京都大学化学研究所研究者情報   [ English | Japanese ]


緒方 博之(おがた ひろゆき)

バイオインフォマティクスセンター 化学生命科学
(理学研究科・薬学研究科 協力講座)
教授
博士(理学)
URL:http://cls.kuicr.kyoto-u.ac.jp/index_J.html
E-mail: ogata@kuicr.kyoto-u.ac.jp
Tel: 0774-38-3270
Fax: 0774-38-3269

研究・教育歴
    1996.10京都大学化学研究所 助手
    1999.4仏国CNRS 博士研究員
    2001.10仏国CNRS 研究員
    2008.10仏国CNRS 主任研究官
    2012.11東京工業大学 特任准教授
    2014.4京都大学化学研究所 教授
専門分野
    バイオインフォマティクス, 比較ゲノム, ゲノム進化, 微生物生態
主な研究テーマ
  1. 巨大ウイルスのゲノム解析
  2. 大規模包括的データに基づく海洋微生物生態系の研究(Tara Oceans)
主な論文・著書
  1. Shimizu Y., Ogata H., Goto S., Type III polyketide synthases: functional classification and phylogenomics. Chembiochem -, - (2016)
  2. Roux, S., Brum, J.R., Dutilh, B.E., Sunagawa, S., Duhaime, M.B., Loy, A., Poulos, B.T., Solonenko, N., Lara, E., Poulain, J., Pesant, S., Kandels-Lewis, S., Dimier, C., Picheral, M., Searson, S., Cruaud, C., Alberti, A., Duarte, C.M., Gasol, J.M., Vaque, D., Tara Oceans Coordinators, Bork, P., Acinas, S.G., Wincker, P., and Sullivan M.B., Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689-693 (2016)  [pubmed]
  3. Blanc-Mathieu R., Ogata H., DNA repair genes in the Megavirales pangenome. Curr Opin Microbiol 31, 94-100 (2016)  [pubmed]
  4. Mihara T., Nasr-Eldin M.A., Chatchawankanphanich O., Bhunchoth A., Phironrit N., Kawasaki T., Nakano M., Fujie M., Ogata H., Yamada T., A Ralstonia solanacearum phage phiRP15 is closely related to Viunalikeviruses and encodes 19 tRNA-related sequences. Virol Rep 6, 61-73 (2016)
  5. Forster D., Dunthorn M., Mahe F., Dolan J.R., Audic S., Bass D., Bittner L., Boutte C., Christen R., Claverie J.-M., Decelle J., Edvardsen B., Egge E., Eikrem W., Gobet A., Kooistra W.H.C.F., Logares R., Massana R., Montresor M., Not F., Ogata H., Pawlowski J., Pernice M.C., Romac S., Shalchian-Tabrizi K., Simon N., Richards T.A., Santini S., Sarno D., Siano R., Vaulot D., Wincker P., Zingone A., de Vargas C., Stoeck T., Benthic protists: the under-charted majority. FEMS Microbiol Ecol 92, fiw120 (2016)  [pubmed]
  6. Bhunchoth A., Blanc-Mathieu R., Mihara T., Nishimura Y, Askora A., Phironrit N., Leksomboon C., Chatchawankanphanich O., Kawasaki T., Nakano M., Fujie M., Ogata H., Yamada, Y., Asian jumbo phages, phiRSL2 and phiRSF1, infect Ralstonia solanacearum and show common features of phiKZ-related phages. Virology 494, 56-66 (2016)  [pubmed]
  7. Mihara T., Nishimura Y., Shimizu Y., Nishiyama H., Yoshikawa G., Uehara H., Hingamp P., Goto S, Ogata H., Linking virus genomes with host taxonomy. Viruses 8, 66 (2016)  [pubmed]
  8. Guidi L., Chaffron S., Bittner L., Eveillard D., Larhlimi A., Roux S., Darzi Y., Audic S., Berline L., Brum J., Coelho L.P., Espinoza J.C., Malviya S., Sunagawa S., Dimier C., Kandels-Lewis S., Picheral M., Poulain J., Searson S.; Tara Oceans Consortium Coordinators, Stemmann L., Not F., Hingamp P., Speich S., Follows M., Karp-Boss L., Boss E., Ogata H., Pesant S., Weissenbach J., Wincker P., Acinas S.G., Bork P., de Vargas C., Iudicone D., Sullivan M.B., Raes J., Karsenti E., Bowler C., Gorsky G., Plankton networks driving carbon export in the oligotrophic ocean. Nature 532, 465-470 (2016)  [pubmed]
  9. Lescot M., Hingamp P., Kojima K.K., Villar E., Romac S., Veluchamy A., Boccara M., Jaillon O., Iudicone D., Bowler C., Wincker P., Claverie J.-M., Ogata H., Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ISME J 10, 1134-1146 (2016)  [pubmed]
  10. Ben Halima N., Khemakhem B., Fendri I., Ogata H., Baril P., Pichon C., Abdelkafi S., Identification of a new oat beta-amylase by functional proteomics. Biochim Biophys Acta 1864, 52-61 (2016)  [pubmed]
  11. Gallot-Lavallee L., Pagarete A., Legendre M., Santini S., Sandaa R.-A., Himmelbauer H., Ogata H., Bratbak G., Claverie J.-M., The 474-kilobase-pair complete genome sequence of CeV-01B, a virus infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae). Genome Announc 3, e01413-15 (2015)  [pubmed]
  12. 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, Mahe 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., Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environ Microbiol 17, 4035-49 (2015)  [pubmed]
  13. 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., Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes. Environ Microbiol Rep doi:10.1111, 1758-2229.12345. (2015)  [pubmed]
  14. Halima NB, Khemakhem B, Fendri I, Ogata H, Baril P, Pichon C, Abdelkafi S., Identification of a new oat beta-amylase by functional proteomics. Biochim Biophys Acta (2015)  [pubmed]
  15. 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, Mahe 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., Patterns of rare and abundant marine microbial eukaryotes. Curr Biol 24, 813-21 (2014)  [pubmed]
  16. 武村政春, 緒方博之, 【特集にあたって】知られざるウイルスの世界をあばく 生物の科学 遺伝 69, 264-267 (2015)
  17. 三原知子, 五斗進, 緒方博之, 海洋巨大ウイルス―ゲノムから見えたきた多様性と生態 生物の科学 遺伝 69, 318-325 (2015)
  18. 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 R.Z, Sonnenschein E.C, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Cacador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro C.M, Luna G.M, Quero G.M, Loscher C.R, Kremp A, DeLorenzo M.E, Ovreas L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer C.P, Ramos S, Magalhaes C, Jude-Lemeilleur F, Aguirre-Macedo M.L, Wang S, Poulton N, Jones S, Collin R, Fuhrman J.A, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov M.M, Baltar F, Bodrossy L, Van De Kamp J, Frampton D.M.F, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder D.C, Kandil M.M, Amaral V, Biancalana F, Santana R, Pedrotti M.L, 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 E.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 K.C, Vezzi A, Lauro F.M, Martin P, Jensen R.M, 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 J.A.H, Barbier M, Turk V, Tinta T, Fuller W.J, Salihoglu I, Serakinci N, Ergoren M.C, Bresnan E, Iriberri J, Nyhus P.A.F, B. Edvardsen, Karlsen H.E, Golyshin P.N, Gasol J.M, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano C.D, Gidley M.L, Zingone A, Danovaro R, Tsiamis G, Clark M.S, Costa A.C, El Bour M, Martins A.M, Collins E.R, Ducluzeau A.-L, Martinez J, Costello M.J, Amaral-Zettler L.A, Gilbert J.A, Davies N, Field D, Glockner F.O., The ocean sampling day consortium. GigaScience 4, 27 (2015)
  19. Takemura M, Yokobori S, Ogata H., Evolution of eukaryotic DNA polymerases via interaction between cells and large DNA viruses. J. Mol. Evol. (2015)
  20. Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Trouble R, Dimier C, Searson S., Open science resources for the discovery and analysis of Tara Oceans data. Sci Data 2, 150023 (2015)  [pubmed]
  21. 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., Ocean plankton. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015)  [pubmed]
  22. de Vargas C, Audic S, Henry N, Decelle J, Mahe 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., Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean. Science 348, 1261605 (2015)  [pubmed]
  23. 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, Sanchez 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., Ocean plankton. Determinants of community structure in the global plankton interactome. Science 348, 1262073 (2015)  [pubmed]
  24. 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., Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science 348, 1261447 (2015)  [pubmed]
  25. 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., Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science 348, 1261498 (2015)  [pubmed]
  26. Clerissi C, Grimsley N, Subirana L, Maria E, Oriol L, Ogata H, Moreau H, Desdevises Y., Prasinovirus distribution in the Northwest Mediterranean Sea is affected by the environment and particularly by phosphate availability. Virology 466-467, 146-57 (2014)  [pubmed]
  27. Johannessen TV, Bratbak G, Larsen A, Ogata H, Egge ES, Edvardsen B, Eikrem W, Sandaa RA., Characterisation of three novel giant viruses reveals huge diversity among viruses infecting Prymnesiales (Haptophyta). Virology 476, 180-8 (2015)  [pubmed]
  28. von Dassow P, John U, Ogata H, Probert I, Bendif el M, 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., Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton. ISME J 9, 1365-77 (2015)  [pubmed]
  29. 緒方博之, 武村政春., 巨大ウイルスがもたらしたパンドラの箱 生物の科学 遺伝 68, 194-199 (2014)
  30. Clerissi C, Grimsley N, Ogata H, Hingamp P, Poulain J, Desdevises Y., 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. Appl Environ Microbiol 80, 3150-60 (2014)  [pubmed]
  31. Wilson WH, Gilg IC, Duarte A, Ogata H., Development of DNA mismatch repair gene, MutS, as a diagnostic marker for detection and phylogenetic analysis of algal Megaviruses. Virology 466-467, 123-128 (2014)  [pubmed]
  32. 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, Mahe 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., Patterns of rare and abundant marine microbial eukaryotes. Curr Biol 24, 813-21 (2014)  [pubmed]
  33. Clerissi C, Grimsley N, Ogata H, Hingamp P, Poulain J, Desdevises Y., 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. Appl Environ Microbiol 80, 3150-60 (2014)  [pubmed]
  34. 緒方博之, 武村政春, 巨大ウイルスがもたらしたパンドラの箱-ウイルス研究はパラダイムシフトを引き起こすか? 生物の科学 遺伝 68, (2014)
  35. Bittner L, Gobet A, Audic S, Romac S, Egge ES, Santini S, Ogata H, Probert I, Edvardsen B, de Vargas C., Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Mol Ecol 22, 87-101 (2013)  [pubmed]
  36. 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., Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J 7, 1678-95 (2013)  [pubmed]
  37. 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., Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209-13 (2013)  [pubmed]
  38. 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., Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ Microbiol (2013)  [pubmed]
  39. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ., Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. J Virol 86, 2380-1 (2012)  [pubmed]
  40. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ., Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. J Virol 86, 2896-7 (2012)  [pubmed]
  41. Abdelkafi S, Abousalham A, Fendri I, Ogata H, Barouh N, Fouquet B, Scheirlinckx F, Villeneuve P, Carriere F., Identification of a new phospholipase D in Carica papaya latex. Gene 499, 243-9 (2012)  [pubmed]
  42. Hamacher K, Greiner T, Ogata H, Van Etten JL, Gebhardt M, Villarreal LP, Cosentino C, Moroni A, Thiel G., Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis. PLoS One 7, e38826 (2012)  [pubmed]
  43. Yoshida-Takashima Y, Yoshida M, Ogata H, Nagasaki K, Hiroishi S, Yoshida T., Cyanophage infection in the bloom-forming cyanobacteria Microcystis aeruginosa in surface freshwater. Microbes Environ 27, 350-5 (2012)  [pubmed]
  44. Ogata H, Ray J, Toyoda K, Sandaa RA, Nagasaki K, Bratbak G, Claverie JM., Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. ISME J 5, 1143-51 (2011)  [pubmed]
  45. Yoshida T, Claverie JM, Ogata H., Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids. Virol J 8, 427 (2011)  [pubmed]
  46. Pagarete A, Le Corguille G, Tiwari B, Ogata H, de Vargas C, Wilson WH, Allen MJ., Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiol Ecol 78, 555-64 (2011)  [pubmed]
  47. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ., Draft genome sequence of the coccolithovirus EhV-84. Stand Genomic Sci 5, 1-11 (2011)  [pubmed]
  48. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ., Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203. J Virol 85, 13468-9 (2011)  [pubmed]
  49. 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., A holistic approach to marine eco-systems biology. PLoS Biol 9, e1001177 (2011)  [pubmed]
  50. Yamada T, Satoh S, Ishikawa H, Fujiwara A, Kawasaki T, Fujie M, Ogata H., A jumbo phage infecting the phytopathogen Ralstonia solanacearum defines a new lineage of the Myoviridae family. Virology 398, 135-47 (2010)  [pubmed]
  51. Ogata H, Monier A, Claverie J.-M., Distribution of Giant Viruses in Marine Environments. Global Change: Mankind-Marine Environment Interactions (2010)
  52. Monier A, Pagarete A, de Vargas C, Allen MJ, Read B, Claverie JM, Ogata H., Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res 19, 1441-9 (2009)  [pubmed]
  53. Abdelkafi S, Ogata H, Barouh N, Fouquet B, Lebrun R, Pina M, Scheirlinckx F, Villeneuve P, Carriere F., Identification and biochemical characterization of a GDSL-motif carboxylester hydrolase from Carica papaya latex. Biochim Biophys Acta 1791, 1048-56 (2009)  [pubmed]
  54. Claverie JM, Ogata H., Ten good reasons not to exclude giruses from the evolutionary picture. Nat Rev Microbiol 7, 615; author reply 615 (2009)  [pubmed]
  55. von Dassow P, Ogata H, Probert I, Wincker P, Da Silva C, Audic S, Claverie JM, de Vargas C., Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. Genome Biol 10, R114 (2009)  [pubmed]
  56. Ogata H, Toyoda K, Tomaru Y, Nakayama N, Shirai Y, Claverie JM, Nagasaki K., Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus. Virol J 6, 178 (2009)  [pubmed]
  57. Claverie JM, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, Ogata H, Abergel C., Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. J Invertebr Pathol 101, 172-80 (2009)  [pubmed]
  58. Claverie J.-M, Abergel C, Ogata H., Mimivirus. Lesser Known Large dsDNA Viruses (2009)
  59. Monier A, Larsen JB, Sandaa RA, Bratbak G, Claverie JM, Ogata H., Marine mimivirus relatives are probably large algal viruses. Virol J 5, 12 (2008)  [pubmed]
  60. Yoshida T, Nagasaki K, Takashima Y, Shirai Y, Tomaru Y, Takao Y, Sakamoto S, Hiroishi S, Ogata H., Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies. J Bacteriol 190, 1762-72 (2008)  [pubmed]
  61. Monier A, Claverie JM, Ogata H., Taxonomic distribution of large DNA viruses in the sea. Genome Biol 9, R106 (2008)  [pubmed]
  62. Ogata H, Claverie JM., How to infect a Mimivirus. Science 321, 1305-6 (2008)  [pubmed]
  63. Blanc G, Ogata H, Robert C, Audic S, Suhre K, Vestris G, Claverie JM, Raoult D., Reductive genome evolution from the mother of Rickettsia. PLoS Genet 3, e14 (2007)  [pubmed]
  64. Ogata H, Claverie JM., Unique genes in giant viruses: regular substitution pattern and anomalously short size. Genome Res 17, 1353-61 (2007)  [pubmed]
  65. Blanc G, Ogata H, Robert C, Audic S, Claverie JM, Raoult D., Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome. Genome Res 17, 1657-64 (2007)  [pubmed]
  66. Monier A, Claverie JM, Ogata H., Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. BMC Genomics 8, 456 (2007)  [pubmed]
  67. Ogata H, Claverie J.-M., An essential dichotomy of the gene pool of giant DNA viruses. JOBIM 2007 269-270 (2007)
  68. Monier A, Claverie J.-M, Ogata H., Horizontal gene transfer and large DNA viruses. JOBIM 2007 271-273 (2007)
  69. Ogata H, Renesto P., Genomics of Rickettsial Agents. Rickettsial Diseases: Old and New (2007)
  70. 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., Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet 2, e7 (2006)  [pubmed]
  71. Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE., Mimivirus and the emerging concept of "giant" virus. Virus Res 117, 133-44 (2006)  [pubmed]
  72. Renesto P, Samson L, Ogata H, Azza S, Fourquet P, Gorvel JP, Heinzen RA, Raoult D., Identification of two putative rickettsial adhesins by proteomic analysis. Res Microbiol 157, 605-12 (2006)  [pubmed]
  73. Ogata H, La Scola B, Audic S, Renesto P, Blanc G, Robert C, Fournier PE, Claverie JM, Raoult D., Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PLoS Genet 2, e76 (2006)  [pubmed]
  74. Abergel C, Blanc G, Monchois V, Renesto P, Sigoillot C, Ogata H, Raoult D, Claverie JM., Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity. Mol Biol Evol 23, 2112-22 (2006)  [pubmed]
  75. Renesto P, Abergel C, Decloquement P, Moinier D, Azza S, Ogata H, Fourquet P, Gorvel JP, Claverie JM., Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. J Virol 80, 11678-85 (2006)  [pubmed]
  76. Ogata H, Raoult D., Genomics of Rickettsia. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (2006)
  77. Rovery C, Renesto P, Crapoulet N, Matsumoto K, Parola P, Ogata H, Raoult D., Transcriptional response of Rickettsia conorii exposed to temperature variation and stress starvation. Res Microbiol 156, 211-8 (2005)  [pubmed]
  78. Ogata H, Claverie JM., Metagrowth: a new resource for the building of metabolic hypotheses in microbiology. Nucleic Acids Res 33, D321-4 (2005)  [pubmed]
  79. Ogata H, Raoult D, Claverie JM., A new example of viral intein in Mimivirus. Virol J 2, 8 (2005)  [pubmed]
  80. Ogata H, Suhre K, Claverie JM., Discovery of protein-coding palindromic repeats in Wolbachia. Trends Microbiol 13, 253-5 (2005)  [pubmed]
  81. Ogata H, Abergel C, Raoult D, Claverie J.-M., Response to comment on "the 1.2-megabase genome sequence of Mimivirus." Science 38, 1114b (2005)
  82. Blanc G, Ngwamidiba M, Ogata H, Fournier PE, Claverie JM, Raoult D., Molecular evolution of rickettsia surface antigens: evidence of positive selection. Mol Biol Evol 22, 2073-83 (2005)  [pubmed]
  83. Ogata H, Renesto P, Audic S, Robert C, Blanc G, Fournier PE, Parinello H, Claverie JM, Raoult D., The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol 3, e248 (2005)  [pubmed]
  84. Zhu Y, Fournier PE, Ogata H, Raoult D., Multispacer typing of Rickettsia prowazekii enabling epidemiological studies of epidemic typhus. J Clin Microbiol 43, 4708-12 (2005)  [pubmed]
  85. Ngwamidiba M, Blanc G, Ogata H, Raoult D, Fournier PE., Phylogenetic study of Rickettsia species using sequences of the autotransporter protein-encoding gene sca2. Ann N Y Acad Sci 1063, 94-9 (2005)  [pubmed]
  86. Renesto P, Ogata H, Audic S, Claverie JM, Raoult D., Some lessons from Rickettsia genomics. FEMS Microbiol Rev 29, 99-117 (2005)  [pubmed]
  87. Crapoulet N, Renesto P, Dumler J. S, Suhre K, Ogata H, Claverie J-M, Raoult D., Tropheryma whipplei genome at the beginning of the post-genomic era. Current Genomics 6, 195-205 (2005)
  88. Ogata H, Robert C, Audic S, Robineau S, Blanc G, Fournier PE, Renesto P, Claverie JM, Raoult D., Rickettsia felis, from culture to genome sequencing. Ann N Y Acad Sci 1063, 26-34 (2005)  [pubmed]
  89. Ogata H., Bioinformatics in France. Japanese Society for Bioinformatics News Letter 11, (2005)
  90. Scorpio DG, Caspersen K, Ogata H, Park J, Dumler JS., Restricted changes in major surface protein-2 (msp2) transcription after prolonged in vitro passage of Anaplasma phagocytophilum. BMC Microbiol 4, 1 (2004)  [pubmed]
  91. Drancourt M, Roux V, Dang LV, Tran-Hung L, Castex D, Chenal-Francisque V, Ogata H, Fournier PE, Crubezy E, Raoult D., Genotyping, Orientalis-like Yersinia pestis, and plague pandemics. Emerg Infect Dis 10, 1585-92 (2004)  [pubmed]
  92. Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM., The 1.2-megabase genome sequence of Mimivirus. Science 306, 1344-50 (2004)  [pubmed]
  93. Fournier PE, Zhu Y, Ogata H, Raoult D., Use of highly variable intergenic spacer sequences for multispacer typing of Rickettsia conorii strains. J Clin Microbiol 42, 5757-66 (2004)  [pubmed]
  94. Raoult D, Ogata H, Audic S, Robert C, Suhre K, Drancourt M, Claverie JM., Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome. Genome Res 13, 1800-9 (2003)  [pubmed]
  95. Renesto P, Crapoulet N, Ogata H, La Scola B, Vestris G, Claverie JM, Raoult D., Genome-based design of a cell-free culture medium for Tropheryma whipplei. Lancet 362, 447-9 (2003)  [pubmed]
  96. Claverie JM, Ogata H., The insertion of palindromic repeats in the evolution of proteins. Trends Biochem Sci 28, 75-80 (2003)  [pubmed]
  97. Zeaiter Z, Fournier PE, Ogata H, Raoult D., Phylogenetic classification of Bartonella species by comparing groEL sequences. Int J Syst Evol Microbiol 52, 165-71 (2002)  [pubmed]
  98. Ogata H, Audic S, Abergel C, Fournier PE, Claverie JM., Protein coding palindromes are a unique but recurrent feature in Rickettsia. Genome Res 12, 808-16 (2002)  [pubmed]
  99. Ogata H, Audic S, Claverie J.-M., Selfish DNA and the origin of genes. Science 291, 252-253 (2001)
  100. Ogata H, Audic S, Renesto-Audiffren P, Fournier PE, Barbe V, Samson D, Roux V, Cossart P, Weissenbach J, Claverie JM, Raoult D., Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science 293, 2093-8 (2001)  [pubmed]
  101. Claverie JM, Abergel C, Audic S, Ogata H., Recent advances in computational genomics. Pharmacogenomics 2, 361-72 (2001)  [pubmed]
  102. Ogata H, Fujibuchi W, Goto S, Kanehisa M., A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res 28, 4021-8 (2000)  [pubmed]
  103. Fujibuchi W, Ogata H, Matsuda H, Kanehisa M., Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. Nucleic Acids Res 28, 4029-36 (2000)  [pubmed]
  104. Ogata H, Audic S, Barbe V, Artiguenave F, Fournier PE, Raoult D, Claverie JM., Selfish DNA in protein-coding genes of Rickettsia. Science 290, 347-50 (2000)  [pubmed]
  105. Kawashima S, Ogata H, Kanehisa M., AAindex: Amino Acid Index Database. Nucleic Acids Res 27, 368-9 (1999)  [pubmed]
  106. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M., KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27, 29-34 (1999)  [pubmed]
  107. Bono H, Ogata H, Goto S, Kanehisa M., Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res 8, 203-10 (1998)  [pubmed]
  108. Ogata H, Goto S, Fujibuchi W, Kanehisa M., Computation with the KEGG pathway database. Biosystems 47, 119-28 (1998)  [pubmed]
  109. Bono H, Goto S, Fujibuchi W, Ogata H, Kanehisa M., Systematic Prediction of Orthologous Units of Genes in the Complete Genomes. Genome Inform Ser Workshop Genome Inform 9, 32-40 (1998)  [pubmed]
  110. Fujibuchi W, Kazushige S, Ogata H, Goto S, Kanehisa M., KEGG and DBGET/LinkDB: Integration of biological relationships in divergent molecular biology data. Knowledge Sharing Across Biological and Medical Knowledge Based Systems Technical Report WS-98-04, 35-40 (1998)
  111. Ogata H., Other sequence analysis tools. Introduction to GenomeNet Databases, 2nd edition (1998)
  112. Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, Sato K, Kanehisa M., Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput 175-86 (1997)  [pubmed]
  113. Ogata H, Kanehisa M., A Survey on E. coli Enzymes: Correlation between Metabolic Pathway and Gene Location. ICR Annual Report 1996 52-53 (1997)
  114. Ogata H, Fujibuchi W, Kanehisa M., The size differences among mammalian introns are due to the accumulation of small deletions. FEBS Lett 390, 99-103 (1996)  [pubmed]
  115. Ogata H, Bono H, Fujibuchi W, Goto S, Kanehisa M., Analysis of binary relations and hierarchies of enzymes in the metabolic pathways. Genome Informatics 7, 128-136 (1996)
  116. Ogata H, Kanehisa M., Function analysis using protein databases. Biophysics 36, 152-154 (1996)
  117. Ogata H, Akiyama Y, Kanehisa M., A genetic algorithm based molecular modeling technique for RNA stem-loop structures. Nucleic Acids Res 23, 419-26 (1995)  [pubmed]
  118. Ogata H, Kanehisa M., Homology search. Inflammation & Immunology 3, 423-429 (1995)
  119. Ogata H, Akiyama Y, Kanehisa M., A computer modeling method for three-dimensional structure of RNA. Genome Informatics 4, 270-274 (1993)


Update: Jul 18,2017