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Hiroyuki Ogata

Directeur de Recherche CNRS

Tel : +33 4 91 82 54 26


Génomique, Bioinformatique, Microbiologie

Adresse :
Institut de Microbiologie de la Méditerranée
Université de la Mediterranée
163 av. de Luminy, Case 934
13288 Marseille Cedex 9, FRANCE
FR-13288, Marseille Cedex 9, France
Fax : +33 4 91 82 54 21

- Publications en PDF, CV

- HDR (14/01/2008)

I’m interested in understanding the evolution of large DNA viruses or "giruses" (for giant viruses) that have large genomes encoding more than 300 and up to over 1000 genes. They hold, as a whole, a hugely rich but the least explored genetic pool, the diversity of which may compare with that of cellular domains. Why giruses have such large genomes ? How did they evolve during their long history of interactions with cellular hosts ? Why are they so different at the genetic sequence level while they share similar morphology at the virion phase of their life ? My approach is genomics and metagenomics combined with state-of-the-art bioinformatics techniques. My current research projects include (1) comparative genomics of giruses isolated from marine unicellular algae, and (2) metagenomics of giruses in aquatic environments all over the world (TARA-GIRUS, Biomarks). In a more broad perspective, I believe that genetic, species and morphological characterization of microbial world on our planet is an essential step towards advancing current biology. This might parallel with the efforts of naturalists in 18th century, who collected and classified macro-organisms, finally leading to "Systema Naturae" of Carl Linnaeus and, a hundred year later, to "On the Origin of Species" by Charles R. Darwin. I wish my research will contribute to this research field and sometimes leads to a good paper (in Nature or Science, hopefully ;)

  1. 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 (2014) Patterns of Rare and Abundant Marine Microbial Eukaryotes. Curr Biol. ; :,2014 Apr 2 - PMID:24704080

  2. 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 (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature.499 ;7457:209-13,2013 Jul 11 - PMID:23760476

  3. 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 (2013) Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. ; :,2013 Apr 11 - PMID:23575371

  4. Bittner L, Gobet A, Audic S, Romac S, Egge ES, Santini S, Ogata H, Probert I, Edvardsen B, de Vargas C (2013) Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Mol Ecol. ; :,2013 Jan 22 - PMID:23163508

  5. Abdelkafi S, Abousalham A, Fendri I, Ogata H, Barouh N, Fouquet B, Scheirlinckx F, Villeneuve P, Carriere F (2012) Identification of a new phospholipase D in Carica papaya latex. Gene.499 ;2:243-9,2012 May 15 - PMID:22450361

  6. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2012) Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. J Virol.86 ;5:2896-7,2012 Mar  - PMID:22328700

  7. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2012) Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. J Virol.86 ;4:2380-1,2012 Feb  - PMID:22282334

  8. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2011) Draft Genome Sequence of the Coccolithovirus Emiliania huxleyi Virus 203. J Virol.85 ;24:13468-9,2011 Dec  - PMID:22106382

  9. Pagarete A, Le Corguillé G, Tiwari B, Ogata H, de Vargas C, Wilson WH, Allen MJ (2011) Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiol Ecol.78 ;3:555-64,2011 Dec  - PMID:22066669

  10. 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 (2011) A Holistic Approach to Marine Eco-Systems Biology. PLoS Biol.9 ;10:e1001177,2011 Oct  - PMID:22028628

  11. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2011) Draft genome sequence of the coccolithovirus EhV-84. Stand Genomic Sci.5 ;1:1-11,2011 Oct 15 - PMID:22180805

  12. Yoshida T, Claverie JM, Ogata H (2011) Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids. Virol J.8 ;1:427,2011 Sep 7 - PMID:21899737

  13. Ogata H, Ray J, Toyoda K, Sandaa RA, Nagasaki K, Bratbak G, Claverie JM (2011) Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. ISME J.5 ;7:1143-51,2011 Jul  - PMID:21248859

  14. Yamada T, Satoh S, Ishikawa H, Fujiwara A, Kawasaki T, Fujie M, Ogata H (2010) A jumbo phage infecting the phytopathogen Ralstonia solanacearum defines a new lineage of the Myoviridae family. Virology.398 ;1:135-47,2010 Mar 1 - PMID:20034649

  15. Ogata H., Monier A., Claverie JM (2010) Distribution of Giant Viruses in Marine Environments. 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

  16. Claverie JM, Ogata H (2009) Ten good reasons not to exclude giruses from the evolutionary picture. Nat Rev Microbiol.7 ;8:615 ; author reply 615,2009 Aug  - PMID:19561626

  17. Ogata H, Toyoda K, Tomaru Y, Nakayama N, Shirai Y, Claverie JM, Nagasaki K (2009) Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus. Virol J.6 ;1:178,2009 Oct 27 - PMID:19860921

  18. Abdelkafi S, Ogata H, Barouh N, Fouquet B, Lebrun R, Pina M, Scherlinckx F, Villeneuve P, Carriere F (2009) Identification and biochemical characterization of a GDSL-motif carboxylester hydrolase from Carica papaya latex. Biochim Biophys Acta.1791 ;11:1048-56,2009 Nov - PMID:19555778

  19. Monier A, Pagarete A, de Vargas C, Allen MJ, Read B, Claverie JM, Ogata H (2009) Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res.19 ;8:1441-9,2009 Aug - PMID:19451591

  20. Claverie JM, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, Ogata H, Abergel C (2009) Mimivirus&Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. J Invertebr Pathol.101 ;3:172-80,2009 Jul - PMID:19457438

  21. von Dassow P, Ogata H, Probert I, Wincker P, Da Silva C, Audic S, Claverie JM, de Vargas C (2009) Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. Genome Biol.10 ;10:R114,2009 Oct 15 - PMID:19832986

  22. Claverie JM, Abergel C, Ogata H (2009) Mimivirus. Curr Top Microbiol Immunol.328 ;:89-121,2009  - PMID:19216436

  23. Monier A, Claverie JM, Ogata H (2008) Taxonomic distribution of large DNA viruses in the sea. Genome Biol.9 ;7:R106,2008 Jul 3 - PMID:18598358

  24. Ogata H, Claverie JM (2008) Microbiology. How to infect a Mimivirus. Science.321 ;5894:1305-6,2008 Sep 5 - PMID:18772426

  25. Yoshida T, Nagasaki K, Takashima Y, Shirai Y, Tomaru Y, Takao Y, Sakamoto S, Hiroishi S, Ogata H (2008) Ma-LMM01 Infecting Toxic Microcystis aeruginosa Illuminates Diverse Cyanophage Genome Strategies. J Bacteriol. ;190(5):1762-72,2008 Mar 1 - PMID:18065537

  26. Monier A, Larsen JB, Sandaa RA, Bratbak G, Claverie JM, Ogata H (2008) Marine mimivirus relatives are probably large algal viruses. Virol J.5 ;1:12,2008 Jan 23 - PMID:18215256

  27. Monier A, Claverie JM, Ogata H (2007) Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. BMC Genomics.8 ;1:456,2007 Dec 10 - PMID:18070355

  28. Blanc G, Ogata H, Robert C, Audic S, Claverie JM, Raoult D (2007) Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome. Genome Res.17 ;11:1657-64,2007 Nov - PMID:17916642

  29. Ogata H, Claverie JM (2007) Unique genes in giant viruses: regular substitution pattern and anomalously short size. Genome Res.17 ;9:1353-61,2007 Sep - PMID:17652424

  30. Ogata H and Renesto P (2007) Genomics of Rickettsial Agents. Didier Raoult and Philippe Parola eds, Rickettsial Diseases : Old and New,2007

  31. Blanc G, Ogata H, Robert C, Audic S, Suhre K, Vestris G, Claverie JM, Raoult D (2007) Reductive Genome Evolution from the Mother of Rickettsia. PLoS Genet.3 ;1:e14,2007 Jan 19 - PMID:17238289

  32. Abergel C , Blanc G , Monchois V, Renesto P, Sigoillot C , Ogata H, Raoult D, Claverie JM (2006) Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity. Mol Biol Evol.23 ;11:2112-22,2006 Nov - PMID:16891376

  33. Ogata H, {La Scola} B, Audic S, Renesto P, Blanc G, Robert C, Fournier PE, Claverie JM, Raoult D (2006) Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PLoS Genet.2 ;5:e76,2006 May - PMID:16703114

  34. Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE (2006) Mimivirus and the emerging concept of "giant" virus. Virus Res.117 ;1:133-44,2006 Apr - PMID:16469402

  35. Ogata H and Raoult D (2006) Genomics of Rickettsia Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (John Wiley & Sons),2006

  36. 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 (2006) Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet.2 ;1:e7,2006 Jan - PMID:16415984

  37. Ngwamidiba M, Blanc G, Ogata H, Raoult D, Fournier PE. (2005) Phylogenetic Study of Rickettsia Species Using Sequences of the Autotransporter Protein-Encoding Gene sca2. Ann N Y Acad Sci. ;1063:94-9,2005 Dec - PMID:16481498

  38. Ogata H, Robert C, Audic S, Robineau S, Blanc G, Fournier PE, Renesto P, Claverie JM, Raoult D. (2005) Rickettsia felis, from Culture to Genome Sequencing. Ann N Y Acad Sci. ;1063:26-34,2005 Dec - PMID:16481487

  39. Zhu Y, Fournier PE, Ogata H, Raoult D. (2005) Multispacer Typing of Rickettsia prowazekii Enabling Epidemiological Studies of Epidemic Typhus. J Clin Microbiol. ;43(9):4708-12,2005 Sep - PMID:16145131

  40. Ogata H, Renesto P, Audic S, Robert C, Blanc G, Fournier PE, Parinello H, Claverie JM, Raoult D (2005) The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol.3 ;8:e248,2005 Aug - PMID:15984913

  41. Ogata H, Abergel C, Raoult D, Claverie JM (2005) Response to Comment on The 1.2-Megabase Genome Sequence of Mimivirus Science, Vol 308, Issue 5725, 1114 Science, Vol 308, Issue 5725, 1114,2005 Jun

  42. Ogata H, Suhre K, Claverie JM. (2005) Discovery of protein-coding palindromic repeats in Wolbachia. Trends Microbiol. ;13(6):253-5,2005 Jun - PMID:15936655

  43. Crapoulet N, Renesto P, Dumler JS, Suhre K, Ogata H, Claverie JM and Raoult D. (2005) Tropheryma whipplei genome at the beginning of the post-genomic era. Current genomics Vol. 6, No. 3, Pp. 195-205,2005

  44. Rovery C, Renesto P, Crapoulet N, Matsumoto K, Parola P, Ogata H, Raoult D (2005) Transcriptional response of Rickettsia conorii exposed to temperature variation and stress starvation. Res Microbiol.156 ;2:211-8,2005 Mar - PMID:15748986

  45. Ogata H, Raoult D, Claverie JM. (2005) A new example of viral intein in Mimivirus. Virol J. ;2(1):8,2005 Feb 11 - PMID:15707490

  46. Renesto P, Ogata H, Audic S, Claverie JM, Raoult D. (2005) Some lessons from Rickettsia genomics. FEMS Microbiol Rev. ;29(1):99-117,2005 Jan - PMID:15652978

  47. Ogata H and Claverie JM (2005) Metagrowth: a new resource for the building of metabolic hypotheses in microbiology Nucleic Acids Res. ;33 Database Issue:D321-4,2005 Jan 1 - PMID:15608207

  48. Fournier PE, Zhu Y, Ogata H, Raoult D. (2004) Use of highly variable intergenic spacer sequences for multispacer typing of Rickettsia conorii strains. J Clin Microbiol. 2004 Dec ;42(12):5757-66. - PMID:15583310

  49. Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. (2004) The 1.2-Mb Genome Sequence of Mimivirus. Science. 2004 Nov 19 ;306(5700):1344-50. Epub 2004 Oct 14. - PMID:15486256

  50. Drancourt M., Roux V., Dang L.V., Tran-Hung L., Castex D., Chenal-Francisque V., Ogata H., Fournier P.-E., Crubezy E. and Raoult D. (2004) Genotyping, Orientalis-like Yersinia pestis, and plague pandemics Emerg. Infect. Dis., 10, 585-592,2004 Aug

  51. Scorpio DG, Caspersen K, Ogata H, Park J, Dumler JS (2004) Restricted changes in major surface protein-2 (msp2) transcriptionafter prolonged in vitro passage of Anaplasma phagocytophilum BMC Microbiol. 2004 Jan 8 ;4(1):1. - PMID:14713314

  52. Raoult D, Ogata H, Audic S, Robert C, Suhre K, Drancourt M, Claverie JM (2003) Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome. Genome Res 2003 Aug ;13(8):1800-9. - PMID:12902375

  53. Renesto P, Crapoulet N, Ogata H, La Scola B, Vestris G, Claverie JM, Raoult D (2003) Genome-based design of a cell-free culture medium for Tropheryma whipplei. Lancet 2003 Aug 9 ;362(9382):447-9. - PMID:12927433

  54. Claverie JM, Ogata H (2003) The insertion of palindromic repeats in the evolution of proteins. Trends Biochem Sci 2003 Feb ;28(2):75-80. - PMID:12575994

  55. Ogata H, Audic S, Abergel C, Fournier PE, Claverie JM (2002) Protein coding palindromes are a unique but recurrent feature in Rickettsia. Genome Res 2002 May ;12(5):808-16. - PMID:11997347

  56. Zeaiter Z, Fournier PE, Ogata H, Raoult D (2002) Phylogenetic classification of Bartonella species by comparing groEL sequences. Int J Syst Evol Microbiol 2002 Jan ;52(Pt 1):165-71. - PMID:11837299

  57. Claverie JM, Abergel C, Audic S, Ogata H (2001) Recent advances in computational genomics. Pharmacogenomics 2001 Nov ;2(4):361-72. - PMID:11722286

  58. Ogata H, Audic S, Renesto-Audiffren P, Fournier PE, Barbe V, Samson D, Roux V, Cossart P, Weissenbach J, Claverie JM, Raoult D (2001) Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science 2001 Sep 14 ;293(5537):2093-8. - PMID:11557893

  59. Ogata H, Fujibuchi W, Goto S, Kanehisa M (2000) A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res 2000 Oct 15 ;28(20):4021-8. - PMID:11024183

  60. Fujibuchi W, Ogata H, Matsuda H, Kanehisa M (2000) Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. Nucleic Acids Res 2000 Oct 15 ;28(20):4029-36. - PMID:11024184

  61. Ogata H, Audic S, Barbe V, Artiguenave F, Fournier PE, Raoult D, Claverie JM (2000) Selfish DNA in protein-coding genes of Rickettsia. Science 2000 Oct 13 ;290(5490):347-50. - PMID:11030655

  62. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999 Jan 1 ;27(1):29-34. - PMID:9847135

  63. Kawashima S, Ogata H, Kanehisa M (1999) AAindex: Amino Acid Index Database. Nucleic Acids Res 1999 Jan 1 ;27(1):368-9. - PMID:9847231

  64. Ogata H, Goto S, Fujibuchi W, Kanehisa M (1998) Computation with the KEGG pathway database. Biosystems 1998 Jun-Jul ;47(1-2):119-28. - PMID:9715755

  65. Bono H, Ogata H, Goto S, Kanehisa M (1998) Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res 1998 Mar ;8(3):203-10. - PMID:9521924

  66. Bono H, Goto S, Fujibuchi W, Ogata H, Kanehisa M (1998) Systematic Prediction of Orthologous Units of Genes in the Complete Genomes. Genome Inform Ser Workshop Genome Inform 1998 ;9:32-40. - PMID:11072319

  67. Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, Sato K, Kanehisa M (1997) Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput 1997 ;:175-86. - PMID:9390290

  68. Ogata H, Fujibuchi W, Kanehisa M (1996) The size differences among mammalian introns are due to the accumulation of small deletions. FEBS Lett 1996 Jul 15 ;390(1):99-103. - PMID:8706839

  69. Ogata H, Akiyama Y, Kanehisa M (1995) A genetic algorithm based molecular modeling technique for RNA stem-loop structures. Nucleic Acids Res 1995 Feb 11 ;23(3):419-26. - PMID:7533901