Pierre Pontarotti

165

Documents

Publications

	Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality Mohamad Maatouk , Vicky Merhej , Pierre Pontarotti , Ahmad Ibrahim , Jean-Marc Rolain Microorganisms, 2023, 11 (8), pp.1933. ⟨10.3390/microorganisms11081933⟩ Article dans une revue hal-04275003v1
	Insights into RAG evolution from the identification of “missing link” family A RAGL transposons Eliza C Martin , Lorlane Le Targa , Louis Tsakou-Ngouafo , Tzu-Pei Fan , Che-Yi Lin Molecular Biology and Evolution, 2023, ⟨10.1093/molbev/msad232⟩ Article dans une revue hal-04243785v2
	Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms Seydina Diene , Pierre Pontarotti , Saïd Azza , Nicholas Armstrong , Lucile Pinault Cells, 2023, 12 (13), pp.1752. ⟨10.3390/cells12131752⟩ Article dans une revue hal-04275581v1
	Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals K. Brener-Raffalli , Jeremie Vidal-Dupiol , M. Adjeroud , Olivier REY , P. Romans Peer Community Journal, 2022, 2, pp.e13. ⟨10.24072/pcjournal.79⟩ Article dans une revue hal-03239787v1
	RadA, a Key Gene of the Circadian Rhythm of Escherichia coli Aissatou Bailo Diallo , Soraya Mezouar , Asma Boumaza , Oksana Fiammingo , Benjamin Coiffard International Journal of Molecular Sciences, 2022, 23 (11), pp.6136. ⟨10.3390/ijms23116136⟩ Article dans une revue hal-03684665v1
	HLA-H02:07 Is a Membrane-Bound Ligand of Denisovan Origin That Protects against Lysis by Activated Immune Effectors Lucas Hubert , Julien Paganini , Christophe Picard , Jacques Chiaroni , Laurent Abi-Rached Journal of Immunology, 2022, pp.ji2100358. ⟨10.4049/jimmunol.2100358⟩ Article dans une revue hal-03471956v1*
	COVID-19 Pandemic: Escape of Pathogenic Variants and MHC Evolution Pierre Pontarotti , Julien Paganini International Journal of Molecular Sciences, 2022, 23 (5), pp.2665. ⟨10.3390/ijms23052665⟩ Article dans une revue hal-03592872v1
	Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia) Didier Aurelle , Marine Pratlong , Nicolas Oury , Anne Haguenauer , Pauline Gélin Genetica, 2022, 150, pp.247-262. ⟨10.1007/s10709-022-00165-7⟩ Article dans une revue hal-03774130v1
	HLA-H02:07 Is a Membrane-Bound Ligand of Denisovan Origin That Protects against Lysis by Activated Immune Effectors Lucas Hubert , Julien Paganini , Christophe Picard , Jacques Chiaroni , Laurent Abi-Rached Journal of Immunology, 2021, 208 (1), pp.49-53. ⟨10.4049/jimmunol.2100358⟩ Article dans une revue hal-03869640v1*
	Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum M. Pratlong , A. Haguenauer , K. Brener , G. Mitta , E. Toulza Peer Community Journal, 2021, 1, pp.e31. ⟨10.24072/pcjournal.12⟩ Article dans une revue hal-03454660v2
	The piggyBac-derived protein 5 (PGBD5) transposes both the closely and the distantly related piggyBac-like elements Tcr-pble and Ifp2 Laura Helou , Linda Beauclair , Hugues Dardente , Benoit Piegu , Louis Tsakou-Ngouafo Journal of Molecular Biology, 2021, 433 (7), pp.1-16. ⟨10.1016/j.jmb.2021.166839⟩ Article dans une revue hal-03149600v1
	Could β-Lactam Antibiotics Block Humoral Immunity? Cléa Melenotte , Pierre Pontarotti , Lucile Pinault , Jean-Louis Mège , Christian Devaux Frontiers in Immunology, 2021, 12, ⟨10.3389/fimmu.2021.680146⟩ Article dans une revue hal-03366413v1
	Self-Peptidome Variation Shapes Individual Immune Responses Pierre Pontarotti , Laurent Abi-Rached , Jung-Hua Yeh , Julien Paganini Trends in Genetics, 2021, 37 (5), pp.414-420. ⟨10.1016/j.tig.2020.10.001⟩ Article dans une revue hal-03366604v1
	Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica Sihem Hannat , Pierre Pontarotti , Philippe Colson , Marie-Line Kuhn , Eric Galiana Frontiers in Microbiology, 2021, 12, ⟨10.3389/fmicb.2021.662762⟩ Article dans une revue hal-03308205v1
	A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin Seydina M Diene , Lucile Pinault , Sophie Alexandra Baron , Saïd Azza , Nicholas Armstrong Scientific Reports, 2021, 11, ⟨10.1038/s41598-021-89600-x⟩ Article dans une revue hal-03371030v1
	A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin Seydina Diene , Lucile Pinault , Sophie Alexandra Baron , Saïd Azza , Nicholas Armstrong Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-89600-x⟩ Article dans une revue hal-03366566v1
	Search for MHC/TCR-Like Systems in Living Organisms Julien Paganini , Pierre Pontarotti Frontiers in Immunology, 2021, 12, ⟨10.3389/fimmu.2021.635521⟩ Article dans une revue hal-03370044v1
	Could β-Lactam Antibiotics Block Humoral Immunity? Cléa Melenotte , Pierre Pontarotti , Lucile Pinault , Jean-Louis Mège , Christian Devaux Frontiers in Immunology, 2021, 12, pp.680146. ⟨10.3389/fimmu.2021.680146⟩ Article dans une revue hal-03370420v1
	Self-Peptidome Variation Shapes Individual Immune Responses Pierre Pontarotti , Laurent Abi-Rached , Jung-Hua Yeh , Julien Paganini Trends in Genetics, 2021, 37 (5), pp.414 - 420. ⟨10.1016/j.tig.2020.10.001⟩ Article dans une revue hal-03370438v1
	A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin Seydina Diene , Lucile Pinault , Sophie Alexandra Baron , Saïd Azza , Nicholas Armstrong Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-89600-x⟩ Article dans une revue hal-03281982v1
	Search for MHC/TCR-Like Systems in Living Organisms Julien Paganini , Pierre Pontarotti Frontiers in Immunology, 2021, 12, ⟨10.3389/fimmu.2021.635521⟩ Article dans une revue hal-03280513v1
	Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea Seydina Diene , Lucile Pinault , Nicholas Armstrong , Said Azza , Vivek Keshri Life, 2020, 10 (11), pp.280. ⟨10.3390/life10110280⟩ Article dans une revue hal-03366589v1
	Origins of the RAG Transposome and the MHC Louis Tsakou-Ngouafo , Julien Paganini , Jim Kaufman , Pierre Pontarotti Current Trends in Immunology, 2020, 41 (7), pp.561-571. ⟨10.1016/j.it.2020.05.002⟩ Article dans une revue hal-03161998v1
	Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea Seydina M Diene , Lucile Pinault , Nicholas Armstrong , Said Azza , Vivek Keshri Life, 2020, 10 (11), pp.280. ⟨10.3390/life10110280⟩ Article dans une revue hal-03047404v1
	A protein of the metallo-hydrolase/oxidoreductase superfamily with both beta-lactamase and ribonuclease activity is linked with translation in giant viruses Philippe Colson , Lucile Pinault , Said Azza , Nicholas Armstrong , Eric Chabriere Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-78658-8⟩ Article dans une revue hal-03371039v1
	A protein of the metallo-hydrolase/oxidoreductase superfamily with both beta-lactamase and ribonuclease activity is linked with translation in giant viruses Philippe Colson , Lucile Pinault , Said Azza , Nicholas Armstrong , Eric Chabriere Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-78658-8⟩ Article dans une revue hal-03366581v1
	Origins of the RAG Transposome and the MHC Louis Tsakou-Ngouafo , Julien Paganini , Jim Kaufman , Pierre Pontarotti Current Trends in Immunology, 2020, ⟨10.1016/j.it.2020.05.002⟩ Article dans une revue hal-02868436v1
	A protein of the metallo-hydrolase/oxidoreductase superfamily with both beta-lactamase and ribonuclease activity is linked with translation in giant viruses Philippe Colson , Lucile Pinault , Said Azza , Nicholas Armstrong , Eric Chabriere Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-78658-8⟩ Article dans une revue hal-03149225v1
	Origins of the RAG Transposome and the MHC Louis Tsakou-Ngouafo , Julien Paganini , Jim Kaufman , Pierre Pontarotti Trends in Immunology, 2020, 41 (7), pp.561-571. ⟨10.1016/j.it.2020.05.002⟩ Article dans une revue hal-03371051v1
	Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases Vivek Keshri , Eric Chabrière , Lucile Pinault , Philippe Colson , Seydina M Diene International Journal of Molecular Sciences, 2020, 21 (17), pp.6260. ⟨10.3390/ijms21176260⟩ Article dans une revue hal-03047280v1
	Identification of RAG-like transposons in protostomes suggests their ancient bilaterian origin Eliza C Martin , Célia Vicari , Louis Tsakou-Ngouafo , Pierre Pontarotti , Andrei J Petrescu Mobile DNA, 2020, 11 (1), ⟨10.1186/s13100-020-00214-y⟩ Article dans une revue hal-03047226v1
	HLAIb worldwide genetic diversity: new HLA-H alleles and haplotype structure description Julien Paganini , Laurent Abi-Rached , Philippe Gouret , Pierre Pontarotti , Jacques Chiaroni Molecular Immunology, 2019, 112, pp.40-50. ⟨10.1016/j.molimm.2019.04.017⟩ Article dans une revue hal-03371942v1
	The functional convergence of antibiotic resistance in β‐lactamases is not conferred by a simple convergent substitution of amino acid Vivek Keshri , Kevin Arbuckle , Olivier Chabrol , Jean‐marc Rolain , Didier Raoult Evolutionary Applications, 2019, ⟨10.1111/eva.12835⟩ Article dans une revue hal-02263608v1
	Human metallo-β-lactamase enzymes degrade penicillin Seydina Diene , Lucile Pinault , Vivek Keshri , Nicholas Armstrong , Saber Khelaifia Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-48723-y⟩ Article dans une revue hal-02479402v1
	The functional convergence of antibiotic resistance in β‐lactamases is not conferred by a simple convergent substitution of amino acid Vivek Keshri , Kevin Arbuckle , Olivier Chabrol , Jean‐marc Rolain , Didier Raoult Evolutionary Applications, 2019, 12 (9), pp.1812-1822. ⟨10.1111/eva.12835⟩ Article dans une revue hal-03047294v1
	An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees Vivek Keshri , Seydina Diene , Adrien Estienne , Justine Dardaillon , Olivier Chabrol Antimicrobial Agents and Chemotherapy, 2019, 63 (5), ⟨10.1128/AAC.02319-18⟩ Article dans une revue hal-02159541v1
	Transposon molecular domestication and the evolution of the RAG recombinase Yuhang Zhang , Tat Cheung Cheng , Guangrui Huang , Qingyi Lu , Marius Surleac Nature, 2019, 569 (7754), pp.79-84. ⟨10.1038/s41586-019-1093-7⟩ Article dans une revue hal-02262562v1
	Human metallo-β-lactamase enzymes degrade penicillin Seydina M Diene , Lucile Pinault , Vivek Keshri , Nicholas Armstrong , Saber Khelaifia Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-48723-y⟩ Article dans une revue hal-03047415v1
	HLAIb worldwide genetic diversity: New HLA-H alleles and haplotype structure description Julien Paganini , Laurent Abi-Rached , Philippe Gouret , Pierre Pontarotti , Jacques Chiaroni Molecular Immunology, 2019, 112, pp.40-50. ⟨10.1016/j.molimm.2019.04.017⟩ Article dans une revue hal-02137704v1
	Why do arthropods secrete β-lactams? Pierre Pontarotti , Didier Raoult International Journal of Antimicrobial Agents, 2019, 53 (4), pp.370. ⟨10.1016/j.ijantimicag.2018.11.006⟩ Article dans une revue hal-02262479v1
	Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members Vivek Keshri , Arup Panda , Anthony Levasseur , Jean-Marc Rolain , Pierre Pontarotti Genome Biology and Evolution, 2018, 10 (4), pp.1106-1114. ⟨10.1093/gbe/evy028⟩ Article dans une revue hal-02057304v1
	Detecting the molecular basis of phenotypic convergence Olivier Chabrol , Manuela Royer-Carenzi , Pierre Pontarotti , Gilles Didier Methods in Ecology and Evolution, 2018, 9 (11), pp.2170-2180. ⟨10.1111/2041-210X.13071⟩ Article dans une revue hal-01532965v1
	Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes Philippe Colson , Anthony Levasseur , Bernard La Scola , Vikas Sharma , Arshan Nasir Frontiers in Microbiology, 2018, 9, ⟨10.3389/fmicb.2018.02668⟩ Article dans une revue hal-01948086v1
	Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium Arup Panda , Michel Drancourt , Tamir Tuller , Pierre Pontarotti Scientific Reports, 2018, 8, pp.14817. ⟨10.1038/s41598-018-33261-w⟩ Article dans une revue hal-02000575v1
	In silico analysis of Schmidtea mediterranea TIR domain-containing proteins Landry Laure Tsoumtsa , Seynabou Sougoufora , Cedric Torre , Emmanuel Lemichez , Pierre Pontarotti Developmental and Comparative Immunology, 2018, 86, pp.214-218. ⟨10.1016/j.dci.2018.05.004⟩ Article dans une revue hal-01858942v1
	Evolutionary and expression analyses reveal a pattern of ancient duplications and functional specializations in the diversification of the Downstream of Kinase (DOK) genes Geoffrey Guittard , Pierre Pontarotti , Samuel Granjeaud , Magda Rodrigues , Laurent Abi-Rached Developmental and Comparative Immunology, 2018, 84, pp.193-198. ⟨10.1016/j.dci.2018.02.011⟩ Article dans une revue inserm-02148721v1
	A Phylogenomic Study of Acanthamoeba polyphaga Draft Genome Sequences Suggests Genetic Exchanges With Giant Viruses Nisrine Chelkha , Anthony Levasseur , Pierre Pontarotti , Didier Raoult , Bernard La Scola Frontiers in Microbiology, 2018, 9, ⟨10.3389/fmicb.2018.02098⟩ Article dans une revue hal-01910335v1
	Amphioxus functional genomics and the origins of vertebrate gene regulation Ferdinand Marletaz , Panos N. Firbas , Ignacio Maeso , Juan J. Tena , Ozren Bogdanovic Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩ Article dans une revue hal-02000511v1
	Immune diversity sheds light on missing variation in worldwide genetic diversity panels Laurent Abi-Rached , Philippe Gouret , Jung-Hua Yeh , Julie Di Cristofaro , Pierre Pontarotti PLoS ONE, 2018, 13 (10), pp.e0206512. ⟨10.1371/journal.pone.0206512⟩ Article dans une revue hal-01931053v1
	Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum Sandrine Pinos , Pierre Pontarotti , Didier Raoult , Vicky Merhej BMC Evolutionary Biology, 2017, 17 (1), ⟨10.1186/s12862-017-0921-3⟩ Article dans une revue hal-01521244v1
	The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes Anthony Levasseur , Vicky Merhej , Emeline Baptiste , Vikas Sharma , Pierre Pontarotti Genome Biology and Evolution, 2017, 9 (10), pp.2635-2639. ⟨10.1093/gbe/evx208⟩ Article dans une revue hal-01730435v1
	The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates Jose Ricardo Morales Poole , Sheng Feng Huang , Anlong Xu , Justine Bayet , Pierre Pontarotti Immunogenetics, 2017, 69 (6), pp.391 - 400. ⟨10.1007/s00251-017-0979-5⟩ Article dans une revue hal-01598270v1
	Evolutionary and polymorphism analyses reveal the central role of BTN3A2 in the concerted evolution of the BTN3 gene family Hassnae Afrache , Pierre Pontarotti , Laurent Abi-Rached , Daniel Olive Immunogenetics, 2017, 69 (6), pp.379 - 390. ⟨10.1007/s00251-017-0980-z⟩ Article dans une revue hal-01785307v1
	Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree? Marine Pratlong , Corinne Rancurel , Pierre Pontarotti , D. Aurelle Zoologica Scripta, 2017, 46 (3), pp.363-371. ⟨10.1111/zsc.12208⟩ Article dans une revue hal-01474009v1
	Convergent evolution of the adaptive immune response in jawed vertebrates and cyclostomes: An evolutionary biology approach based study Jose Ricardo Morales Poole , Julien Paganini , Pierre Pontarotti Developmental and Comparative Immunology, 2017, 75, pp.120 - 126. ⟨10.1016/j.dci.2017.02.011⟩ Article dans une revue hal-01622250v1
	MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales Sourabh Jain , Arup Panda , Philippe Colson , Didier Raoult , Pierre Pontarotti Viruses, 2017, 9 (4), pp.72 - 72. ⟨10.3390/v9040072⟩ Article dans une revue hal-01573785v1
	Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination Shengfeng Huang , Xin Tao , Shaochun Yu , Yuhang Yu , Peiyi Li Cell, 2016, 166 (1), pp.102 - 114. ⟨10.1016/j.cell.2016.05.032⟩ Article dans une revue hal-01486940v1
	Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Jérémy Pasquier , Cédric Cabau , Thuy Thao Vi Nguyen , Elodie Jouanno , Dany Severac BMC Genomics, 2016, 17 (1), pp.368. ⟨10.1186/s12864-016-2709-z⟩ Article dans une revue hal-01487023v1
	Origin and Evolution of Rickettsial Plasmids Khalid El Karkouri , Pierre Pontarotti , Didier Raoult , Pierre-Edouard Fournier PLoS ONE, 2016, 11 (2), pp.e0147492. ⟨10.1371/journal.pone.0147492⟩ Article dans une revue hal-01459537v1
	Mimivirus inaugurated in the 21st century the beginning of a reclassification of viruses Vikas Sharma , Philippe Colson , Pierre Pontarotti , Didier Raoult Current Opinion in Microbiology, 2016, 31, pp.16-24. ⟨10.1016/j.mib.2015.12.010⟩ Article dans une revue hal-01308970v1
	MIMIVIRE is a defence system in mimivirus that confers resistance to virophage Anthony Levasseur , Meriem Bekliz , Eric Chabrière , Pierre Pontarotti , Bernard La Scola Nature, 2016, 531 (7593), pp.249-252. ⟨10.1038/nature17146⟩ Article dans une revue hal-01306166v1
	Genomic resources and their influence on the detection of the signal of positive selection in genome scans S. Manel , Charles Perrier , Marine Pratlong , Laurent Abi-Rached , Julien Paganini Molecular Ecology, 2016, 25 (1), pp.170-184. ⟨10.1111/mec.13468⟩ Article dans une revue hal-02336047v1
	Compartmentalization in PVC super-phylum: evolution and impact Sandrine Pinos , Pierre Pontarotti , Didier Raoult , Jean Pierre Baudoin , Isabelle Pagnier Biology Direct, 2016, 11, ⟨10.1186/s13062-016-0144-3⟩ Article dans une revue hal-01455631v1
	Welcome to pandoraviruses at the 'Fourth TRUC' club Vikas Sharma , Philippe Colson , Olivier Chabrol , Patrick Scheid , Pierre Pontarotti Frontiers in Microbiology, 2015, 6 (423), ⟨10.3389/fmicb.2015.00423⟩ Article dans une revue hal-01211489v1
	The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies M. Pratlong , A. Haguenauer , O. Chabrol , C. Klopp , P. Pontarotti Molecular Ecology Resources, 2015, 15 (5), pp.1205--1215. ⟨10.1111/1755-0998.12383⟩ Article dans une revue hal-01445149v1
	Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club Vikas Sharma , Philippe Colson , Olivier Chabrol , Pierre Pontarotti , Didier Raoult Frontiers in Microbiology, 2015, 6, pp.722. ⟨10.3389/fmicb.2015.00722⟩ Article dans une revue hal-01304145v1
	The genome of the white-rot fungus [i]Pycnoporus cinnabarinus[/i]: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown Anthony Levasseur , Anne Lomascolo , Olivier Chabrol , Francisco J Ruiz-Dueñas , Eva Boukhris-Uzan BMC Genomics, 2014, 15 (1), pp.486. ⟨10.1186/1471-2164-15-486⟩ Article dans une revue hal-01204353v1
	The Proto-MHC of Placozoans, a Region Specialized in Cellular Stress and Ubiquitination/Proteasome Pathways Jaanus Suurväli , Luc Jouneau , Dominique Thepot Thépot , Simona Grusea , Pierre Pontarotti Journal of Immunology, 2014, 193 (6), pp.2891 - 2901. ⟨10.4049/jimmunol.1401177⟩ Article dans une revue hal-01633156v1
	Mycobacteriophage-drived diversification of Mycobacterium abscessus Mohamed Sassi , Philippe Gouret , Olivier Chabrol , Pierre Pontarotti , Michel Drancourt Biology Direct, 2014, 9 (1), pp.19. ⟨10.1186/1745-6150-9-19⟩ Article dans une revue hal-01304426v1
	African Relapsing Fever Borreliae Genomospecies Revealed by Comparative Genomics Haitham Elbir , Laurent Abi-Rached , Pierre Pontarotti , Niyaz Yoosuf , Michel Drancourt Frontiers in Public Health, 2014, 2, ⟨10.3389/fpubh.2014.00043⟩ Article dans une revue hal-01785565v1
	DNA-Dependent RNA Polymerase Detects Hidden Giant Viruses in Published Databanks Vikas Sharma , Philippe Colson , Roch Giorgi , Pierre Pontarotti , Didier Raoult Genome Biology and Evolution, 2014, 6 (7), ⟨10.1093/gbe/evu128⟩ Article dans une revue hal-01308942v1
	Choosing the best ancestral character state reconstruction method. Manuela Royer-Carenzi , Pierre Pontarotti , Gilles Didier Mathematical Biosciences, 2013, 242 (1), pp.95-109. ⟨10.1016/j.mbs.2012.12.003⟩ Article dans une revue hal-00830797v1
	To Tree or Not to Tree? Genome-Wide Quantification of Recombination and Reticulate Evolution during the Diversification of Strict Intracellular Bacteria Antonio Hernández-López , Olivier Chabrol , Manuela Royer-Carenzi , Vicky Merhej , Pierre Pontarotti Genome Biology and Evolution, 2013, 5 (12), pp.2305-2317. ⟨10.1093/gbe/evt178⟩ Article dans une revue hal-01107523v1
	An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales. Phuong Thi Le , Hemalatha Golaconda Ramulu , Laurent Guijarro , Julien Paganini , Philippe Gouret BMC Evolutionary Biology, 2012, 12 (1), pp.243. ⟨10.1186/1471-2148-12-243⟩ Article dans une revue inserm-00789846v1
	The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response. Hassnae Afrache , Philippe Gouret , Shanaiz Ainouche , Pierre Pontarotti , Daniel Olive Immunogenetics, 2012, 64 (11), pp.781-94. ⟨10.1007/s00251-012-0619-z⟩ Article dans une revue hal-00831095v1
	GLADX: an automated approach to analyze the lineage-specific loss and pseudogenization of genes. Jacques Dainat , Julien Paganini , Pierre Pontarotti , Philippe Gouret PLoS ONE, 2012, 7 (6), pp.e38792. ⟨10.1371/journal.pone.0038792⟩ Article dans une revue hal-00831091v1
	Controversies in modern evolutionary biology: the imperative for error detection and quality control. Francisco Prosdocimi , Benjamin Linard , Pierre Pontarotti , Olivier Poch , Julie Thompson BMC Genomics, 2012, 13 (1), pp.5. ⟨10.1186/1471-2164-13-5⟩ Article dans une revue inserm-00682055v1
	Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes. Julien Paganini , Amandine Campan-Fournier , Martine da Rocha , Philippe Gouret , Pierre Pontarotti PLoS ONE, 2012, 7 (11), pp.e50875. ⟨10.1371/journal.pone.0050875⟩ Article dans une revue hal-00831026v1
	Correction : GPR50 is the mammalian ortholog of Mel1c: Evidence of rapid evolution in mammals Laurence Dufourny , A. Levasseur , Martine Migaud , I. Callebaut , P. Pontarotti BMC Evolutionary Biology, 2012, 12 (Article 28), pp.1-3. ⟨10.1186/1471-2148-8-105⟩ Article dans une revue hal-01129620v1
	FunGene-DB: a web-based tool for Polyporales strains authentication. David Navarro , Anne Favel , Olivier Chabrol , Pierre Pontarotti , Mireille Haon Journal of Biotechnology, 2012, 161 (3), pp.383-6. ⟨10.1016/j.jbiotec.2012.06.023⟩ Article dans une revue hal-00831085v1
	The genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa. Otmane Lamrabet , Vicky Merhej , Pierre Pontarotti , Didier Raoult , Michel Drancourt PLoS ONE, 2012, 7 (4), pp.e34754. ⟨10.1371/journal.pone.0034754⟩ Article dans une revue hal-00831103v1
	The rhizome of life: what about metazoa? Hemalatha G Ramulu , Didier Raoult , Pierre Pontarotti Frontiers in Cellular and Infection Microbiology, 2012, 2, pp.50. ⟨10.3389/fcimb.2012.00050⟩ Article dans une revue hal-00831099v1
	The chordate proteome history database. Anthony Levasseur , Julien Paganini , Jacques Dainat , Julie D Thompson , Olivier Poch Evolutionary Bioinformatics, 2012, 8, pp.437-47. ⟨10.4137/EBO.S9186⟩ Article dans une revue hal-00831115v1
	Oocyte-somatic cells interactions, lessons from evolution. Cathy Charlier , Jérôme Montfort , Olivier Chabrol , Daphné Brisard , Thuy Thao Vi Nguyen BMC Genomics, 2012, 13 (1), pp.560. ⟨10.1186/1471-2164-13-560⟩ Article dans une revue hal-00753310v1
	Peptidoglycan: a post-genomic analysis. Caroline Cayrou , Bernard Henrissat , Philippe Gouret , Pierre Pontarotti , Michel Drancourt BMC Microbiology, 2012, 12, pp.294. ⟨10.1186/1471-2180-12-294⟩ Article dans une revue hal-00831025v1
	The Rhizome of Life: The Sympatric Rickettsia felis Paradigm Demonstrates the Random Transfer of DNA Sequences Vicky Merhej , Cedric Notredame , Manuela Royer-Carenzi , Pierre Pontarotti , Didier Raoult Molecular Biology and Evolution, 2011, 28 (11), pp.3213-3223. ⟨10.1093/molbev/msr239⟩ Article dans une revue hal-01105200v1
	The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics Anthony Levasseur , Pierre Pontarotti Biology Direct, 2011, 18 (6), pp.11. ⟨10.1186/1745-6150-6-11⟩ Article dans une revue hal-02645551v1
	Compound Poisson Approximation and Testing for Gene Clusters with Multigene Families Simona Grusea , Etienne Pardoux , Olivier Chabrol , Pierre Pontarotti Journal of Computational Biology, 2011, 18 (4), pp.579-594. ⟨10.1089/cmb.2010.0043⟩ Article dans une revue hal-00636411v1
	Origin and evolution of TRIM proteins: new insights from the complete TRIM repertoire of zebrafish and pufferfish Pierre Boudinot , Lieke M van Der Aa , Luc Jouneau , Louis Du Pasquier , Pierre Pontarotti PLoS ONE, 2011, 6 (7), pp.e22022. ⟨10.1371/journal.pone.0022022⟩ Article dans une revue hal-00831143v1
	Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits. Stephanie Bertrand , Alain Camasses , Ildiko Somorjai , Mohamed R Belgacem , Olivier Chabrol Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (22), pp.9160-5. ⟨10.1073/pnas.1014235108⟩ Article dans une revue hal-00831149v1
	Was the ancestral MHC involved in innate immunity Anthony Levasseur , Pierre Pontarotti European Journal of Immunology, 2010, 40 (10), pp.2682-2685. ⟨10.1002/eji.201040856⟩ Article dans une revue hal-02655486v1
	Exploring laccase-like multicopper oxidase genes from the ascomycete Trichoderma reesei: a functional, phylogenetic and evolutionary study Anthony Levasseur , Markku Saloheimo , David Navarro , Martina Andberg , Pierre Pontarotti BMC Biochemistry, 2010, 11, pp.32. ⟨10.1186/1471-2091-11-32⟩ Article dans une revue hal-02658923v1
	Nme Gene Family Evolutionary History Reveals Pre-Metazoan Origins and High Conservation between Humans and the Sea Anemone, Nematostella vectensis Thomas Desvignes , Pierre Pontarotti , Julien Bobe PLoS ONE, 2010, 5:11 (e15506), pp.1-12. ⟨10.1371/journal.pone.0015506⟩ Article dans une revue hal-01204995v1
	PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. Philippe Gouret , Julie Thompson , Pierre Pontarotti BMC Bioinformatics, 2009, 10 (1), pp.298. ⟨10.1186/1471-2105-10-298⟩ Article dans une revue inserm-00663932v1
	The TP53INP2 protein is required for autophagy in mammalian cells. Jonathan Nowak , Cendrine Archange , Joël Tardivel-Lacombe , Pierre Pontarotti , Marie-Josèphe Pébusque Molecular Biology of the Cell, 2009, 20 (3), pp.870-81. ⟨10.1091/mbc.E08-07-0671⟩ Article dans une revue hal-00831186v1
	Gene birth, death, and divergence: the different scenarios of reproduction-related gene evolution. Xin Tian , Géraldine Pascal , Sophie Fouchécourt , Pierre Pontarotti , Philippe Monget Biology of Reproduction, 2009, 80 (4), pp.616-21. ⟨10.1095/biolreprod.108.073684⟩ Article dans une revue hal-00831221v1
	Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Vicky Merhej , Manuela Royer-Carenzi , Pierre Pontarotti , Didier Raoult Biology Direct, 2009, 4, pp.13. ⟨10.1186/1745-6150-4-13⟩ Article dans une revue hal-00831226v1
	Origin and evolution of the vertebrate leukocyte receptors: the lesson from tunicates. Ivana Zucchetti , Rosaria de Santis , Simona Grusea , Pierre Pontarotti , Louis Du Pasquier Immunogenetics, 2009, 61 (6), pp.463-81. ⟨10.1007/s00251-009-0373-z⟩ Article dans une revue hal-00831237v1
	CASSIOPE: an expert system for conserved regions searches Virginie Lopez Rascol , Anthony Levasseur , Olivier Chabrol , Simona Grusea , Philippe Gouret BMC Bioinformatics, 2009, 10, pp.284 Article dans une revue hal-02661323v1
	Nme protein family evolutionary history, a vertebrate perspective Thomas Desvignes , Pierre Pontarotti , Christian Fauvel , Julien Bobe BMC Evolutionary Biology, 2009, 9:256, pp.1-25. ⟨10.1186/1471-2148-9-256⟩ Article dans une revue hal-02663889v1
	FOLy: An integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds Anthony Levasseur , François Piumi , Pedro M Coutinho , Corinne Rancurel , Michèle Asther Fungal Genetics and Biology, 2008, 45 (5), pp.638-645. ⟨10.1016/j.fgb.2008.01.004⟩ Article dans une revue hal-02666159v1
	Evolution of major histocompatibility complex by "en bloc" duplication before mammalian radiation Elodie Darbo , Etienne Danchin , Michael Mcdermott , Pierre Pontarotti Immunogenetics, 2008, 60 (8), pp.423-438. ⟨10.1007/s00251-008-0301-7⟩ Article dans une revue hal-02664403v1
	Nuclear localization of a novel human syntaxin 1B isoform Sandrine Pereira , Annick Massacrier , Patrice Roll , Alain Vérine , Marie-Christine Etienne-Grimaldi Gene, 2008, 423 (2), pp.160-71. ⟨10.1016/j.gene.2008.07.010⟩ Article dans une revue hal-00831154v1
	Strategies for reliable exploitation of evolutionary concepts in high throughput biology. Anthony Levasseur , Pierre Pontarotti , Olivier Poch , Julie D. Thompson Evolutionary Bioinformatics, 2008, 4, pp.121-37 Article dans une revue inserm-00368022v1
	The use of evolutionary biology concepts for genome annotation Etienne Danchin , Anthony Levasseur , Virginie Lopez Rascol , Philippe Gouret , Pierre Pontarotti Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2007, 308B (1), pp.26-36. ⟨10.1002/jez.b.21131⟩ Article dans une revue hal-02658043v1
	Molecular evolution of the human SRPX2 gene that causes brain disorders of the Rolandic and Sylvian speech areas Barbara Royer , Dinesh C Soares , Paul N Barlow , Ronald E Bontrop , Patrice Roll BMC Genetics, 2007, 8, pp.72. ⟨10.1186/1471-2156-8-72⟩ Article dans une revue hal-03509486v1
	Bromodomain testis-specific protein is expressed in mouse oocyte and evolves faster than its ubiquitously expressed paralogs BRD2, -3, and -4 Amélie Paillisson , Anthony Levasseur , Philippe Gouret , Isabelle Callebaut , Martine Bontoux Genomics, 2007, 89 (2), pp.215-223. ⟨10.1016/j.ygeno.2006.09.002⟩ Article dans une revue hal-00131215v1
	Atypical structure and phylogenomic evolution of the new eutherian oocyte- and embryo-expressed KHDC1/DPPA5/ECAT1/OOEP gene family Alice Pierre , Mathieu M. Gautier , I. Callebaut , Martine Bontoux , Eric Jeanpierre Genomics, 2007, 90 (5), pp.583-594 Article dans une revue hal-02666732v1
	Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution Anthony Levasseur , Ludovic Orlando , Xavier Bailly , Michel C. Milinkovitch , Etienne Danchin Biological Reviews, 2007, 82 (4), pp.551-572. ⟨10.1111/j.1469-185X.2007.00024.x⟩ Article dans une revue hal-02668139v1
	Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family Anthony Levasseur , Philippe Gouret , Laurence Lesage-Meessen , Michèle Asther , Marcel M. Asther BMC Evolutionary Biology, 2006, 6 (92), 11 p. ⟨10.1186/1471-2148-6-92⟩ Article dans une revue hal-02660242v1
	Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals Etienne Danchin , Philippe Gouret , Pierre Pontarotti BMC Evolutionary Biology, 2006, 6 (5), 10 p. ⟨10.1186/1471-2148-6-5⟩ Article dans une revue hal-02668451v1
	A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example. Nathalie Balandraud , Philippe Gouret , Etienne G. J. Danchin , M Blanc , D Zinn BMC Genomics, 2005, 6, pp.153. ⟨10.1186/1471-2164-6-153⟩ Article dans une revue inserm-00091307v1
	FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform Philippe Gouret , Vérane Vitiello , Nathalie Balandraud , André Gilles , Pierre Pontarotti BMC Bioinformatics, 2005, 6, 21 p. ⟨10.1186/1471-2105-6-198⟩ Article dans une revue hal-02681213v1
	Towards the reconstruction of the bilaterian ancestral pre-MHC region Etienne Danchin , Pierre Pontarotti Trends in Genetics, 2004, 20 (12), pp.587-591. ⟨10.1016/j.tig.2004.09.009⟩ Article dans une revue hal-02677408v1
	The major histocompatibility complex origin Etienne Danchin , Vérane Vitiello , Alexandre Vienne , Olivier Richard , Philippe Gouret Immunological Reviews, 2004, 198, pp.216-232 Article dans une revue hal-02682552v1
	Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome Etienne Danchin , Pierre Pontarotti Journal of Molecular Evolution, 2004, 59 (5), pp.587-597. ⟨10.1007/s00239-004-2648-1⟩ Article dans une revue hal-02677409v1
	Endogenous retroviral sequence is fused to FGFR1 kinase in the 8p12 stem-cell myeloproliferative disorder with t(8;19)(p12;q13.3) Géraldine Guasch , Cornel Popovici , Francine Mugneret , Max Chaffanet , Pierre Pontarotti Blood, 2003, 101 (1), pp.286-288. ⟨10.1182/blood-2002-02-0577⟩ Article dans une revue hal-03634435v1
	Evolution of the proto-MHC ancestral region Alexandre Vienne , Takashi Shiina , Laurent Abi-Rached , Etienne Danchin , Vérane Vitiello Immunogenetics, 2003, 55 (7), pp.429-436. ⟨10.1007/s00251-003-0601-x⟩ Article dans une revue hal-02683166v1
	Conservation of the MHC-like region throughout evolution Etienne Danchin , Laurent Abi-Rached , André Gilles , Pierre Pontarotti Immunogenetics, 2003, 55 (3), pp.141-148. ⟨10.1007/s00251-003-0562-0⟩ Article dans une revue hal-02681710v1
	A first map of the porcine major histocompatibility complex class I region F. Velten , Claire Rogel Gaillard , Christine Renard , Pierre Pontarotti , R. Tazi-Ahnini Tissue Antigens, 1998, 51, pp.183-194 Article dans une revue hal-02688540v1
	Molecular linkage of the human CTLA4 and CD28 Ig-superfamily genes in yeast artificial chromosomes Nathalie Buonavista , Christine Balzano , Pierre Pontarotti , Denis Le Paslier , Pierre Golstein Genomics, 1992, 13 (3), pp.856-861. ⟨10.1016/0888-7543(92)90169-s⟩ Article dans une revue hal-03104217v1

	Methods to identify and study the evolution of pseudogenes using a phylogenetic approach Jacques Dainat , Pierre Pontarotti Laura Poliseno. Pseudogenes. Functions and Protocols, 2324, Springer US, pp.21-34, 2021, 978-1-0716-1502-7. ⟨10.1007/978-1-0716-1503-4_2⟩ Chapitre d'ouvrage hal-03389474v1
	DDE Transposon as Public Goods Louis Tsakou-Ngouafo , Célia Vicari , Laura Helou , Vivek Keshri , Sabyasachi Das Evolutionary Biology—A Transdisciplinary Approach, Springer International Publishing, pp.337 - 357, 2020, ⟨10.1007/978-3-030-57246-4_14⟩ Chapitre d'ouvrage hal-03043351v1
	DDE Transposon as Public Goods Louis Tsakou-Ngouafo , Célia Vicari , Laura Helou , Vivek Keshri , Sabyasachi Das Evolutionary Biology—A Transdisciplinary Approach, Springer International Publishing, pp.337-357, 2020, ⟨10.1007/978-3-030-57246-4_14⟩ Chapitre d'ouvrage hal-03370014v1
	A Proposed Terminology of Convergent Evolution George R. Mcghee , Isabelle Hue , Justine Dardaillon , Pierre Pontarotti Origin and Evolution of Biodiversity, Springer International Publishing, 361p., 2019, 978-3-319-95953-5. ⟨10.1007/978-3-319-95954-2_18⟩ Chapitre d'ouvrage hal-02418230v1
	Road map to study convergent evolution: A proposition for evolutionary systems biology approaches Pierre Pontarotti , Isabelle Hue Evolutionary Biology : Convergent Evolution, Evolution of Complex Traits, Concepts and Methods, Springer International Publishing, 422 p., 2016, 978-3-319-41323-5. ⟨10.1007/978-3-319-41324-2_1⟩ Chapitre d'ouvrage hal-02801520v1
	CD277 an Immune Regulator of T Cell Function and Tumor Cell Recognition Jose Francisco Zambrano-Zaragoza , Nassima Messal , Sonia Pastor , Emmanuel Scotet , Marc Bonneville Advances in Cancer Therapy, In Tech, pp.411-428, 2011, 978-953-307-703-1. ⟨10.5772/24915⟩ Chapitre d'ouvrage hal-00827306v1
	Integration of evolutionary biology concepts for functional annotation and automation of complex research in evolution: the multi-agent software system DAGOBAH Philippe Gouret , Julien Paganini , Jacques Dainat , Dorra Louati , Elodie Darbo evolutionary biology-concepts biodiversity, macroevolution and genome evolution Evolutionary Biology - Concept Biodiversity, Macroevolution and Genome Evolution, SPRINGER, pp.71-87, 2011, 978-3-642-20762-4. ⟨10.1007/978-3-642-20763-1_5⟩ Chapitre d'ouvrage hal-00827323v1
	12th evolutionary biology meeting at marseilles Meeting report Pierre Pontarotti , Francisco Prosdocimi Evolutionary Biology Concept, Modeling, and Application, springer, pp.7-10, 2009 Chapitre d'ouvrage hal-00827684v1
	An Overview of Evolutionary Biology Concepts for Functional Annotation : Advances and Challenges Anthony Levasseur , Pierre Pontarotti Evolutionary Biology from Concept to Application, SPRINGER, pp.209-215, 2008, 978-3-540-78992-5. ⟨10.1007/978-3-540-78993-2_13⟩ Chapitre d'ouvrage hal-00827379v1
	A Possible Relationship Between the Phylogenetic Branch Lengths and the Chaetognath rRNA Paralog Gene Functionalities : Ubiquitous, Tissue-Specific or Pseudogenes. Roxane-Marie Barthelemy , Michel Grino , Pierre Pontarotti , Jean-Paul Casanova , Eric Faure Evolutionary Biology from Concept to Application, SPRINGER, pp.155-164, 2008 Chapitre d'ouvrage hal-00827395v1
	Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters Etienne Danchin , Pierre Pontarotti , Eric A. Gaucher Ancestral Sequence Reconstruction, Oxford University Press, 272 p., 2007, 978-0199545575 Chapitre d'ouvrage hal-02820457v1
	Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters Etienne G. J. Danchin , Eric A. Gaucher , Pierre Pontarotti Ancestral Sequence Reconstruction, oxford university press, pp.252, 2007, 9780199299188 Chapitre d'ouvrage hal-00827430v1
	The MHC big bang : duplication and exons shuffling during the chordate evolution. An hypothetico-deductive approach Laurent Abi Rached , Pierre Pontarotti The Major Histocompatibility Complex: Evolution, Structure, and Function, springer verlag japan, pp.561, 2000, 978-4431702764 Chapitre d'ouvrage hal-00828020v1
	Physical mapping of human chromosome 6. John Trowsdale , S. Beck , J.M. Boyle , D. Campbell , H.M. Cann Human genome analysis., Biomedical and Health Research IOS PRESS, pp.101-115, 1998 Chapitre d'ouvrage hal-00828081v1
	Geography and History of the Genes in the Human MHC: Can We Predict MHC Organization in Nonhuman Primates? R. Tazi Ahnini , J. Henry , Pierre Pontarotti Molecular Biology and Evolution of Blood Group and MHC Antigens in Primates, Springer-Verlag GmbH, pp.325-338, 1997 Chapitre d'ouvrage hal-00827530v1
	Molecular organization and evolution of the chromosomal region containing the human major histocompatibility complex Giovanna Chimini , Pierre Pontarotti Immunogenetics of the Major Histocompatibility Complex, Verlag Chemic International Publishers, New York, pp.65-99, 1991 Chapitre d'ouvrage hal-00827645v1
	Polymorphism and diversity in the murine class I gene family : a study of spontaneous mutants J. Geliebter , A. Kumar , F. Boriello , S. Hemmi , K. Kesari Evolution and vertebrate immunity :the antigen-receptor and MHC gene families, University of Texas Press, pp.315-323, 1987 Chapitre d'ouvrage hal-00827604v1

	Analyse phylogénomique des duplications géniques chez les poissons téléostéens : une approche PAR RNASeq Julien Bobe , Yann Guiguen , John H. Postlethwait , Laurent Journot , Christophe C. Klopp [Rapport de recherche] ANR-10-GENM-017, University of Oregon; Centre National de la Recherche Scientifique (CNRS); Aix Marseille Université (AMU); INRA SCRIBE Station Commune de Recherche en Ichtyophysiologie. Biodiversité et Environnement. 2015 Rapport hal-02801550v1
	Interactions ovocyte-cellules somatiques, une étude de génomique comparative chez les vertébrés - Oscile Julien Bobe , Svetlana Uzbekova , Pierre Pontarotti , Franck Chesnel [Contrat] ANR-08-GENM-033, INRA. 2013 Rapport hal-02808395v1

	Convergent evolution: concepts, database, roadmap and case studies Isabelle Hue , Justine Dardaillon , Pierre Pontarotti , George Mc Ghee AEEB: Evolutionary Biology Meeting, Sep 2017, Marseille, France. pp.189, 2017, 21st Evolutionary Biology Meeting Poster de conférence hal-02734433v1
	The PhyloFish project: an RNA-Seq approach coupled to high throughput phylogenomic analyses to study whole genome duplication impact on teleosts Jérémy Pasquier , Cédric Cabau , P. Gouret , L. Journot , Christophe C. Klopp 17. Evolutionary Biology Meeting at Marseilles, Sep 2013, Marseille, France. 2013, 17th Evolutionary Biology Meeting at Marseilles Poster de conférence hal-02745585v1
	Gene annotation with evolutionary support in teleosts with a focus on the salmonid lineage Julien Bobe , M. Westerfield , Pierre Pontarotti , Christophe C. Klopp , Laurent Journot 1. International Conference on Integrative Salmonid Biology ICISB, Jun 2012, Oslo, Norway. 2012, ICISB 2012 Poster de conférence hal-02746168v1
	Histoire évolutive des gènes de la famille Nme chez les vertébrés et implication dans la compétence ovocytaire au développement chez les poissons Thomas Desvignes , Pierre Pontarotti , Christian Fauvel , Julien Bobe Journées des doctorants de l'Ifremer, Oct 2010, Brest, France. 2010 Poster de conférence hal-02822027v1

	Holobiont diversity in heterogeneous and anthropized marine environments D. Aurelle , Christelle Desnues , Stephane Sartoretto , Emma Rozis , Sonia Bouchard Ecology and Evolution: New perspectives and societal challenges, SFE² GfÖ EEF Joint meeting, International Conference on Ecological Sciences, Nov 2022, Metz, France Communication dans un congrès hal-03947518v1
	Immunogenetics in the age of next generation sequencing and the need for dedicated analytical solutions Laurent Abi Rached , Philippe Gouret , Juang-Hua Yeh , Christophe Picard , Pierre Pontarotti HLA, 2019, Tours, France. pp.384 Communication dans un congrès hal-02526687v1
	Coral plasticity and holobiont dynamics under thermal stress: intrapopulational, interpopulational and interspecific variability Kelly Brener , Marine Pratlong , Jérémie Vidal-Dupiol , Mehdi Adjeroud , Pascal Romans 13th International Coral Reef Symposium, Jun 2016, Honolulu, United States. pp.38-39 Communication dans un congrès hal-03965848v1
	Integration of European eel transcriptome into the PHYLOFISH project, a high throughput phylogenomic analysis designed to study teleost gene evolution after whole genome duplication Jérémy Pasquier , Cédric Cabau , P. Gouret , L. Journot , Christophe C. Klopp Eel genome symposium 2014, Jan 2014, Leiden, Netherlands Communication dans un congrès hal-02743789v1
	Interactions ovocyte-cellules somatiques, une étude de génomique comparative chez les vertébrés Julien Bobe , Svetlana Uzbekova , Pierre Pontarotti , Franck Chesnel 9. Journées AGENAE, Mar 2012, La Rochelle, France Communication dans un congrès hal-02747100v1
	Oscile Cathy Charlier , Jérôme Montfort , Olivier Chabrol , François Moreews , M. Salhab VIIIe Colloque Agenae / Genanimal, Nov 2010, Bordeaux, France Communication dans un congrès inria-00540830v1
	The Nme family: gene repertoire and evolutionary history Thomas Desvignes , Pierre Pontarotti , Christian Fauvel , Julien Bobe 8. International Congress of the NDP Kinase/Nm23/awd Family - From basic science to clinical application, Oct 2010, Heidelberg, Germany Communication dans un congrès hal-02818522v1
	Nme protein family evolutionary history, a vertebrate perspective with emphasis on the teleost group Thomas Desvignes , Pierre Pontarotti , Christian Fauvel , Julien Bobe Evolutionary biology 2009: Phylogenetics, speciation, co-evolution, development, genomes, life histories, plasticity.. What is new ?, Jun 2009, Rennes, France Communication dans un congrès hal-02752933v1
	La phylogénie à l'heure de l'annotation fonctionnellle des génomes Philippe Monget , Pierre Pontarotti Séminaire AIP INRA 2005-2007. Séquençage et Ressources Génétiques "du séquençage à la biologie intégrative", Nov 2007, Paris, France Communication dans un congrès hal-02752018v1

	Evolutionary Biology—A Transdisciplinary Approach Pierre Pontarotti Springer International Publishing, 2020, ⟨10.1007/978-3-030-57246-4⟩ Ouvrages hal-03047851v1
	Evolution, Origin of Life, Concepts and Methods Pierre Pontarotti Springer International Publishing, 2019, ⟨10.1007/978-3-030-30363-1⟩ Ouvrages hal-03047853v1
	Evolution, Origin of Life, Concepts and Methods Pierre Pontarotti Springer International Publishing, 2019, ⟨10.1007/978-3-030-30363-1⟩ Ouvrages hal-02418178v1
	Evolutionary Biology: Exobiology and Evolutionary Mechanisms Pierre Pontarotti SPRINGER, pp.304, 2013, 978-3-642-38211-6 Ouvrages hal-00828085v1
	Evolutionary biology : mechanisms and trends Pierre Pontarotti springer, pp.364, 2012 Ouvrages hal-00828007v1
	Evolutionary Biology - Concept Biodiversity, Macroevolution and Genome Evolution Pierre Pontarotti springer, pp.345, 2011, 978-3-642-20762-4 Ouvrages hal-00828088v1
	Evolutionary Biology - Concepts, Molecular and Morphological Evolution Pierre Pontarotti springer, pp.360, 2010, 978-3-642-12339-9 Ouvrages hal-00828096v1
	Evolutionary Biology - Concept, Modeling and Application Pierre Pontarotti SPRINGER, pp.398, 2009, 978-3-642-00951-8 Ouvrages hal-00828099v1
	Evolutionary Biology from Concept to Application Pierre Pontarotti SPRINGER, pp.220, 2008 Ouvrages hal-00828101v1

	Sequencing, de novo assembly and annotation of the genome of the scleractinian coral, Pocillopora acuta Jeremie Vidal-Dupiol , Cristian Chaparro , Marine Pratlong , Pierre Pontarotti , Christoph Grunau 2021 Pré-publication, Document de travail hal-03239739v1
	Population genomics of Pocillopora corals: insights from RAD-sequencing Didier Aurelle , Marine Pratlong , Nicolas Oury , Anne Haguenauer , Pauline Gélin 2021 Pré-publication, Document de travail hal-03374944v1
	A metallo-beta-lactamase with both beta-lactamase and ribonuclease activity is linked with traduction in giant viruses Philippe Colson , Lucile Pinault , Said Azza , Nicholas Armstrong , Eric Chabriere 2020 Pré-publication, Document de travail hal-03047394v1

Pierre Pontarotti

Publications

Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality

Insights into RAG evolution from the identification of “missing link” family A RAGL transposons

Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms

Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals

RadA, a Key Gene of the Circadian Rhythm of Escherichia coli

HLA-H*02:07 Is a Membrane-Bound Ligand of Denisovan Origin That Protects against Lysis by Activated Immune Effectors

COVID-19 Pandemic: Escape of Pathogenic Variants and MHC Evolution

Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia)

HLA-H*02:07 Is a Membrane-Bound Ligand of Denisovan Origin That Protects against Lysis by Activated Immune Effectors

Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum

The piggyBac-derived protein 5 (PGBD5) transposes both the closely and the distantly related piggyBac-like elements Tcr-pble and Ifp2

Could β-Lactam Antibiotics Block Humoral Immunity?

Self-Peptidome Variation Shapes Individual Immune Responses

Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica

A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin

A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin

Search for MHC/TCR-Like Systems in Living Organisms

Could β-Lactam Antibiotics Block Humoral Immunity?

Self-Peptidome Variation Shapes Individual Immune Responses

A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin

Search for MHC/TCR-Like Systems in Living Organisms

Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea

Origins of the RAG Transposome and the MHC

Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea

A protein of the metallo-hydrolase/oxidoreductase superfamily with both beta-lactamase and ribonuclease activity is linked with translation in giant viruses

A protein of the metallo-hydrolase/oxidoreductase superfamily with both beta-lactamase and ribonuclease activity is linked with translation in giant viruses

Origins of the RAG Transposome and the MHC

A protein of the metallo-hydrolase/oxidoreductase superfamily with both beta-lactamase and ribonuclease activity is linked with translation in giant viruses

Origins of the RAG Transposome and the MHC

Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases

Identification of RAG-like transposons in protostomes suggests their ancient bilaterian origin

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

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

Human metallo-β-lactamase enzymes degrade penicillin

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

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

Transposon molecular domestication and the evolution of the RAG recombinase

Human metallo-β-lactamase enzymes degrade penicillin

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

Why do arthropods secrete β-lactams?

Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members

Detecting the molecular basis of phenotypic convergence

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

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

In silico analysis of Schmidtea mediterranea TIR domain-containing proteins

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

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

Amphioxus functional genomics and the origins of vertebrate gene regulation

Immune diversity sheds light on missing variation in worldwide genetic diversity panels

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

The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes

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

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

Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree?

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

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

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

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.

Origin and Evolution of Rickettsial Plasmids

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

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

Genomic resources and their influence on the detection of the signal of positive selection in genome scans

Compartmentalization in PVC super-phylum: evolution and impact

Welcome to pandoraviruses at the 'Fourth TRUC' club

The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies

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

The genome of the white-rot fungus [i]Pycnoporus cinnabarinus[/i]: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown

The Proto-MHC of Placozoans, a Region Specialized in Cellular Stress and Ubiquitination/Proteasome Pathways

Mycobacteriophage-drived diversification of Mycobacterium abscessus

African Relapsing Fever Borreliae Genomospecies Revealed by Comparative Genomics

DNA-Dependent RNA Polymerase Detects Hidden Giant Viruses in Published Databanks

Choosing the best ancestral character state reconstruction method.

To Tree or Not to Tree? Genome-Wide Quantification of Recombination and Reticulate Evolution during the Diversification of Strict Intracellular Bacteria

An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales.

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

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

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

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