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Chantal Abergel Directeur de Recherche CNRS Tel:+33 4 91 82 54 22

Le groupe expérimental que je dirige, travaille à l’isolement de nouveaux membres des familles de virus géants déjà connues et à la découverte de nouvelles familles en prospectant des environnements exotiques et en utilisant d’autres hôtes qu’Acanthamoeba. Des études de génomiques, transcritomiques et protéomiques sont systématiquement réalisées afin d’étudier l’évolution des virus dont nous disposons, ainsi que les échanges possibles entre chacun des virus et leurs hôtes cellulaires. Dans ce contexte, il est nécessaire de coordonner nos efforts avec le groupe de bioinformaticiens du laboratoire. Nous développons également les outils analytiques nécessaires à l’étude de la physiologie de nos virus géants en combinant de la génétique, de la biologie structurale et de la biologie cellulaire avec de l’expression in vivo et de l’imagerie par microscopie électronique et à fluorescence

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Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes. ; Zhang HH, Zhou QZ, Wang PL, Xiong XM, Luchetti A, Raoult D, Levasseur A, Santini S, Abergel C, Legendre M, Drezen JM, Béliveau C, Cusson M, Jiang SH, Bao HO, Sun C, Bureau TE, Cheng PF, Han MJ, Zhang Z, Zhang XG, Dai FY ; Mob DNA.9;:19,2018 june ; 2018-06-01 ; PMID 29946369
  3. Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly. ; Okamoto K, Miyazaki N, Reddy HKN, Hantke MF, Maia FRNC, Larsson DSD, Abergel C, Claverie JM, Hajdu J, Murata K, Svenda M ; Virology.516;:239-245,2018 Mar ; 2018-03-01 ; PMID 29407382
  4. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. ; Okamoto K, Miyazaki N, Song C, Maia FRNC, Reddy HKN, Abergel C, Claverie JM, Hajdu J, Svenda M, Murata K ; Sci Rep.7;1:13291,2017 Oct 16 ; 2017-10-16 ; PMID 29038566
  5. Noumeavirus replication relies on a transient remote control of the host nucleus. ; Fabre E, Jeudy S, Santini S, Legendre M, Trauchessec M, Couté Y, Claverie JM, Abergel C ; Nat Commun.8;:15087,2017 Apr 21 ; 2017-04-21 ; PMID 28429720
  6. The rare sugar N-acetylated viosamine is a major component of mimivirus fibers. ; Piacente F, De Castro C, Jeudy S, Gaglianone M, Laugieri ME, Notaro A, Salis A, Damonte G, Abergel C, Tonetti MG ; J Biol Chem.;:,2017 Mar 17 ; 2017-03-17 ; PMID 28314774
  7. Giant viruses: update, enigmas, controversies and perspectives ; Claverie JM, Abergel C ; Médecine/Sciences ;32(12) 1087-1096,2016 Dec ; 2016-12-20 ; PMID 28044972
  8. Les virus géants : des fossiles vivants de cellules primitives ? ; Abergel C, Claverie JM ; Pour la Science 469 : 50-53,2016 dec ; 2016-12-01 ;
  9. Les virus ont-ils joué un rôle dans l’apparition du noyau ? ; Abergel C, Claverie JM ; Pour la Science 469 : 46.,2016 dec ; 2016-12-01 ;
  10. Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser. ; Ekeberg T, Svenda M, Seibert MM, Abergel C, Maia FR, Seltzer V, DePonte DP, Aquila A, Andreasson J, Iwan B, Jonsson O, Westphal D, Odic D, Andersson I, Barty A, Liang M, Martin AV, Gumprecht L, Fleckenstein H, Bajt S, Barthelmess M, Coppola N, Claverie JM, Loh ND, Bostedt C, Bozek JD, Krzywinski J, Messerschmidt M, Bogan MJ, Hampton CY, Sierra RG, Frank M, Shoeman RL, Lomb L, Foucar L, Epp SW, Rolles D, Rudenko A, Hartmann R, Hartmann A, Kimmel N, Holl P, Weidenspointner G, Rudek B, Erk B, Kassemeyer S, Schlichting I, Struder L, Ullrich J, Schmidt C, Krasniqi F, Hauser G, Reich C, Soltau H, Schorb S, Hirsemann H, Wunderer C, Graafsma H, Chapman H, Hajdu J ; Sci Data.3;:160060,2016 aug ; 2016-08-01 ; PMID 27479754
  11. CRISPR-Cas-like system in giant viruses: why MIMIVIRE is not likely to be an adaptive immune system. ; Claverie JM, Abergel C ; Virol Sin.;:,2016 Jun 13 ; 2016-06-13 ; PMID 27315813
  12. Giant viruses: The difficult breaking of multiple epistemological barriers. ; Claverie JM, Abergel C ; Stud Hist Philos Biol Biomed Sci.;:,2016 Mar 10 ; 2016-03-10 ; PMID 26972873
  13. Diversité des virus géants ; Abergel C, Claverie JM ; Virologie, Vol 20, n◦ 1, 2016 jan ; 2016-01-28 ;
  14. Complete Genome Sequence of a New Member of the Marseilleviridae Recovered from the Brackish Submarine Spring in the Cassis Port-Miou Calanque, France. ; Doutre G, Arfib B, Rochette P, Claverie JM, Bonin P, Abergel C ; Genome Announc.3;6:,2011 nov ; 2015-11-01 ; PMID 26607881
  15. On a ouvert la glacière de Pandore ; Claverie JM, Abergel C ; Biofutur 369: 54-55.,2015 oct ; 2015-10-01 ;
  16. The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus. ; Abergel C, Legendre M, Claverie JM ; FEMS Microbiol Rev.;:,2015 Sep 20 ; 2015-09-20 ; PMID 26391910
  17. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. ; Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;:,2015 Sep 8 ; 2015-09-08 ; PMID 26351664
  18. mRNA maturation in giant viruses: variation on a theme. ; Priet S, Lartigue A, Debart F, Claverie JM, Abergel C ; Nucleic Acids Res.;:,2015 Mar 16 ; 2015-03-16 ; PMID 25779049
  19. Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser. ; Ekeberg T, Svenda M, Abergel C, Maia FR, Seltzer V, Claverie JM, Hantke M, Jonsson O, Nettelblad C, van der Schot G, Liang M, DePonte DP, Barty A, Seibert MM, Iwan B, Andersson I, Loh ND, Martin AV, Chapman H, Bostedt C, Bozek JD, Ferguson KR, Krzywinski J, Epp SW, Rolles D, Rudenko A, Hartmann R, Kimmel N, Hajdu J ; Phys Rev Lett.114;9:098102,2015 Mar 6 ; 2015-01-06 ; PMID 25793853
  20. Pandoravirus ; Claverie J.-M., Abergel C ; McGraw-Hill Year book of Science and Technology - 2015. (John Renie, ed.);pp 226-227;ISBN 978-0-07-183576-3 ISSN 0076-2016,2015 ; 2015-01-01 ;
  21. La découverte de Mimivirus redéfinit la notion même de virus. ; Claverie JM, Abergel C ; Philippe Cramer (ed.), Le défi des maladies infectieuses, Edition Docis, Paris. , pp 85-89 ; 2014-12-18 ;
  22. The Megavirus chilensis Cu,Zn-Superoxide Dismutase: the first viral structure of a typical CCS-independent hyperstable dimeric enzyme. ; Lartigue A, Burlat B, Coutard B, Chaspoul F, Claverie JM, Abergel C ; J Virol.;:,2014 Oct 29 ; 2014-10-29 ; PMID 25355875
  23. Genome analysis of the first Marseilleviridae representative from Australia indicates that most of its genes contribute to the virus fitness. ; Doutre G, Philippe N, Abergel C, Claverie JM ; J Virol.;:,2014 Oct 1 ; 2014-10-01 ; PMID 25275139
  24. From extraordinary endocytobionts to Pandoraviruses. Comment on Scheid et al.: Some secrets are revealed: Parasitic keratitis amoebae as vectors of the scarcely described pandoraviruses to humans. ; Claverie JM, Abergel C ; Parasitol Res.;:,2014 Aug 19 ; 2014-08-19 ; PMID 25134945
  25. A complement to the modern crystallographer s toolbox: caged gadolinium complexes with versatile binding modes. ; Stelter M, Molina R, Jeudy S, Kahn R, Abergel C, Hermoso JA ; Acta Crystallogr D Biol Crystallogr.70;Pt 6:1506-16,2014 Jun ; 2014-06-01 ; PMID 24914962
  26. Paléovirologie : Pithovirus : un virus géant venu du fond des âges ; Claverie J-M, Abergel C ; Biofutur 33 (352), 50-51,2014 Mar 4 ; 2014-04-03 ;
  27. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. ; Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;111 (11): 4274–4279,2014 Mar 3 ; 2014-01-03 ; PMID 24591590
  28. Pithovirus sibericum:awakening of a giant virus of more than 30 000 years. ; Abergel C, Claverie JM ; Med Sci (Paris).30;3:329-31,2014 Mar ; 2014-01-01 ; PMID 24685225
  29. Les virus sont-ils vraiment des virus ? ; Claverie J.-M. & Abergel C ; Virologie 17: 217-228,2013 Dec 1 ; 2013-12-01 ;
  30. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. ; Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C ; Science.341;6143:281-6,2013 Jul 19 ; 2013-07-19 ; PMID 23869018
  31. Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. ; Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, Barbe V, Wommack KE, Noordeloos AA, Brussaard CP, Claverie JM ; Proc Natl Acad Sci U S A.110;26:10800-5,2013 Jun 25 ; 2013-06-25 ; PMID 23754393
  32. Characterization of a UDP-N-acetylglucosamine biosynthetic pathway encoded by the giant DNA virus Mimivirus. ; Piacente F, Bernardi C, Marin M, Blanc G, Abergel C, Tonetti MG ; Glycobiology.;:,2013 Oct 9 ; 2013-01-09 ; PMID 24107487
  33. Open questions about giant viruses. ; Claverie JM, Abergel C ; Adv Virus Res.85;:25-56,2013 ; 2013-01-01 ; PMID 23439023
  34. Preliminary crystallographic analysis of a polyadenylate synthase from Megavirus. ; Lartigue A, Jeudy S, Bertaux L, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.69;Pt 1:53-6,2013 Jan 1 ; 2013-01-01 ; PMID 23295487
  35. Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. ; Jeudy S, Abergel C, Claverie JM, Legendre M ; PLoS Genet.8;12:e1003122,2012 Dec ; 2012-12-12 ; PMID 23271980
  36. Preliminary crystallographic analysis of the Megavirus superoxide dismutase. ; Lartigue A, Philippe N, Jeudy S, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.68;Pt 12:1557-9,2012 Dec 1 ; 2012-12-01 ; PMID 23192047
  37. The Concept of Virus in the Post-Megavirus Era ; Claverie JM, Abergel C ; Springer, Guenther Witzany Editor, Viruses: Essential Agents of Life: 187-202,2012 November ; 2012-11-20 ;
  38. Les virus géants, vestiges d'organismes cellulaires. ; Claverie JM, Abergel C ; Pour la Science 415: 30-33,2012 May ; 2012-05-01 ;
  39. Giant DNA Virus Mimivirus Encodes Pathway for Biosynthesis of Unusual Sugar 4-Amino-4,6-dideoxy-D-glucose (Viosamine). ; Piacente F, Marin M, Molinaro A, De Castro C, Seltzer V, Salis A, Damonte G, Bernardi C, Claverie JM, Abergel C, Tonetti M ; J Biol Chem.287;5:3009-18,2012 Jan 27 ; 2012-01-27 ; PMID 22157758
  40. Genomics of Megavirus and the elusive fourth domain of Life. ; Legendre M, Arslan D, Abergel C, Claverie JM ; Commun Integr Biol.5;1:102-6,2012 Jan 1 ; 2012-01-01 ; PMID 22482024
  41. Megavirus réécrit l'évolution des virus à ADN. ; Claverie JM, Abergel C ; Biofutur 327 (Décembre, p11),2011 ; 2011-12-01 ;
  42. Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. ; Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.108;42:17486-91,2011 Oct 18 ; 2011-10-18 ; PMID 21987820
  43. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. ; Yoon CH, Schwander P, Abergel C, Andersson I, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek J, Chapman HN, Claverie JM, Coppola N, DePonte DP, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann E, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Kiskinova M, Liang M, Loh NT, Lomb L, Maia FR, Martin AV, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert M, Seltzer V, Shoeman RL, Sierra RG, Soltau H, Starodub D, Steinbrener J, Stier G, Strüder L, Svenda M, Ullrich J, Weidenspointner G, White TA, Wunderer C, Ourmazd A ; Opt Express.19;17:16542-9,2011 Aug 15 ; 2011-07-15 ; PMID 21935018
  44. Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. ; Legendre M, Santini S, Rico A, Abergel C, Claverie JM ; Virol J.8;1:99,2011 Mar 4 ; 2011-01-04 ; PMID 21375749
  45. Single mimivirus particles intercepted and imaged with an X-ray laser. ; Seibert MM, Ekeberg T, Maia FR, Svenda M, Andreasson J, Jonsson O, Odic D, Iwan B, Rocker A, Westphal D, Hantke M, Deponte DP, Barty A, Schulz J, Gumprecht L, Coppola N, Aquila A, Liang M, White TA, Martin A, Caleman C, Stern S, Abergel C, Seltzer V, Claverie JM, Bostedt C, Bozek JD, Boutet S, Miahnahri AA, Messerschmidt M, Krzywinski J, Williams G, Hodgson KO, Bogan MJ, Hampton CY, Sierra RG, Starodub D, Andersson I, Bajt S, Barthelmess M, Spence JC, Fromme P, Weierstall U, Kirian R, Hunter M, Doak RB, Marchesini S, Hau-Riege SP, Frank M, Shoeman RL, Lomb L, Epp SW, Hartmann R, Rolles D, Rudenko A, Schmidt C, Foucar L, Kimmel N, Holl P, Rudek B, Erk B, Homke A, Reich C, Pietschner D, Weidenspointner G, Struder L, Hauser G, Gorke H, Ullrich J, Schlichting I, Herrmann S, Schaller G, Schopper F, Soltau H, Kuhnel KU, Andritschke R, Schroter CD, Krasniqi F, Bott M, Schorb S, Rupp D, Adolph M, Gorkhover T, Hirsemann H, Potdevin G, Graafsma H, Nilsson B, Chapman HN, Hajdu J ; Nature.470;7332:78-81,2011 Feb 3 ; 2011-01-03 ; PMID 21293374
  46. The mimivirus R355 gene product: preliminary crystallographic analysis of a putative ubiquitin-like protein-specific protease. ; Jeudy S, Lartigue A, Mansuelle P, Ogata Y, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.67;Pt 1:169-72,2011 Jan 1 ; 2011-01-01 ; PMID 21206054
  47. The Conserved Candida albicans CA3427 Gene Product Defines a New Family of Proteins Exhibiting the Generic Periplasmic Binding Protein Structural Fold. ; Santini S, Claverie JM, Mouz N, Rousselle T, Maza C, Monchois V, Abergel C ; PLoS One.6;4:e18528,2011 ; 2011-01-01 ; PMID 21494601
  48. Family Mimiviridae. ; Claverie JM, Abergel C ; Virus Taxonomy, ninth report of the International Committee on Taxonomy of Viruses (ICTV) , Elsevier, Academic Press, ISBN : 978-0-12-384684-6. pp223-228,2011 ; 2011-01-01 ;
  49. Preliminary crystallographic analysis of a possible transcription factor encoded by the mimivirus L544 gene. ; Ciaccafava A, Lartigue A, Mansuelle P, Jeudy S, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.67;Pt 8:922-5,2011 Aug 1 ; 2011-01-01 ; PMID 21821896
  50. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. ; Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, Byrne D, Lartigue A, Lescot M, Bernadac A, Poulain J, Abergel C, Claverie JM ; Genome Res.20;5:664-74,2010 May ; 2010-04-01 ; PMID 20360389
  51. Identification of an L-rhamnose synthetic pathway in two nucleo-cytoplasmic large dna viruses. ; Parakkottil-Chothi M, Duncan GA, Armirotti A, Abergel C, Gurnon JR, Van Etten JL, Bernardi C, Damonte G, Tonetti M ; J Virol.84;17:8829-38,2010 Sep ; 2010-01-10 ; PMID 20538863
  52. Mimivirus: the emerging paradox of quasi-autonomous viruses. ; Claverie JM, Abergel C ; Trends Genet.;pp. 431-437 :,2010 Aug 7 ; 2010-01-07 ; PMID 20696492
  53. Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions. ; Trapani S, Schoehn G, Navaza J, Abergel C ; Acta Crystallogr D Biol Crystallogr.66;Pt 5:514-21,2010 May ; 2010-01-01 ; PMID 20445226
  54. Mimivirus&Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. ; Claverie JM, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, Ogata H, Abergel C ; J Invertebr Pathol.101;3:172-80,2009 Jul ; 2009-01-17 ; PMID 19457438
  55. Dissecting the unique nucleotide specificity of Mimivirus nucleoside diphosphate kinase. ; Jeudy S, Lartigue A, Claverie JM, Abergel C ; J Virol.83;14:7142-50,2009 Jul ; 2009-01-13 ; PMID 19439473
  56. Mimivirus and its Virophage. ; Claverie JM, Abergel C ; Annu Rev Genet.43;:49-66,2009 ; 2009-01-04 ; PMID 19653859
  57. Mimivirus. ; Claverie JM, Abergel C, Ogata H ; Curr Top Microbiol Immunol.328;:89-121,2009 ; 2009-01-01 ; PMID 19216436
  58. The polyadenylation site of Mimivirus transcripts obeys a stringent hairpin rule. ; Byrne D, Grzela R, Lartigue A, Audic S, Chenivesse S, Encinas S, Claverie JM, Abergel C ; Genome Res.19;7:1233-42,2009 Jul ; 2009-01-01 ; PMID 19403753
  59. Comparative analysis of Acinetobacters: three genomes for three lifestyles. ; Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, Bataille E, Dossat C, Gas S, Kreimeyer A, Lenoble P, Oztas S, Poulain J, Segurens B, Robert C, Abergel C, Claverie JM, Raoult D, Médigue C, Weissenbach J, Cruveiller S ; PLoS ONE.3;3:e1805,2008 ; 2008-01-01 ; PMID 18350144
  60. Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase. ; Santini S, Monchois V, Mouz N, Sigoillot C, Rousselle T, Claverie JM, Abergel C ; BMC Struct Biol.8;:33,2008 ; 2008-01-01 ; PMID 18652651
  61. Virus-Encoded Aminoacyl-tRNA Synthetases: Structural and Functional Characterization of Mimivirus TyrRS and MetRS. ; Abergel C, Rudinger-Thirion J , Giegé R, Claverie JM ; J Virol.81;22:12406-17,2007 Nov ; 2007-10-01 ; PMID 17855524
  62. Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria. ; Abergel C, Monchois V, Byrne D, Chenivesse S, Lembo F, Lazzaroni JC, Claverie JM ; Proc Natl Acad Sci U S A.104;15:6394-9,2007 Apr 10 ; 2007-04-10 ; PMID 17405861
  63. Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. ; P. Renesto , C. Abergel , P. Decloquement , D. Moinier , S. Azza , H. Ogata , P. Fourquet , J.P. Gorvel , J.M. Claverie ; J Virol.80;23:11678-85,2006 Dec ; 2006-09-01 ; PMID 16971431
  64. Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity. ; Abergel C , Blanc G , Monchois V, Renesto P, Sigoillot C , Ogata H, Raoult D, Claverie JM ; Mol Biol Evol.23;11:2112-22,2006 Nov ; 2006-08-01 ; PMID 16891376
  65. Combining experimental data for structure determination of flexible multimeric macromolecules by molecular replacement. ; Trapani S, Abergel C, Gutsche I, Horcajada C, Fita I, Navaza J ; Acta Crystallogr D Biol Crystallogr.62;Pt 5:467-75,2006 May ; 2006-05-01 ; PMID 16627938
  66. Mimivirus and the emerging concept of "giant" virus. ; Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE ; Virus Res.117;1:133-44,2006 Apr ; 2006-04-01 ; PMID 16469402
  67. Comparative genomics of multidrug resistance in Acinetobacter baumannii. ; Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, Poirel L, Richet H, Robert C, Mangenot S, Abergel C, Nordmann P, Weissenbach J, Raoult D, Claverie JM ; PLoS Genet.2;1:e7,2006 Jan ; 2006-01-01 ; PMID 16415984
  68. The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides. ; Jeudy S, Claverie JM, Abergel C ; J Bioenerg Biomembr.38;3-4:247-54,2006 Aug ; 2006-01-01 ; PMID 16957983
  69. Preliminary crystallographic analysis of the Escherichia coli YeaZ protein using the anomalous signal of a gadolinium derivative. ; Jeudy S, Stelter M, Coutard B, Kahn R, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.61;Pt 9:848-51,2005 Sep 1 ; 2005-09-01 ; PMID 16511176
  70. Response to Comment on The 1.2-Megabase Genome Sequence of Mimivirus Science, Vol 308, Issue 5725, 1114 ; Ogata H, Abergel C, Raoult D, Claverie JM ; Science, Vol 308, Issue 5725, 1114,2005 Jun ; 2005-06-20 ;
  71. Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase. ; Jeudy S, Coutard B, Lebrun R, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.61;Pt 6:569-72,2005 Jun 1 ; 2005-06-01 ; PMID 16511098
  72. Insight into Molecular Stability and Physiological Properties of the Diheme Cytochrome CYC(41) from the Acidophilic Bacterium Acidithiobacillus ferrooxidans. ; Malarte G, Leroy G, Lojou E, Abergel C, Bruschi M, Giudici-Orticoni MT. ; Biochemistry;44(17):6471-81,2005 May 3 ; 2005-05-01 ; PMID 15850381
  73. Mimivirus TyrRS: preliminary structural and functional characterization of the first amino-acyl tRNA synthetase found in a virus. ; Abergel C, Chenivesse S, Byrne D, Suhre K, Arondel V, Claverie JM ; Acta Crystallogr Sect F Struct Biol Cryst Commun.61;Pt 2:212-5,2005 Feb 1 ; 2005-02-01 ; PMID 16510997
  74. The 1.2-Mb Genome Sequence of Mimivirus. ; Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. ; Science. 2004 Nov 19;306(5700):1344-50. Epub 2004 Oct 14. ; 2004-10-14 ; PMID 15486256
  75. Spectacular improvement of X-ray diffraction through fast desiccation of protein crystals. ; Abergel C. ; Acta Crystallogr D Biol Crystallogr. 2004 Aug;60(Pt 8):1413-6. ; 2004-08-01 ; PMID 15272164
  76. 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. ; Poirot O, Suhre K, Abergel C, O'Toole E, Notredame C ; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. ; 2004-07-01 ; PMID 15215345
  77. CaspR: a web-server for automated molecular replacement using homology modelling. ; Claude JB, Suhre K, Notredame C, Claverie JM, Abergel C ; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9. ; 2004-07-01 ; PMID 15215460
  78. Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis ; Enault F, Suhre K, Poirot O, Abergel C, Claverie JM ; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W336-9. ; 2004-07-01 ; PMID 15215406
  79. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. ; O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C. ; J Mol Biol. 2004 Jul 2;340(2):385-95. ; 2004-07-01 ; PMID 15201059
  80. Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. ; Enault F, Suhre K, Poirot O, Abergel C, Claverie JM ; Nucleic Acids Res 2003 Jul 1;31(13):3720-2. ; 2003-07-01 ; PMID 12824402
  81. The structure of Acidithiobacillus ferrooxidans c(4)-cytochrome: a model for complex-induced electron transfer tuning. ; Abergel C, Nitschke W, Malarte G, Bruschi M, Claverie JM, Giudici-Orticoni MT ; Structure (Camb) 2003 May;11(5):547-55. ; 2003-05-01 ; PMID 12737820
  82. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. ; Abergel C, Coutard B, Byrne D, Chenivesse S, Claude JB, Deregnaucourt C, Fricaux T, Gianesini-Boutreux C, Jeudy S, Lebrun R, Maza C, Notredame C, Poirot O, Suhre K, Varagnol M, Claverie JM. ; J Struct Funct Genomics. 2003;4(2-3):141-57. ; 2003-01-01 ; PMID 14649299
  83. Using T-Coffee to assess the reliability of multiple sequence alignments. ; Notredame C. and Abergel C. ; Bioinformatics and Genomes (M.A. Andrade, ed.) Horizon Scientific Press, Wymondham,UK, pp 27-49 ; 2003-01-01 ;
  84. In Search of new anti-bacterial target genes: a comparative/structural genomics approach. ; Claverie JM, Monchois V, Audic S, Poirot O, Abergel C ; Comb Chem High Throughput Screen 2002 Nov;5(7):511-22. ; 2002-11-01 ; PMID 12470264
  85. Protein coding palindromes are a unique but recurrent feature in Rickettsia. ; Ogata H, Audic S, Abergel C, Fournier PE, Claverie JM ; Genome Res 2002 May;12(5):808-16. ; 2002-05-01 ; PMID 11997347
  86. Proficient target selection in structural genomic by In vitro protein expression on Gateway recombination plasmids. ; Monchois V., Vincentelli R., Abergel C., Deregnaucourt C., Claverie J.-M. and Monchois V. ; Cell-Free Translation Systems (Spirin Ed.) Springer Verlag : () 197- 202. ; 2002-01-01 ;
  87. Recent advances in computational genomics. ; Claverie JM, Abergel C, Audic S, Ogata H ; Pharmacogenomics 2001 Nov;2(4):361-72. ; 2001-11-01 ; PMID 11722286
  88. DNA gyrase-mediated natural resistance to fluoroquinolones in Ehrlichia spp. ; Maurin M, Abergel C, Raoult D ; Antimicrob Agents Chemother 2001 Jul;45(7):2098-105. ; 2001-07-01 ; PMID 11408229
  89. Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme. ; Monchois V, Abergel C, Sturgis J, Jeudy S, Claverie JM ; J Biol Chem 2001 May 25;276(21):18437-41. ; 2001-05-01 ; PMID 11278658
  90. Crystallization and preliminary crystallographic study of the peptidoglycan-associated lipoprotein from Escherichia coli. ; Abergel C, Walburger A, Chenivesse S, Lazdunski C ; Acta Crystallogr D Biol Crystallogr 2001 Feb;57(Pt 2):317-9. ; 2001-02-01 ; PMID 11173492
  91. Crystallization and preliminary crystallographic study of a recombinant phospholipase D from cowpea (Vigna unguiculata L. Walp). ; Abergel C, Abousalham A, Chenivesse S, Riviere M, Moustacas-Gardies AM, Verger R ; Acta Crystallogr D Biol Crystallogr 2001 Feb;57(Pt 2):320-2. ; 2001-02-01 ; PMID 11173493
  92. Crystallization and preliminary crystallographic study of the periplasmic domain of the Escherichia coli TolR protein. ; Abergel C, Journet L, Chenivesse S, Gavioli M, Lloubes R ; Acta Crystallogr D Biol Crystallogr 2001 Feb;57(Pt 2):323-5. ; 2001-02-01 ; PMID 11173494
  93. Crystallization and preliminary crystallographic study of b0220, an 'ORFan' protein of unknown function from Escherichia coli. ; Abergel C, Monchois V, Chenivesse S, Jeudy S, Claverie JM ; Acta Crystallogr D Biol Crystallogr 2000 Dec;56 Pt 12:1694-5. ; 2000-12-01 ; PMID 11092949
  94. Crystallization and preliminary crystallographic study of an extremophile cytochrome c4 from Thiobacillus ferrooxidans. ; Abergel C, Bruschi M, Chenivesse S, Guasco S, Leroy G, Guidici-Orticoni MT ; Acta Crystallogr D Biol Crystallogr 2000 Nov;56 ( Pt 11):1432-3. ; 2000-11-01 ; PMID 11053842
  95. Structure of the Escherichia coli TolB protein determined by MAD methods at 1.95 A resolution. ; Abergel C, Bouveret E, Claverie JM, Brown K, Rigal A, Lazdunski C, Benedetti H ; Structure Fold Des 1999 Oct 15;7(10):1291-300. ; 1999-10-01 ; PMID 10545334
  96. Crystallization and preliminary crystallographic study of HIP/PAP, a human C-lectin overexpressed in primary liver cancers. ; Abergel ; Acta ; 1999-08-01 ; PMID 10417404
  97. Author correction: triple association of CDC25-, dbl- and Sec7-related domains in mammalian guanine nucleotide exchange factors ; Abergel ; Trends ; 1999-05-01 ; PMID 10322431
  98. Hidden dUTPase sequence in human immunodeficiency virus type 1 gp120. ; Abergel C, Robertson DL, Claverie JM ; J Virol 1999 Jan;73(1):751-3. ; 1999-01-01 ; PMID 9847382
  99. A New Strategy and Software System for the Design of Functional Signatures in Protein Sequences, in Perspective in Structural Biology. ; Claverie J.-M., Lopez F. and Abergel C ; Indian Acad. Sciences and the Universities Press,Hyderabad, India.(M. Vijayan, ed.). Chap. 51: () 680- 700. ; 1999-01-01 ;
  100. Triple association of CDC25-, Dbl- and Sec7-related domains in mammalian guanine-nucleotide-exchange factors. ; Abergel C, Chavrier P, Claverie JM ; Trends Biochem Sci 1998 Dec;23(12):472-3. ; 1998-12-01 ; PMID 9868368
  101. Crystallization and preliminary crystallographic study of a component of the Escherichia coli tol system: TolB. ; Abergel C, Rigal A, Chenivesse S, Lazdunski C, Claverie JM, Bouveret E, Benedetti H ; Acta Crystallogr D Biol Crystallogr 1998 Jan 1;54 ( Pt 1):102-4. ; 1998-01-01 ; PMID 9761825
  102. SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments. ; Audic S, Lopez F, Claverie JM, Poirot O, Abergel C ; Proteins 1997 Oct;29(2):252-7. ; 1997-10-01 ; PMID 9329089
  103. Biochemical and spectroscopic characterization of two new cytochromes isolated from Desulfuromonas acetoxidans. ; Bruschi M, Woudstra M, Guigliarelli B, Asso M, Lojou E, Petillot Y, Abergel C ; Biochemistry 1997 Sep 2;36(35):10601-8. ; 1997-09-02 ; PMID 9271490
  104. Identification of specificity-determining residues in antibodies. ; Padlan EA, Abergel C, Tipper JP ; FASEB J 1995 Jan;9(1):133-9. ; 1995-01-01 ; PMID 7821752
  105. Structural significance of sequence variability in antibody complementarity-determining regions. ; Abergel C, Tipper JP, Padlan EA ; Res Immunol 1994 Jan;145(1):49-53. ; 1994-01-01 ; PMID 8008969
  106. Crystallographic studies and primary structure of the antitumor monoclonal CC49 Fab'. ; Abergel C, Padlan EA, Kashmiri SV, Milenic D, Calvo B, Schlom J ; Proteins 1993 Dec;17(4):438-43. ; 1993-12-01 ; PMID 8108385
  107. Isoform purification of gastric lipases. Towards crystallization. ; Moreau H, Abergel C, Carriere F, Ferrato F, Fontecilla-Camps JC, Cambillau C, Verger R ; J Mol Biol 1992 May 5;225(1):147-53. ; 1992-05-01 ; PMID 1583687
  108. A strong propensity toward loop formation characterizes the expressed reading frames of the D segments at the Ig H and T cell receptor loci. ; Abergel C, Claverie JM ; Eur J Immunol 1991 Dec;21(12):3021-5. ; 1991-12-01 ; PMID 1660812
  109. Systematic use of the incomplete factorial approach in the design of protein crystallization experiments. ; Abergel C, Moulard M, Moreau H, Loret E, Cambillau C, Fontecilla-Camps JC ; J Biol Chem 1991 Oct 25;266(30):20131-8. ; 1991-10-01 ; PMID 1939074
  110. Crystallization and preliminary X-ray diffraction data of the Fab fragment of a monoclonal antibody against apamin, a bee venom neurotoxin. ; Devaux C, Defendini ML, Alzari PM, Abergel C, Granier C, Fontecilla-Camps JC, Alzar PM ; FEBS Lett 1991 Jul 29;286(1-2):64-6. ; 1991-07-01 ; PMID 1747157
  111. Crystallization and preliminary X-ray study of a recombinant cutinase from Fusarium solani pisi. ; Abergel C, Martinez C, Fontecilla-Camps J, Cambillau C, de Geus P, Lauwereys M ; J Mol Biol 1990 Sep 20;215(2):215-6. ; 1990-09-01 ; PMID 2213880
  112. Crystallization and preliminary X-ray study of AaH IT2, and insect-specific toxin from the scorpion Androctonus australis Hector. ; Abergel C, Loret E, Rochat H, Fontecilla-Camps JC ; J Mol Biol 1990 Aug 5;214(3):637-8. ; 1990-08-01 ; PMID 2388262
  113. X-ray crystal structure determination and refinement at 1.9 A resolution of isolectin I from the seeds of Lathyrus ochrus. ; Bourne Y, Abergel C, Cambillau C, Frey M, Rouge P, Fontecilla-Camps JC ; J Mol Biol 1990 Jul 20;214(2):571-84. ; 1990-07-01 ; PMID 2380988
  114. Conformational analysis of T immunogenic peptides by circular dichroism spectroscopy. ; Abergel C, Loret E, Claverie JM ; Eur J Immunol 1989 Oct;19(10):1969-72. ; 1989-10-01 ; PMID 2511030

Contacter cette personne
Chantal Abergel Directeur de Recherche CNRS
Jean-Marie Alempic Technicien de la recherche Tel:+33 4 91 82 54 25

Je participe à la remise en culture d’échantillons environnementaux dans le but d’isoler de nouveaux virus infectant A. castellanii et de les caractériser (profils protéique, extraction d’ADN, visualisation en coloration négative, analyse des cycles infectieux en microscopie optique (DAPI)).
Je suis également chargé de l’installation du modèle Paramecium au laboratoire (mise en culture et maintien des cellules).
Je développe et met en place des protocoles d’ouverture de nos virus géants qui permettrons de réaliser l’étude de l’organisation de l’ADN des Mimiviridae, d’identifier en conditions natives la présence d’activité enzymatiques dans les virions (endonucléases, RNAses, Méthylases…).
Des protocoles de défibrillation permettront également de caractériser les sucres composant les fibrilles des capsides des différents virus de la famille des Megaviridae dont nous disposons au laboratoire.

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. ; Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;:,2015 Sep 8 ; 2015-09-08 ; PMID 26351664

Contacter cette personne
Jean-Marie Alempic Technicien de la recherche
B
Lionel Bertaux Ingénieur d’études CNRS Tel:+33 4 91 82 54 42

Au sein du groupe expérimental du laboratoire je partage mon activité entre la biologie cellulaire/virologie et la microscopie électronique. Je participe à l’étude de l’origine et du devenir de l’ADN des virus géants au cours de leurs cycles infectieux ainsi qu’à celle des virophages qui parasitent les virus géants. Je gère et entretiens les stocks de virus pour notre usage et celui de collaborateurs français et internationaux. En parallèle de mon activité expérimentale, je suis l’assistant de prévention du laboratoire.

Lien ORCID

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. ; Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;:,2015 Sep 8 ; 2015-09-08 ; PMID 26351664
  3. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. ; Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;111 (11): 4274–4279,2014 Mar 3 ; 2014-01-03 ; PMID 24591590
  4. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. ; Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C ; Science.341;6143:281-6,2013 Jul 19 ; 2013-07-19 ; PMID 23869018
  5. Preliminary crystallographic analysis of a polyadenylate synthase from Megavirus. ; Lartigue A, Jeudy S, Bertaux L, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.69;Pt 1:53-6,2013 Jan 1 ; 2013-01-01 ; PMID 23295487

Contacter cette personne
Lionel Bertaux Ingénieur d’études CNRS
C
Eugene Christo-Foroux Doctorant Tel:+33 4 91 82 54 33

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839

Contacter cette personne
Eugene Christo-Foroux Doctorant
Jean-Michel Claverie PU-PH, Directeur du laboratoire Tel:+33 4 91 82 54 20

BioSketch :
Jean-Michel Claverie is full professor of Genomics and Bioinformatics at the School of Medicine of Aix-Marseille University, director of the Mediterranean Institute of Microbiology, and head of the Structural and Genomic Information Laboratory, a unit of the French National Research Center (CNRS) that he founded in 1996.
He got his initial training both in biochemistry, computer science and theoretical particle physics at the University of Paris and combined his multidisciplinary education into a Doctorate (Dr. Sc.) on the subject of mathematical modeling of biological system in 1977. He then successively hold research positions at the Jacques Monod Institute (CNRS) in Paris, then at the Salk Institute in La Jolla, before creating in 1982 one of the first pre-Internet era computational biology laboratory at the Pasteur Institute (Paris) where he remained until 1990. He then returned to the USA, at the National Center for Biotechnology Information (NCBI, NLM-NIH, Bethesda) where he participated to the exciting beginning of the genomic era, as a NIH senior Fogarty scientist, until 1995. Before returning to France, he spent one year as director of bioinformatics at Incyte pharmaceuticals (Palo Alto).
Owing to his theoretical background, Jean-Michel Claverie worked on a wide range of topics ranging from the mathematical modeling of ultracentrifugation experiments, microbial and human genetics, cellular immunology, and more recently microbial genomics. Following the discovery and initial characterization of Mimivirus, the first "giant" virus in 2003, he then focused on the search for more giant and/or unconventional viruses in increasingly exotic environments. In the last ten years, his laboratory described four new families encompassing the largest known viruses in terms of particle and genome sizes : the Mega/Mimiviridae, the Pandoraviruses, Pithovirus and Mollivirus. The last two viruses were revived from 30,000 year-old Siberian permafrost, opening the field of "Paleovirology". While continuously searching for more ancient and/or exotic viruses, his laboratory is also involved in deciphering the biology and evolutionary origin of these giant viruses. The laboratory’s approaches include structural, molecular, and cellular biology, high throughput proteomics, genome and transcriptome sequencing, environmental sampling, large-scale comparative genomics and metagenomics, together with the development of relevant bioinformatics methods for sequence analysis and data mining.
Dr. Jean-Michel Claverie co-authored more than 220 scientific publications, as well as the best-seller book "Bioinformatics for Dummies". He was a member of the Board of reviewing editors of Science for 10 years (2002-2012). He was recipient of the CNRS Silver medal in 2003, and a Knight in the National Order of the Academic Palms (2016).

EDUCATION 1977 Dr. Sc. "Mathematical modelling and simulation of biological systems", Institut Jacques Monod, University Paris 7, France 1972 Master (DEA) in Biochemistry, University Paris 7, Paris, France 1973 Master (DEA) in Applied Computer Science, Univ. Paris 6, Paris, France 1974 Master (DEA) in Theoretical Physics, University Paris 6 & 7 & 11, Paris, France

CURRENT POSITION(S) 2004 – today Professor of Medicine (PU/PH), Biostatistics and Genomics, Aix-Marseille Univ. & APHM 2008 – today Head, Mediterranean Institute of Microbiology (CNRS-AMU), France 1995 – today Founder & head, Structural & Genomic Information Lab. (CNRS-AMU), Marseille, France

PREVIOUS POSITIONS 1996 – 2004 Senior CNRS researchers (Director level 1) 1990 – 1995 Senior Fogarty visiting Scientist, NCBI-National Institutes of Health, Bethesda, USA 1982 – 1992 Head of laboratory (Computational Biology), Institut Pasteur, Paris, France 1989 – 1990 Professor of Immunology, Rouen University, Rouen, France 1975 – 1995 CNRS researcher (from junior to director grade, with on leave periods when abroad)

Lien ORCID

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. ACDtool: a web-server extending the original Audic-Claverie statistical test to the comparison of large data sets of counts. ; Jean-Michel Claverie, Thi Ngan Ta ; biorxiv, doi: https://doi.org/10.1101/304568,2018 march ; 2018-04-20 ;
  3. Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly. ; Okamoto K, Miyazaki N, Reddy HKN, Hantke MF, Maia FRNC, Larsson DSD, Abergel C, Claverie JM, Hajdu J, Murata K, Svenda M ; Virology.516;:239-245,2018 Mar ; 2018-03-01 ; PMID 29407382
  4. New genomic data and analyses challenge the traditional vision of animal epithelium evolution. ; Belahbib H, Renard E, Santini S, Jourda C, Claverie JM, Borchiellini C, Le Bivic A ; BMC Genomics.19;1:393,2018 May 24 ; 2018-01-24 ; PMID 29793430
  5. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. ; Okamoto K, Miyazaki N, Song C, Maia FRNC, Reddy HKN, Abergel C, Claverie JM, Hajdu J, Svenda M, Murata K ; Sci Rep.7;1:13291,2017 Oct 16 ; 2017-10-16 ; PMID 29038566
  6. Comparative genomics of Chrysochromulina Ericina Virus (CeV) and other microalgae-infecting large DNA viruses highlight their intricate evolutionary relationship with the established Mimiviridae family. ; Gallot-Lavallee L, Blanc G, Claverie JM ; J Virol.;:,2017 Apr 26 ; 2017-04-26 ; PMID 28446675
  7. Noumeavirus replication relies on a transient remote control of the host nucleus. ; Fabre E, Jeudy S, Santini S, Legendre M, Trauchessec M, Couté Y, Claverie JM, Abergel C ; Nat Commun.8;:15087,2017 Apr 21 ; 2017-04-21 ; PMID 28429720
  8. Complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa ; Villain A, Kojadinovic M, Puppo C, Prioretti L, Hubert P, Zhang Y, Grégori G, Roulet A, Roques C, Claverie JM, Gontero B & Guillaume Blanc ; Mitochondrial DNA Part B, 2:1, 97-98,2017 Feb ; 2017-02-16 ;
  9. Giant viruses: update, enigmas, controversies and perspectives ; Claverie JM, Abergel C ; Médecine/Sciences ;32(12) 1087-1096,2016 Dec ; 2016-12-20 ; PMID 28044972
  10. Les virus géants : des fossiles vivants de cellules primitives ? ; Abergel C, Claverie JM ; Pour la Science 469 : 50-53,2016 dec ; 2016-12-01 ;
  11. Les virus ont-ils joué un rôle dans l’apparition du noyau ? ; Abergel C, Claverie JM ; Pour la Science 469 : 46.,2016 dec ; 2016-12-01 ;
  12. Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser. ; Ekeberg T, Svenda M, Seibert MM, Abergel C, Maia FR, Seltzer V, DePonte DP, Aquila A, Andreasson J, Iwan B, Jonsson O, Westphal D, Odic D, Andersson I, Barty A, Liang M, Martin AV, Gumprecht L, Fleckenstein H, Bajt S, Barthelmess M, Coppola N, Claverie JM, Loh ND, Bostedt C, Bozek JD, Krzywinski J, Messerschmidt M, Bogan MJ, Hampton CY, Sierra RG, Frank M, Shoeman RL, Lomb L, Foucar L, Epp SW, Rolles D, Rudenko A, Hartmann R, Hartmann A, Kimmel N, Holl P, Weidenspointner G, Rudek B, Erk B, Kassemeyer S, Schlichting I, Struder L, Ullrich J, Schmidt C, Krasniqi F, Hauser G, Reich C, Soltau H, Schorb S, Hirsemann H, Wunderer C, Graafsma H, Chapman H, Hajdu J ; Sci Data.3;:160060,2016 aug ; 2016-08-01 ; PMID 27479754
  13. CRISPR-Cas-like system in giant viruses: why MIMIVIRE is not likely to be an adaptive immune system. ; Claverie JM, Abergel C ; Virol Sin.;:,2016 Jun 13 ; 2016-06-13 ; PMID 27315813
  14. Benthic protists: the under-charted majority. ; Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra WH, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T ; FEMS Microbiol Ecol.;:,2016 Jun 5 ; 2016-05-05 ; PMID 27267932
  15. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ; Lescot M, Hingamp P, Kojima KK, Villar E, Romac S, Veluchamy A, Boccara M, Jaillon O, Iudicone D, Bowler C, Wincker P, Claverie JM, Ogata H ; ISME J.;:,2016 may ; 2016-05-01 ; PMID 26613339
  16. Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits. ; Bordez L, Jourand P, Ducousso M, Carriconde F, Cavaloc Y, Santini S, Claverie JM, Wantiez L, Leveau A, Amir H ; Mol Ecol.;:,2016 Mar 19 ; 2016-03-19 ; PMID 26994404
  17. Giant viruses: The difficult breaking of multiple epistemological barriers. ; Claverie JM, Abergel C ; Stud Hist Philos Biol Biomed Sci.;:,2016 Mar 10 ; 2016-03-10 ; PMID 26972873
  18. Diversité des virus géants ; Abergel C, Claverie JM ; Virologie, Vol 20, n◦ 1, 2016 jan ; 2016-01-28 ;
  19. The 474-Kilobase-Pair Complete Genome Sequence of CeV-01B, a Virus Infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae). ; Gallot-Lavallée L, Pagarete A, Legendre M, Santini S, Sandaa RA, Himmelbauer H, Ogata H, Bratbak G, Claverie JM ; Genome Announc.3;6:,2015 dec ; 2015-12-01 ; PMID 26634761
  20. Complete Genome Sequence of a New Member of the Marseilleviridae Recovered from the Brackish Submarine Spring in the Cassis Port-Miou Calanque, France. ; Doutre G, Arfib B, Rochette P, Claverie JM, Bonin P, Abergel C ; Genome Announc.3;6:,2011 nov ; 2015-11-01 ; PMID 26607881
  21. The human gene damage index as a gene-level approach to prioritizing exome variants. ; Itan Y, Shang L, Boisson B, Patin E, Bolze A, Moncada-Vélez M, Scott E, Ciancanelli MJ, Lafaille FG, Markle JG, Martinez-Barricarte R, de Jong SJ, Kong XF, Nitschke P, Belkadi A, Bustamante J, Puel A, Boisson-Dupuis S, Stenson PD, Gleeson JG, Cooper DN, Quintana-Murci L, Claverie JM, Zhang SY, Abel L, Casanova JL ; Proc Natl Acad Sci U S A.;:,2015 Oct 19 ; 2015-10-19 ; PMID 26483451
  22. On a ouvert la glacière de Pandore ; Claverie JM, Abergel C ; Biofutur 369: 54-55.,2015 oct ; 2015-10-01 ;
  23. In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem. ; Philippe N, Maigre L, Santini S, Pinet E, Claverie JM, Davin-Régli AV, Pagès JM, Masi M ; PLoS One.10;9:e0138828,2015 sep ; 2015-09-23 ; PMID 26398358
  24. The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus. ; Abergel C, Legendre M, Claverie JM ; FEMS Microbiol Rev.;:,2015 Sep 20 ; 2015-09-20 ; PMID 26391910
  25. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. ; Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;:,2015 Sep 8 ; 2015-09-08 ; PMID 26351664
  26. Draft Genome Sequence of an Alphaproteobacterium Associated with the Mediterranean Sponge Oscarella lobularis. ; Jourda C, Santini S, Rocher C, Le Bivic A, Claverie JM ; Genome Announc.3;5:,2015 sept ; 2015-09-01 ; PMID 26337883
  27. Mitochondrial Genome Sequence of the Glass Sponge Oopsacas minuta. ; Jourda C, Santini S, Rocher C, Le Bivic A, Claverie JM ; Genome Announc.3;4:,2015 ; 2015-07-30 ; PMID 26227597
  28. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. ; Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Forn I, Forster D, Guillou L, Jaillon O, Kooistra WH, Logares R, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simon N, Stoeck T, Vaulot D, Zingone A, de Vargas C ; Environ Microbiol. doi: 10.1111/1462-2920.12955,2015 ; 2015-06-28 ; PMID 26119494
  29. mRNA maturation in giant viruses: variation on a theme. ; Priet S, Lartigue A, Debart F, Claverie JM, Abergel C ; Nucleic Acids Res.;:,2015 Mar 16 ; 2015-03-16 ; PMID 25779049
  30. Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser. ; Ekeberg T, Svenda M, Abergel C, Maia FR, Seltzer V, Claverie JM, Hantke M, Jonsson O, Nettelblad C, van der Schot G, Liang M, DePonte DP, Barty A, Seibert MM, Iwan B, Andersson I, Loh ND, Martin AV, Chapman H, Bostedt C, Bozek JD, Ferguson KR, Krzywinski J, Epp SW, Rolles D, Rudenko A, Hartmann R, Kimmel N, Hajdu J ; Phys Rev Lett.114;9:098102,2015 Mar 6 ; 2015-01-06 ; PMID 25793853
  31. Pandoravirus ; Claverie J.-M., Abergel C ; McGraw-Hill Year book of Science and Technology - 2015. (John Renie, ed.);pp 226-227;ISBN 978-0-07-183576-3 ISSN 0076-2016,2015 ; 2015-01-01 ;
  32. La découverte de Mimivirus redéfinit la notion même de virus. ; Claverie JM, Abergel C ; Philippe Cramer (ed.), Le défi des maladies infectieuses, Edition Docis, Paris. , pp 85-89 ; 2014-12-18 ;
  33. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton. ; von Dassow P, John U, Ogata H, Probert I, Bendif EM, Kegel JU, Audic S, Wincker P, Da Silva C, Claverie JM, Doney S, Glover DM, Flores DM, Herrera Y, Lescot M, Garet-Delmas MJ, de Vargas C ; ISME J.;:,2014 Dec 2 ; 2014-12-02 ; PMID 25461969
  34. The Megavirus chilensis Cu,Zn-Superoxide Dismutase: the first viral structure of a typical CCS-independent hyperstable dimeric enzyme. ; Lartigue A, Burlat B, Coutard B, Chaspoul F, Claverie JM, Abergel C ; J Virol.;:,2014 Oct 29 ; 2014-10-29 ; PMID 25355875
  35. Genome analysis of the first Marseilleviridae representative from Australia indicates that most of its genes contribute to the virus fitness. ; Doutre G, Philippe N, Abergel C, Claverie JM ; J Virol.;:,2014 Oct 1 ; 2014-10-01 ; PMID 25275139
  36. From extraordinary endocytobionts to Pandoraviruses. Comment on Scheid et al.: Some secrets are revealed: Parasitic keratitis amoebae as vectors of the scarcely described pandoraviruses to humans. ; Claverie JM, Abergel C ; Parasitol Res.;:,2014 Aug 19 ; 2014-08-19 ; PMID 25134945
  37. Expanding the Mimiviridae family using asparagine synthase as a sequence bait. ; Mozar M, Claverie JM ; Virology.;:,2014 Jun 4 ; 2014-06-04 ; PMID 24908633
  38. Paléovirologie : Pithovirus : un virus géant venu du fond des âges ; Claverie J-M, Abergel C ; Biofutur 33 (352), 50-51,2014 Mar 4 ; 2014-04-03 ;
  39. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. ; Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;111 (11): 4274–4279,2014 Mar 3 ; 2014-01-03 ; PMID 24591590
  40. Patterns of Rare and Abundant Marine Microbial Eukaryotes. ; Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WH, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards TA, de Vargas C, Massana R ; Curr Biol.;:,2014 Apr 2 ; 2014-01-02 ; PMID 24704080
  41. Pithovirus sibericum:awakening of a giant virus of more than 30 000 years. ; Abergel C, Claverie JM ; Med Sci (Paris).30;3:329-31,2014 Mar ; 2014-01-01 ; PMID 24685225
  42. Les virus sont-ils vraiment des virus ? ; Claverie J.-M. & Abergel C ; Virologie 17: 217-228,2013 Dec 1 ; 2013-12-01 ;
  43. Giant virus in the sea: Extending the realm of Megaviridae to Viridiplantae. ; Claverie JM ; Commun Integr Biol.6;6:e25685,2013 Nov 1 ; 2013-11-01 ; PMID 24563700
  44. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. ; Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C ; Science.341;6143:281-6,2013 Jul 19 ; 2013-07-19 ; PMID 23869018
  45. Pan genome of the phytoplankton Emiliania underpins its global distribution. ; Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, Young J, Aguilar M, Claverie JM, Frickenhaus S, Gonzalez K, Herman EK, Lin YC, Napier J, Ogata H, Sarno AF, Shmutz J, Schroeder D, de Vargas C, Verret F, von Dassow P, Valentin K, Van de Peer Y, Wheeler G, Dacks JB, Delwiche CF, Dyhrman ST, Glockner G, John U, Richards T, Worden AZ, Zhang X, Grigoriev IV, Allen AE, Bidle K, Borodovsky M, Bowler C, Brownlee C, Cock JM, Elias M, Gladyshev VN, Groth M, Guda C, Hadaegh A, Iglesias-Rodriguez MD, Jenkins J, Jones BM, Lawson T, Leese F, Lindquist E, Lobanov A, Lomsadze A, Malik SB, Marsh ME, Mackinder L, Mock T, Mueller-Roeber B, Pagarete A, Parker M, Probert I, Quesneville H, Raines C, Rensing SA, Riano-Pachon DM, Richier S, Rokitta S, Shiraiwa Y, Soanes DM, van der Giezen M, Wahlund TM, Williams B, Wilson W, Wolfe G, Wurch LL ; Nature.499;7457:209-13,2013 Jul 11 ; 2013-07-11 ; PMID 23760476
  46. Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. ; Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, Barbe V, Wommack KE, Noordeloos AA, Brussaard CP, Claverie JM ; Proc Natl Acad Sci U S A.110;26:10800-5,2013 Jun 25 ; 2013-06-25 ; PMID 23754393
  47. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ; Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H ; ISME J.;:,2013 Apr 11 ; 2013-04-11 ; PMID 23575371
  48. Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses. ; Jeanniard A, Dunigan DD, Gurnon JR, Agarkova IV, Kang M, Vitek J, Duncan G, McClung OW, Larsen M, Claverie JM, Van Etten JL, Blanc G ; BMC Genomics.14;1:158,2013 Mar 8 ; 2013-01-08 ; PMID 23497343
  49. Open questions about giant viruses. ; Claverie JM, Abergel C ; Adv Virus Res.85;:25-56,2013 ; 2013-01-01 ; PMID 23439023
  50. Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. ; Jeudy S, Abergel C, Claverie JM, Legendre M ; PLoS Genet.8;12:e1003122,2012 Dec ; 2012-12-12 ; PMID 23271980
  51. The Concept of Virus in the Post-Megavirus Era ; Claverie JM, Abergel C ; Springer, Guenther Witzany Editor, Viruses: Essential Agents of Life: 187-202,2012 November ; 2012-11-20 ;
  52. Les virus géants, vestiges d'organismes cellulaires. ; Claverie JM, Abergel C ; Pour la Science 415: 30-33,2012 May ; 2012-05-01 ;
  53. Giant DNA Virus Mimivirus Encodes Pathway for Biosynthesis of Unusual Sugar 4-Amino-4,6-dideoxy-D-glucose (Viosamine). ; Piacente F, Marin M, Molinaro A, De Castro C, Seltzer V, Salis A, Damonte G, Bernardi C, Claverie JM, Abergel C, Tonetti M ; J Biol Chem.287;5:3009-18,2012 Jan 27 ; 2012-01-27 ; PMID 22157758
  54. The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. ; Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E, Lucas S, Pangilinan J, Proschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Lomsadze A, Borodovsky M, Claverie JM, Grigoriev IV, Van Etten JL ; Genome Biol.13;5:R39,2012 May 25 ; 2012-01-25 ; PMID 22630137
  55. Genomics of Megavirus and the elusive fourth domain of Life. ; Legendre M, Arslan D, Abergel C, Claverie JM ; Commun Integr Biol.5;1:102-6,2012 Jan 1 ; 2012-01-01 ; PMID 22482024
  56. Review of the book: "Life from an RNA world: the ancestor within" by M Yarus. Harvard Univ. Press. ; Claverie JM ; The Quarterly Review of Biology 87: 66-67,2012 Jan ; 2012-01-01 ;
  57. Megavirus réécrit l'évolution des virus à ADN. ; Claverie JM, Abergel C ; Biofutur 327 (Décembre, p11),2011 ; 2011-12-01 ;
  58. A Holistic Approach to Marine Eco-Systems Biology. ; Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P ; PLoS Biol.9;10:e1001177,2011 Oct ; 2011-11-01 ; PMID 22028628
  59. Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. ; Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.108;42:17486-91,2011 Oct 18 ; 2011-10-18 ; PMID 21987820
  60. Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids. ; Yoshida T, Claverie JM, Ogata H ; Virol J.8;1:427,2011 Sep 7 ; 2011-09-07 ; PMID 21899737
  61. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. ; Yoon CH, Schwander P, Abergel C, Andersson I, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek J, Chapman HN, Claverie JM, Coppola N, DePonte DP, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann E, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Kiskinova M, Liang M, Loh NT, Lomb L, Maia FR, Martin AV, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert M, Seltzer V, Shoeman RL, Sierra RG, Soltau H, Starodub D, Steinbrener J, Stier G, Strüder L, Svenda M, Ullrich J, Weidenspointner G, White TA, Wunderer C, Ourmazd A ; Opt Express.19;17:16542-9,2011 Aug 15 ; 2011-07-15 ; PMID 21935018
  62. Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. ; Ogata H, Ray J, Toyoda K, Sandaa RA, Nagasaki K, Bratbak G, Claverie JM ; ISME J.5;7:1143-51,2011 Jul ; 2011-07-01 ; PMID 21248859
  63. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella. ; Audic S, Lescot M, Claverie JM, Cloeckaert A, Zygmunt MS ; BMC Evol Biol.11;1:200,2011 Jul 11 ; 2011-01-11 ; PMID 21745361
  64. Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. ; Legendre M, Santini S, Rico A, Abergel C, Claverie JM ; Virol J.8;1:99,2011 Mar 4 ; 2011-01-04 ; PMID 21375749
  65. Single mimivirus particles intercepted and imaged with an X-ray laser. ; Seibert MM, Ekeberg T, Maia FR, Svenda M, Andreasson J, Jonsson O, Odic D, Iwan B, Rocker A, Westphal D, Hantke M, Deponte DP, Barty A, Schulz J, Gumprecht L, Coppola N, Aquila A, Liang M, White TA, Martin A, Caleman C, Stern S, Abergel C, Seltzer V, Claverie JM, Bostedt C, Bozek JD, Boutet S, Miahnahri AA, Messerschmidt M, Krzywinski J, Williams G, Hodgson KO, Bogan MJ, Hampton CY, Sierra RG, Starodub D, Andersson I, Bajt S, Barthelmess M, Spence JC, Fromme P, Weierstall U, Kirian R, Hunter M, Doak RB, Marchesini S, Hau-Riege SP, Frank M, Shoeman RL, Lomb L, Epp SW, Hartmann R, Rolles D, Rudenko A, Schmidt C, Foucar L, Kimmel N, Holl P, Rudek B, Erk B, Homke A, Reich C, Pietschner D, Weidenspointner G, Struder L, Hauser G, Gorke H, Ullrich J, Schlichting I, Herrmann S, Schaller G, Schopper F, Soltau H, Kuhnel KU, Andritschke R, Schroter CD, Krasniqi F, Bott M, Schorb S, Rupp D, Adolph M, Gorkhover T, Hirsemann H, Potdevin G, Graafsma H, Nilsson B, Chapman HN, Hajdu J ; Nature.470;7332:78-81,2011 Feb 3 ; 2011-01-03 ; PMID 21293374
  66. Radiographie ... biologique. ; Claverie JM ; Biofutur 319, 10,2011 ; 2011-01-01 ;
  67. The Conserved Candida albicans CA3427 Gene Product Defines a New Family of Proteins Exhibiting the Generic Periplasmic Binding Protein Structural Fold. ; Santini S, Claverie JM, Mouz N, Rousselle T, Maza C, Monchois V, Abergel C ; PLoS One.6;4:e18528,2011 ; 2011-01-01 ; PMID 21494601
  68. Family Mimiviridae. ; Claverie JM, Abergel C ; Virus Taxonomy, ninth report of the International Committee on Taxonomy of Viruses (ICTV) , Elsevier, Academic Press, ISBN : 978-0-12-384684-6. pp223-228,2011 ; 2011-01-01 ;
  69. The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. ; Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J, Polle J, Salamov A, Terry A, Yamada T, Dunigan DD, Grigoriev IV, Claverie JM, Van Etten JL ; Plant Cell.22;9:2943-55,2010 Sep ; 2010-09-01 ; PMID 20852019
  70. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. ; Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, Byrne D, Lartigue A, Lescot M, Bernadac A, Poulain J, Abergel C, Claverie JM ; Genome Res.20;5:664-74,2010 May ; 2010-04-01 ; PMID 20360389
  71. Gene expression in proliferating cells of the dinoflagellate Alexandrium catenella (Dinophyceae). ; Toulza E, Shin MS, Blanc G, Audic S, Laabir M, Collos Y, Claverie JM, Grzebyk D ; Appl Environ Microbiol.76;13:4521-9,2010 Jul ; 2010-01-30 ; PMID 20435767
  72. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. ; Dereeper A, Audic S, Claverie JM, Blanc G ; BMC Evol Biol.10;1:8,2010 Jan 12 ; 2010-01-12 ; PMID 20067610
  73. Mimivirus: the emerging paradox of quasi-autonomous viruses. ; Claverie JM, Abergel C ; Trends Genet.;pp. 431-437 :,2010 Aug 7 ; 2010-01-07 ; PMID 20696492
  74. Mimivirus, un géant parmi les microbes. ; Claverie JM, Aurias A ; Biofutur 309 : 46-48.(en Français),2010 ; 2010-01-01 ;
  75. Distribution of Giant Viruses in Marine Environments. ; Ogata H., Monier A., Claverie JM ; Global Change: Mankind-Marine Environment Interactions - Proceedings of the 13th French-Japanese Oceanography Symposium, Ceccaldi H.-J. et al. eds., Springer Science/Business Media B.V. ,2010 ; 2010-01-01 ;
  76. Brucella microti: the genome sequence of an emerging pathogen. ; Audic S, Lescot M, Claverie JM, Scholz HC ; BMC Genomics.10;1:352,2009 Aug 4 ; 2009-08-04 ; PMID 19653890
  77. Ten good reasons not to exclude giruses from the evolutionary picture. ; Claverie JM, Ogata H ; Nat Rev Microbiol.7;8:615; author reply 615,2009 Aug ; 2009-01-29 ; PMID 19561626
  78. Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus. ; Ogata H, Toyoda K, Tomaru Y, Nakayama N, Shirai Y, Claverie JM, Nagasaki K ; Virol J.6;1:178,2009 Oct 27 ; 2009-01-27 ; PMID 19860921
  79. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. ; Monier A, Pagarete A, de Vargas C, Allen MJ, Read B, Claverie JM, Ogata H ; Genome Res.19;8:1441-9,2009 Aug ; 2009-01-18 ; PMID 19451591
  80. Mimivirus&Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. ; Claverie JM, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, Ogata H, Abergel C ; J Invertebr Pathol.101;3:172-80,2009 Jul ; 2009-01-17 ; PMID 19457438
  81. Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. ; von Dassow P, Ogata H, Probert I, Wincker P, Da Silva C, Audic S, Claverie JM, de Vargas C ; Genome Biol.10;10:R114,2009 Oct 15 ; 2009-01-15 ; PMID 19832986
  82. Dissecting the unique nucleotide specificity of Mimivirus nucleoside diphosphate kinase. ; Jeudy S, Lartigue A, Claverie JM, Abergel C ; J Virol.83;14:7142-50,2009 Jul ; 2009-01-13 ; PMID 19439473
  83. Mimivirus and its Virophage. ; Claverie JM, Abergel C ; Annu Rev Genet.43;:49-66,2009 ; 2009-01-04 ; PMID 19653859
  84. Mimivirus. ; Claverie JM, Abergel C, Ogata H ; Curr Top Microbiol Immunol.328;:89-121,2009 ; 2009-01-01 ; PMID 19216436
  85. The polyadenylation site of Mimivirus transcripts obeys a stringent hairpin rule. ; Byrne D, Grzela R, Lartigue A, Audic S, Chenivesse S, Encinas S, Claverie JM, Abergel C ; Genome Res.19;7:1233-42,2009 Jul ; 2009-01-01 ; PMID 19403753
  86. The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii. ; Lescot M, Audic S, Robert C, Nguyen TT, Blanc G, Cutler SJ, Wincker P, Couloux A, Claverie JM, Raoult D, Drancourt M ; PLoS Genet.4;9:e1000185,2008 Sep ; 2008-09-01 ; PMID 18787695
  87. Taxonomic distribution of large DNA viruses in the sea. ; Monier A, Claverie JM, Ogata H ; Genome Biol.9;7:R106,2008 Jul 3 ; 2008-07-03 ; PMID 18598358
  88. Microbiology. How to infect a Mimivirus. ; Ogata H, Claverie JM ; Science.321;5894:1305-6,2008 Sep 5 ; 2008-05-01 ; PMID 18772426
  89. Marine mimivirus relatives are probably large algal viruses. ; Monier A, Larsen JB, Sandaa RA, Bratbak G, Claverie JM, Ogata H ; Virol J.5;1:12,2008 Jan 23 ; 2008-01-23 ; PMID 18215256
  90. Mimivirus. ; Claverie JM ; Encyclopedia of Virology, 5 vols. (B.W.J. Mahy and M.H.V. Van Regenmortel, Editors), pp. 311-319 Oxford: Elsevier ,2008 ; 2008-01-01 ;
  91. Comparative analysis of Acinetobacters: three genomes for three lifestyles. ; Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, Bataille E, Dossat C, Gas S, Kreimeyer A, Lenoble P, Oztas S, Poulain J, Segurens B, Robert C, Abergel C, Claverie JM, Raoult D, Médigue C, Weissenbach J, Cruveiller S ; PLoS ONE.3;3:e1805,2008 ; 2008-01-01 ; PMID 18350144
  92. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. ; Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O ; Nucleic Acids Res.36;Web Server issue:W465-9,2008 Jul 1 ; 2008-01-01 ; PMID 18424797
  93. Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase. ; Santini S, Monchois V, Mouz N, Sigoillot C, Rousselle T, Claverie JM, Abergel C ; BMC Struct Biol.8;:33,2008 ; 2008-01-01 ; PMID 18652651
  94. Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. ; Monier A, Claverie JM, Ogata H ; BMC Genomics.8;1:456,2007 Dec 10 ; 2007-12-10 ; PMID 18070355
  95. Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome. ; Blanc G, Ogata H, Robert C, Audic S, Claverie JM, Raoult D ; Genome Res.17;11:1657-64,2007 Nov ; 2007-11-01 ; PMID 17916642
  96. La Bioinformatique. ; Claverie JM ; Les Techniques de l`Ingénieur - in press,2007 ; 2007-10-28 ;
  97. Virus-Encoded Aminoacyl-tRNA Synthetases: Structural and Functional Characterization of Mimivirus TyrRS and MetRS. ; Abergel C, Rudinger-Thirion J , Giegé R, Claverie JM ; J Virol.81;22:12406-17,2007 Nov ; 2007-10-01 ; PMID 17855524
  98. Unique genes in giant viruses: regular substitution pattern and anomalously short size. ; Ogata H, Claverie JM ; Genome Res.17;9:1353-61,2007 Sep ; 2007-09-01 ; PMID 17652424
  99. Bioinformatics for Dummies, 2nd Edition. ; Claverie JM, Notredame C ; Wiley, 436p,2007 ; 2007-06-01 ;
  100. Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria. ; Abergel C, Monchois V, Byrne D, Chenivesse S, Lembo F, Lazzaroni JC, Claverie JM ; Proc Natl Acad Sci U S A.104;15:6394-9,2007 Apr 10 ; 2007-04-10 ; PMID 17405861
  101. Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria. ; Audic S, Robert C, Campagna B, Parinello H, Claverie JM, Raoult D, Drancourt M ; PLoS Genet.3;8:e138,2007 Aug 24 ; 2007-01-24 ; PMID 17722982
  102. Reductive Genome Evolution from the Mother of Rickettsia. ; Blanc G, Ogata H, Robert C, Audic S, Suhre K, Vestris G, Claverie JM, Raoult D ; PLoS Genet.3;1:e14,2007 Jan 19 ; 2007-01-01 ; PMID 17238289
  103. Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data. ; Unneberg P, Claverie JM ; PLoS ONE.2;2:e254,2007 ; 2007-01-01 ; PMID 17330142
  104. Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. ; P. Renesto , C. Abergel , P. Decloquement , D. Moinier , S. Azza , H. Ogata , P. Fourquet , J.P. Gorvel , J.M. Claverie ; J Virol.80;23:11678-85,2006 Dec ; 2006-09-01 ; PMID 16971431
  105. Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity. ; Abergel C , Blanc G , Monchois V, Renesto P, Sigoillot C , Ogata H, Raoult D, Claverie JM ; Mol Biol Evol.23;11:2112-22,2006 Nov ; 2006-08-01 ; PMID 16891376
  106. Viruses take center stage in cellular evolution. ; Claverie JM ; Genome Biology, 7:110,2006 ; 2006-06-19 ; PMID 16787527
  107. Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. ; Ogata H, {La Scola} B, Audic S, Renesto P, Blanc G, Robert C, Fournier PE, Claverie JM, Raoult D ; PLoS Genet.2;5:e76,2006 May ; 2006-05-01 ; PMID 16703114
  108. Mimivirus and the emerging concept of "giant" virus. ; Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE ; Virus Res.117;1:133-44,2006 Apr ; 2006-04-01 ; PMID 16469402
  109. Characterization of mimivirus DNA topoisomerase IB suggests horizontal gene transfer between eukaryal viruses and bacteria. ; Benarroch D, Claverie JM, Raoult D, Shuman S ; J Virol.80;1:314-21,2006 Jan ; 2006-01-01 ; PMID 16352556
  110. Comparative genomics of multidrug resistance in Acinetobacter baumannii. ; Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, Poirel L, Richet H, Robert C, Mangenot S, Abergel C, Nordmann P, Weissenbach J, Raoult D, Claverie JM ; PLoS Genet.2;1:e7,2006 Jan ; 2006-01-01 ; PMID 16415984
  111. Crystal structure of Escherichia coli DkgA, a broad-specificity aldo-keto reductase. ; Jeudy S, Monchois V, Maza C, Claverie JM, Aberg C ; Proteins.62;1:302-7,2006 Jan 1 ; 2006-01-01 ; PMID 16284956
  112. The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides. ; Jeudy S, Claverie JM, Abergel C ; J Bioenerg Biomembr.38;3-4:247-54,2006 Aug ; 2006-01-01 ; PMID 16957983
  113. Determination of strongly overlapping signaling activity from microarray data. ; Bidaut G, Suhre K, Claverie JM, Ochs MF ; BMC Bioinformatics.7;:99,2006 ; 2006-01-01 ; PMID 16507110
  114. Rickettsia felis, from Culture to Genome Sequencing. ; Ogata H, Robert C, Audic S, Robineau S, Blanc G, Fournier PE, Renesto P, Claverie JM, Raoult D. ; Ann N Y Acad Sci. ;1063:26-34,2005 Dec ; 2005-12-01 ; PMID 16481487
  115. Mimivirus gene promoters exhibit an unprecedented conservation among all eukaryotes. ; Suhre K, Audic S, Claverie JM ; Proc Natl Acad Sci U S A.102;41:14689-93,2005 Oct 11 ; 2005-10-11 ; PMID 16203998
  116. Characterization of the Naturally Occurring Oxacillinase of Acinetobacter baumannii. ; Heritier C, Poirel L, Fournier PE, Claverie JM, Raoult D, Nordmann P. ; Antimicrob Agents Chemother. 49(10):4174-9,2005 Oct ; 2005-10-01 ; PMID 16189095
  117. Fewer genes, more noncoding RNA. ; Claverie JM. ; Science. 309(5740):1529-30,2005 Sep 2 ; 2005-09-01 ; PMID 16141064
  118. The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. ; Ogata H, Renesto P, Audic S, Robert C, Blanc G, Fournier PE, Parinello H, Claverie JM, Raoult D ; PLoS Biol.3;8:e248,2005 Aug ; 2005-08-01 ; PMID 15984913
  119. Mimivirus relatives in the Sargasso sea. ; Ghedin E, Claverie JM ; Virol J.2;:62,2005 Aug 16 ; 2005-08-01 ; PMID 16105173
  120. Response to Comment on The 1.2-Megabase Genome Sequence of Mimivirus Science, Vol 308, Issue 5725, 1114 ; Ogata H, Abergel C, Raoult D, Claverie JM ; Science, Vol 308, Issue 5725, 1114,2005 Jun ; 2005-06-20 ;
  121. Giant viruses in the oceans : the 4th Algal Virus Workshop. ; Claverie JM. ; Virol J. ;2(1):52,2005 Jun 20 ; 2005-06-20 ; PMID 15967028
  122. Discovery of protein-coding palindromic repeats in Wolbachia. ; Ogata H, Suhre K, Claverie JM. ; Trends Microbiol.;13(6):253-5,2005 Jun ; 2005-06-01 ; PMID 15936655
  123. Tropheryma whipplei genome at the beginning of the post-genomic era. ; Crapoulet N, Renesto P, Dumler JS, Suhre K, Ogata H, Claverie JM and Raoult D. ; Current genomics Vol. 6, No. 3, Pp. 195-205,2005 ; 2005-04-28 ;
  124. A new example of viral intein in Mimivirus. ; Ogata H, Raoult D, Claverie JM. ; Virol J. ;2(1):8,2005 Feb 11 ; 2005-02-01 ; PMID 15707490
  125. French public research--saved? ; Claverie JM. ; Science.;307(5713):1169,2005 Feb 25 ; 2005-02-01 ; PMID 15731408
  126. Mimivirus TyrRS: preliminary structural and functional characterization of the first amino-acyl tRNA synthetase found in a virus. ; Abergel C, Chenivesse S, Byrne D, Suhre K, Arondel V, Claverie JM ; Acta Crystallogr Sect F Struct Biol Cryst Commun.61;Pt 2:212-5,2005 Feb 1 ; 2005-02-01 ; PMID 16510997
  127. Some lessons from Rickettsia genomics. ; Renesto P, Ogata H, Audic S, Claverie JM, Raoult D. ; FEMS Microbiol Rev.;29(1):99-117,2005 Jan ; 2005-01-01 ; PMID 15652978
  128. Metagrowth: a new resource for the building of metabolic hypotheses in microbiology ; Ogata H and Claverie JM ; Nucleic Acids Res.;33 Database Issue:D321-4,2005 Jan 1 ; 2005-01-01 ; PMID 15608207
  129. Un virus encore plus géant que les autres. ; Claverie JM ; Médecine Science 21 : 15-16,2005 ; 2005-01-01 ;
  130. Bayesian decomposition analysis of bacterial phylogenomic profiles. ; Bidaut G, Suhre K, Claverie JM, Ochs MF. ; Am J Pharmacogenomics;5(1):63-70,2005 ; 2005-01-01 ; PMID 15727490
  131. Molecular evolution of rickettsia surface antigens: evidence of positive selection. ; G. Blanc , M. Ngwamidiba , H. Ogata , P.E. Fournier , J.M. Claverie , D. Raou ; Mol Biol Evol.22;10:2073-83,2005 Oct ; 2005-01-01 ; PMID 15972845
  132. Phydbac ; F. Enault , K. Suhre , J.M. Claverie ; BMC Bioinformatics.6;:247,2005 ; 2005-01-01 ; PMID 16221304
  133. The 1.2-Mb Genome Sequence of Mimivirus. ; Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. ; Science. 2004 Nov 19;306(5700):1344-50. Epub 2004 Oct 14. ; 2004-10-14 ; PMID 15486256
  134. Dictionary of Bioinformatics and Computational Biology ; John M. Hancock (Editor), Marketa J. Zvelebil (Editor), J.-M. Claverie ; Dictionary of Bioinformatics and Computational Biology, J. M. Hancock & M.J. Zvelebil editors, Wiley-Liss, Hoboken, USA ; 2004-08-01 ;
  135. CaspR: a web-server for automated molecular replacement using homology modelling. ; Claude JB, Suhre K, Notredame C, Claverie JM, Abergel C ; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9. ; 2004-07-01 ; PMID 15215460
  136. Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis ; Enault F, Suhre K, Poirot O, Abergel C, Claverie JM ; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W336-9. ; 2004-07-01 ; PMID 15215406
  137. FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. ; Suhre, Claverie JM ; Nucleic Acids Res. 2004 Jan 1; 32 Database issue: D273-6. ; 2004-01-01 ; PMID 14681411
  138. Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome. ; Raoult D, Ogata H, Audic S, Robert C, Suhre K, Drancourt M, Claverie JM ; Genome Res 2003 Aug;13(8):1800-9. ; 2003-08-01 ; PMID 12902375
  139. Genome-based design of a cell-free culture medium for Tropheryma whipplei. ; Renesto P, Crapoulet N, Ogata H, La Scola B, Vestris G, Claverie JM, Raoult D ; Lancet 2003 Aug 9;362(9382):447-9. ; 2003-08-01 ; PMID 12927433
  140. Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. ; Enault F, Suhre K, Poirot O, Abergel C, Claverie JM ; Nucleic Acids Res 2003 Jul 1;31(13):3720-2. ; 2003-07-01 ; PMID 12824402
  141. Genomic correlates of hyperthermostability, an update. ; Suhre K, Claverie JM ; J Biol Chem 2003 May 9;278(19):17198-202. ; 2003-05-01 ; PMID 12600994
  142. The structure of Acidithiobacillus ferrooxidans c(4)-cytochrome: a model for complex-induced electron transfer tuning. ; Abergel C, Nitschke W, Malarte G, Bruschi M, Claverie JM, Giudici-Orticoni MT ; Structure (Camb) 2003 May;11(5):547-55. ; 2003-05-01 ; PMID 12737820
  143. A giant virus in amoebae. ; La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie JM, Rao ; Science 2003 Mar 28;299(5615):2033. ; 2003-03-01 ; PMID 12663918
  144. The insertion of palindromic repeats in the evolution of proteins. ; Claverie JM, Ogata H ; Trends Biochem Sci 2003 Feb;28(2):75-80. ; 2003-02-01 ; PMID 12575994
  145. Positional clustering of differentially expressed genes on human chromosomes 20, 21 and 22. ; Megy K, Audic S, Claverie JM ; Genome Biol 2003;4(2):P1. ; 2003-01-10 ; PMID 12620117
  146. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. ; Abergel C, Coutard B, Byrne D, Chenivesse S, Claude JB, Deregnaucourt C, Fricaux T, Gianesini-Boutreux C, Jeudy S, Lebrun R, Maza C, Notredame C, Poirot O, Suhre K, Varagnol M, Claverie JM. ; J Struct Funct Genomics. 2003;4(2-3):141-57. ; 2003-01-01 ; PMID 14649299
  147. Bioinformatics for Dummies ; Claverie J.-M., Notredame C. ; John Wiley & Sons, New York ; 2003-01-01 ;
  148. In Search of new anti-bacterial target genes: a comparative/structural genomics approach. ; Claverie JM, Monchois V, Audic S, Poirot O, Abergel C ; Comb Chem High Throughput Screen 2002 Nov;5(7):511-22. ; 2002-11-01 ; PMID 12470264
  149. Heart-specific genes revealed by expressed sequence tag (EST) sampling. ; Megy K, Audic S, Claverie JM ; Genome Biol 2002;3(12):RESEARCH0074. ; 2002-11-01 ; PMID 12537563
  150. Heart specific genes revealed by EST sampling. ; Megy K, Audic S, Claverie JM ; Genome Biol 2002 Aug 16;3(9):PREPRINT0008. ; 2002-08-01 ; PMID 12225578
  151. Protein coding palindromes are a unique but recurrent feature in Rickettsia. ; Ogata H, Audic S, Abergel C, Fournier PE, Claverie JM ; Genome Res 2002 May;12(5):808-16. ; 2002-05-01 ; PMID 11997347
  152. Proficient target selection in structural genomic by In vitro protein expression on Gateway recombination plasmids. ; Monchois V., Vincentelli R., Abergel C., Deregnaucourt C., Claverie J.-M. and Monchois V. ; Cell-Free Translation Systems (Spirin Ed.) Springer Verlag : () 197- 202. ; 2002-01-01 ;
  153. Recent advances in computational genomics. ; Claverie JM, Abergel C, Audic S, Ogata H ; Pharmacogenomics 2001 Nov;2(4):361-72. ; 2001-11-01 ; PMID 11722286
  154. Mechanisms of evolution in Rickettsia conorii and R. prowazekii. ; Ogata H, Audic S, Renesto-Audiffren P, Fournier PE, Barbe V, Samson D, Roux V, Cossart P, Weissenbach J, Claverie JM, Raoult D ; Science 2001 Sep 14;293(5537):2093-8. ; 2001-09-01 ; PMID 11557893
  155. Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme. ; Monchois V, Abergel C, Sturgis J, Jeudy S, Claverie JM ; J Biol Chem 2001 May 25;276(21):18437-41. ; 2001-05-01 ; PMID 11278658
  156. [Transcriptome analysis in cancerology: bioinformatics aspects] ; Claverie JM ; Bull Cancer 2001 Mar;88(3):269-76. ; 2001-03-01 ; PMID 11313204
  157. Gene number. What if there are only 30,000 human genes? ; Claverie JM ; Science 2001 Feb 16;291(5507):1255-7. ; 2001-02-01 ; PMID 11233450
  158. Bioinformatics of transcriptome analysis in Cancer Biology. ; Claverie J.-M. ; Bull. Cancer 88: 269-276. ; 2001-01-01 ;
  159. Le dècryptage du gènome humain : du fantasme ? la rèalitè mèdicale ; Claverie J.-M. ; Concours Medical 123: 429-429. ; 2001-01-01 ;
  160. Crystallization and preliminary crystallographic study of b0220, an 'ORFan' protein of unknown function from Escherichia coli. ; Abergel C, Monchois V, Chenivesse S, Jeudy S, Claverie JM ; Acta Crystallogr D Biol Crystallogr 2000 Dec;56 Pt 12:1694-5. ; 2000-12-01 ; PMID 11092949
  161. Identification of odorant receptors from the Alpine marmot (Marmota marmota). ; Matarazzo V, Tirard A, Renucci M, Botto JM, Bel MC, Claverie JM, Belaich A, Clement JL ; Cell Mol Biol (Noisy-le-grand) 2000 Nov;46(7):1249-58. ; 2000-11-01 ; PMID 11075954
  162. Structural and genomic correlates of hyperthermostability. ; Cambillau C, Claverie JM ; J Biol Chem 2000 Oct 20;275(42):32383-6. ; 2000-10-01 ; PMID 10940293
  163. Selfish DNA in protein-coding genes of Rickettsia. ; Ogata H, Audic S, Barbe V, Artiguenave F, Fournier PE, Raoult D, Claverie JM ; Science 2000 Oct 13;290(5490):347-50. ; 2000-10-01 ; PMID 11030655
  164. From bioinformatics to computational biology. ; Claverie JM ; Genome Res 2000 Sep;10(9):1277-9. ; 2000-09-01 ; PMID 10984445
  165. Reverse transcriptase-polymerase chain reaction validation of 25 orphan genes from Escherichia coli K-12 MG1655. ; Alimi JP, Poirot O, Lopez F, Claverie JM ; Genome Res 2000 Jul;10(7):959-66. ; 2000-07-01 ; PMID 10899145
  166. Patterns of variant polyadenylation signal usage in human genes. ; Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D ; Genome Res 2000 Jul;10(7):1001-10. ; 2000-07-01 ; PMID 10899149
  167. Do we need a huge new centre to annotate the human genome? ; Claverie JM ; Nature 2000 Jan 6;403(6765):12. ; 2000-01-01 ; PMID 10638729
  168. EST databases as multi-conditional gene expression datasets. ; Ewing RM, Claverie JM ; Pac Symp Biocomput 2000;:430-42. ; 2000-01-01 ; PMID 10902191
  169. Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets. ; Ewing R, Poirot O, Claverie JM ; In Silico Biol 1999-2000;1(4):197-213. ; 2000-01-01 ; PMID 11479934
  170. The Detection of Putative Recombinant Sequence Using BLAST. ; BenKahla A., Robertson D.L., Beaudoing E., Claverie J.-M. ; Proceedings of the German Conference on Bioinformatics. : 3- 9. ; 2000-01-01 ;
  171. Structure of the Escherichia coli TolB protein determined by MAD methods at 1.95 A resolution. ; Abergel C, Bouveret E, Claverie JM, Brown K, Rigal A, Lazdunski C, Benedetti H ; Structure Fold Des 1999 Oct 15;7(10):1291-300. ; 1999-10-01 ; PMID 10545334
  172. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. ; Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM. ; Genome Res. 1999 Oct;9(10):950-9. ; 1999-10-01 ; PMID 10523523
  173. Computational methods for the identification of differential and coordinated gene expression. ; Claverie JM ; Hum Mol Genet 1999;8(10):1821-32. ; 1999-05-01 ; PMID 10469833
  174. Hidden dUTPase sequence in human immunodeficiency virus type 1 gp120. ; Abergel C, Robertson DL, Claverie JM ; J Virol 1999 Jan;73(1):751-3. ; 1999-01-01 ; PMID 9847382
  175. A New Strategy and Software System for the Design of Functional Signatures in Protein Sequences, in Perspective in Structural Biology. ; Claverie J.-M., Lopez F. and Abergel C ; Indian Acad. Sciences and the Universities Press,Hyderabad, India.(M. Vijayan, ed.). Chap. 51: () 680- 700. ; 1999-01-01 ;
  176. Triple association of CDC25-, Dbl- and Sec7-related domains in mammalian guanine-nucleotide-exchange factors. ; Abergel C, Chavrier P, Claverie JM ; Trends Biochem Sci 1998 Dec;23(12):472-3. ; 1998-12-01 ; PMID 9868368
  177. Self-identification of protein-coding regions in microbial genomes. ; Audic S, Claverie JM ; Proc Natl Acad Sci U S A 1998 Aug 18;95(17):10026-31. ; 1998-08-01 ; PMID 9707594
  178. Computational methods for exon detection. ; Claverie JM ; Mol Biotechnol 1998 Aug;10(1):27-48. ; 1998-08-01 ; PMID 9779421
  179. Quantitative analysis of the T cell repertoire selected by a single peptide-major histocompatibility complex. ; Gapin L, Fukui Y, Kanellopoulos J, Sano T, Casrouge A, Malier V, Beaudoing E, Gautheret D, Claverie JM, Sasazuki T, Kourilsky P ; J Exp Med 1998 Jun 1;187(11):1871-83. ; 1998-06-01 ; PMID 9607927
  180. Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. ; Gautheret D, Poirot O, Lopez F, Audic S, Claverie JM ; Genome Res 1998 May;8(5):524-30. ; 1998-05-01 ; PMID 9582195
  181. Visualizing the competitive recognition of TATA-boxes in vertebrate promoters. ; Audic S, Claverie JM ; Trends Genet 1998 Jan;14(1):10-1. ; 1998-01-01 ; PMID 9448460
  182. Crystallization and preliminary crystallographic study of a component of the Escherichia coli tol system: TolB. ; Abergel C, Rigal A, Chenivesse S, Lazdunski C, Claverie JM, Bouveret E, Benedetti H ; Acta Crystallogr D Biol Crystallogr 1998 Jan 1;54 ( Pt 1):102-4. ; 1998-01-01 ; PMID 9761825
  183. SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments. ; Audic S, Lopez F, Claverie JM, Poirot O, Abergel C ; Proteins 1997 Oct;29(2):252-7. ; 1997-10-01 ; PMID 9329089
  184. The significance of digital gene expression profiles. ; Audic S, Claverie JM ; Genome Res 1997 Oct;7(10):986-95. ; 1997-10-01 ; PMID 9331369
  185. Exon detection by similarity searches. ; Claverie JM ; Methods Mol Biol 1997;68:283-313. ; 1997-01-01 ; PMID 9055264
  186. Computational methods for the identification of genes in vertebrate genomic sequences. ; Claverie JM ; Hum Mol Genet 1997;6(10):1735-44. ; 1997-01-01 ; PMID 9300666
  187. The difficulty of identifying genes in anonymous vertebrate sequences. ; Claverie JM, Poirot O, Lopez F ; Comput Chem 1997;21(4):203-14. ; 1997-01-01 ; PMID 9415985
  188. Detection of eukaryotic promoters using Markov transition matrices. ; Audic S, Claverie JM ; Comput Chem 1997;21(4):223-7. ; 1997-01-01 ; PMID 9440929
  189. The statistical significance of nucleotide position-weight matrix matches. ; Claverie JM, Audic S ; Comput Appl Biosci 1996 Oct;12(5):431-9. ; 1996-10-01 ; PMID 8996792
  190. Effective large-scale sequence similarity searches. ; Claverie JM ; Methods Enzymol 1996;266:212-27. ; 1996-01-01 ; PMID 8743687
  191. Nef and Gag synthetic peptide priming of antibody responses to HIV type 1 antigens in mice and primates. ; Vaslin B, Claverie JM, Benveniste O, Barre-Sinoussi FC, Dormont D ; AIDS Res Hum Retroviruses 1994 Oct;10(10):1241-50. ; 1994-10-01 ; PMID 7531460
  192. A streamlined random sequencing strategy for finding coding exons. ; Claverie JM ; Genomics 1994 Oct;23(3):575-81. ; 1994-10-01 ; PMID 7851885
  193. Alu alert. ; Claverie JM, Makalowski W ; Nature 1994 Oct 27;371(6500):752. ; 1994-10-01 ; PMID 7935834
  194. Some useful statistical properties of position-weight matrices. ; Claverie JM ; Comput Chem 1994 Sep;18(3):287-94. ; 1994-09-01 ; PMID 7952899
  195. Detecting frame shifts by amino acid sequence comparison. ; Claverie JM ; J Mol Biol 1993 Dec 20;234(4):1140-57. ; 1993-12-01 ; PMID 7903399
  196. Identification of T cell peptides from C gamma 2ab involved in IgG2ab T cell-induced allotypic suppression. Relationship with the MHC haplotype of the suppressor T cell-donor Igha mice. ; Majlessi L, Roth C, Benaroch P, Claverie JM, Kourilsky P, Bordenave G ; J Immunol 1993 Aug 1;151(3):1263-72. ; 1993-08-01 ; PMID 8335928
  197. Database of ancient sequences. ; Claverie JM ; Nature 1993 Jul 1;364(6432):19-20. ; 1993-07-01 ; PMID 8316293
  198. Ancient conserved regions in new gene sequences and the protein databases. ; Green P, Lipman D, Hillier L, Waterston R, States D, Claverie JM ; Science 1993 Mar 19;259(5102):1711-6. ; 1993-03-01 ; PMID 8456298
  199. Dense Alu clustering and a potential new member of the NF kappa B family within a 90 kilobase HLA class III segment. ; Iris FJ, Bougueleret L, Prieur S, Caterina D, Primas G, Perrot V, Jurka J, Rodriguez-Tome P, Claverie JM, Dausset J, et al. ; Nat Genet 1993 Feb;3(2):137-45. ; 1993-02-01 ; PMID 8499947
  200. Characterization and chromosomal assignment of a human cDNA encoding a protein related to the murine 102-kDa cadherin-associated protein (alpha-catenin). ; Claverie JM, Hardelin JP, Legouis R, Levilliers J, Bougueleret L, Mattei MG, Petit C ; Genomics 1993 Jan;15(1):13-20. ; 1993-01-01 ; PMID 8432524
  201. Antibodies and reactive T cells against the malaria heat-shock protein Pf72/Hsp70-1 and derived peptides in individuals continuously exposed to Plasmodium falciparum. ; Behr C, Sarthou JL, Rogier C, Trape JF, Dat MH, Michel JC, Aribot G, Dieye A, Claverie JM, Druihle P, et al. ; J Immunol 1992 Nov 15;149(10):3321-30. ; 1992-11-01 ; PMID 1431109
  202. Correlations in intronless DNA. ; Prabhu VV, Claverie JM ; Nature 1992 Oct 29;359(6398):782. ; 1992-10-01 ; PMID 1436053
  203. Identifying coding exons by similarity search: alu-derived and other potentially misleading protein sequences. ; Claverie JM ; Genomics 1992 Apr;12(4):838-41. ; 1992-04-01 ; PMID 1572661
  204. Random association between the peptide repertoire of A2.1 class I and several different DR class II molecules. ; Sette A, Vitiello A, Farness P, Furze J, Sidney J, Claverie JM, Grey HM, Chesnut R ; J Immunol 1991 Dec 1;147(11):3893-900. ; 1991-12-01 ; PMID 1658152
  205. A strong propensity toward loop formation characterizes the expressed reading frames of the D segments at the Ig H and T cell receptor loci. ; Abergel C, Claverie JM ; Eur J Immunol 1991 Dec;21(12):3021-5. ; 1991-12-01 ; PMID 1660812
  206. The candidate gene for the X-linked Kallmann syndrome encodes a protein related to adhesion molecules. ; Legouis R, Hardelin JP, Levilliers J, Claverie JM, Compain S, Wunderle V, Millasseau P, Le Paslier D, Cohen D, Caterina D, et al. ; Cell 1991 Oct 18;67(2):423-35. ; 1991-10-01 ; PMID 1913827
  207. Biased amino acid distributions in regions of the T cell receptors and MHC molecules potentially involved in their association. ; Prochnicka-Chalufour A, Casanova JL, Avrameas S, Claverie JM, Kourilsky P ; Int Immunol 1991 Sep;3(9):853-64. ; 1991-09-01 ; PMID 1931813
  208. WOBB.C: a portable software package for defining and searching ambiguous sequence patterns. ; Claverie JM, Sauvaget I ; Protein Seq Data Anal 1991 Aug;4(2):119-21. ; 1991-08-01 ; PMID 1946329
  209. Identification of a major human immunodeficiency virus-1 reverse transcriptase epitope recognized by mouse CD4+ T lymphocytes. ; Haas G, David R, Frank R, Gausepohl H, Devaux C, Claverie JM, Pierres M ; Eur J Immunol 1991 Jun;21(6):1371-7. ; 1991-06-01 ; PMID 1710563
  210. Smoothing profiles with sliding windows: better to wear a hat! ; Claverie JM, Daulmerie C ; Comput Appl Biosci 1991 Jan;7(1):113-5. ; 1991-01-01 ; PMID 2004269
  211. Structure of the ecdysone-inducible P1 gene of Drosophila melanogaster. ; Maschat F, Dubertret ML, Therond P, Claverie JM, Lepesant JA ; J Mol Biol 1990 Jul 20;214(2):359-72. ; 1990-07-01 ; PMID 1696317
  212. Protein instruction. ; Claverie JM ; Nature 1990 May 10;345(6271):121-2. ; 1990-05-01 ; PMID 2186280
  213. K-tuple frequency analysis: from intron/exon discrimination to T-cell epitope mapping. ; Claverie JM, Sauvaget I, Bougueleret L ; Methods Enzymol 1990;183:237-52. ; 1990-01-01 ; PMID 1690334
  214. Conformational analysis of T immunogenic peptides by circular dichroism spectroscopy. ; Abergel C, Loret E, Claverie JM ; Eur J Immunol 1989 Oct;19(10):1969-72. ; 1989-10-01 ; PMID 2511030
  215. MHC restriction, alloreactivity, and thymic education: a common link? ; Kourilsky P, Claverie JM ; Cell 1989 Feb 10;56(3):327-9. ; 1989-02-01 ; PMID 2492449
  216. Extensive structural homology between H-2 K/D/L antigens and non-polymorphic class I Qa, Tla and 37 molecules suggests they may act as peptide carriers. ; Prochnicka-Chalufour A, Casanova JL, Kourilsky P, Claverie JM ; Res Immunol 1989 Feb;140(2):133-44. ; 1989-02-01 ; PMID 2740613
  217. MHC-antigen interaction: what does the T cell receptor see? ; Kourilsky P, Claverie JM ; Adv Immunol 1989;45:107-93. ; 1989-01-01 ; PMID 2665438
  218. Implications of a Fab-like structure for the T-cell receptor. ; Claverie JM, Prochnicka-Chalufour A, Bougueleret L ; Immunol Today 1989 Jan;10(1):10-4. ; 1989-01-01 ; PMID 2665768
  219. How important is the direct recognition of polymorphic MHC residues by TCR in the generation of the T-cell repertoire? ; Kourilsky P, Claverie JM, Prochnicka-Chalufour A, Spetz-Hagberg AL, Larsson-Sciard EL ; Cold Spring Harb Symp Quant Biol 1989;54 Pt 1:93-103. ; 1989-01-01 ; PMID 2700950
  220. T-immunogenic peptides are constituted of rare sequence patterns. Use in the identification of T epitopes in the human immunodeficiency virus gag protein. ; Claverie JM, Kourilsky P, Langlade-Demoyen P, Chalufour-Prochnicka A, Dadaglio G, Tekaia F, Plata F, Bougueleret L ; Eur J Immunol 1988 Oct;18(10):1547-53. ; 1988-10-01 ; PMID 2461306
  221. Objective comparison of exon and intron sequences by means of 2-dimensional data analysis methods. ; Bougueleret L, Tekaia F, Sauvaget I, Claverie JM ; Nucleic Acids Res 1988 Mar 11;16(5):1729-38. ; 1988-03-01 ; PMID 3353220
  222. Sequence patterns in protein kinases. ; Bairoch A, Claverie JM ; Nature 1988 Jan 7;331(6151):22. ; 1988-01-01 ; PMID 3340146
  223. Rare sequence motifs are common constituents of hypervariable antibody regions. ; Chalufour A, Bougueleret L, Claverie JM, Kourilsky P ; Ann Inst Pasteur Immunol 1987 Sep-Oct;138(5):671-85. ; 1987-09-01 ; PMID 3125843
  224. [Quality control of multicenter evaluation studies of the in vitro activity of antibiotics] ; Tekaia F, Derlot E, Claverie JM, Courvalin P ; Pathol Biol (Paris) 1987 Jun;35(5 Pt 2):687-91. ; 1987-06-01 ; PMID 3309798
  225. Working principles in the immune system implied by the peptidic self model. ; Kourilsky P, Chaouat G, Rabourdin-Combe C, Claverie JM ; Proc Natl Acad Sci U S A 1987 May;84(10):3400-4. ; 1987-05-01 ; PMID 3494999
  226. Isolation and characterisation of a murine cDNA clone highly homologous to the yeast L29 ribosomal protein gene. ; Belhumeur P, Paterno GD, Boileau G, Claverie JM, Skup D ; Nucleic Acids Res 1987 Feb 11;15(3):1019-29. ; 1987-02-01 ; PMID 2434927
  227. Variability analysis of the human and mouse T-cell receptor beta chains. ; Bougueleret L, Claverie JM ; Immunogenetics 1987;26(4-5):304-8. ; 1987-01-01 ; PMID 3653942
  228. The peptidic self model: a reassessment of the role of the major histocompatibility complex molecules in the restriction of the T-cell response. ; Claverie JM, Kourilsky P ; Ann Inst Pasteur Immunol 1986 Nov-Dec;137D(3):425-42. ; 1986-11-01 ; PMID 3103648
  229. Relevance of the lariat model to the splicing of the H-2 gene family. ; Bougueleret L, Claverie JM ; Eur J Biochem 1986 Oct 15;160(2):279-84. ; 1986-10-01 ; PMID 3769928
  230. PseqIP: a nonredundant and exhaustive protein sequence data bank generated from 4 major existing collections. ; Claverie JM, Bricault L ; Proteins 1986 Sep;1(1):60-5. ; 1986-09-01 ; PMID 3449852
  231. The peptidic self model: a hypothesis on the molecular nature of the immunological self. ; Kourilsky P, Claverie JM ; Ann Inst Pasteur Immunol 1986 Jul-Aug;137D(1):3-21. ; 1986-07-01 ; PMID 3489434
  232. [Neg-entropy and local information content: a new approach to the analysis of nucleotide and amino-acid sequences] ; Claverie JM, Bougueleret L, Ooi T ; Tanpakushitsu Kakusan Koso 1986 Jun;(29 Suppl):111-22. ; 1986-06-01 ; PMID 3534948
  233. Heuristic informational analysis of sequences. ; Claverie JM, Bougueleret L ; Nucleic Acids Res 1986 Jan 10;14(1):179-96. ; 1986-01-01 ; PMID 3753763
  234. A new protein sequence data bank. ; Claverie JM, Sauvaget I ; Nature 1985 Nov 7-13;318(6041):19. ; 1985-11-01 ; PMID 4058589
  235. Computer generation and statistical analysis of a data bank of protein sequences translated from GenBank. ; Claverie JM, Sauvaget I, Bougueleret L ; Biochimie 1985 May;67(5):437-43. ; 1985-05-01 ; PMID 3927990
  236. Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters. ; Claverie JM, Sauvaget I ; Comput Appl Biosci 1985;1(2):95-104. ; 1985-01-01 ; PMID 3880336
  237. Sequencing the erbA gene of avian erythroblastosis virus reveals a new type of oncogene. ; Debuire B, Henry C, Bernissa M, Biserte G, Claverie JM, Saule S, Martin P, Stehelin D ; Science 1984 Jun 29;224(4656):1456-9. ; 1984-06-01 ; PMID 6328658
  238. A common philosophy and FORTRAN 77 software package for implementing and searching sequence databases. ; Claverie JM ; Nucleic Acids Res 1984 Jan 11;12(1 Pt 1):397-407. ; 1984-01-01 ; PMID 6546424
  239. T lymphoma variants with specifically altered growth in semi-solid media. ; Claverie JM, Cohn M ; Int J Cancer 1983 Nov 15;32(5):641-3. ; 1983-11-01 ; PMID 6642758
  240. A new simple method to determine the diffusion coefficient from active enzyme centrifugation experiments. ; Claverie JM ; Arch Biochem Biophys 1980 Jun;202(1):160-7. ; 1980-06-01 ; PMID 7396532
  241. Mutations of Chinese hamster somatic cells from 2-deoxygalactose sensitivity to resistance. ; Claverie JM, de Souza AC, Thirion JP ; Genetics 1979 Jun;92(2):563-72. ; 1979-06-01 ; PMID 488705
  242. Sedimentation studies of the reversible dimer-tetramer transition kinetics of concanavalin A. ; Huet M, Claverie JM ; Biochemistry 1978 Jan 24;17(2):236-41. ; 1978-01-01 ; PMID 619990
  243. Phosphorylation of intracellular fructose in Bacillus subtilis mediated by phosphoenolpyruvate-1-fructose phosphotransferase. ; Delobbe A, Chalumeau H, Claverie JM, Gay P ; Eur J Biochem 1976 Jul 15;66(3):485-91. ; 1976-07-01 ; PMID 821752
  244. Sedimentation of generalized systems of interacting particles. III. Concentration-dependent sedimentation and extension to other transport methods. ; Claverie JM ; Biopolymers 1976 May;15(5):843-57. ; 1976-05-01 ; PMID 9925410
  245. Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations. ; Claverie JM, Dreux H, Cohen R ; Biopolymers 1975 Aug;14(8):1685-1700. ; 1975-08-01 ; PMID 1156660
  246. Sedimentation of generalized systems of interacting particles. II. Active enzyme centrifugation--theory and extensions of its validity range. ; Cohen R, Claverie JM ; Biopolymers 1975 Aug;14(8):1701-16. ; 1975-08-01 ; PMID 1156661
  247. [Research on anti-inflammatory indazoles] ; Claverie JM, Mattioda G ; Farmaco [Sci] 1973 Jul;28(7):523-7. ; 1973-07-01 ; PMID 4718399
  248. cc ; Claverie JM ; dd,2012 May ; 0000-00-00 ;

Contacter cette personne
Jean-Michel Claverie PU-PH, Directeur du laboratoire
G
Lucie Gallot Tel:

Mes centres d’intérêt principaux concernent l’évolution des organismes et des génomes ; et plus particulièrement l’évolution des virus géants et de leurs hôtes cellulaires, dont les trajectoires évolutives s’entrecroisent.

Mon travail de thèse s’articule en deux axes complémentaires :

Analyse génomique d’un virus en particulier, CeV, qui infecte une algue ; et comparaison avec les autres membres de sa famille pour étudier les modes d’évolutions de ces virus.
Analyse des séquences virales présentes dans les assemblages eucaryotes, afin de

étendre le spectre de séquences virales étudiées en s’affranchissant des restrictions dues aux méthodes classiques d’obtention de matériel génétique de virus (isolation de virions à partir d’hôtes cultivables, connus) tout en conservant les informations liées à leur écologie, en partie perdues lors d’analyses métagénomiques
mettre en évidence les processus par lesquels l’interaction des virus géants avec des cellules a mené à l’évolution du génome de ces dernières, et expliciter ces innovations génétiques.

Thèse soutenue le 7 novembre 2017:
Génomique des virus géants, des virophages, et échanges génétiques avec leurs hôtes eucaryotes
Discipline : Biologie
Spécialité : Génomique et Bioinformatique
jury :
Elisabeth Herniou Rapportrice
Marie-Agnès Petit Rapportrice
Gwenaël Piganeau Examinatrice
Christophe Robaglia Examinateur
Guillaume Blanc Co-directeur de thèse
Jean-Michel Claverie Co-directeur de thèse

Bibliographie:

  1. Comparative genomics of Chrysochromulina Ericina Virus (CeV) and other microalgae-infecting large DNA viruses highlight their intricate evolutionary relationship with the established Mimiviridae family. ; Gallot-Lavallee L, Blanc G, Claverie JM ; J Virol.;:,2017 Apr 26 ; 2017-04-26 ; PMID 28446675
  2. A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. ; Gallot-Lavallée L, Blanc G ; Viruses.9;1:,2017 Jan 20 ; 2017-01-20 ; PMID 28117696
  3. Giant viruses at the core of microscopic wars with global impacts. ; Villain A, Gallot-Lavallée L, Blanc G, Maumus F ; Curr Opin Virol.17;:130-137,2016 Apr 15 ; 2016-04-15 ; PMID 27088734
  4. The 474-Kilobase-Pair Complete Genome Sequence of CeV-01B, a Virus Infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae). ; Gallot-Lavallée L, Pagarete A, Legendre M, Santini S, Sandaa RA, Himmelbauer H, Ogata H, Bratbak G, Claverie JM ; Genome Announc.3;6:,2015 dec ; 2015-12-01 ; PMID 26634761
  5. Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses. ; Blanc G, Gallot-Lavallée L, Maumus F ; Proc Natl Acad Sci U S A.;:,2015 Aug 24 ; 2015-08-24 ; PMID 26305943

Contacter cette personne
Lucie Gallot
Elsa Garcin Tel:

Lien ORCID

Bibliographie:

  1. TranscriptSNPView: a genome-wide catalog of mouse coding variation. ; Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J, van der Weyden L, Bradley A, Birney E, Adams DJ. ; Nat Genet. 2006 Aug;38(8):853. ; 2006-08-01 ; PMID 16874317

Contacter cette personne
Elsa Garcin
J
Sandra Jeudy Chargé de Recherche CNRS Tel:+33 4 91 82 54 41

Je m’associe à la démarche du laboratoire afin d’avancer dans la compréhension des virus géants et des mécanismes qu’ils utilisent pour prendre le contrôle de la cellule hôte.

Je suis plus particulièrement impliquée dans :

l’étude des Marseilleviridae et leur niveau de dépendance au noyau cellulaire
la caractérisation du virophage et l’étude de la relation hôte/virus/virophage
l’étude de la méthylation de l’ADN chez les virus géants

Lien ORCID

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. Noumeavirus replication relies on a transient remote control of the host nucleus. ; Fabre E, Jeudy S, Santini S, Legendre M, Trauchessec M, Couté Y, Claverie JM, Abergel C ; Nat Commun.8;:15087,2017 Apr 21 ; 2017-04-21 ; PMID 28429720
  3. The rare sugar N-acetylated viosamine is a major component of mimivirus fibers. ; Piacente F, De Castro C, Jeudy S, Gaglianone M, Laugieri ME, Notaro A, Salis A, Damonte G, Abergel C, Tonetti MG ; J Biol Chem.;:,2017 Mar 17 ; 2017-03-17 ; PMID 28314774
  4. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. ; Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;:,2015 Sep 8 ; 2015-09-08 ; PMID 26351664
  5. A complement to the modern crystallographer s toolbox: caged gadolinium complexes with versatile binding modes. ; Stelter M, Molina R, Jeudy S, Kahn R, Abergel C, Hermoso JA ; Acta Crystallogr D Biol Crystallogr.70;Pt 6:1506-16,2014 Jun ; 2014-06-01 ; PMID 24914962
  6. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. ; Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;111 (11): 4274–4279,2014 Mar 3 ; 2014-01-03 ; PMID 24591590
  7. Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. ; Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, Barbe V, Wommack KE, Noordeloos AA, Brussaard CP, Claverie JM ; Proc Natl Acad Sci U S A.110;26:10800-5,2013 Jun 25 ; 2013-06-25 ; PMID 23754393
  8. Preliminary crystallographic analysis of a polyadenylate synthase from Megavirus. ; Lartigue A, Jeudy S, Bertaux L, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.69;Pt 1:53-6,2013 Jan 1 ; 2013-01-01 ; PMID 23295487
  9. Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. ; Jeudy S, Abergel C, Claverie JM, Legendre M ; PLoS Genet.8;12:e1003122,2012 Dec ; 2012-12-12 ; PMID 23271980
  10. Preliminary crystallographic analysis of the Megavirus superoxide dismutase. ; Lartigue A, Philippe N, Jeudy S, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.68;Pt 12:1557-9,2012 Dec 1 ; 2012-12-01 ; PMID 23192047
  11. The mimivirus R355 gene product: preliminary crystallographic analysis of a putative ubiquitin-like protein-specific protease. ; Jeudy S, Lartigue A, Mansuelle P, Ogata Y, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.67;Pt 1:169-72,2011 Jan 1 ; 2011-01-01 ; PMID 21206054
  12. Preliminary crystallographic analysis of a possible transcription factor encoded by the mimivirus L544 gene. ; Ciaccafava A, Lartigue A, Mansuelle P, Jeudy S, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.67;Pt 8:922-5,2011 Aug 1 ; 2011-01-01 ; PMID 21821896
  13. Dissecting the unique nucleotide specificity of Mimivirus nucleoside diphosphate kinase. ; Jeudy S, Lartigue A, Claverie JM, Abergel C ; J Virol.83;14:7142-50,2009 Jul ; 2009-01-13 ; PMID 19439473
  14. Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex. ; Jeudy S, Boehmer T, Berke IC, Schwartz TU ; Mol Cell.30;6:721-31,2008 Jun 20 ; 2008-01-20 ; PMID 18570875
  15. Crystal structure of nucleoporin Nic96 reveals a novel, intricate helical domain architecture. ; Jeudy S, Schwartz TU ; J Biol Chem.282;48:34904-12,2007 Nov 30 ; 2007-01-30 ; PMID 17897938
  16. Crystal structure of Escherichia coli DkgA, a broad-specificity aldo-keto reductase. ; Jeudy S, Monchois V, Maza C, Claverie JM, Aberg C ; Proteins.62;1:302-7,2006 Jan 1 ; 2006-01-01 ; PMID 16284956
  17. The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides. ; Jeudy S, Claverie JM, Abergel C ; J Bioenerg Biomembr.38;3-4:247-54,2006 Aug ; 2006-01-01 ; PMID 16957983
  18. Preliminary crystallographic analysis of the Escherichia coli YeaZ protein using the anomalous signal of a gadolinium derivative. ; Jeudy S, Stelter M, Coutard B, Kahn R, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.61;Pt 9:848-51,2005 Sep 1 ; 2005-09-01 ; PMID 16511176
  19. Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase. ; Jeudy S, Coutard B, Lebrun R, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.61;Pt 6:569-72,2005 Jun 1 ; 2005-06-01 ; PMID 16511098
  20. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. ; Abergel C, Coutard B, Byrne D, Chenivesse S, Claude JB, Deregnaucourt C, Fricaux T, Gianesini-Boutreux C, Jeudy S, Lebrun R, Maza C, Notredame C, Poirot O, Suhre K, Varagnol M, Claverie JM. ; J Struct Funct Genomics. 2003;4(2-3):141-57. ; 2003-01-01 ; PMID 14649299
  21. Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme. ; Monchois V, Abergel C, Sturgis J, Jeudy S, Claverie JM ; J Biol Chem 2001 May 25;276(21):18437-41. ; 2001-05-01 ; PMID 11278658
  22. Crystallization and preliminary crystallographic study of b0220, an 'ORFan' protein of unknown function from Escherichia coli. ; Abergel C, Monchois V, Chenivesse S, Jeudy S, Claverie JM ; Acta Crystallogr D Biol Crystallogr 2000 Dec;56 Pt 12:1694-5. ; 2000-12-01 ; PMID 11092949

Contacter cette personne
Sandra Jeudy Chargé de Recherche CNRS
L
Audrey Lartigue Ingénieur de Recherche CNRS Tel:+33 4 91 82 54 42

Mes activités à l’IGS s’articulent à l’interface entre la biologie cellulaire et la biochimie des protéines.

Je travaille sur des gènes sélectionnés pour leur intérêt fondamental ou appliqué et produit les protéines correspondantes dans la bactérie, afin d’en résoudre les structures 3D et les caractériser biochimiquement. Je produis également ces protéines dans les cellules Acanthamoeba afin d’étudier leurs fonctions dans la cellule infectée au cours du cycle infectieux. Je développe et met en place les protocoles adaptés à l’analyse de leur fonction moléculaire et cellulaire (radioactivité, pull-down, thermal shift…).

Je participe également à la remise en culture d’échantillons environnementaux dans le but d’isoler de nouveaux membres des familles de virus dont nous disposons au laboratoire et d’identifier de nouveaux virus qui pourraient correspondre à de nouvelles familles.

Lien ORCID

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. ; Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;:,2015 Sep 8 ; 2015-09-08 ; PMID 26351664
  3. mRNA maturation in giant viruses: variation on a theme. ; Priet S, Lartigue A, Debart F, Claverie JM, Abergel C ; Nucleic Acids Res.;:,2015 Mar 16 ; 2015-03-16 ; PMID 25779049
  4. The Megavirus chilensis Cu,Zn-Superoxide Dismutase: the first viral structure of a typical CCS-independent hyperstable dimeric enzyme. ; Lartigue A, Burlat B, Coutard B, Chaspoul F, Claverie JM, Abergel C ; J Virol.;:,2014 Oct 29 ; 2014-10-29 ; PMID 25355875
  5. Preliminary crystallographic analysis of a polyadenylate synthase from Megavirus. ; Lartigue A, Jeudy S, Bertaux L, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.69;Pt 1:53-6,2013 Jan 1 ; 2013-01-01 ; PMID 23295487
  6. Preliminary crystallographic analysis of the Megavirus superoxide dismutase. ; Lartigue A, Philippe N, Jeudy S, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.68;Pt 12:1557-9,2012 Dec 1 ; 2012-12-01 ; PMID 23192047
  7. The mimivirus R355 gene product: preliminary crystallographic analysis of a putative ubiquitin-like protein-specific protease. ; Jeudy S, Lartigue A, Mansuelle P, Ogata Y, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.67;Pt 1:169-72,2011 Jan 1 ; 2011-01-01 ; PMID 21206054
  8. Preliminary crystallographic analysis of a possible transcription factor encoded by the mimivirus L544 gene. ; Ciaccafava A, Lartigue A, Mansuelle P, Jeudy S, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.67;Pt 8:922-5,2011 Aug 1 ; 2011-01-01 ; PMID 21821896
  9. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. ; Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, Byrne D, Lartigue A, Lescot M, Bernadac A, Poulain J, Abergel C, Claverie JM ; Genome Res.20;5:664-74,2010 May ; 2010-04-01 ; PMID 20360389
  10. Mimivirus&Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. ; Claverie JM, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, Ogata H, Abergel C ; J Invertebr Pathol.101;3:172-80,2009 Jul ; 2009-01-17 ; PMID 19457438
  11. Dissecting the unique nucleotide specificity of Mimivirus nucleoside diphosphate kinase. ; Jeudy S, Lartigue A, Claverie JM, Abergel C ; J Virol.83;14:7142-50,2009 Jul ; 2009-01-13 ; PMID 19439473
  12. The polyadenylation site of Mimivirus transcripts obeys a stringent hairpin rule. ; Byrne D, Grzela R, Lartigue A, Audic S, Chenivesse S, Encinas S, Claverie JM, Abergel C ; Genome Res.19;7:1233-42,2009 Jul ; 2009-01-01 ; PMID 19403753
  13. Relationship between responsiveness of cancer cells to Oncostatin M and/or IL-6 and survival of stage III melanoma patients treated with tumour-infiltrating lymphocytes. ; Lacreusette A, Lartigue A, Nguyen JM, Barbieux I, Pandolfino MC, Paris F, Khammari A, Dréno B, Jacques Y, Blanchard F, Godard A ; J Pathol.216;4:451-9,2008 Dec ; 2008-01-01 ; PMID 18798220

Contacter cette personne
Audrey Lartigue Ingénieur de Recherche CNRS
Didier Léandri Professeur, Université du Sud Toulon-Var Tel:334-918-25420

Pr Leandri obtained Ph.D. degrees in mechanics in 1993 and Dr. Sc (HDR) “Undersea Robotics” from Institut National Polytechnique of Toulouse in 1999. During 1987-2000, he was head of research group in undersea vehicles and undersea robotics for French Navy at “Centre Technique des Systèmes Navals” (French MOD). Since 2000, he is full professor at engineer school “Institut Supérieur des Ingénieurs de Toulon et du Var” (University of Toulon). His main interest lies in the area of undersea robotics systems for water and sediments sampling and undersea mechatronics systems. He leads the studies and developments of many undersea systems :

Supercavitation vehicle
Lightweight glider (world record of lowest angle of fly in 2006)
Autonomous vehicle and undersea weapon F17-mod2 and ASMX
SSBN “Triomphant” and SSN “Amethyste” weapons systems

Bibliographie:

  1. Analysis of Some Solutions to Protect the Tombolo of GIENS ; Lacroix Y, Van Van Than, Leandri D, Liardet P ; World Academy of Science, Engineering and Technology International Journal of Environmental, Ecological, Geological and Geophysical Engineering Vol:9, No:3, 2015 ; 2015-01-01 ;
  2. Analysis of a Coupled Hydro-Sedimentological Numerical Model for the Tombolo of GIENS ; Lacroix Y, Van Van Than, Leandri D, Liardet P ; World Academy of Science, Engineering and Technology International Journal of Environmental, Ecological, Geological and Geophysical Engineering Vol:9, No:3, 2015 ; 2015-01-01 ;

Contacter cette personne
Didier Léandri Professeur, Université du Sud Toulon-Var
Matthieu Legendre Chargé de Recherche CNRS Tel:+33 4 91 82 54 31

Ma thématique principale de recherche tourne autour des virus géants, de leur histoire évolutive, de leur contenu et régulation génique, ainsi que des interactions avec leur hôte cellulaire.

D’où viennent ces virus étranges ?
Pourquoi leurs génomes sont-ils si complexes ?
Comment leurs multiples gènes sont-ils exprimés au cours du cycle infectieux ?

Voici les grandes questions auxquelles je tente de répondre.

Pour étudier ces virus je m’appuie sur des méthodes d’analyse bioinformatique des données de séquençage à haut débit (dites NGS). Un large panel de données "omique" et de méthodes d’analyse me permettent d’aborder l’étude de ces virus :

La génomique (assemblage, annotation) donne accès aux séquences complètes des génomes viraux
La génomique comparative et les méthodes d’analyse et de reconstruction phylogénique donnent des indices sur leur trajectoire évolutive
L’analyse des profils d’expression de leurs gènes et des éléments qui contrôlent leur régulation
au niveau du transcriptome par RNA-seq
au niveau du protéome par spectrométrie de masse
Les modifications épigénétiques globales de l’ADN (la méthylation notamment).

L’analyse et l’intégration de ces nombreuses données me permettent d’interagir avec les expérimentalistes du laboratoire et d’élaborer ensemble des hypothèses sur la biologie de ces virus.

Lien ORCID

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes. ; Zhang HH, Zhou QZ, Wang PL, Xiong XM, Luchetti A, Raoult D, Levasseur A, Santini S, Abergel C, Legendre M, Drezen JM, Béliveau C, Cusson M, Jiang SH, Bao HO, Sun C, Bureau TE, Cheng PF, Han MJ, Zhang Z, Zhang XG, Dai FY ; Mob DNA.9;:19,2018 june ; 2018-06-01 ; PMID 29946369
  3. Noumeavirus replication relies on a transient remote control of the host nucleus. ; Fabre E, Jeudy S, Santini S, Legendre M, Trauchessec M, Couté Y, Claverie JM, Abergel C ; Nat Commun.8;:15087,2017 Apr 21 ; 2017-04-21 ; PMID 28429720
  4. The 474-Kilobase-Pair Complete Genome Sequence of CeV-01B, a Virus Infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae). ; Gallot-Lavallée L, Pagarete A, Legendre M, Santini S, Sandaa RA, Himmelbauer H, Ogata H, Bratbak G, Claverie JM ; Genome Announc.3;6:,2015 dec ; 2015-12-01 ; PMID 26634761
  5. The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus. ; Abergel C, Legendre M, Claverie JM ; FEMS Microbiol Rev.;:,2015 Sep 20 ; 2015-09-20 ; PMID 26391910
  6. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. ; Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;:,2015 Sep 8 ; 2015-09-08 ; PMID 26351664
  7. Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity. ; Gemayel R, Chavali S, Pougach K, Legendre M, Zhu B, Boeynaems S, van der Zande E, Gevaert K, Rousseau F, Schymkowitz J, Babu MM, Verstrepen KJ ; Mol Cell.;:,2015 Aug 5 ; 2015-09-05 ; PMID 26257283
  8. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. ; Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;111 (11): 4274–4279,2014 Mar 3 ; 2014-01-03 ; PMID 24591590
  9. Evolution and Diversity in Human Herpes Simplex Virus Genomes. ; Szpara ML, Gatherer D, Ochoa A, Greenbaum B, Dolan A, Bowden RJ, Enquist LW, Legendre M, Davison AJ ; J Virol.;:,2013 Nov 13 ; 2013-11-13 ; PMID 24227835
  10. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. ; Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C ; Science.341;6143:281-6,2013 Jul 19 ; 2013-07-19 ; PMID 23869018
  11. Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. ; Jeudy S, Abergel C, Claverie JM, Legendre M ; PLoS Genet.8;12:e1003122,2012 Dec ; 2012-12-12 ; PMID 23271980
  12. Background-dependent effects of polyglutamine variation in the Arabidopsis thaliana gene ELF3. ; Undurraga SF, Press MO, Legendre M, Bujdoso N, Bale J, Wang H, Davis SJ, Verstrepen KJ, Queitsch C ; Proc Natl Acad Sci U S A.;:,2012 Nov 5 ; 2012-11-05 ; PMID 23129635
  13. Genomics of Megavirus and the elusive fourth domain of Life. ; Legendre M, Arslan D, Abergel C, Claverie JM ; Commun Integr Biol.5;1:102-6,2012 Jan 1 ; 2012-01-01 ; PMID 22482024
  14. Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. ; Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.108;42:17486-91,2011 Oct 18 ; 2011-10-18 ; PMID 21987820
  15. A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. ; Szpara ML, Tafuri YR, Parsons L, Shamim SR, Verstrepen KJ, Legendre M, Enquist LW ; PLoS Pathog.7;10:e1002282,2011 Oct ; 2011-10-13 ; PMID 22022263
  16. Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. ; Legendre M, Santini S, Rico A, Abergel C, Claverie JM ; Virol J.8;1:99,2011 Mar 4 ; 2011-01-04 ; PMID 21375749
  17. Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways. ; Martini E, Borde V, Legendre M, Audic S, Regnault B, Soubigou G, Dujon B, Llorente B ; PLoS Genet.7;9:e1002305,2011 Sep ; 2011-01-01 ; PMID 21980306
  18. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. ; Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, Byrne D, Lartigue A, Lescot M, Bernadac A, Poulain J, Abergel C, Claverie JM ; Genome Res.20;5:664-74,2010 May ; 2010-04-01 ; PMID 20360389
  19. Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences. ; Gemayel R, Vinces MD, Legendre M, Verstrepen KJ ; Annu Rev Genet.44;:445-77,2010 Aug ; 2010-01-25 ; PMID 20809801
  20. Unstable tandem repeats in promoters confer transcriptional evolvability. ; Vinces MD, Legendre M*, Caldara M, Hagihara M, Verstrepen KJ ; Science.324;5931:1213-6,2009 May 29 ; 2009-01-29 ; PMID 19478187
  21. Efficacy of RNA amplification is dependent on sequence characteristics: implications for gene expression profiling using a cDNA microarray. ; Duftner N, Larkins-Ford J, Legendre M, Hofmann HA ; Genomics.91;1:108-17,2008 Jan ; 2008-01-01 ; PMID 18006269
  22. Using the SERV Applet to Detect Tandem Repeats in DNA Sequences and to Predict Their Variability ; Legendre M, Verstrepen KJ ; Cold Srping Harbor Protocols; 2008; doi:10.1101/pdb.ip50, 2008 Jan ; 2008-01-01 ;
  23. Sequence-based estimation of minisatellite and microsatellite repeat variability. ; Legendre M, Pochet N, Pak T, Verstrepen KJ ; Genome Res.17;12:1787-96,2007 Dec ; 2007-01-01 ; PMID 17978285
  24. RNA stem-loops: to be or not to be cleaved by RNAse III. ; Ritchie W, Legendre M, Gautheret D ; RNA.13;4:457-62,2007 Apr ; 2007-01-01 ; PMID 17299129
  25. Differential repression of alternative transcripts: a screen for miRNA targets. ; Legendre M, Ritchie W, Lopez F, Gautheret D ; PLoS Comput Biol.2;5:e43,2006 May ; 2006-01-01 ; PMID 16699595
  26. Computing expectation values for RNA motifs using discrete convolutions. ; Lambert A, Legendre M, Fontaine JF, Gautheret D ; BMC Bioinformatics.6;:118,2005 ; 2005-01-01 ; PMID 15892887
  27. Profile-based detection of microRNA precursors in animal genomes. ; Legendre M, Lambert A, Gautheret D ; Bioinformatics.21;7:841-5,2005 Apr 1 ; 2005-01-01 ; PMID 15509608
  28. Seeking RNA motifs in genomic sequences ; Legendre M, Gautheret D ; Handbook of RNA Biochemistry (Hartmann OK, Bindereif A, Schon A, Westhof E) Volume 2. Pages 577-594,2004 Jan ; 2004-01-01 ;
  29. The ERPIN server: an interface to profile-based RNA motif identification. ; Lambert A, Fontaine JF, Legendre M, Leclerc F, Permal E, Major F, Putzer H, Delfour O, Michot B, Gautheret D ; Nucleic Acids Res.32;Web Server issue:W160-5,2004 Jul 1 ; 2004-01-01 ; PMID 15215371
  30. Sequence determinants in human polyadenylation site selection. ; Legendre M, Gautheret D ; BMC Genomics.4;1:7,2003 Feb 25 ; 2003-01-25 ; PMID 12600277

Contacter cette personne
Matthieu Legendre Chargé de Recherche CNRS
M
Dorothée Murat Maître de conférences Université de la Méditerranée Tel:

Microbiologie, Biologie Cellulaire, Biologie moléculaire, Microscopie.

Projet de recherche : Mécanismes d’infection des virus géants.

Enseignement : Enseignant chercheur (section 67). Campus Aix-Montperrin et Luminy.

Bibliographie:

  1. Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly. ; Okamoto K, Miyazaki N, Reddy HKN, Hantke MF, Maia FRNC, Larsson DSD, Abergel C, Claverie JM, Hajdu J, Murata K, Svenda M ; Virology.516;:239-245,2018 Mar ; 2018-03-01 ; PMID 29407382
  2. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. ; Okamoto K, Miyazaki N, Song C, Maia FRNC, Reddy HKN, Abergel C, Claverie JM, Hajdu J, Svenda M, Murata K ; Sci Rep.7;1:13291,2017 Oct 16 ; 2017-10-16 ; PMID 29038566

Contacter cette personne
Dorothée Murat Maître de conférences Université de la Méditerranée
N
Anna Notaro Doctorante Tel:+33 4 91 82 54 32

Publications:

Piacente F, De Castro C, Jeudy S, Gaglianone M, Laugieri ME, Notaro A, Salis A, Damonte G, Abergel C, Tonetti MG (2017) The rare sugar N-acetylated viosamine is a major component of mimivirus fibers. J Biol Chem. ; :,2017 Mar 17 - PMID:28314774

Bibliographie:

  1. The rare sugar N-acetylated viosamine is a major component of mimivirus fibers. ; Piacente F, De Castro C, Jeudy S, Gaglianone M, Laugieri ME, Notaro A, Salis A, Damonte G, Abergel C, Tonetti MG ; J Biol Chem.;:,2017 Mar 17 ; 2017-03-17 ; PMID 28314774

Contacter cette personne
Anna Notaro Doctorante
P
Nadège Philippe Ingénieur de Recherche CNRS Tel:+33 4 91 82 54 32

L’un des défis majeurs de notre projet de caractérisation détaillée des cycles viraux reste la mise au point de techniques de manipulations génétiques. Je suis chargée de développer le système CRISPR/Cas9 chez Acanthamoeba castellanii, ce qui nous permettra de réaliser la mutagénèse de l’amibe et des virus qui l’infectent.
Pour cela, je mets au point des outils permettant de produire une protéine de type Cas9 (SpCas9, Cpf1, C2c2, SaCas9…) de façon constitutive ou inductible chez l’amibe, et d’exprimer dans la cellule des ARN guides ciblant des gènes d’intérêt que nous souhaitons muter (transfection directe d’ARN ou de vecteurs d’expression).
Je participe aussi à la recherche de nouvelles familles de virus géants avec de nouveaux hôtes (Acanthamoeba environnementales, Dictyostelium discoideum, Paramecium tetraurelia dont les génomes sont connus et qui sont génétiquement modifiables). J’ai implémenté le système Dictyostelium discoideum au laboratoire.
Je contribue également à la remise en culture d’échantillons environnementaux d’origines diverses, dans le but d’isoler de nouveaux virus géants qui viendront étoffer nos connaissances.

Lien ORCID

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem. ; Philippe N, Maigre L, Santini S, Pinet E, Claverie JM, Davin-Régli AV, Pagès JM, Masi M ; PLoS One.10;9:e0138828,2015 sep ; 2015-09-23 ; PMID 26398358
  3. Genome analysis of the first Marseilleviridae representative from Australia indicates that most of its genes contribute to the virus fitness. ; Doutre G, Philippe N, Abergel C, Claverie JM ; J Virol.;:,2014 Oct 1 ; 2014-10-01 ; PMID 25275139
  4. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. ; Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C ; Science.341;6143:281-6,2013 Jul 19 ; 2013-07-19 ; PMID 23869018
  5. Preliminary crystallographic analysis of the Megavirus superoxide dismutase. ; Lartigue A, Philippe N, Jeudy S, Abergel C ; Acta Crystallogr Sect F Struct Biol Cryst Commun.68;Pt 12:1557-9,2012 Dec 1 ; 2012-12-01 ; PMID 23192047
  6. Pathway Complexity of Alzheimer s-Amyloid A 16-22 Peptide Assembly ; Sebastien Santini,Guanghong Wei, Normand Mousseau, Philippe Derreumaux ; Structure, Vol. 12, 1 20, July, 2004, ; 2004-07-05 ;
  7. Sampling the complex energy landscape of a simple beta-hairpin ; Guanghong Wei, Philippe Derreumaux, and Normand Mousseau ; The Journal of Chemical Physics -- October 1, 2003 -- Volume 119, Issue 13, pp. 6403-6406 ; 2003-10-01 ;
  8. Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique ; Guanghong Wei, Normand Mousseau, and Philippe Derreumaux ; The Journal of Chemical Physics -- December 22, 2002 -- Volume 117, Issue 24, pp. 11379-11387 ; 2002-12-22 ;
  9. Insight into protein topology from Monte Carlo simulations ; Philippe Derreumaux ; The Journal of Chemical Physics -- August 15, 2002 -- Volume 117, Issue 7, pp. 3499-3503 ; 2002-08-15 ;
  10. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. ; Brinkmann H, Philippe H. ; Mol Biol Evol. 1999 Jun;16(6):817-25. ; 1999-06-01 ; PMID 10368959

Contacter cette personne
Nadège Philippe Ingénieur de Recherche CNRS
Olivier Poirot Ingénieur d’études CNRS Tel:+33 4 91 82 54 23

Sujets:
-Participation aux multiples activités bioinformatiques du laboratoire, en support de la recherche comme de la plate-forme France-Génomique PACA-Bioinfo
-Développement d’outils interactifs (en PHP, Perl, Java, C, HTML, SQL) d’exploitation de banques de données génomiques (Blast, lookfor, package Emboss), de fouille de données métagénomiques (Seqtinizer).
-Responsable de la mise à jour du site Web (extranet, intranet, Wiki) du laboratoire
-Exploitation de données de protéomique
-Participation à la gestion du parc matériel et logiciel du laboratoire

ORCID ID

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. Neuron-Like Networks Between Ribosomal Proteins Within the Ribosome. ; Poirot O, Timsit Y ; Sci Rep.6;:26485,2016 ; 2016-05-01 ; PMID 27225526
  3. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. ; Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;111 (11): 4274–4279,2014 Mar 3 ; 2014-01-03 ; PMID 24591590
  4. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. ; Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C ; Science.341;6143:281-6,2013 Jul 19 ; 2013-07-19 ; PMID 23869018
  5. Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. ; Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, Barbe V, Wommack KE, Noordeloos AA, Brussaard CP, Claverie JM ; Proc Natl Acad Sci U S A.110;26:10800-5,2013 Jun 25 ; 2013-06-25 ; PMID 23754393
  6. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. ; Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, Byrne D, Lartigue A, Lescot M, Bernadac A, Poulain J, Abergel C, Claverie JM ; Genome Res.20;5:664-74,2010 May ; 2010-04-01 ; PMID 20360389
  7. APDB: a web server to evaluate the accuracy of sequence alignments using structural information. ; Armougom F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C ; Bioinformatics.22;19:2439-40,2006 Oct 1 ; 2006-10-01 ; PMID 17032685
  8. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. ; Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C ; Nucleic Acids Res.34;Web Server issue:W604-8,2006 Jul 1 ; 2006-07-01 ; PMID 16845081
  9. PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. ; Moretti S, Reinier F, Poirot O, Armougom F, Audic S, Keduas V, Notredame C. ; Nucleic Acids Res. ;34(Web Server issue):W600-3,2006 Jul 1 ; 2006-07-01 ; PMID 16845080
  10. 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. ; Poirot O, Suhre K, Abergel C, O'Toole E, Notredame C ; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. ; 2004-07-01 ; PMID 15215345
  11. Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis ; Enault F, Suhre K, Poirot O, Abergel C, Claverie JM ; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W336-9. ; 2004-07-01 ; PMID 15215406
  12. Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. ; Poirot O, O'Toole E, Notredame C ; Nucleic Acids Res 2003 Jul 1;31(13):3503-6. ; 2003-07-01 ; PMID 12824354
  13. Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. ; Enault F, Suhre K, Poirot O, Abergel C, Claverie JM ; Nucleic Acids Res 2003 Jul 1;31(13):3720-2. ; 2003-07-01 ; PMID 12824402
  14. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. ; Abergel C, Coutard B, Byrne D, Chenivesse S, Claude JB, Deregnaucourt C, Fricaux T, Gianesini-Boutreux C, Jeudy S, Lebrun R, Maza C, Notredame C, Poirot O, Suhre K, Varagnol M, Claverie JM. ; J Struct Funct Genomics. 2003;4(2-3):141-57. ; 2003-01-01 ; PMID 14649299
  15. In Search of new anti-bacterial target genes: a comparative/structural genomics approach. ; Claverie JM, Monchois V, Audic S, Poirot O, Abergel C ; Comb Chem High Throughput Screen 2002 Nov;5(7):511-22. ; 2002-11-01 ; PMID 12470264
  16. Reverse transcriptase-polymerase chain reaction validation of 25 orphan genes from Escherichia coli K-12 MG1655. ; Alimi JP, Poirot O, Lopez F, Claverie JM ; Genome Res 2000 Jul;10(7):959-66. ; 2000-07-01 ; PMID 10899145
  17. Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets. ; Ewing R, Poirot O, Claverie JM ; In Silico Biol 1999-2000;1(4):197-213. ; 2000-01-01 ; PMID 11479934
  18. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. ; Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM. ; Genome Res. 1999 Oct;9(10):950-9. ; 1999-10-01 ; PMID 10523523
  19. Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. ; Gautheret D, Poirot O, Lopez F, Audic S, Claverie JM ; Genome Res 1998 May;8(5):524-30. ; 1998-05-01 ; PMID 9582195
  20. SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments. ; Audic S, Lopez F, Claverie JM, Poirot O, Abergel C ; Proteins 1997 Oct;29(2):252-7. ; 1997-10-01 ; PMID 9329089
  21. The difficulty of identifying genes in anonymous vertebrate sequences. ; Claverie JM, Poirot O, Lopez F ; Comput Chem 1997;21(4):203-14. ; 1997-01-01 ; PMID 9415985

Contacter cette personne
Olivier Poirot Ingénieur d’études CNRS
S
Sébastien Santini Ingénieur de Recherche CNRS Tel:+33 4 91 82 54 34

Bioinformatique ; génomique ; assemblage ; analyse de séquences et de génomes ; responsable ressources HPC ; Administration phylogeny.fr et de différents serveurs de la plate-forme ; correspondant formation.

Lien ORCID

Bibliographie:

  1. Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes. ; Zhang HH, Zhou QZ, Wang PL, Xiong XM, Luchetti A, Raoult D, Levasseur A, Santini S, Abergel C, Legendre M, Drezen JM, Béliveau C, Cusson M, Jiang SH, Bao HO, Sun C, Bureau TE, Cheng PF, Han MJ, Zhang Z, Zhang XG, Dai FY ; Mob DNA.9;:19,2018 june ; 2018-06-01 ; PMID 29946369
  2. New genomic data and analyses challenge the traditional vision of animal epithelium evolution. ; Belahbib H, Renard E, Santini S, Jourda C, Claverie JM, Borchiellini C, Le Bivic A ; BMC Genomics.19;1:393,2018 May 24 ; 2018-01-24 ; PMID 29793430
  3. Noumeavirus replication relies on a transient remote control of the host nucleus. ; Fabre E, Jeudy S, Santini S, Legendre M, Trauchessec M, Couté Y, Claverie JM, Abergel C ; Nat Commun.8;:15087,2017 Apr 21 ; 2017-04-21 ; PMID 28429720
  4. Benthic protists: the under-charted majority. ; Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra WH, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T ; FEMS Microbiol Ecol.;:,2016 Jun 5 ; 2016-05-05 ; PMID 27267932
  5. Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits. ; Bordez L, Jourand P, Ducousso M, Carriconde F, Cavaloc Y, Santini S, Claverie JM, Wantiez L, Leveau A, Amir H ; Mol Ecol.;:,2016 Mar 19 ; 2016-03-19 ; PMID 26994404
  6. The 474-Kilobase-Pair Complete Genome Sequence of CeV-01B, a Virus Infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae). ; Gallot-Lavallée L, Pagarete A, Legendre M, Santini S, Sandaa RA, Himmelbauer H, Ogata H, Bratbak G, Claverie JM ; Genome Announc.3;6:,2015 dec ; 2015-12-01 ; PMID 26634761
  7. In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem. ; Philippe N, Maigre L, Santini S, Pinet E, Claverie JM, Davin-Régli AV, Pagès JM, Masi M ; PLoS One.10;9:e0138828,2015 sep ; 2015-09-23 ; PMID 26398358
  8. Draft Genome Sequence of an Alphaproteobacterium Associated with the Mediterranean Sponge Oscarella lobularis. ; Jourda C, Santini S, Rocher C, Le Bivic A, Claverie JM ; Genome Announc.3;5:,2015 sept ; 2015-09-01 ; PMID 26337883
  9. Mitochondrial Genome Sequence of the Glass Sponge Oopsacas minuta. ; Jourda C, Santini S, Rocher C, Le Bivic A, Claverie JM ; Genome Announc.3;4:,2015 ; 2015-07-30 ; PMID 26227597
  10. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. ; Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Forn I, Forster D, Guillou L, Jaillon O, Kooistra WH, Logares R, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simon N, Stoeck T, Vaulot D, Zingone A, de Vargas C ; Environ Microbiol. doi: 10.1111/1462-2920.12955,2015 ; 2015-06-28 ; PMID 26119494
  11. Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport. ; Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D, Acinas SG, Bork P, Boss E, Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Krzic U, Not F, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P ; Science.348;6237:1261447,2015 May 22 ; 2015-05-22 ; PMID 25999514
  12. Patterns of Rare and Abundant Marine Microbial Eukaryotes. ; Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WH, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards TA, de Vargas C, Massana R ; Curr Biol.;:,2014 Apr 2 ; 2014-01-02 ; PMID 24704080
  13. Vampires in the oceans: predatory cercozoan amoebae in marine habitats. ; Berney C, Romac S, Mahé F, Santini S, Siano R, Bass D ; ISME J.7;12:2387-99,2013 Dec ; 2013-12-01 ; PMID 23864128
  14. Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. ; Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, Barbe V, Wommack KE, Noordeloos AA, Brussaard CP, Claverie JM ; Proc Natl Acad Sci U S A.110;26:10800-5,2013 Jun 25 ; 2013-06-25 ; PMID 23754393
  15. Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. ; Bittner L, Gobet A, Audic S, Romac S, Egge ES, Santini S, Ogata H, Probert I, Edvardsen B, de Vargas C ; Mol Ecol.;:,2013 Jan 22 ; 2013-01-22 ; PMID 23163508
  16. Reticulamoeba is a long-branched granofilosean (cercozoa) that is missing from sequence databases. ; Bass D, Yabuki A, Santini S, Romac S, Berney C ; PLoS One.7;12:e49090,2012 ; 2012-12-01 ; PMID 23226495
  17. Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. ; Logares R, Audic S, Santini S, Pernice MC, De Vargas C, Massana R ; ISME J.;:,2012 Apr 26 ; 2012-04-26 ; PMID 22534609
  18. Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. ; Legendre M, Santini S, Rico A, Abergel C, Claverie JM ; Virol J.8;1:99,2011 Mar 4 ; 2011-01-04 ; PMID 21375749
  19. The Conserved Candida albicans CA3427 Gene Product Defines a New Family of Proteins Exhibiting the Generic Periplasmic Binding Protein Structural Fold. ; Santini S, Claverie JM, Mouz N, Rousselle T, Maza C, Monchois V, Abergel C ; PLoS One.6;4:e18528,2011 ; 2011-01-01 ; PMID 21494601
  20. Study of Thermomyces lanuginosa lipase in the presence of tributyrylglycerol and water. ; Santini S, Crowet JM, Thomas A, Paquot M, Vandenbol M, Thonart P, Wathelet JP, Blecker C, Lognay G, Brasseur R, Lins L, Charloteaux B ; Biophys J.96;12:4814-25,2009 Jun 17 ; 2009-01-17 ; PMID 19527641
  21. Characterization of a novel aphid prenyltransferase displaying dual geranyl/farnesyl diphosphate synthase activity. ; Vandermoten S, Charloteaux B, Santini S, Sen SE, Beliveau C, Vandenbol M, Francis F, Brasseur R, Cusson M, Haubruge E ; FEBS Lett.582;13:1928-34,2008 Jun 11 ; 2008-01-11 ; PMID 18466770
  22. Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase. ; Santini S, Monchois V, Mouz N, Sigoillot C, Rousselle T, Claverie JM, Abergel C ; BMC Struct Biol.8;:33,2008 ; 2008-01-01 ; PMID 18652651
  23. Ixodes ricinus tick lipocalins: identification, cloning, phylogenetic analysis and biochemical characterization. ; Beaufays J, Adam B, Decrem Y, Prevot, Santini S, Brasseur R, Brossard M, Lins L, Vanhamme L, Godfroid E ; PLoS ONE.3;12:e3941,2008 ; 2008-01-01 ; PMID 19096708
  24. Ir-LBP, an ixodes ricinus tick salivary LTB4-binding lipocalin, interferes with host neutrophil function. ; Beaufays J, Adam B, Menten-Dedoyart C, Fievez L, Grosjean A, Decrem Y, Prevot, Santini S, Brasseur R, Brossard M, Vanhaeverbeek M, Bureau F, Heinen E, Lins L, Vanhamme L, Godfroid E ; PLoS ONE.3;12:e3987,2008 ; 2008-01-01 ; PMID 19096526
  25. In silico assembly of Alzheimer's Abeta(16-22) peptide into beta-sheets ; Santini S, Mousseau N, Derreumaux P ; J. Am. Chem. Soc. (2004) 126:11509-11516 ; 2004-10-06 ; PMID 15366896
  26. Pathway Complexity of Alzheimer s-Amyloid A 16-22 Peptide Assembly ; Sebastien Santini,Guanghong Wei, Normand Mousseau, Philippe Derreumaux ; Structure, Vol. 12, 1 20, July, 2004, ; 2004-07-05 ;
  27. The helix H1 of the prion is rather stable against environmental perturbations: molecular dynamics of mutation and deletion variants of PrP(90-231) ; Santini S, Derreumaux P ; Cell Mol Life Sci. 2004 Apr;61(7-8):951-60 ; 2004-01-01 ; PMID 15095015
  28. Pathway complexity of Alzheimer's beta-amyloid Abeta16-22 peptide assembly. ; Santini S, Wei G, Mousseau N, Derreumaux P ; Structure.12;7:1245-55,2004 Jul ; 2004-01-01 ; PMID 15242601
  29. Exploring the folding pathways of proteins through energy landscape sampling: Application to Alzheimer's beta-amyloid peptide ; Santini S, Wei G, Mousseau N, Derreumaux P ; Internet Electron. J. Mol. Des. , 2: 564-577. ; 2003-09-01 ;
  30. Impact of the tail and mutations G131V and M129V on prion protein flexibility. ; Santini S, Claude JB, Audic S, Derreumaux P ; Proteins 2003 May 1;51(2):258-65. ; 2003-05-01 ; PMID 12660994

Contacter cette personne
Sébastien Santini Ingénieur de Recherche CNRS
T
Thi Ngan Ta Ingénieur d’études CDD Tel:+33 4 91 82 54 35

Lien ORCID

Bibliographie:

  1. Diversity and evolution of the emerging Pandoraviridae family. ; Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic JM, Beucher L, Philippe N, Bertaux L, Christo-Foroux E, Labadie K, Couté Y, Abergel C, Claverie JM ; Nat Commun.9;1:2285,2018 Jun 11 ; 2018-06-11 ; PMID 29891839
  2. ACDtool: a web-server extending the original Audic-Claverie statistical test to the comparison of large data sets of counts. ; Jean-Michel Claverie, Thi Ngan Ta ; biorxiv, doi: https://doi.org/10.1101/304568,2018 march ; 2018-04-20 ;
  3. Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly. ; Okamoto K, Miyazaki N, Reddy HKN, Hantke MF, Maia FRNC, Larsson DSD, Abergel C, Claverie JM, Hajdu J, Murata K, Svenda M ; Virology.516;:239-245,2018 Mar ; 2018-03-01 ; PMID 29407382
  4. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. ; Okamoto K, Miyazaki N, Song C, Maia FRNC, Reddy HKN, Abergel C, Claverie JM, Hajdu J, Svenda M, Murata K ; Sci Rep.7;1:13291,2017 Oct 16 ; 2017-10-16 ; PMID 29038566
  5. Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean. ; Nishimura Y, Watai H, Honda T, Mihara T, Omae K, Roux S, Blanc-Mathieu R, Yamamoto K, Hingamp P, Sako Y, Sullivan MB, Goto S, Ogata H, Yoshida T ; mSphere.2;2:,01 2017 ; 2017-04-01 ; PMID 28261669
  6. The rare sugar N-acetylated viosamine is a major component of mimivirus fibers. ; Piacente F, De Castro C, Jeudy S, Gaglianone M, Laugieri ME, Notaro A, Salis A, Damonte G, Abergel C, Tonetti MG ; J Biol Chem.;:,2017 Mar 17 ; 2017-03-17 ; PMID 28314774
  7. Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser. ; Ekeberg T, Svenda M, Seibert MM, Abergel C, Maia FR, Seltzer V, DePonte DP, Aquila A, Andreasson J, Iwan B, Jonsson O, Westphal D, Odic D, Andersson I, Barty A, Liang M, Martin AV, Gumprecht L, Fleckenstein H, Bajt S, Barthelmess M, Coppola N, Claverie JM, Loh ND, Bostedt C, Bozek JD, Krzywinski J, Messerschmidt M, Bogan MJ, Hampton CY, Sierra RG, Frank M, Shoeman RL, Lomb L, Foucar L, Epp SW, Rolles D, Rudenko A, Hartmann R, Hartmann A, Kimmel N, Holl P, Weidenspointner G, Rudek B, Erk B, Kassemeyer S, Schlichting I, Struder L, Ullrich J, Schmidt C, Krasniqi F, Hauser G, Reich C, Soltau H, Schorb S, Hirsemann H, Wunderer C, Graafsma H, Chapman H, Hajdu J ; Sci Data.3;:160060,2016 aug ; 2016-08-01 ; PMID 27479754
  8. Benthic protists: the under-charted majority. ; Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra WH, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T ; FEMS Microbiol Ecol.;:,2016 Jun 5 ; 2016-05-05 ; PMID 27267932
  9. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ; Lescot M, Hingamp P, Kojima KK, Villar E, Romac S, Veluchamy A, Boccara M, Jaillon O, Iudicone D, Bowler C, Wincker P, Claverie JM, Ogata H ; ISME J.;:,2016 may ; 2016-05-01 ; PMID 26613339
  10. Linking Virus Genomes with Host Taxonomy. ; Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H, Hingamp P, Goto S, Ogata H ; Viruses.8;3:,2016 march ; 2016-03-01 ; PMID 26938550
  11. Plankton networks driving carbon export in the oligotrophic ocean. ; Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G ; Nature.;:,2016 Feb 10 ; 2016-01-10 ; PMID 26863193
  12. The 474-Kilobase-Pair Complete Genome Sequence of CeV-01B, a Virus Infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae). ; Gallot-Lavallée L, Pagarete A, Legendre M, Santini S, Sandaa RA, Himmelbauer H, Ogata H, Bratbak G, Claverie JM ; Genome Announc.3;6:,2015 dec ; 2015-12-01 ; PMID 26634761
  13. The human gene damage index as a gene-level approach to prioritizing exome variants. ; Itan Y, Shang L, Boisson B, Patin E, Bolze A, Moncada-Vélez M, Scott E, Ciancanelli MJ, Lafaille FG, Markle JG, Martinez-Barricarte R, de Jong SJ, Kong XF, Nitschke P, Belkadi A, Bustamante J, Puel A, Boisson-Dupuis S, Stenson PD, Gleeson JG, Cooper DN, Quintana-Murci L, Claverie JM, Zhang SY, Abel L, Casanova JL ; Proc Natl Acad Sci U S A.;:,2015 Oct 19 ; 2015-10-19 ; PMID 26483451
  14. Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes. ; Clerissi C, Desdevises Y, Romac S, Audic S, de Vargas C, Acinas SG, Casotti R, Poulain J, Wincker P, Hingamp P, Ogata H, Grimsley N ; Environ Microbiol Rep.;:,2015 Oct 16 ; 2015-10-16 ; PMID 26472079
  15. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. ; Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;:,2015 Sep 8 ; 2015-09-08 ; PMID 26351664
  16. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. ; Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Forn I, Forster D, Guillou L, Jaillon O, Kooistra WH, Logares R, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simon N, Stoeck T, Vaulot D, Zingone A, de Vargas C ; Environ Microbiol. doi: 10.1111/1462-2920.12955,2015 ; 2015-06-28 ; PMID 26119494
  17. The ocean sampling day consortium. ; Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Loscher CR, Kremp A, DeLorenzo ME, OvreasL, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhaes C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid el H, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PA, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glockner FO ; Gigascience.4;:27,June 2015 ; 2015-06-27 ; PMID 26097697
  18. Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean. ; de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Lukes J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E, Acinas SG, Bork P, Boss E, Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Krzic U, Not F, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P ; Science.348;6237:1261605,2015 May 22 ; 2015-05-22 ; PMID 25999516
  19. Ocean plankton. Structure and function of the global ocean microbiome. ; Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P, Acinas SG, Bork P, Boss E, Bowler C, de Vargas C, Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Krzic U, Not F, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P ; Science.348;6237:1261359,2015 May 22 ; 2015-05-22 ; PMID 25999513
  20. Ocean plankton. Patterns and ecological drivers of ocean viral communities. ; Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB, Acinas SG, Bork P, Boss E, Bowler C, Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Krzic U, Not F, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P ; Science.348;6237:1261498,2015 May 22 ; 2015-05-22 ; PMID 25999515
  21. Ocean plankton. Determinants of community structure in the global plankton interactome. ; Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J, Acinas SG, Bork P, Boss E, De Vargas , Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Krzic U, Not F, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P ; Science.348;6237:1262073,2015 May 22 ; 2015-05-22 ; PMID 25999517
  22. Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport. ; Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D, Acinas SG, Bork P, Boss E, Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Krzic U, Not F, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P ; Science.348;6237:1261447,2015 May 22 ; 2015-05-22 ; PMID 25999514
  23. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton. ; von Dassow P, John U, Ogata H, Probert I, Bendif EM, Kegel JU, Audic S, Wincker P, Da Silva C, Claverie JM, Doney S, Glover DM, Flores DM, Herrera Y, Lescot M, Garet-Delmas MJ, de Vargas C ; ISME J.;:,2014 Dec 2 ; 2014-12-02 ; PMID 25461969
  24. The Megavirus chilensis Cu,Zn-Superoxide Dismutase: the first viral structure of a typical CCS-independent hyperstable dimeric enzyme. ; Lartigue A, Burlat B, Coutard B, Chaspoul F, Claverie JM, Abergel C ; J Virol.;:,2014 Oct 29 ; 2014-10-29 ; PMID 25355875
  25. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. ; Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG ; Environ Microbiol.16;9:2659-71,2014 Sep ; 2014-09-01 ; PMID 24102695
  26. Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine Samples by Using High-Throughput Sequencing Analyses of PCR-Amplified DNA Polymerase and Major Capsid Protein Genes. ; Clerissi C, Grimsley N, Ogata H, Hingamp P, Poulain J, Desdevises Y ; Appl Environ Microbiol.80;10:3150-60,2014 May ; 2014-05-01 ; PMID 24632251
  27. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. ; Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM ; Proc Natl Acad Sci U S A.;111 (11): 4274–4279,2014 Mar 3 ; 2014-01-03 ; PMID 24591590
  28. Patterns of Rare and Abundant Marine Microbial Eukaryotes. ; Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WH, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards TA, de Vargas C, Massana R ; Curr Biol.;:,2014 Apr 2 ; 2014-01-02 ; PMID 24704080
  29. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. ; Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C ; Science.341;6143:281-6,2013 Jul 19 ; 2013-07-19 ; PMID 23869018
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  192. Phylogenetic classification of Bartonella species by comparing groEL sequences. ; Zeaiter Z, Fournier PE, Ogata H, Raoult D ; Int J Syst Evol Microbiol 2002 Jan;52(Pt 1):165-71. ; 2002-01-01 ; PMID 11837299
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  199. Mechanisms of evolution in Rickettsia conorii and R. prowazekii. ; Ogata H, Audic S, Renesto-Audiffren P, Fournier PE, Barbe V, Samson D, Roux V, Cossart P, Weissenbach J, Claverie JM, Raoult D ; Science 2001 Sep 14;293(5537):2093-8. ; 2001-09-01 ; PMID 11557893
  200. Chemosensitivity prediction by transcriptional profiling. ; Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR. ; Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10787-92. ; 2001-09-01 ; PMID 11553813
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  202. Crystallographic approach to identification of cyclin-dependent kinase 4 (CDK4)-specific inhibitors by using CDK4 mimic CDK2 protein. ; Ikuta M, Kamata K, Fukasawa K, Honma T, Machida T, Hirai H, Suzuki-Takahashi I, Hayama T, Nishimura S. ; J Biol Chem. 2001 Jul 20;276(29):27548-54. ; 2001-07-20 ; PMID 11335721
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  206. Activity of a specific inhibitor of the BCR-ABL tyrosine kinase in the blast crisis of chronic myeloid leukemia and acute lymphoblastic leukemia with the Philadelphia chromosome. ; Druker BJ, Sawyers CL, Kantarjian H, Resta DJ, Reese SF, Ford JM, Capdeville R, Talpaz M. ; N Engl J Med. 2001 Apr 5;344(14):1038-42. ; 2001-04-05 ; PMID 11287973
  207. Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. ; Druker BJ, Talpaz M, Resta DJ, Peng B, Buchdunger E, Ford JM, Lydon NB, Kantarjian H, Capdeville R, Ohno-Jones S, Sawyers CL. ; N Engl J Med. 2001 Apr 5;344(14):1031-7. ; 2001-04-05 ; PMID 11287972
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  209. Crystallization and preliminary crystallographic study of a recombinant phospholipase D from cowpea (Vigna unguiculata L. Walp). ; Abergel C, Abousalham A, Chenivesse S, Riviere M, Moustacas-Gardies AM, Verger R ; Acta Crystallogr D Biol Crystallogr 2001 Feb;57(Pt 2):320-2. ; 2001-02-01 ; PMID 11173493
  210. An alternative-exon database and its statistical analysis. ; Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O, Zhang MQ. ; DNA Cell Biol. 2000 Dec;19(12):739-56. ; 2000-12-01 ; PMID 11177572
  211. Identification of odorant receptors from the Alpine marmot (Marmota marmota). ; Matarazzo V, Tirard A, Renucci M, Botto JM, Bel MC, Claverie JM, Belaich A, Clement JL ; Cell Mol Biol (Noisy-le-grand) 2000 Nov;46(7):1249-58. ; 2000-11-01 ; PMID 11075954
  212. A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. ; Ogata H, Fujibuchi W, Goto S, Kanehisa M ; Nucleic Acids Res 2000 Oct 15;28(20):4021-8. ; 2000-10-01 ; PMID 11024183
  213. Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. ; Fujibuchi W, Ogata H, Matsuda H, Kanehisa M ; Nucleic Acids Res 2000 Oct 15;28(20):4029-36. ; 2000-10-01 ; PMID 11024184
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  215. Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. ; Irizarry K, Kustanovich V, Li C, Brown N, Nelson S, Wong W, Lee CJ. ; Nat Genet. 2000 Oct;26(2):233-6. ; 2000-10-01 ; PMID 11017085
  216. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. ; Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. ; Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12182-6. ; 2000-10-01 ; PMID 11027309
  217. NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods. ; Ota S, Li WH. ; Mol Biol Evol. 2000 Sep;17(9):1401-9. ; 2000-09-01 ; PMID 10958856
  218. 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. ; Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P. ; Genome Biol. 2000;1(2):RESEARCH0003. ; 2000-08-04 ; PMID 11178228
  219. Inhibition of p38 MAP kinase as a therapeutic strategy. ; Lee JC, Kumar S, Griswold DE, Underwood DC, Votta BJ, Adams JL. ; Immunopharmacology. 2000 May;47(2-3):185-201. ; 2000-05-01 ; PMID 10878289
  220. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. ; Croft L, Schandorff S, Clark F, Burrage K, Arctander P, Mattick JS. ; Nat Genet. 2000 Apr;24(4):340-1. ; 2000-04-01 ; PMID 10742092
  221. A gene expression database for the molecular pharmacology of cancer. ; Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN. ; Nat Genet. 2000 Mar;24(3):236-44. ; 2000-03-01 ; PMID 10700175
  222. A regulator of G protein signaling interaction surface linked to effector specificity. ; Sowa ME, He W, Wensel TG, Lichtarge O. ; Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1483-8. ; 2000-02-01 ; PMID 10677488
  223. RNA processing and human disease. ; Philips AV, Cooper TA. ; Cell Mol Life Sci. 2000 Feb;57(2):235-49. ; 2000-02-01 ; PMID 10766020
  224. The family of Caenorhabditis elegans tyrosine kinase receptors: similarities and differences with mammalian receptors. ; Popovici C, Roubin R, Coulier F, Pontarotti P, Birnbaum D. ; Genome Res. 1999 Nov;9(11):1026-39. ; 1999-11-01 ; PMID 10568743
  225. CDK inhibition and cancer therapy. ; Garrett MD, Fattaey A. ; Curr Opin Genet Dev. 1999 Feb;9(1):104-11. ; 1999-02-01 ; PMID 10072351
  226. KEGG: Kyoto Encyclopedia of Genes and Genomes. ; Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M ; Nucleic Acids Res 1999 Jan 1;27(1):29-34. ; 1999-01-01 ; PMID 9847135
  227. AAindex: Amino Acid Index Database. ; Kawashima S, Ogata H, Kanehisa M ; Nucleic Acids Res 1999 Jan 1;27(1):368-9. ; 1999-01-01 ; PMID 9847231
  228. Abnormalities in the p34cdc2-related PITSLRE protein kinase gene complex (CDC2L) on chromosome band 1p36 in melanoma. ; Nelson MA, Ariza ME, Yang JM, Thompson FH, Taetle R, Trent JM, Wymer J, Massey-Brown K, Broome-Powell M, Easton J, Lahti JM, Kidd VJ. ; Cancer Genet Cytogenet. 1999 Jan 15;108(2):91-9. ; 1999-01-01 ; PMID 9973934
  229. The Protein Mutant Database. ; Kawabata T, Ota M, Nishikawa K. ; Nucleic Acids Res. 1999 Jan 1;27(1):355-7. ; 1999-01-01 ; PMID 9847227
  230. Determining number of clusters and prototype locations via multi-scale clustering. ; Nakamura E, Kehtarnavaz N. ; Pattern Recognition Letters 1998 Dec;19(14):1265-1283. ; 1998-12-05 ;
  231. SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex. ; Wang R, Liu L, Lai L, Tang Y. ; J Molec Model. 1998 Dec;4(12):379-394. ; 1998-12-01 ;
  232. Structure of human cyclin-dependent kinase inhibitor p19INK4d: comparison to known ankyrin-repeat-containing structures and implications for the dysfunction of tumor suppressor p16INK4a. ; Baumgartner R, Fernandez-Catalan C, Winoto A, Huber R, Engh RA, Holak TA. ; Structure. 1998 Oct 15;6(10):1279-90. ; 1998-10-15 ; PMID 9782052
  233. Computation with the KEGG pathway database. ; Ogata H, Goto S, Fujibuchi W, Kanehisa M ; Biosystems 1998 Jun-Jul;47(1-2):119-28. ; 1998-06-01 ; PMID 9715755
  234. Phosphorylation of PITSLRE p110 isoforms accompanies their processing by caspases during Fas-mediated cell death. ; Tang D, Gururajan R, Kidd VJ. ; J Biol Chem. 1998 Jun 26;273(26):16601-7. ; 1998-06-01 ; PMID 9632733
  235. How do kinases transfer phosphoryl groups? ; Matte A, Tari LW, Delbaere LT. ; Structure. 1998 Apr 15;6(4):413-9. ; 1998-04-15 ; PMID 9562560
  236. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. ; Bono H, Ogata H, Goto S, Kanehisa M ; Genome Res 1998 Mar;8(3):203-10. ; 1998-03-01 ; PMID 9521924
  237. New Drosophila introns originate by duplication. ; Tarrio R, Rodriguez-Trelles F, Ayala FJ. ; Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1658-62. ; 1998-02-17 ; PMID 9465072
  238. Systematic Prediction of Orthologous Units of Genes in the Complete Genomes. ; Bono H, Goto S, Fujibuchi W, Ogata H, Kanehisa M ; Genome Inform Ser Workshop Genome Inform 1998;9:32-40. ; 1998-01-01 ; PMID 11072319
  239. Identification of functional surfaces of the zinc binding domains of intracellular receptors. ; Lichtarge O, Yamamoto KR, Cohen FE. ; J Mol Biol. 1997 Dec 5;274(3):325-37. ; 1997-12-01 ; PMID 9405143
  240. The protein kinase resource. ; Smith CM, Shindyalov IN, Veretnik S, Gribskov M, Taylor SS, Ten Eyck LF, Bourne PE. ; Trends Biochem Sci. 1997 Nov;22(11):444-6. ; 1997-11-01 ; PMID 9397688
  241. A genomic perspective on protein families. ; Tatusov RL, Koonin EV, Lipman DJ. ; Science. 1997 Oct 24;278(5338):631-7. ; 1997-10-24 ; PMID 9381173
  242. The regulation of splice-site selection, and its role in human disease. ; Cooper TA, Mattox W. ; Am J Hum Genet. 1997 Aug;61(2):259-66. ; 1997-08-01 ; PMID 9311728
  243. Protein kinase inhibition: natural and synthetic variations on a theme. ; Taylor SS, Radzio-Andzelm E. ; Curr Opin Chem Biol. 1997 Aug;1(2):219-26. ; 1997-08-01 ; PMID 9667861
  244. Structures of the tyrosine kinase domain of fibroblast growth factor receptor in complex with inhibitors. ; Mohammadi M, McMahon G, Sun L, Tang C, Hirth P, Yeh BK, Hubbard SR, Schlessinger J. ; Science. 1997 May 9;276(5314):955-60. ; 1997-05-09 ; PMID 9139660
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Thi Ngan Ta Ingénieur d’études CDD
V
Adrien Villain Doctorant Tel:+33 4 91 82 54 36

Mon projet de thèse, en collaboration avec l’Unité de Bioénergétique et Ingénierie des Protéines, consiste à étudier la diatomée d’eau douce Asterionella formosa par des approches de génomique (séquençage de novo, méta-génomique, génomique comparative). Nous nous intéressons particulièrement aux interactions qui ont lieu entre la diatomée et les bactéries présentes en co-culture. Mieux comprendre ces échanges et identifier le rôle de chaque bactérie dans la communauté permettrait de renforcer les associations favorables et d’optimiser la croissance de l’algue, ou sa capacité à stocker des lipides (dans l’optique d’une production de bio-carburant par exemple).

Bibliographie:

  1. Complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa ; Villain A, Kojadinovic M, Puppo C, Prioretti L, Hubert P, Zhang Y, Grégori G, Roulet A, Roques C, Claverie JM, Gontero B & Guillaume Blanc ; Mitochondrial DNA Part B, 2:1, 97-98,2017 Feb ; 2017-02-16 ;
  2. Giant viruses at the core of microscopic wars with global impacts. ; Villain A, Gallot-Lavallée L, Blanc G, Maumus F ; Curr Opin Virol.17;:130-137,2016 Apr 15 ; 2016-04-15 ; PMID 27088734

Contacter cette personne
Adrien Villain Doctorant
Alejandro Villalta Doctorant Tel:0491825432

Mon Projet de thèse consiste à étudier des protéines de virus géants riches en cystéines, dont les fonctions sont inconnues. Pour cela je les exprime dans la bactérie afin de les caractériser biochimiquement et en résoudre la structure 3D. De plus, j'étudie leur expression dans Acanthamoeba afin d’observer leur localisation dans un contexte infectieux, toujours dans le but d'élucider leur fonction.

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    Contacter cette personne
    Alejandro Villalta Doctorant