.4137/EBO.S9186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418167PMC
August 2012

Controversies in modern evolutionary biology: the imperative for error detection and quality control.

BMC Genomics 2012 Jan 4;13. Epub 2012 Jan 4.

Department of Integrated Structural Biology, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) CNRS/INSERM/Université de Strasbourg, 1 rue Laurent Fries, Illkirch, F-67404, France.

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http://dx.doi.org/10.1186/1471-2164-13-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3311146PMC
January 2012

The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences.

Mol Biol Evol 2011 Nov;28(11):3213-23

Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, CNRS-IRD UMR6236-198, Université de la Méditerranée, Faculté de Médecine, Marseille, France.

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http://dx.doi.org/10.1093/molbev/msr239DOI Listing
November 2011

Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits.

Proc Natl Acad Sci U S A 2011 May 12;108(22):9160-5. Epub 2011 May 12.

Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7232, Université Pierre et Marie Curie Paris 06, Observatoire Océanologique, F-66651 Banyuls-sur-Mer, France.

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http://www.pnas.org/content/108/22/9160.full.pdf
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http://www.pnas.org/cgi/doi/10.1073/pnas.1014235108
Publisher Site
http://dx.doi.org/10.1073/pnas.1014235108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107284PMC
May 2011

Gene gain and loss events in Rickettsia and Orientia species.

Biol Direct 2011 Feb 8;6. Epub 2011 Feb 8.

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE, CNRS-IRD UMR 6236 IFR48 Faculté de Médecine, Université de la Méditerranée, Marseille, France.

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http://dx.doi.org/10.1186/1745-6150-6-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055210PMC
February 2011

The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics.

Biol Direct 2011 Feb 18;6:11. Epub 2011 Feb 18.

INRA, UMR1163 de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.

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http://link.springer.com/content/pdf/10.1186%2F1745-6150-6-1
Web Search
http://www.biology-direct.com/content/6/1/11
Publisher Site
http://dx.doi.org/10.1186/1745-6150-6-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3052240PMC
February 2011

Was the ancestral MHC involved in innate immunity?

Eur J Immunol 2010 Oct;40(10):2682-5

UMR 1163, INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM. Universités de Provence et de la Méditerranée, ESIL, Marseille Cedex 09, France.

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http://dx.doi.org/10.1002/eji.201040856DOI Listing
October 2010

Exploring laccase-like multicopper oxidase genes from the ascomycete Trichoderma reesei: a functional, phylogenetic and evolutionary study.

BMC Biochem 2010 Aug 24;11:32. Epub 2010 Aug 24.

UMR-1163, INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.

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http://www.biomedcentral.com/1471-2091/11/32
Publisher Site
http://dx.doi.org/10.1186/1471-2091-11-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939539PMC
August 2010

Nme protein family evolutionary history, a vertebrate perspective.

BMC Evol Biol 2009 Oct 23;9:256. Epub 2009 Oct 23.

INRA, UR1037 SCRIBE, IFR140, Ouest-Genopole, F-35000 Rennes, France.

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http://dx.doi.org/10.1186/1471-2148-9-256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777172PMC
October 2009

Metaphylogeny of 82 gene families sheds a new light on chordate evolution.

Int J Biol Sci 2006 10;2(2):32-7. Epub 2006 Apr 10.

Phylogenomics Laboratory, EA 3781 Evolution Biologique, Université de Provence, 13331 Marseille Cedex 03, France.

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http://dx.doi.org/10.7150/ijbs.2.32DOI Listing
September 2009

CASSIOPE: an expert system for conserved regions searches.

BMC Bioinformatics 2009 Sep 10;10:284. Epub 2009 Sep 10.

EBM UMR 6632 LATP, 3 place V Hugo - 13 331 Marseille cedex 03 France.

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http://dx.doi.org/10.1186/1471-2105-10-284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756280PMC
September 2009

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees.

BMC Bioinformatics 2009 Sep 19;10:298. Epub 2009 Sep 19.

UMR 6632, Evolutionary Biology and Modeling, University of Provence, Marseille, France.

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http://dx.doi.org/10.1186/1471-2105-10-298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759962PMC
September 2009

Origin and evolution of the vertebrate leukocyte receptors: the lesson from tunicates.

Immunogenetics 2009 Jun 30;61(6):463-81. Epub 2009 Apr 30.

Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.

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http://dx.doi.org/10.1007/s00251-009-0373-zDOI Listing
June 2009

Gene birth, death, and divergence: the different scenarios of reproduction-related gene evolution.

Biol Reprod 2009 Apr 7;80(4):616-21. Epub 2009 Jan 7.

Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique-Université François Rabelais de Tours-Haras Nationaux, Nouzilly, France.

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http://dx.doi.org/10.1095/biolreprod.108.073684DOI Listing
April 2009

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria.

Biol Direct 2009 Apr 10;4:13. Epub 2009 Apr 10.

Faculty of Medicine, Unit for Research on Emergent and Tropical Infectious Diseases, CNRS-IRD UMR 6236 IFR48, University of the Mediterranean, Marseilles, France.

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http://dx.doi.org/10.1186/1745-6150-4-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688493PMC
April 2009

The TP53INP2 protein is required for autophagy in mammalian cells.

Mol Biol Cell 2009 Feb 3;20(3):870-81. Epub 2008 Dec 3.

Institut National de la Santé et de la Recherche Médicale U624, Stress Cellulaire, 13288 Marseille Cedex 9, France.

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http://dx.doi.org/10.1091/mbc.e08-07-0671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633384PMC
February 2009

Evolution of major histocompatibility complex by "en bloc" duplication before mammalian radiation.

Immunogenetics 2008 Aug 17;60(8):423-38. Epub 2008 Jun 17.

LATP UMR 6632 CNRS Evolution biologique et Modélisation, Université de Provence, case 19, 3 place Victor Hugo, 13331 Marseille Cedex 03, France.

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http://dx.doi.org/10.1007/s00251-008-0301-7DOI Listing
August 2008

The differential expression of ribosomal 18S RNA paralog genes from the chaetognath Spadella cephaloptera.

Cell Mol Biol Lett 2007 24;12(4):573-83. Epub 2007 Jun 24.

Biodiversity and Environment, Université de Provence, case 18, 3 Place V. Hugo, 13331, Marseille cedex 3, France.

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http://www.degruyter.com/view/j/cmble.2007.12.issue-4/s11658
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http://dx.doi.org/10.2478/s11658-007-0026-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6275777PMC
May 2008

FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.

Fungal Genet Biol 2008 May 26;45(5):638-45. Epub 2008 Jan 26.

UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 Avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France.

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http://dx.doi.org/10.1016/j.fgb.2008.01.004DOI Listing
May 2008

Strategies for reliable exploitation of evolutionary concepts in high throughput biology.

Evol Bioinform Online 2008 May 8;4:121-37. Epub 2008 May 8.

Phylogenomics Laboratory, EA 3781 Evolution Biologique, Université de Provence, 13331 Marseille, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614184PMC
May 2008

GPR50 is the mammalian ortholog of Mel1c: evidence of rapid evolution in mammals.

BMC Evol Biol 2008 Apr 9;8:105. Epub 2008 Apr 9.

Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France.

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http://dx.doi.org/10.1186/1471-2148-8-105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323367PMC
April 2008

Atypical structure and phylogenomic evolution of the new eutherian oocyte- and embryo-expressed KHDC1/DPPA5/ECAT1/OOEP gene family.

Genomics 2007 Nov 3;90(5):583-94. Epub 2007 Oct 3.

Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université F. Rabelais de Tours Haras Nationaux, 37380 Nouzilly, France.

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http://linkinghub.elsevier.com/retrieve/pii/S088875430700145
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http://dx.doi.org/10.1016/j.ygeno.2007.06.003DOI Listing
November 2007

Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution.

Biol Rev Camb Philos Soc 2007 Nov;82(4):551-72

Phylogenomics Laboratory, EA 3781 Evolution Biologique Université de Provence, Case 19, Pl. V. Hugo, 13331 Marseille Cedex 03, France.

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http://dx.doi.org/10.1111/j.1469-185X.2007.00024.xDOI Listing
November 2007

Ancestral animal genomes reconstruction.

Curr Opin Immunol 2007 Oct 15;19(5):542-6. Epub 2007 Aug 15.

Phylogenomics Laboratory, EA 3781 Evolution Biologique Université de Provence, Case 19, Pl. V. Hugo, 13331 Marseille Cedex 03, France.

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http://dx.doi.org/10.1016/j.coi.2007.06.009DOI Listing
October 2007

Bromodomain testis-specific protein is expressed in mouse oocyte and evolves faster than its ubiquitously expressed paralogs BRD2, -3, and -4.

Genomics 2007 Feb 16;89(2):215-23. Epub 2006 Oct 16.

Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France.

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http://dx.doi.org/10.1016/j.ygeno.2006.09.002DOI Listing
February 2007

The use of evolutionary biology concepts for genome annotation.

J Exp Zool B Mol Dev Evol 2007 Jan;308(1):26-36

Glycogenomics and Biomedical Structural Biology, AFMB Laboratory, UMR 6098, CNRS, Universités d'Aix-Marseille I et II, 13288 Marseille, France.

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http://dx.doi.org/10.1002/jez.b.21131DOI Listing
January 2007

Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family.

BMC Evol Biol 2006 Nov 8;6:92. Epub 2006 Nov 8.

Phylogenomics Laboratory, EA 3781 Evolution Biologique Université de Provence, Case 19, Pl, V, Hugo, 13331 Marseille Cedex 03, France.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-6-92DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1660568PMC
November 2006

Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals.

BMC Evol Biol 2006 Jan 18;6. Epub 2006 Jan 18.

Phylogenomics Laboratory, EA 3781 EGEE, Universite de Provence, Marseilles, France.

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http://dx.doi.org/10.1186/1471-2148-6-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1382263PMC
January 2006

The phylogenetic analysis of tetraspanins projects the evolution of cell-cell interactions from unicellular to multicellular organisms.

Genomics 2005 Dec 20;86(6):674-84. Epub 2005 Oct 20.

State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China.

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http://dx.doi.org/10.1016/j.ygeno.2005.08.004DOI Listing
December 2005

FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform.

BMC Bioinformatics 2005 Aug 5;6:198. Epub 2005 Aug 5.

EA 3781 EGEE (Evolution, Genome, Environment), Université de Provence, Case 36, Pl. V. Hugo, 13331 Marseille Cedex 03, France.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-6-198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1188056PMC
August 2005

Towards the reconstruction of the bilaterian ancestral pre-MHC region.

Trends Genet 2004 Dec;20(12):587-91

EA 3781 Evolution, Genome and Environment, Equipe Phylogénomique, Université de Provence, 03 Pl. V. Hugo, Case 36, 13331 Marseille Cedex 03, France.

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http://dx.doi.org/10.1016/j.tig.2004.09.009DOI Listing
December 2004

Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome.

J Mol Evol 2004 Nov;59(5):587-97

EA EGEE (Evolution, Genome, Environment), Phylogenomics Laboratory, Université de Provence, Marseilles, France.

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http://dx.doi.org/10.1007/s00239-004-2648-1DOI Listing
November 2004

Frontline: Characterization of BT3 molecules belonging to the B7 family expressed on immune cells.

Eur J Immunol 2004 Aug;34(8):2089-99

INSERM UMR 599, Université de la Méditerranée, Cancer and Immunology Institute of Marseille, IFR 137, 27 Boulevard Lei Roure, F-13009 Marseille, France.

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http://doi.wiley.com/10.1002/eji.200425227
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http://dx.doi.org/10.1002/eji.200425227DOI Listing
August 2004

The major histocompatibility complex origin.

Immunol Rev 2004 Apr;198:216-32

Phylogenomics Laboratory, Université d'Aix Marseille I, Marseille, France.

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http://dx.doi.org/10.1111/j.0105-2896.2004.00132.xDOI Listing
April 2004

Evolution of the proto-MHC ancestral region: more evidence for the plesiomorphic organisation of human chromosome 9q34 region.

Immunogenetics 2003 Oct 3;55(7):429-36. Epub 2003 Oct 3.

EA Biodiversité 2202, Université de Provence, Place V. Hugo, 13331 Marseille cedex 3, France.

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http://link.springer.com/10.1007/s00251-003-0601-x
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October 2003

Systematic phylogenomic evidence of en bloc duplication of the ancestral 8p11.21-8p21.3-like region.

Mol Biol Evol 2003 Aug 30;20(8):1290-8. Epub 2003 May 30.

EA Biodiversité 2202, Université de Provence, Marseille, France.

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http://dx.doi.org/10.1093/molbev/msg127DOI Listing
August 2003

A co-evolution perspective of the TNFSF and TNFRSF families in the immune system.

Trends Immunol 2003 Jul;24(7):387-94

Institut de Cancérologie et d'Immunologie de Marseille, Université de la Méditerranée, INSERM, Unite 119, 27 Boulevard Lei Roure, 13009, Marseille, France.

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July 2003

Conservation of the MHC-like region throughout evolution.

Immunogenetics 2003 Jun 7;55(3):141-148. Epub 2003 May 7.

EA Biodiversité 2202, Phylogenomics Laboratory, Université de Provence, Case 36 Pl. V.Hugo, 13331, Marseilles Cedex 3, France.

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http://dx.doi.org/10.1007/s00251-003-0562-0DOI Listing
June 2003

Endogenous retroviral sequence is fused to FGFR1 kinase in the 8p12 stem-cell myeloproliferative disorder with t(8;19)(p12;q13.3).

Blood 2003 Jan 28;101(1):286-8. Epub 2002 Jun 28.

INSERM U119, the Institut de Cancérologie et d'Immunologie de Marseille, France.

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http://dx.doi.org/10.1182/blood-2002-02-0577DOI Listing
January 2003

The LAP family: a phylogenetic point of view.

Trends Genet 2002 Oct;18(10):494-7

U119 INSERM, Molecular Oncology and Institut Paoli-Calmettes, Molecular Pharmacology, 27, Bd Leï Roure, 13009 Marseille, France.

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http://dx.doi.org/10.1016/s0168-9525(02)02738-5DOI Listing
October 2002

Evidence of en bloc duplication in vertebrate genomes.

Nat Genet 2002 May 22;31(1):100-5. Epub 2002 Apr 22.

INSERM Unité 119, 27 bd Leï Roure, 13009 Marseille, France.

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http://dx.doi.org/10.1038/ng855DOI Listing
May 2002

Cutting edge: recruitment of the ancestral fyn gene during emergence of the adaptive immune system.

J Immunol 2002 Mar;168(6):2595-8

Institut de Cancérologie et d'Immunologie de Marseille, Marseille, France.

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http://dx.doi.org/10.4049/jimmunol.168.6.2595DOI Listing
March 2002

Leukocyte Ig-like receptor complex (LRC) in mice and men.

Trends Immunol 2002 Feb;23(2):81-8

Centre for Clinical Immunology and Biomedical Statistics, Murdoch University and Royal Perth Hospital, WA, Australia.

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February 2002