Pierre Pontarotti

directeur de recherche émérite au CNRS.
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Publications

The Phylogenomic Approach Suggests That Butyrophilins Have Ligands Beyond Gamma–Delta Receptors

Ludovic Marenco , Daniel Olive , Pierre Pontarotti

International Journal of Molecular Sciences, 2026, 27 (2), pp.741. ⟨10.3390/ijms27020741⟩

Article dans une revue hal-05468860v1

APOBEC cellular enzymes as ‘court jesters’ in SARS-CoV-2 evolution

Philippe Colson , Pierre Pontarotti , Jacques Fantini , Anthony Levasseur , Christian Devaux et al.

Virus Genes, 2026, Mar 14., Online ahead of print. ⟨10.1007/s11262-026-02227-w⟩

Article dans une revue hal-05558515v1

“Fertile” Mutations in SARS ‐ CoV ‐2 RNA More Frequently Occurred in Hairpin Loops That Determine Virus Evolution

Philippe Colson , Pierre Pontarotti , Jacques Fantini , Anthony Levasseur , Christian Devaux et al.

APMIS, 2025, 133 (12), pp.e70113. ⟨10.1111/apm.70113⟩

Article dans une revue hal-05454460v1

The disappearance of ORF8 in human-adapted coronaviruses: the Cheshire cat paradigm

Philippe Colson , Anthony Levasseur , Hervé Chaudet , Christian Devaux , Jacques Fantini et al.

Virus Genes, 2025, Online ahead of print. ⟨10.1007/s11262-025-02196-6⟩

Article dans une revue hal-05371351v1
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HLA Class Ib and MICA/MICB Expression in Human Tissues and Cell Types: Reshuffling Immune Players

Laurent Abi-Rached , Pierre Faux , Julien Paganini , Jacques Chiaroni , Pierre Pontarotti et al.

HLA: Immune Response Genetics, 2025, 106 (3), ⟨10.1111/tan.70390⟩

Article dans une revue hal-05248853v1
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Mechanisms of acquisition of the vanA operon among vancomycin-resistant Staphylococcus aureus genomes: The tip of the iceberg?

Tram Vo , Pierre Pontarotti , Jean-Marc Rolain , Vicky Merhej

International Journal of Antimicrobial Agents, 2024, 63 (6), pp.107154. ⟨10.1016/j.ijantimicag.2024.107154⟩

Article dans une revue hal-04785869v1

Intrinsically linked lineage-specificity of transposable elements and lncRNAs reshapes transcriptional regulation species- and tissue-specifically

Jie Lin , Yijin Wu , Wei Xiong , Sha He , Pierre Pontarotti et al. Article dans une revue hal-04498089v1
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Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic

Philippe Colson , Hervé Chaudet , Jérémy Delerce , Pierre Pontarotti , Anthony Levasseur et al.

Journal of Infection, 2024, 88 (5), pp.106150. ⟨10.1016/j.jinf.2024.106150⟩

Article dans une revue hal-04795807v1

Resistance‐associated mutations to the anti‐SARS‐CoV‐2 agent nirmatrelvir: Selection not induction

Philippe Colson , Jérémy Delerce , Pierre Pontarotti , Christian Devaux , Bernard La Scola et al.

Journal of Medical Virology, 2024, 96 (2), ⟨10.1002/jmv.29462⟩

Article dans une revue hal-04463077v1

Mechanisms of acquisition of the vanA operon among vancomycin-resistant Staphylococcus aureus genomes: The tip of the iceberg?

Tram Vo , Pierre Pontarotti , Jean-Marc Rolain , Vicky Merhej

International Journal of Antimicrobial Agents, 2024, 63 (6), pp.107154. ⟨10.1016/j.ijantimicag.2024.107154⟩

Article dans une revue hal-04677856v1
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“Outlaw” mutations in quasispecies of SARS-CoV-2 inhibit replication

Philippe Colson , Jacques Fantini , Jeremy Delerce , Wahiba Bader , Anthony Levasseur et al.

Emerging microbes & infections, 2024, 13 (1), ⟨10.1080/22221751.2024.2368211⟩

Article dans une revue hal-04795753v1

Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic

Philippe Colson , Hervé Chaudet , Jérémy Delerce , Pierre Pontarotti , Anthony Levasseur et al.

Journal of Infection, 2024, 88 (5), pp.106150. ⟨10.1016/j.jinf.2024.106150⟩

Article dans une revue hal-04675387v1

Resistance‐associated mutations to the anti‐SARS‐CoV‐2 agent nirmatrelvir: Selection not induction

Philippe Colson , Jérémy Delerce , Pierre Pontarotti , Christian Devaux , Bernard La Scola et al.

Journal of Medical Virology, 2024, 96 (2), ⟨10.1002/jmv.29462⟩

Article dans une revue hal-04789246v1
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The IL-17 pathway intertwines with neurotrophin and TLR/IL-1R pathways since its domain shuffling origin

Shenghui Chen , Huiping Fan , Chenrui Ran , Yun Hong , Huixiong Feng et al.

Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (19), pp.e2400903121. ⟨10.1073/pnas.2400903121⟩

Article dans une revue hal-04564576v1
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Is it time to switch to a formulation other than the live attenuated poliovirus vaccine to prevent poliomyelitis?

Christian Albert Devaux , Pierre Pontarotti , Anthony Levasseur , Philippe Colson , Didier Raoult

Frontiers in Public Health, 2024, 11, pp.1284337. ⟨10.3389/fpubh.2023.1284337⟩

Article dans une revue hal-04403097v1
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The emergence, spread and vanishing of a French SARS‐CoV‐2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule

Philippe Colson , Philippe Gautret , Jeremy Delerce , Hervé Chaudet , Pierre Pontarotti et al.

Journal of Medical Virology, 2023, 95 (1), ⟨10.1002/jmv.28102⟩

Article dans une revue hal-03805866v1
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Integration of the immune memory into the pathogen‐driven MHC polymorphism hypothesis

Jacek Radwan , Chirine Kohi , Maciej Ejsmond , Julien Paganini , Pierre Pontarotti

HLA: Immune Response Genetics, In press, ⟨10.1111/tan.15216⟩

Article dans une revue hal-04201789v2
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From viral democratic genomes to viral wild bunch of quasispecies

Philippe Colson , Wahiba Bader , Jacques Fantini , Pierre Dudouet , Anthony Levasseur et al.

Journal of Medical Virology, 2023, 95 (11), ⟨10.1002/jmv.29209⟩

Article dans une revue hal-04275773v1

The return of the “Mistigri” (virus adaptative gain by gene loss) through the SARS‐CoV‐2 XBB.1.5 chimera that predominated in 2023

Philippe Colson , Jérémy Delerce , Jacques Fantini , Pierre Pontarotti , Bernard La Scola et al.

Journal of Medical Virology, 2023, 95 (10), pp.e29146. ⟨10.1002/jmv.29146⟩

Article dans une revue hal-04243842v1
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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 et al.

Cells, 2023, 12 (13), pp.1752. ⟨10.3390/cells12131752⟩

Article dans une revue hal-04275581v1
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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 et al.

Molecular Biology and Evolution, 2023, ⟨10.1093/molbev/msad232⟩

Article dans une revue hal-04243785v2
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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 et al.

Microorganisms, 2023, 11 (8), pp.1933. ⟨10.3390/microorganisms11081933⟩

Article dans une revue hal-04275003v1
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Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia)

Didier Aurelle , Marine Pratlong , Nicolas Oury , Anne Haguenauer , Pauline Gélin et al.

Genetica, 2022, 150 (5), pp.247-262. ⟨10.1007/s10709-022-00165-7⟩

Article dans une revue hal-03774130v1
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Parallel evolution of amphioxus and vertebrate small-scale gene duplications

Marina Brasó-Vives , Ferdinand Marlétaz , Amina Echchiki , Federica Mantica , Rafael D Acemel et al.

Genome Biology, 2022, 23 (1), pp.243. ⟨10.1186/s13059-022-02808-6⟩

Article dans une revue hal-03860371v1
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Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals

K. Brener-Raffalli , Jeremie Vidal-Dupiol , M. Adjeroud , Olivier REY , P. Romans et al.

Peer Community Journal, 2022, 2, pp.e13. ⟨10.24072/pcjournal.79⟩

Article dans une revue hal-03239787v1
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RadA, a Key Gene of the Circadian Rhythm of Escherichia coli

Aissatou Bailo Diallo , Soraya Mezouar , Asma Boumaza , Oksana Fiammingo , Benjamin Coiffard et al.

International Journal of Molecular Sciences, 2022, 23 (11), pp.6136. ⟨10.3390/ijms23116136⟩

Article dans une revue hal-03684665v1

HLA-H*02:07 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 et al.

Journal of Immunology, 2022, pp.ji2100358. ⟨10.4049/jimmunol.2100358⟩

Article dans une revue hal-03471956v1
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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
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A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin

Seydina Diene , Lucile Pinault , Sophie Alexandra Baron , Saïd Azza , Nicholas Armstrong et al.

Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-89600-x⟩

Article dans une revue hal-03281982v1
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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
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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 et al.

Frontiers in Microbiology, 2021, 12, ⟨10.3389/fmicb.2021.662762⟩

Article dans une revue hal-03308205v1
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Could β-Lactam Antibiotics Block Humoral Immunity?

Cléa Melenotte , Pierre Pontarotti , Lucile Pinault , Jean-Louis Mège , Christian Devaux et al.

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

Seydina M Diene , Lucile Pinault , Sophie Alexandra Baron , Saïd Azza , Nicholas Armstrong et al.

Scientific Reports, 2021, 11, ⟨10.1038/s41598-021-89600-x⟩

Article dans une revue hal-03371030v1
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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
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Could β-Lactam Antibiotics Block Humoral Immunity?

Cléa Melenotte , Pierre Pontarotti , Lucile Pinault , Jean-Louis Mège , Christian Devaux et al.

Frontiers in Immunology, 2021, 12, pp.680146. ⟨10.3389/fimmu.2021.680146⟩

Article dans une revue hal-03370420v1
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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
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Separate the wheat from the chaff: genomic scan for local adaptation in the red coral <i>Corallium rubrum</i>

Marine Pratlong , Anne Haguenauer , K. Brener , G. Mitta , E. Toulza et al.

Peer Community Journal, 2021, 1, pp.e31. ⟨10.24072/pcjournal.12⟩

Article dans une revue hal-03454660v2
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HLA-H*02:07 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 et al.

Journal of Immunology, 2021, 208 (1), pp.49-53. ⟨10.4049/jimmunol.2100358⟩

Article dans une revue hal-03869640v1
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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 et al.

Journal of Molecular Biology, 2021, 433 (7), pp.1-16. ⟨10.1016/j.jmb.2021.166839⟩

Article dans une revue hal-03149600v1
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A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin

Seydina Diene , Lucile Pinault , Sophie Alexandra Baron , Saïd Azza , Nicholas Armstrong et al.

Scientific Reports, 2021, 11 (1), pp.10062. ⟨10.1038/s41598-021-89600-x⟩

Article dans une revue hal-03366566v1
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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 et al.

Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-78658-8⟩

Article dans une revue hal-03366581v1
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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 et al.

Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-78658-8⟩

Article dans une revue hal-03149225v1
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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 et al.

Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-78658-8⟩

Article dans une revue hal-03371039v1
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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 et al.

Mobile DNA, 2020, 11 (1), ⟨10.1186/s13100-020-00214-y⟩

Article dans une revue hal-03047226v1
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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 et al.

International Journal of Molecular Sciences, 2020, 21 (17), pp.6260. ⟨10.3390/ijms21176260⟩

Article dans une revue hal-03047280v1
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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
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Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea

Seydina M Diene , Lucile Pinault , Nicholas Armstrong , Said Azza , Vivek Keshri et al.

Life, 2020, 10 (11), pp.280. ⟨10.3390/life10110280⟩

Article dans une revue hal-03047404v1
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Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea

Seydina Diene , Lucile Pinault , Nicholas Armstrong , Said Azza , Vivek Keshri et al.

Life, 2020, 10 (11), pp.280. ⟨10.3390/life10110280⟩

Article dans une revue hal-03366589v1

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

Julien Paganini , Laurent Abi-Rached , Philippe Gouret , Pierre Pontarotti , Jacques Chiaroni et al.

Molecular Immunology, 2019, 112, pp.40-50. ⟨10.1016/j.molimm.2019.04.017⟩

Article dans une revue hal-03371942v1
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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 et al.

Evolutionary Applications, 2019, 12 (9), pp.1812-1822. ⟨10.1111/eva.12835⟩

Article dans une revue hal-03047294v1
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An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees

Vivek Keshri , Seydina Diene , Adrien Estienne , Justine Dardaillon , Olivier Chabrol et al.

Antimicrobial Agents and Chemotherapy, 2019, 63 (5), ⟨10.1128/AAC.02319-18⟩

Article dans une revue hal-02159541v1
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Transposon molecular domestication and the evolution of the RAG recombinase

Yuhang Zhang , Tat Cheung Cheng , Guangrui Huang , Qingyi Lu , Marius Surleac et al.

Nature, 2019, 569 (7754), pp.79-84. ⟨10.1038/s41586-019-1093-7⟩

Article dans une revue hal-02262562v1
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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 et al.

Evolutionary Applications, 2019, ⟨10.1111/eva.12835⟩

Article dans une revue hal-02263608v1
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Human metallo-β-lactamase enzymes degrade penicillin

Seydina M Diene , Lucile Pinault , Vivek Keshri , Nicholas Armstrong , Saber Khelaifia et al.

Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-48723-y⟩

Article dans une revue hal-03047415v1
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Human metallo-β-lactamase enzymes degrade penicillin

Seydina Diene , Lucile Pinault , Vivek Keshri , Nicholas Armstrong , Saber Khelaifia et al.

Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-48723-y⟩

Article dans une revue hal-02479402v1

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

Julien Paganini , Laurent Abi-Rached , Philippe Gouret , Pierre Pontarotti , Jacques Chiaroni et al.

Molecular Immunology, 2019, 112, pp.40-50. ⟨10.1016/j.molimm.2019.04.017⟩

Article dans une revue hal-02137704v1
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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 et al.

Developmental and Comparative Immunology, 2018, 84, pp.193-198. ⟨10.1016/j.dci.2018.02.011⟩

Article dans une revue hal-04772664v1
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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
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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
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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 et al.

Frontiers in Microbiology, 2018, 9, ⟨10.3389/fmicb.2018.02668⟩

Article dans une revue hal-01948086v1
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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 et al.

Developmental and Comparative Immunology, 2018, 84, pp.193-198. ⟨10.1016/j.dci.2018.02.011⟩

Article dans une revue inserm-02148721v1
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Amphioxus functional genomics and the origins of vertebrate gene regulation

Ferdinand Marletaz , Panos N. Firbas , Ignacio Maeso , Juan J. Tena , Ozren Bogdanovic et al.

Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩

Article dans une revue hal-02000511v1
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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 et al.

Frontiers in Microbiology, 2018, 9, ⟨10.3389/fmicb.2018.02098⟩

Article dans une revue hal-01910335v1

In silico analysis of Schmidtea mediterranea TIR domain-containing proteins

Landry Laure Tsoumtsa , Seynabou Sougoufora , Cedric Torre , Emmanuel Lemichez , Pierre Pontarotti et al.

Developmental and Comparative Immunology, 2018, 86, pp.214-218. ⟨10.1016/j.dci.2018.05.004⟩

Article dans une revue hal-01858942v1

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 et al.

Genome Biology and Evolution, 2018, 10 (4), pp.1106-1114. ⟨10.1093/gbe/evy028⟩

Article dans une revue hal-02057304v1
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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 et al.

PLoS ONE, 2018, 13 (10), pp.e0206512. ⟨10.1371/journal.pone.0206512⟩

Article dans une revue hal-01931053v1
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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-04243712v1
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Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree?

Marine Pratlong , Corinne Rancurel , Pierre Pontarotti , Didier 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
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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
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The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes

Anthony Levasseur , Vicky Merhej , Emeline Baptiste , Vikas Sharma , Pierre Pontarotti et al.

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
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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
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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⟩

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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⟩

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

Shengfeng Huang , Xin Tao , Shaochun Yuan , Yuhang Zhang , Peiyi Li et al.

Cell, 2016, 166 (1), pp.102-114. ⟨10.1016/j.cell.2016.05.032⟩

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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 et al.

BMC Genomics, 2016, 17 (1), pp.368. ⟨10.1186/s12864-016-2709-z⟩

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

Anthony Levasseur , Meriem Bekliz , Eric Chabrière , Pierre Pontarotti , Bernard La Scola et al.

Nature, 2016, 531 (7593), pp.249-252. ⟨10.1038/nature17146⟩

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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⟩

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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⟩

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

Shengfeng Huang , Xin Tao , Shaochun Yu , Yuhang Yu , Peiyi Li et al.

Cell, 2016, 166 (1), pp.102 - 114. ⟨10.1016/j.cell.2016.05.032⟩

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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 et al.

Molecular Ecology, 2016, 25 (1), pp.170-184. ⟨10.1111/mec.13468⟩

Article dans une revue hal-02336047v1
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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 et al.

Molecular Ecology Resources, 2015, 15 (5), pp.1205--1215. ⟨10.1111/1755-0998.12383⟩

Article dans une revue istex hal-01445149v1
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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⟩

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Welcome to pandoraviruses at the 'Fourth TRUC' club

Vikas Sharma , Philippe Colson , Olivier Chabrol , Patrick Scheid , Pierre Pontarotti et al.

Frontiers in Microbiology, 2015, 6 (423), ⟨10.3389/fmicb.2015.00423⟩

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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 et al.

BMC Genomics, 2014, 15 (1), pp.486. ⟨10.1186/1471-2164-15-486⟩

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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), pp.1603-1610. ⟨10.1093/gbe/evu128⟩

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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
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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⟩

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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 et al.

Journal of Immunology, 2014, 193 (6), pp.2891 - 2901. ⟨10.4049/jimmunol.1401177⟩

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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 et al.

Genome Biology and Evolution, 2013, 5 (12), pp.2305-2317. ⟨10.1093/gbe/evt178⟩

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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⟩

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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⟩

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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

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

David Navarro , Anne Favel , Olivier Chabrol , Pierre Pontarotti , Mireille Haon et al.

Journal of Biotechnology, 2012, 161 (3), pp.383-6. ⟨10.1016/j.jbiotec.2012.06.023⟩

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Correction : GPR50 is the mammalian ortholog of Mel1c: Evidence of rapid evolution in mammals

Laurence Dufourny , A. Levasseur , Martine Migaud , I. Callebaut , P. Pontarotti et al.

BMC Evolutionary Biology, 2012, 12 (Article 28), pp.1-3. ⟨10.1186/1471-2148-8-105⟩

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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 et al.

PLoS ONE, 2012, 7 (11), pp.e50875. ⟨10.1371/journal.pone.0050875⟩

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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
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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
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The chordate proteome history database.

Anthony Levasseur , Julien Paganini , Jacques Dainat , Julie D Thompson , Olivier Poch et al.

Evolutionary Bioinformatics, 2012, 8, pp.437-47. ⟨10.4137/EBO.S9186⟩

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Oocyte-somatic cells interactions, lessons from evolution.

Cathy Charlier , Jérôme Montfort , Olivier Chabrol , Daphné Brisard , Thuy Thao Vi Nguyen et al.

BMC Genomics, 2012, 13 (1), pp.560. ⟨10.1186/1471-2164-13-560⟩

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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⟩

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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⟩

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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 et al.

BMC Evolutionary Biology, 2012, 12 (1), pp.243. ⟨10.1186/1471-2148-12-243⟩

Article dans une revue inserm-00789846v1
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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
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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
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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 et al.

PLoS ONE, 2011, 6 (7), pp.e22022. ⟨10.1371/journal.pone.0022022⟩

Article dans une revue hal-00831143v1
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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⟩

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Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits.

Stephanie Bertrand , Alain Camasses , Ildiko Somorjai , Mohamed R Belgacem , Olivier Chabrol et al.

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
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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 et al.

BMC Biochemistry, 2010, 11, pp.32. ⟨10.1186/1471-2091-11-32⟩

Article dans une revue hal-02658923v1

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
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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
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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
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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 (article de synthèse) hal-00831221v1

The TP53INP2 protein is required for autophagy in mammalian cells.

Jonathan Nowak , Cendrine Archange , Joël Tardivel-Lacombe , Pierre Pontarotti , Marie-Josèphe Pébusque et al.

Molecular Biology of the Cell, 2009, 20 (3), pp.870-81. ⟨10.1091/mbc.E08-07-0671⟩

Article dans une revue hal-00831186v1

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 istex hal-00831237v1

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
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CASSIOPE: an expert system for conserved regions searches

Virginie Lopez Rascol , Anthony Levasseur , Olivier Chabrol , Simona Grusea , Philippe Gouret et al.

BMC Bioinformatics, 2009, 10, pp.284

Article dans une revue hal-02661323v1
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<em>Nme</em> 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
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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

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 et al.

Fungal Genetics and Biology, 2008, 45 (5), pp.638-645. ⟨10.1016/j.fgb.2008.01.004⟩

Article dans une revue istex hal-02666159v1
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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.121-137. ⟨10.4137/ebo.s597⟩

Article dans une revue hal-04127572v1

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 istex hal-02664403v1

Nuclear localization of a novel human syntaxin 1B isoform

Sandrine Pereira , Annick Massacrier , Patrice Roll , Alain Vérine , Marie-Christine Etienne-Grimaldi et al.

Gene, 2008, 423 (2), pp.160-71. ⟨10.1016/j.gene.2008.07.010⟩

Article dans une revue istex hal-00831154v1

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 et al.

Biological Reviews, 2007, 82 (4), pp.551-572. ⟨10.1111/j.1469-185X.2007.00024.x⟩

Article dans une revue istex hal-02668139v1
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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 istex hal-02658043v1
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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 et al.

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 et al.

Genomics, 2007, 89 (2), pp.215-223. ⟨10.1016/j.ygeno.2006.09.002⟩

Article dans une revue istex 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 et al.

Genomics, 2007, 90 (5), pp.583-594. ⟨10.1016/j.ygeno.2007.06.003⟩

Article dans une revue hal-02666732v1
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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
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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 et al.

BMC Evolutionary Biology, 2006, 6 (92), 11 p. ⟨10.1186/1471-2148-6-92⟩

Article dans une revue hal-02660242v1
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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 et al.

BMC Genomics, 2005, 6, pp.153. ⟨10.1186/1471-2164-6-153⟩

Article dans une revue inserm-00091307v1
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FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform

Philippe Gouret , Vérane Vitiello , Nathalie Balandraud , André Gilles , Pierre Pontarotti et al.

BMC Bioinformatics, 2005, 6, 21 p. ⟨10.1186/1471-2105-6-198⟩

Article dans une revue hal-02681213v1

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 istex hal-02677409v1

The major histocompatibility complex origin

Etienne Danchin , Vérane Vitiello , Alexandre Vienne , Olivier Richard , Philippe Gouret et al.

Immunological Reviews, 2004, 198, pp.216-232

Article dans une revue hal-02682552v1

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 istex hal-02677408v1

Evolution of the proto-MHC ancestral region

Alexandre Vienne , Takashi Shiina , Laurent Abi-Rached , Etienne Danchin , Vérane Vitiello et al.

Immunogenetics, 2003, 55 (7), pp.429-436. ⟨10.1007/s00251-003-0601-x⟩

Article dans une revue istex hal-02683166v1

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 et al.

Blood, 2003, 101 (1), pp.286-288. ⟨10.1182/blood-2002-02-0577⟩

Article dans une revue hal-03634435v1

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 istex 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 et al.

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 istex hal-03104217v1
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Characterization of the novel transposon Tn7722 harboring bla NDM-1 : Insights into the evolutionary dynamics of resistance in Klebsiella pneumoniae

Tram Vo , Aïcha Hamieh , Marc Levy , Pierre Pontarotti , Jean-Marc Rolain et al.

2026

Pré-publication, Document de travail (working paper) hal-05526118v1

Long-Term Intra-Host Evolution of SARS-CoV-2 in an Immunocompromised Patient: Recombination and Within-Host Mutations Driving Viral Adaptation

Emilie Burel , Pierre Pontarotti , Jacques Fantini , Jean-Christophe Lagier , Pierre Edouard Fournier

2025

Pré-publication, Document de travail hal-05015227v1
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Symbiotic status does not preclude hybridisation in Mediterranean octocorals

Didier Aurelle , Anne Haguenauer , Marc Bally , Frédéric Zuberer , Jean-Baptiste Ledoux et al.

2024

Pré-publication, Document de travail hal-04568927v1
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Pre-Columbian treponemes clarify worldwide spread of treponematosis

Matteo Gueyrard , Pierre Pontarotti , Michel Drancourt , Laurent Abi-Rached

2024

Pré-publication, Document de travail hal-04403114v1
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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 et al.

2021

Pré-publication, Document de travail hal-03239739v1
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Population genomics of Pocillopora corals: insights from RAD-sequencing

Didier Aurelle , Marine Pratlong , Nicolas Oury , Anne Haguenauer , Pauline Gélin et al.

2021

Pré-publication, Document de travail hal-03374944v1
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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 et al.

2020

Pré-publication, Document de travail hal-03047394v1

Holobiont diversity in heterogeneous and anthropized marine environments

D. Aurelle , Christelle Desnues , Stephane Sartoretto , Emma Rozis , Sonia Bouchard et al.

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 et al.

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 et al.

13th International Coral Reef Symposium, Jun 2016, Honolulu, United States. pp.38-39

Communication dans un congrès hal-03965848v1
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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 Klopp et al.

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

The <em>Nme</em> 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

Oscile

Cathy Charlier , Jérôme Montfort , Olivier Chabrol , François Moreews , M. Salhab et al.

VIIIe Colloque Agenae / Genanimal, Nov 2010, Bordeaux, France

Communication dans un congrès inria-00540830v1

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
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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
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DDE Transposon as Public Goods

Louis Tsakou-Ngouafo , Célia Vicari , Laura Helou , Vivek Keshri , Sabyasachi Das et al.

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
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DDE Transposon as Public Goods

Louis Tsakou-Ngouafo , Célia Vicari , Laura Helou , Vivek Keshri , Sabyasachi Das et al.

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 et al.

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 et al.

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

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

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

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 et al.

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 et al.

Evolution and vertebrate immunity :the antigen-receptor and MHC gene families, University of Texas Press, pp.315-323, 1987

Chapitre d'ouvrage hal-00827604v1

Epigenetic and genetic mechanisms of trained adaptation to global warming in corals

Jeremie Vidal-Dupiol , Eve R Toulza , Christoph Grunau , Olivier Rey , David Roquis et al.

EVOLUTION 2018 - 2nd Joint Congress on Evolutionary Biology, Aug 2018, Montellier, France.

Poster de conférence hal-03969153v1
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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 Klopp et al.

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 Klopp , Laurent Journot et al.

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 <em>Nme</em> 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

Analyse phylogénomique des duplications géniques chez les poissons téléostéens : une approche PAR RNASeq

Julien Bobe , Yann Guiguen , John H. Postlethwait , Laurent Journot , Christophe Klopp et al.

[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 (rapport de recherche) 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 (rapport contrat/projet) hal-02808395v1