Reprint may be requested to ogata@* (* --> kuicr.kyoto-u.ac.jp)
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Original articles (peer reviewed)

  1. Sunagawa S., Acinas S.G., Bork P., Bowler C., Tara Oceans Coordinators, Eveillard D., Gorsky G., Guidi L., Iudicone D., Karsenti E., Lombard F., Ogata H., Pesant S., Sullivan M.B., Wincker P., de Vargas C.
    Tara Oceans: towards global ocean ecosystems biology.
    Nat. Rev. Microbiol. (2020).

  2. Tominaga K., Morimoto D., Nishimura Y., Ogata H., YoshidaT.
    In silico prediction of virus-host interactions for marine Bacteroidetes with the use of metagenome-assembled genomes.
    Front. Microbiol., 11, 738 (2020).

  3. Prodinger F., Endo H., Gotoh Y., Li Y., Morimoto D., Omae K., Tominaga K., Blanc-Mathieu R., Takano Y., Hayashi T., Nagasaki K., Yoshida T., Ogata H.
    An optimized metabarcoding method for Mimiviridae.
    Microorganisms, 8, E506 (2020). pubmed

  4. Martinez-Hernandez F., Luo E., Tominaga K., Ogata H., Yoshida T., DeLong E.F., Martinez-Garcia M.
    Diel cycling of the cosmopolitan abundant Pelagibacter virus 37-F6: one of the most abundant viruses on earth.
    Environ. Microbiol. Rep., 12, 214-219 (2020). pubmed

  5. Sakurai T., Nishiyama H., Nagai T., Goto S., Ogata H., Kudo M.
    Deficiency of Gankyrin in the small intestine is associated with augmented colitis accompanied by altered bacterial composition of intestinal microbiota.
    BMC Gastroenterol., 20, 12 (2020). pubmed

  6. Aramaki T., Blanc-Mathieu R., Endo H., Ohkubo K., Kanehisa M., Goto S., Ogata H.
    KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold.
    Bioinformatics, btz859 (2019). pubmed

  7. Ibarbalz F.M., Henry N., Brandao M.C., Martini S., Busseni G., Byrne H., Coelho L.P., Endo H., Gasol J.M., Gregory A.C, Mahe F., Rigonato J., Royo-Llonch M., Salazar G., Sanz-Saez I, Scalco E., Soviadan D., Zayed A.A., Zingone A., Labadie K., Ferland J., Marec C., Kandels S., Picheral M., Dimier C., Poulain J., Pisarev S., Carmichael M., Pesant S., Tara Oceans Coordinators, Babin M., Boss E., Iudicone D., Jaillon O., Acinas S.G., Ogata H., Pelletier E., Stemmann L., Sullivan M.B., Sunagawa S., Bopp L., de Vargas C., Karp-Boss L., Wincker P., Lombard F., Bowler C., Zinger L.
    Global trends in marine plankton diversity across kingdoms of life.
    Cell, 179, 1084-1097.e21 (2019). pubmed

  8. Salazar G., Paoli L., Alberti A., Huerta-Cepas J., Ruscheweyh H.-J., Cuenca M., Field C.M., Coelho L.P., Cruaud C., Engelen S., Gregory A.C., Labadie K., Marec C., Pelletier E., Royo-Llonch M., Roux S., Sanchez P., Uehara H., Zayed A.A., Zeller G., Carmichae M., Dimier C., Ferland J., Kandels S., Picheral M., Pisarev S., Poulain J., Tara Oceans Coordinators, Acinas S.G., Babin M., Bork P., Bowler C., de Vargas C., Guidi L., Hingamp P., Iudicone D., Karp-Boss L., Karsenti E., Ogata H., Pesant S., Speich S., Sullivan M.B., Wincker P., Sunagawa S.
    Gene expression changes and community turnover differentially shape the global ocean metatranscriptome.
    Cell, 179, 1068-1083.e21 (2019). pubmed

  9. Okazaki Y., Nishimura Y., Yoshida T., Ogata H., Nakano S.
    Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake.
    Environ. Microbiol., 21, 4740-4754 (2019). pubmed

  10. Castillo Y.M., Mangot J.-F., Benites F., Logares R., Kuronishi M., Ogata H., Jaillon O., Massana R., Sebastian M., Vaque D.
    Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics.
    Mol. Ecol., 28, 4272-4289 (2019). pubmed

  11. Li Y., Endo H., Gotoh Y., Watai H., Ogawa N., Blanc-Mathieu R., Yoshida T., Ogata H.
    The earth is small for "leviathans": long distance dispersal of giant viruses across aquatic environments.
    Microbes Environ., 34, 334-339 (2019). pubmed

  12. Aoki K., Hagiwara R., Akashi M., Murata K., Ogata H., Takemura M.
    Fifteen marseilleviruses newly isolated from three water samples in Japan reveal a local diversity of Marseilleviridae.
    Front. Microbiol., 10, 1152 (2019). pubmed

  13. Gregory A.C., Zayed A.A., Conceicao-Neto N., Temperton B., Bolduc B., Alberti A., Ardyna M., Arkhipova K., Carmichael M., Cruaud C., Dimier C., Dominguez-Huerta G., Ferland J., Kandels S., Liu Y., Marec C., Pesant S., Picheral M., Pisarev S., Poulain J., Tremblay J.E., Vik D.; Tara Oceans Coordinators, Babin M., Bowler C., Culley A.I., de Vargas C., Dutilh B.E., Iudicone D., Karp-Boss L., Roux S., Sunagawa S., Wincker P., Sullivan M.B.
    Marine DNA viral macro- and microdiversity from pole to pole.
    Cell, 177, 1109-1123.e14 (2019). pubmed

  14. Yoshikawa G., Blanc-Mathieu R., Song C., Kayama Y., Mochizuki T., Murata K., Ogata H., Takemura M.
    Medusavirus, a novel large DNA virus discovered from hot spring water.
    J. Virol., 93, e02130-18 (2019). pubmed

  15. Inoue M., Nakamoto I., Omae K., Oguro T., Ogata H., Yoshida T., Sako Y.
    Structural and phylogenetic diversity of anaerobic carbon-monoxide dehydrogenases.
    Front. Microbiol. 9, 3353 (2019). pubmed

  16. Caputi L., Carradec Q., Eveillard D., Kirilovsky A., Pelletier, Pierella Karlusich J.J., Vieira F.R.J., Villar E., Chaffron S., Malviya S., Scalco E., Acinas S.G., Alberti A., Aury J.-M., Benoiston A.-S., Bertrand A., Biard T., Bittner L., Boccara M., Brum J.R., Brunet C., Busseni G., Carratala A., Claustre H., Coelho L.P., Colin S., D’Aniello S., Da Silva C., Del Core M., Dore H., Gasparini S., Kokoszka F., Jamet J.-L., Lejeusne C., Lepoivre C., Lescot M., Lima-Mendez G., Lombard F., Lukes J., Maillet N., Madoui M.-A., Martinez E., Mazzocchi M.G., Neou M.B., Paz-Yepes J., Poulain J., Ramondenc S., Romagnan J.-B., Roux S., Manta D.S., Sanges R., Speich S., Sprovieri M., Sunagawa S., Taillander V., Tanaka A., Tirichine L., Trottier C., Uitz J., Veluchamy A., Vesela J., Vincent F., Yau S., Kandels-Lewis S., Searson S., Dimier C., Picheral M., Tara Oceans Coordinators, Bork P., Boss E., de Vargas C., Follows M.J., Grimsley N., Guidi L., Hingamp P., Karsenti E., Sordino P., Stemmann L., Sullivan M.B., Tagliabue A., Zingone A., Garczarek L., d’Ortenzio F., Testor P., Not F., Ribera d’Alcala M., Wincker P., Bowler C., Iudicone D.
    Community-level responses to iron availability in open ocean planktonic ecosystems. Global Biogeochem. Cycles, 33, 391-419 (2019).

  17. Roux S., Adriaenssens E.M., Dutilh B.E., Koonin E.V., Kropinski A.M., Krupovic M., Kuhn J.H., Lavigne R., Brister J.R., Varsani A., Amid C., Aziz R.K., Bordenstein S.R., Bork P., Breitbart M., Cochrane G.R., Daly R.A., Desnues C., Duhaime M.B., Emerson J.B., Enault F., Fuhrman J.A., Hingamp P., Hugenholtz P., Hurwitz B.L., Ivanova N.N., Labonte J.M., Lee K.-B., Malmstrom R.R., Martinez-Garcia M., Mizrachi I., Ogata H., Paez-Espino D., Petit M.-A., Putonti C., Rattei T., Reyes A., Rodriguez-Valera F., Rosario K., Schriml L., Schulz F., Steward G.F., Sullivan M.B., Sunagawa S., Suttle C.A., Temperton B., Tringe S.G., Vega Thurber R., Webster N.S., Whiteson K.L., Wilhelm S.W., Wommack K.E., Woyke T., Wrighton K., Yilmaz P., Yoshida T., Young M.J., Yutin N., Allen L.Z., Kyrpides N.C., Eloe-Fadrosh E.A.
    Minimum Information about Uncultivated Virus Genomes (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses.
    Nat. Biotechnol., 37, 29-37 (2019). pubmed

  18. Piredda R., Claverie J.-M., Decelle J., de Vargas C., Dunthorn M., Edvardsen B., Eikrem W., Forster D., Kooistra W.H.C.F., Logares R., Massana R., Montresor M., Not F., Ogata H., Pawlowski J., Romac S., Sarno D., Stoeck T., Zingone A.
    Diatom diversity through HTS-metabarcoding in coastal European seas.
    Sci. Rep., 8, 18059 (2018). pubmed

  19. Li Y., Hingamp P., Watai H., Endo H., Yoshida T., Ogata H.
    Degenerate PCR primers to reveal the diversity of giant viruses in coastal waters.
    Viruses, 10, E496 (2018). pubmed

  20. Endo H., Ogata H., Suzuki K.
    Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean.
    Sci. Rep., 8, 10916 (2018). pubmed

  21. Arai W., Taniguchi T., Goto S., Moriya Y., Uehara H., Takemoto K., Ogata H., Takami H.
    MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes.
    Biosci. Biotechnol. Biochem., 82, 1515-1517 (2018). pubmed

  22. Mihara T., Koyano H., Hingamp P., Grimsley N., Goto S., Ogata H.
    Taxon richness of "Megaviridae" exceeds those of Bacteria and Archaea in the ocean.
    Microbes Environ., 33, 162-171 (2018). pubmed

  23. Yoshikawa G., Askora A., Blanc-Mathieu R., Kawasaki T., Li Y., Nakano M., Ogata H., Yamada T.
    Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes.
    Sci. Rep., 8, 4486 (2018). pubmed

  24. Yoshida T., Nishimura Y., Watai H., Haruki N., Morimoto D., Kaneko H., Honda T., Yamamoto K., Hingamp P., Sako Y., Goto S., Ogata H.
    Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan.
    ISME J., 12, 1287-1295 (2018). pubmed

  25. Carradec Q., Pelletier E., Da Silva C., Alberti A., Seeleuthner Y., Blanc-Mathieu R., Lima-Mendez G., Rocha F., Tirichine L., Labadie K., Kirilovsky A., Bertrand A., Engelen S., Madoui M.-A., Meheust R., Poulain J., Romac S., Richter D., Yoshikawa G., Dimier C., Kandels-Lewis S., Picheral M., Searson S., Tara Oceans Coordinators, Jaillon O., Aury J.-M., Karsenti E., Sullivan M.B., Sunagawa S., Bork P., Not F., Hingamp P., Raes J., Guidi L., Ogata H., de Vargas C., Iudicone D., Bowler C., Wincker P.
    A global ocean atlas of eukaryotic genes.
    Nat. Commun., 9, 373, doi:10.1038/s41467-017-02342-1 (2018). pubmed

  26. Seeleuthner Y., Mondy S., Lombard V., Carradec Q., Pelletier E., Wessner M., Leconte J., Mangot J.F., Poulain J., Labadie K., Logares R., Sunagawa S., de Berardinis V., Salanoubat M., Dimier C., Kandels-Lewis S., Picheral M., Searson S., Tara Oceans Coordinators, Pesant S., Poulton N., Stepanauskas R., Bork P., Bowler C., Hingamp P., Sullivan M.B., Iudicone D., Massana R., Aury J.M., Henrissat B., Karsenti E., Jaillon O., Sieracki M., de Vargas C., Wincker P.
    Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.
    Nat. Commun., 9, 310, doi:10.1038/s41467-017-02235-3. (2018). pubmed

  27. Nishiyama H., Nagai T., Kudo M., Okazaki Y., Azuma Y., Watanabe T., Susumu G., Ogata H., Sakurai T.
    Supplementation of pancreatic digestive enzymes alters the composition of intestinal microbiota in mice.
    Biochem. Biophys. Res. Commun., pii: S0006-291X(17)32108-3., (2017). pubmed

  28. Alberti A., Poulain J., Engelen S., Labadie K., Romac S., Ferrera I., Albini G., Aury J.M., Belser C., Bertrand A., Cruaud C., Da Silva C., Dossat C., Gavory F., Gas S., Guy J., Haquelle M., Jacoby E., Jaillon O., Lemainque A., Pelletier E., Samson G., Wessner M.; Genoscope Technical Team, Acinas S.G., Royo-Llonch M., Cornejo-Castillo F.M., Logares R., Fernandez-Gomez B., Bowler C., Cochrane G., Amid C., Hoopen P.T., De Vargas C., Grimsley N., Desgranges E., Kandels-Lewis S., Ogata H., Poulton N., Sieracki M.E., Stepanauskas R., Sullivan M.B., Brum J.R., Duhaime M.B., Poulos B.T., Hurwitz B.L.; Tara Oceans Consortium Coordinators, Pesant S., Karsenti E., Wincker P.
    Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
    Sci. Data, 4, 170093, doi:10.1038/sdata.2017.93. (2017). pubmed

  29. Matsui T., Yoshikawa G.,, Mihara T., Chatchawankanphanich O., Kawasaki T., Nakano M., Fujie M., Ogata H., Yamada T.
    Replications of two closely related groups of jumbo phages show different level of dependence on host-encoded RNA polymerase.
    Front. Microbiol., 8, 1010, doi:10.3389/fmicb.2017.01010 (2017). Open Access pubmed

  30. Nishimura Y., Yoshida T., Kuronishi M., Uehara H., Ogata H., Goto S.
    ViPTree: the viral proteomic tree server.
    Bioinformatics, 33, 2379-2380, doi:10.1093/bioinformatics/btx157 (2017). Author Manuscript Free Access pubmed

  31. Shimizu Y., Ogata H., Goto S.
    Discriminating the reaction types of plant type III polyketide synthases.
    Bioinformatics, 33, 1937-1943, doi:10.1093/bioinformatics/btx112 (2017). Free Access pubmed

  32. Nishimura Y., Watai H., Honda T., Mihara T., Omae K., Roux S., Blanc-Mathieu R., Yamamoto K., Hingamp P., Sako Y., Sullivan M.B., Goto S., Ogata H., Yoshida T.
    Environmental viral genomes shed new light on virus-host interactions in the ocean.
    mSphere, 2, e00359-16 (2017). pubmed

  33. 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., Sullivan M.B.
    Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.
    Nature, 537, 689-693 (2016). -- (Ogata H. in the "Tara Oceans Coordinators") pubmed

  34. 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).

  35. 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, doi:10.1093/femsec/fiw120 (2016). pubmed

  36. 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

  37. 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, doi:10.3390/v8030066 (2016). pubmed

  38. 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, doi:10.1038/nature16942. (2016). pubmed

  39. 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, doi:10.1038/ismej.2015.192. (2016). pubmed

  40. 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, doi: 10.1016/j.bbapap.2015.10.001 (2016). pubmed

  41. 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

  42. Massana R., Gobet A., Audic S., Bass D., Bittner L., Boutte C., Chambouvet A., Christen R., Claverie J.-M., Decelle J., Dolan J.R., Dunthorn M., Edvardsen B., Forn I., Forster D., Guillou L., Jaillon O., Kooistra W.H., Logares R., Mahe F., Not F., Ogata H., Pawlowski J., Pernice M.C., 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, 4035-4049 doi:10.1111/1462-2920.12955. (2015). pubmed

  43. Clerissi C., Desdevises Y., Romac S., Audic S., de Vargas C., Acinas S.G., 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., 7, 979-989, doi:10.1111/1758-2229.12345 (2015). pubmed

  44. 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). pubmed open access

  45. Takemura M., Yokobori S., Ogata H.
    Evolution of eukaryotic DNA polymerases via interaction between cells and large DNA viruses.
    J. Mol. Evol., 81, 24-33, DOI: 10.1007/s00239-015-9690-z (2015). pubmed

  46. 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.; Tara Oceans Consortium Coordinators.
    Open science resources for the discovery and analysis of Tara Oceans data.
    Sci. Data, 2, 150023 (2015). pubmed open access

  47. Sunagawa S., Coelho L.P., Chaffron S., Kultima J.R., Labadie K., Salazar G., Djahanschiri B., Zeller G., Mende D.R., Alberti A., Cornejo-Castillo F.M., Costea P.I., Cruaud C., d'Ovidio F., Engelen S., Ferrera I., Gasol J.M., Guidi L., Hildebrand F., Kokoszka F., Lepoivre C., Lima-Mendez G., Poulain J., Poulos B.T., Royo-Llonch M., Sarmento H., Vieira-Silva S., Dimier C., Picheral M., Searson S., Kandels-Lewis S.; Tara Oceans coordinators, 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 M.B., Weissenbach J., Wincker P., Karsenti E., Raes J., Acinas S.G., Bork P..
    Structure and function of the global ocean microbiome.
    Science, 348, 1261359 (2015). pubmed

  48. 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 J.M., 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.; Tara Oceans Coordinators, Acinas S.G., Bork P., Bowler C., Gorsky G., Grimsley N., Hingamp P., Iudicone D., Not F., Ogata H., Pesant S., Raes J., Sieracki M.E., Speich S., Stemmann L., Sunagawa S., Weissenbach J., Wincker P., Karsenti E.
    Eukaryotic plankton diversity in the sunlit ocean.
    Science, 348, 1261605 (2015). pubmed

  49. Lima-Mendez G., Faust K., Henry N., Decelle J., Colin S., Carcillo F., Chaffron S., Ignacio-Espinosa J.C., Roux S., Vincent F., Bittner L., Darzi Y., Wang J., Audic S., Berline L., Bontempi G., Cabello A.M., Coppola L., Cornejo-Castillo F.M., d'Ovidio F., De Meester L., Ferrera I., Garet-Delmas M.J., 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.; Tara Oceans coordinators, Gorsky G., Not F. Ogata H., Speich S., Stemmann L., Weissenbach J., Wincker P., Acinas S.G., Sunagawa S., Bork P., Sullivan M.B., Karsenti E., Bowler C., de Vargas C., Raes J.
    Determinants of community structure in the global plankton interactome.
    Science, 348, 1262073 (2015). pubmed

  50. Villar E., Farrant G.K., Follows M., Garczarek L., Speich S., Audic S., Bittner L., Blanke B., Brum J.R., Brunet C., Casotti R., Chase A., Dolan J.R., d'Ortenzio F., Gattuso J.P., Grima N., Guidi L., Hill C.N., Jahn O., Jamet J.L., Le Goff H., Lepoivre C., Malviya S., Pelletier E., Romagnan J.B., Roux S., Santini S., Scalco E., Schwenck S.M., Tanaka A., Testor P., Vannier T., Vincent F., Zingone A., Dimier C., Picheral M., Searson S., Kandels-Lewis S.; Tara Oceans Coordinators, Acinas S.G., Bork P., Boss E., de Vargas C., Gorsky G., Ogata H., Pesant S., Sullivan M.B., Sunagawa S., Wincker P., Karsenti E., Bowler C., Not F., Hingamp P., Iudicone D.
    Environmental characteristics of Agulhas rings affect interocean plankton transport.
    Science, 348, 1261447 (2015). pubmed

  51. Brum J.R., Ignacio-Espinoza J.C., Roux S., Doulcier G., Acinas S.G., Alberti A., Chaffron S., Cruaud C., de Vargas C., Gasol J.M., Gorsky G., Gregory A.C., Guidi L., Hingamp P., Iudicone D., Not F., Ogata H., Pesant S., Poulos B.T., Schwenck S.M., Speich S., Dimier C., Kandels-Lewis S., Picheral M., Searson S.; Tara Oceans Coordinators, Bork P., Bowler C., Sunagawa S., Wincker P., Karsenti E., Sullivan M.B.
    Patterns and ecological drivers of ocean viral communities.
    Science, 348, 1261498 (2015). pubmed

  52. Johannessen T.V., Bratbak G., Larsen A., Ogata H., Egge E.S., Edvardsen B., Eikrem W., Sandaa R.-A.
    Characterisation of four novel viruses reveal huge diversity among viruses infecting Prymnesiales (Haptophyta).
    Virology, 476, 180-188 (2015). pubmed

  53. von Dassow P., John U., Ogata H., Probert I., Bendif E.M., Kegel J.U., Audic S., Wincker P., Da Silva C., Claverie J.-M., Doney S., Glover D.M., Flores D.M., Herrera Y., Lescot M., Garet-Delmas M.-J., de Vargas C.
    Life cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.
    ISME J., 9(6), 1365-1377 doi:10.1038/ismej.2014.221. (2015). pubmed

  54. 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, 146-157 (2014). pubmed

  55. Logares R., Audic S., Bass D., Bittner L., Boutte C., Christen R., Claverie J.-M., Decelle J., Dolan J.R., Dunthorn M., Edvardsen B., Gobet A., Kooistra W.H., Mahe F., Not F., Ogata H., Pawlowski J., Pernice M.C., Romac S., Shalchian-Tabrizi K., Simon N., Stoeck T., Santini S., Siano R., Wincker P., Zingone A., Richards T.A., de Vargas C., Massana R.
    Patterns of rare and abundant marine microbial eukaryotes.
    Curr Biol., 24, 813-821 (2014). pubmed

  56. Wilson W.H., Gilg I.C., 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

  57. 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, 3150-3160 (2014). pubmed

  58. Logares R., Sunagawa S., Salazar G., Cornejo-Castillo F.M., 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 S.G.
    Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
    Environ Microbiol., 488, 209-213 (2013). pubmed

  59. Read B.A., Kegel J., Klute M.J., Kuo A., Lefebvre S.C., Maumus F., Mayer C., Miller J., Monier A., Salamov A., Young J., Aguilar M., Claverie J.-M., Frickenhaus S., Gonzalez K., Herman E.K., Lin Y.-C., Napier J., Ogata H., Sarno A.F., Shmutz J., Schroeder D., de Vargas C., Verret F., von Dassow P., Valentin K., Van de Peer Y., Wheeler G.; Emiliania huxleyi Annotation Consortium, Dacks J.B., Delwiche C.F., Dyhrman S.T., Glockner G., John U., Richards T., Worden A.Z., Zhang X., Grigoriev I.V.
    Pan genome of the phytoplankton Emiliania underpins its global distribution.
    Nature, 488, 209-213 (2013). pubmed

  60. Hingamp P., Grimsley N., Acinas S.G., Clerissi C., Subirana L., Poulain J., Ferrera I., Sarmento H., Villar E., Lima-Mendez G., Faust K., Sunagawa S., Claverie J.-M., 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, 1678-1695 (2013). pubmed

  61. 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, 350-355 (2012). pubmed

  62. Hamacher K., Greiner T., Ogata H., Van Etten J.L., Gebhardt M., Villarreal L.P., Cosentino C., Moroni A., Thiel G.
    Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.
    PLoS One, 7, e38826 (2012). pubmed

  63. 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, 243-249 (2012). pubmed

  64. Bittner L., Gobet A., Audic S., Romac S., Egge E.S., 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

  65. Nissimov J.I., Worthy C.A., Rooks P., Napier J.A., Kimmance S.A., Henn M.R., Ogata H., Allen M.J.
    Draft genome sequence of four coccolithoviruses: EhV-88, EhV-201, EhV-207 and EhV-208.
    J. Virol., 86, 2896-2897 (2012). pubmed

  66. Nissimov J.I., Worthy C.A., Rooks P., Napier J.A., Kimmance S.A., Henn M.R., Ogata H., Allen M.J.
    Draft genome sequence of the coccolithovirus EhV-202.
    J. Virol., 86, 2380-2381 (2012). pubmed

  67. Karsenti E., Gonzales Acinas S., Bork P, Bowler C, De Vargas C., Raes J., Sullivan M., Arendt D., Benzoni F., Claverie J.-M., Follows M., Jaillon O., Gorsky G., Hingamp P., Iudicone D., Kandels-Lewis S., Krzic U., Not F., Ogata H., Pesant S., Georges Reynaud E., Sardet C., Edward Sieracki M, Speich S., Velayoudon D., Weissenbach J., Wincker P.; the Tara Oceans Consortium
    A holistic approach to marine ecosystems biology.
    PLoS Biol., 9, e1001177 (2011). pubmed

  68. Nissimov J.I., Worthy C.A., Rooks P., Napier J.A., Kimmance S.A., Henn M.R., Ogata H., Allen M.J.
    Draft Genome Sequence of the Coccolithovirus Emiliania huxleyi Virus 203.
    J. Virol., 85, 13468-13469 (2011). pubmed

  69. Nissimov J.I., Worthy C.A., Rooks P., Napier J.A., Kimmance S.A., Henn M.R., Ogata H., Allen M.J.
    Draft genome sequence of the coccolithovirus EhV-84.
    Stand. Genomic Sci., 5, 1-11 (2011). pubmed

  70. Pagarete A., le Corguille G., Tiwari B., Ogata H., de Vargas C., Wilson W.H., Allen M.J.
    Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms.
    FEMS Microbiol. Ecol., 78, 555-564 (2011). pubmed

  71. Yoshida T., Claverie J.-M., Ogata H.
    Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids.
    Virol J., 8, 427 (2011). pubmed

  72. Ogata H., Ray J., Toyoda K., Sandaa R.-A., Nagasaki K., Bratbak G., Claverie J.-M.
    Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment.
    ISME J., 5, 1143-1151 (2011). pubmed

  73. 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, 135-147 (2010). pubmed

  74. Ogata H., Toyoda K., Tomaru Y., Nakayama N., Shirai Y., Claverie J.-M., 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

  75. von Dassow P., Ogata H., Probert I., Wincker P., Da Silva C., Audic S., Claverie J.-M., 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

  76. Claverie J.-M., Ogata H.
    Ten good reasons not to exclude giruses from the evolutionary picture.
    Nat. Rev. Microbiol., 7, 615 (2009). pubmed

  77. Abdelkafi S., Ogata H., Barouh N., Fouquet B. Lebrun R., Pina M., Scherlinckx F., Villeneuve P., Carriere F.
    Identification and biochemical characterization of a GDSL-motif carboxylester hydrolase from Carica papaya latex.
    Biochim. Biophys. Acta, 1791, 1048-1056 (2009). pubmed

  78. Monier A., Pagarete A., de Vargas C., Allen M.J., Read B., Claverie J.-M., Ogata H.
    Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus.
    Genome Res., 19, 1441-1449 (2009). pubmed

  79. Ogata H., Claverie J.-M.
    How to infect a Mimivirus.
    Science, 321, 1305-1306 (2008). pubmed

  80. Monier A., Claverie J.-M., Ogata H.
    Taxonomic distribution of large DNA viruses in the sea.
    Genome Biol., 9, R106 (2008) pubmed

  81. 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, 1762-1772 (2008). pubmed

  82. Monier A., Larsen J.B., Sandaa R.-A., Bratbak G., Claverie J.-M., Ogata H.
    Marine mimivirus relatives are probably large algal viruses.
    Virol J., 5, 12 (2008). pubmed

  83. Monier A., Claverie J.-M., Ogata H.
    Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses.
    BMC Genomics, 8, 456 (2007). pubmed

  84. Blanc G., Ogata H., Robert C., Audic S., Claverie J.-M., Raoult D.
    Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome.
    Genome Res., 17, 1657-1664 (2007). pubmed

  85. Ogata H., Claverie J.-M.
    Unique genes in giant viruses: regular substitution pattern and anomalously short size.
    Genome Res., 17, 1353-1361 (2007). pubmed

  86. Blanc G., Ogata H., Robert C., Audic S., Suhre K., Vestris G., Claverie J.-M., Raoult D.
    Reductive genome evolution from the mother of Rickettsia
    PLoS Genet., 3, e14 (2007). pubmed

  87. Renesto P., Abergel C., Decloquement P., Moinier D., Azza S., Ogata H., Fourquet P., Gorvel J.-P., Claverie J.-M.
    Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products.
    J. Virol., 80, 11678-11685 (2006). pubmed

  88. Abergel C., Blanc G., Monchois V., Renesto-Audiffren P., Sigoillot C., Ogata H., Raoult D., Claverie J.-M.
    Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity.
    Mol. Biol. Evol., 23, 2112-2122 (2006). pubmed

  89. Ogata H., La Scola B., Audic S., Renesto P., Blanc G., Robert C., Fournier P.-E., Claverie J.-M., Raoult D.
    Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens.
    PLoS Genet., 2, e76 (2006). pubmed

  90. Renesto P., Samson L., Ogata H., Azza S., Fourquet P., Gorvel J.-P., Heinzen R. A., Raoult D.
    Identification of two putative rickettsial adhesins by proteomic analysis.
    Res. Microbiol., 157, 605-612 (2006). pubmed

  91. Claverie J.-M., Ogata H., Audic S., Abergel C., Suhre K., Fournier P.-E.
    Mimivirus and the emerging concept of giant virus.
    Virus Res., 117, 133-144 (2006). pubmed

  92. Fournier P.-E., 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 J.-M.
    Comparative genomics of multidrug resistance in Acinetobacter baumannii.
    PLoS Genet., 2, e7 (2006) pubmed

  93. Ngwamidiba M., Blanc G., Ogata H., Raoult D., Fournier P.-E.
    Phylogenetic study of Rickettsia species using sequences of the autotransporter protein-encoding gene sca2.
    Ann. N. Y. Acad. Sci., 1063, 94-99 (2005). pubmed

  94. Zhu Y., Fournier P.-E., Ogata H., Raoult D.
    Multispacer typing of Rickettsia prowazekii enabling epidemiological studies of epidemic typhus.
    J. Clin. Microbiol., 43, 4708-4712 (2005) pubmed

  95. Ogata H., Renesto P., Audic S., Robert C., Blanc G., Fournier P.-E., Parinello H., Claverie J.-M., 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

  96. Blanc G., Ngwamidiba M., Ogata H., Fournier P.-E., Claverie J.-M., Raoult D.
    Molecular evolution of Rickettsia surface antigens: evidence of positive selection.
    Mol. Biol. Evol., 22, 2073-2083 (2005) pubmed
  97. Ogata H., Abergel C., Raoult D., Claverie J.-M.
    Response to comment on "the 1.2-megabase genome sequence of Mimivirus"
    Science, 308, 1114b (2005) Free access

  98. Ogata H., Suhre, K., Claverie J.-M.
    Discovery of protein-coding palindromic repeats in Wolbachia.
    Trends Microbiol., 13, 253-255 (2005). pubmed

  99. Ogata H., Raoult, D., Claverie J.-M.
    A new example of viral intein in Mimivirus.
    Virol. J., 2, 8 (2005). pubmed

  100. Ogata H., Claverie J.-M.
    Metagrowth: a new resource for the building of metabolic hypotheses in microbiology.
    Nucleic Acids Res., 33, Database Issue:D321-4 (2005). pubmed

  101. 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, 211-218 (2005). pubmed

  102. Fournier P.-E., Zhu Y., Ogata H., Raoult D.
    Use of highly variable intergenic spacer sequences for multispacer typing of Rickettsia conorii strains.
    J. Clin. Microbiol., 42, 5757-5766 (2004). pubmed

  103. Raoult D., Audic S., Robert C., Abergel C., Renesto P., Ogata H., La Scola B., Suzan M., Claverie J.-M.
    The 1.2-megabase genome sequence of Mimivirus.
    Science, 306, 1344-1350 (2004). pubmed

  104. Drancourt M., Roux V., Dang L.V., Tran-Hung L., Castex D., Chenal-Francisque V., Ogata H., Fournier P.-E., Crubezy E., Raoult D.
    Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.
    Emerg. Infect. Dis., 10, 1585-1592 (2004). pubmed

  105. Scorpio D.G., Caspersen K., Ogata H., Park J., Dumler J.S.
    Restricted changes in major surface protein-2 (msp2) transcription after prolonged in vitro passage of Anaplasma phagocytophilum.
    BMC Microbiol., 4, 1 (2004). pubmed

  106. Renesto P., Crapoulet N., Ogata H., La Scola B., Vestris G., Claverie J.-M., Raoult D.
    Genome-based design of a cell-free culture medium for Tropheryma whipplei.
    Lancet, 362, 447-449 (2003). pubmed

  107. Raoult D., Ogata H., Audic S., Robert C., Suhre K., Drancourt M., Claverie J.-M.
    Tropheryma whipplei Twist: a human pathogenic actinobacteria with a reduced genome.
    Genome Res., 13, 1800-1809 (2003). pubmed

  108. Ogata H., Audic S., Abergel C., Fournier P.-E, Claverie J.-M.
    Protein coding palindromes are a unique but recurrent feature in Rickettsia.
    Genome Res., 12, 808-816 (2002). pubmed

  109. Zeaiter Z., Fournier P.-E., Ogata H., Raoult D.
    Phylogenetic classification of Bartonella species by comparing groEL sequences.
    Int. J. Syst. Evol. Microbiol., 52, 165-171 (2002). pubmed

  110. Ogata H., Audic S., Renesto-Audiffren P., Fournier P.-E., Barbe V., Samson D., Roux V., Cossart P., Weissenbach J., Claverie J.-M., Raoult D.
    Mechanisms of evolution in Rickettsia conorii and R. prowazekii.
    Science, 293, 2093-2098 (2001). pubmed

  111. Ogata H., Audic S., Claverie J.-M.
    Selfish DNA and the origin of genes.
    Science, 291, 252-253 (2001). - Letter Science

  112. Ogata H., Audic S., Barbe V., Artiguenave F., Fournier P.-E., Raoult D., Claverie J.-M.
    Selfish DNA in protein coding genes of Rickettsia.
    Science, 290, 347-350 (2000). pubmed

  113. 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, 4029-4036 (2000). pubmed

  114. 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, 4021-4028 (2000). pubmed

  115. 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

  116. Kawashima S., Ogata H., Kanehisa M.
    AAindex: amino acid index database.
    Nucleic Acids Res., 27, 368-369 (1999). pubmed

  117. Ogata H., Goto S., Fujibuchi W., Kanehisa M.
    Computation with the KEGG pathway database.
    BioSystems, 47, 119-128 (1998). pubmed

  118. Bono H., Ogata H., Goto S., Kanehisa M.
    Reconstruction of amino acid biosynthesis pathways from the complete genome sequence.
    Genome Res., 8, 203-210 (1998). pubmed

  119. 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

  120. Ogata H., Akiyama Y., Kanehisa M.
    A genetic algorithm based molecular modeling technique for RNA stem-loop structures.
    Nucleic Acids Res., 23, 419-426 (1995). pubmed


Review articles (peer reviewed)

  1. Ogata H.
    Habitat Alterations by viruses: strategies by tupanviruses and others.
    Microbes Environ, 33, 117-119 (2018). pubmed

  2. Shimizu Y., Ogata H., Goto S.
    Type III polyketide synthases: functional classification and phylogenomics.
    ChemBioChem, 18, 50-65 (2017). pubmed

  3. Blanc-Mathieu R., Ogata H.
    DNA repair genes in the Megavirales pangenome.
    Curr. Opin. Microbiol., 31, 94-100 (2016). pubmed

  4. Claverie J.-M., 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, 172-180 (2009). pubmed

  5. Ogata H., Robert C., Audic S., Robineau S., Blanc G., Fournier P.-E., Renesto P., Claverie J.-M., Raoult D.
    Rickettsia felis, from Culture to Genome Sequencing.
    Ann. N. Y. Acad. Sci., 1063,26-34 (2005). pubmed

  6. 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). Abstract

  7. Renesto P., Ogata H., Audic S., Claverie J.-M., Raoult D.
    Some lessons from Rickettsia genomics. FEMS Microbiol. Rev., 29, 99-117 (2005). pubmed

  8. Claverie J.-M., Ogata H.
    The insertion of palindromic repeats in the evolution of proteins.
    Trends Biochemical Sci., 28, 75-80 (2003). pubmed

  9. Claverie J.-M., Abergel C., Audic S., Ogata H.
    Recent advances in computational genomics.
    Pharmacogenomics, 2, 361-372 (2001). pubmed


Conference proceedings (peer reviewed)

  1. Monier A., Claverie J.-M., Ogata H.
    Horizontal gene transfer and large DNA viruses.
    JOBIM 2007, 271-273 (2007) (July 10-12, Marseille, Poster presentation)

  2. Ogata H., Claverie J.-M.
    An essential dichotomy of the gene pool of giant DNA viruses.
    JOBIM 2007, 269-270 (2007) (July 10-12, Marseille, Poster presentation)

  3. Fujibuchi W., Kazushige S., Ogata H., Goto S., Kanehisa M.
    KEGG and DBGET/LinkDB: Integration of biological relationships in divergent molecular biology data.
    In "Knowledge Sharing Across Biological and Medical Knowledge Based Systems", Technical Report WS-98-04, 35-40, AAAI Press (1998).

  4. Bono H., Goto S., Fujibuchi W., Ogata, H., Kanehisa, M.
    Systematic prediction of orthologous units of genes in the complete genomes.
    Genome Informatics, 9, 32-40 (1998). pubmed

  5. 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.
    Pacific Symp. Biocomputing, 175-186 (1997). pubmed

  6. 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).

  7. Ogata H., Akiyama Y., Kanehisa M.
    A computer modeling method for the three-dimensional structure of RNA.
    Genome Informatics, 4, 270-274, (1993).


Book chapters

  1. Ogata H., Takemura M.
    A decade of giant virus genomics: surprising discoveries opening new questions.
    in "Global Virology I: Identifying and Investigating Viral Diseases", Shapshak P. et al. eds. Springer New York Heidelberg Dordrecht London (2015). Springer

  2. Ogata H., Monier A., Claverie J.-M.
    Distribution of Giant Viruses in Marine Environments.
    in "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. (2011). Springer

  3. Claverie J.-M., Abergel C., Ogata H.
    Mimivirus.
    in "Lesser Known Large dsDNA Viruses", Van Etten J.L. ed., Springer-Verlag, Berlin Heidelberg. (2009). pubmed

  4. Ogata H., Renesto P.
    Genomics of Rickettsial Agents.
    in "Rickettsial Diseases: Old and New", Raoult D. and Parola P. eds., Informa Healthcare, New York, London. (2007).

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

  6. Ogata H.
    Other sequence analysis tools. (8th Chap.)
    in "Introduction to GenomeNet Databases, 2nd edition", Takagi T. and Kanehisa M eds. Kyoritsu Shuppan, Tokyo (1998). -- in Japanese


Other articles

  1. 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).

  2. 三原知子, 五斗進, 緒方博之
    海洋巨大ウイルス―ゲノムから見えてきた多様性と生態
    生物の科学 遺伝, 69, 318-325 (2015).

  3. 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).

  4. Ogata H.
    Bioinformatics in France.
    Japanese Society for Bioinformatics News Letter, Number 11 (2005). -- in Japanese

  5. Ogata H., Kanehisa M.
    A Survey on E. coli Enzymes: Correlation between Metabolic Pathway and Gene Location.
    ICR Annual Report 1996, 52-53, (1997).

  6. Ogata H., Kanehisa M.
    Function analysis using protein databases.
    Biophysics, 36, 152-154, (1996). -- in Japanese

  7. Ogata H., Kanehisa M.
    Homology search.
    Inflammation & Immunology, 3, 423-429, (1995). -- in Japanese


Invited talks

  1. Ogata H., Blanc-Mathieu R., Kaneko H., Endo H.
    Global genetic data reveal lineages of giant viruses and other eukaryotic viruses associated with the carbon export efficiency.
    4th Ringberg Symposium on Giant Virus Biology [November 17-29, 2019, Ringberg Castle, Tegernsee, Germany, Oral presentation on Nov 19 by Ogata H.]

  2. Ogata H.
    Eukaryotic giant viruses: update on their evolution, diversity and ecology.
    ELSI Thermophiles seminar - Microbes from the Hadean Hel [August 30, 2019, ELSI, Tokyo Institute of Technology; Oral presentation]

  3. Ogata H.
    Do viruses enhance the carbon export down to the deep ocean?
    Gordon Research Conference - Applied and Environmental Microbiology: Shaping the Earth’s Microverse [July 14-19, 2019, Mt. Holyoke College; Oral presentation on July 15 by Ogata H.]

  4. 緒方博之
    地球規模海洋オミクスデータに基づく巨大ウイルスと生物炭素ポンプの関係の解明.
    第2回感染症診断と治療におけるゲノム解析 [March 15, 2019, 東海大学伊勢原キャンパス; Oral presentation]

  5. 緒方博之
    海洋ウイルス:どこから来て、何をしているのか?
    第33回 国際生物学賞記念シンポジウム (December 5-6, 2017, つくば国際会議場, presentation on December 6)

  6. Ogata H.
    Multi-omics approach to assess viral impact on marine plankton.
    KAUST Global Ocean Genome Workship (KAUST, Saudi Arabia, October 29 to November 1, presentation on Oct. 30)

  7. 緒方博之
    何故に今頃ネオウイルス学?
    環境微生物系学会合同大会2017 (August 29-31, 2017, Tohoku University, Oral presentation Aug. 29)

  8. 緒方博之, Blanc-Mathieu R., Hingamp P., 西村陽介, 李岩沢, 吉田天士
    マルチオミクス解析が明らかにする洋ウイルスの多様性と存在意義.
    日本進化学会第19回大会 (August 24-26, 2017, Kyoto University, Oral presentation Aug. 24)

  9. Ogata H., Blanc-Mathieu R., Hingamp P., Nishimura Y., Li Y., Yoshida T.
    Towards unveiling pivotal roles of viruses in marine ecosystems.
    The 73rd Fujihara Seminar, International Conference "Molecular Life of Diatoms" (July 9-13, 2017, Kobe, Oral presentation July 13)

  10. Ogata H.
    Biodiversity of marine plankton revealed by Tara Oceans' eco-systems approach.
    Tara Coral Conference (April 24-25, 2017, National Taiwan Ocean University, Oral presentation April 24)

  11. 緒方博之
    遺伝子科学の昨今、生物学からのアプローチ.
    2016年度日仏会館科学シンポジウム「遺伝子の科学」(Dec 3, 2016, 日仏会館ホール, Oral presentation)

  12. Ogata H.
    Tara Oceans expedition and giant viruses in marine ecosystems.
    Biodiversity and Chemical Biology of Marine and Terrestrial Life in the Philippine Region (Oct 16-20, 2016, Bohol, Philippines, Oral presentation Oct 17)

  13. 緒方博之
    ウイルスは生命か?-巨大ウイルスを中心に-.
    第56回生物物理若手の会夏の学校(Sept 2-5, 2016,支笏湖ユースホステル,Oral presentation Sept 4)

  14. 緒方博之
    海洋巨大ウイルスの多様性と宿主予測.
    水圏微生物研究フォーラム(Aug 9-10, 2016,東京大学大気海洋研究所,Oral presentation Aug 9)

  15. 緒方博之
    海洋ウイルス:環境ゲノムから見る多様性・相互作用・分布.
    日本海洋学会2016年度春季大会(Mar 14-18, 2016,東京大学本郷キャンパス, Oral presentation March 17)

  16. 緒方博之
    海洋巨大ウイルスの多様性と進化.
    JT生命誌研究館セミナー(Mar 18, 2015,JT生命誌研究館, Oral presentation)

  17. 緒方博之
    海洋巨大ウイルスの進化と生態.
    京都大学生態研センターセミナー(Feb 20, 2015, 生態研センター, Oral presentation)

  18. Ogata H.
    Marine viral genomics: from genetic diversity to ecological implications.
    Sweden-Kyoto Symposium (Sept 11-12, 2014, Stockholm University/Karolinska Institute, Oral presentation Sept 12/Karolinska Institute)

  19. Ogata H.
    Recent bioinformatics development in quantitative metagenomics.
    The 3rd International Seminar on Biodiversity and Evolution (June 6, 2014, Kyoto Kyoiku Bunka Center, Kyoto, Oral presentation)

  20. Ogata H.
    Giruses in the Ocean: from diversity to their ecological significance (in Japanese).
    Annual meeting of the Sciety of Genome Microbiology Japan - Symposium 1 (7-9 March 2014, Tokyo University of Agriculture, Tokyo, Oral presentation on the 8th March)

  21. Ogata H.
    Giant viruses: a unique entry to the natural diversity of DNA processing genes.
    Second Bioscience and Biotechnology International Symposium: The Nucleic Acid World - Interface between Biology and Chemistry. (29 Jan 2014, Suzukakedai Campus, Tokyo Institute of Technology. Oral presentation)

  22. Ogata H.
    Quantifying nucleo-cytoplasmic large DNA viruses in marine ecosystems.
    International Symposium on Giant Virus Biology (17-20 Nov 2013, Ringberg Castle, Tegernsee, Germany, Oral presentation, Nov. 19)

  23. Ogata H.
    The wonder world of small giants in the sea.
    Lecture at Tokyo Institute of Technology, Tokyo (May 14, 2012, Ookayama, Oral presentation, May 14)

  24. Ogata H.
    The girus gene pool.
    ANR/ARP workshop: International conference on the Viruses of the Environement (March 22-23, 2011, Heidelberg, Oral presentation, Mar. 23)

  25. Ogata H., Hingamp P., Santini S.
    Genomics and metagenomics of marine giruses.
    ANR/ARP workshop: Combining high througput genomics, quantitative imaging, in situ oceanographic and satellite data and modeling to better understand plankton ecosystems at the planetary level (January 10-11, 2011, Villefranche, Oral presentation, Jan 11)

  26. Ogata H.
    Mimivirus and other giants of the virus world.
    Fourth European Congress of Virology (April 7-11, 2010, Cernobbio, Italy, Oral presentation, April 7)

  27. Ogata H.
    The goal of Tara-Girus.
    Tara Retreat Meeting (February 1-3, 2010, Heidlberg, Germany, Oral presentation, February 1)

  28. Ogata H.
    Mimivirus, its sisters and cousins: towards revealing the hidden world of giant viruses.
    Seminar Observatoire Oceanologique de Villefranche-sur-Mer (December 10, 2009, Villefranche-sur-Mer)

  29. Ogata H.
    Host-like genes in giant DNA viruses.
    Lecture at Kyoto University (December 19-22, 2008, Kyoto, Oral presentation)

  30. Ogata H.
    Aquatic viruses: manipulators of host metabolism and a reservoir of new genes.
    Lecture at Universite Blaise-Pascal and Universite D'Auvergne (November 26, 2008, Aubiere, Oral presentation)

  31. Ogata H.
    New insights into the evolutionary behaviour of giant virus genomes.
    Bioinformatics Colloquium (October 24, 2007, Munich, Oral presentation) link

  32. Ogata H., Monier A., Claverie J.-M.
    Virus-host genome comparison.
    E. huxleyi Genome Jamboree (March 19-20, 2007, Roscoff, Oral presentation March 19)

  33. Ogata H.
    Genome sequence of Rickettsia bellii suggests the role of amoebae in ancestral gene transfers between intracellular pathogens.
    International symposium on the comparative biology of the alpha-proteobacteria (April 26-29, 2006, Blacksburg, Virginia, Oral presentation April 27)

  34. Ogata H.
    Comparative evolutionary genomics of Rickettsia.
    CBRC (March 24, 2006, Tokyo, Oral presentation)

  35. Ogata H.
    Lessons from Genomics of Rickettsia and Tropheryma.
    International Symposium From Genomics to Chemical Genomics - 10th Anniversary of KEGG (December 15-16, 2005, Kyoto, Oral presentation Dec. 15)

  36. Ogata H.
    Mimivirus & Evolution du Vivant.
    Reunion Evolution Virale (November 7-8, 2005, Montpelliker, Oral presentation Nov. 7)

  37. Ogata H.
    What have we learned from microbial genome projects.
    Workshop GENOMED-HEALTH, (March 4-5, 2005, Tunis, Oral presentation March 4)

  38. Ogata H.
    Rickettsia and Tropheryma: Lessons from small parasitic bacterial genomes.
    Second JSPS Forum, "Postgenome", (November 28, 2003, Strasbourg)

  39. Ogata H., Abergel C., Audic S., Enault F., Notredame C., Suhre S., Claverie J.-M.
    Bioinformatics and structural genomics of intracellular pathogens and E. coli.
    E. coli Workshop: Towards New Biology in 21st Century, (October 15-17, 2003, Awaji, Japan)

  40. Ogata H.
    Genome sequence of Tropheryma whipplei Twist: a small human pathogen of the high G+C Gram-positive bacteria.
    HAMAP Workshop on Microbial Annotation (June 2-4, 2003).

  41. Ogata H.
    Mechanisms of genome evolution in Rickettsia.
    International Summer School - From Genome to Life, (2002).
  42. Ogata H.
    Unexpected selfish DNA in protein coding regions of Rickettsia.
    4th Annual Conference on Computational Genomics (TIGR), (2000).

  43. Ogata H., Fujibuchi, W., Goto, S., Kanehisa M.
    Integrated analysis of metabolic pathways, sequence evolution and genome organization.
    Dagstuhl Seminar - Modeling and Simulation of Gene Regulation and Metabolic Pathways, (1998).
  44. Ogata H., Kanehisa M.
    A graph theoretical approach for comparative analysis of genomic structures and biochemical pathways.
    Glaxo Wellcome Symposium on Bioinformatics '98, (1998).
  45. Ogata H.
    The new age of bioinformatics.
    A tutuorial at Communications Research Laboratory, Ministry of Posts & Telecommunications, Kobe(1997).

Oral presentations (Conferences, workshops, seminars)

  1. 金子博人, Blanc-Mathieu R., 遠藤 寿, 緒方博之
    海洋ウイルスと地球の炭素循環:TARAオミクスデータの解析による発見.
    インテリジェントバイオインフォマティクス研究チームセミナー [December 20, 2019, AIST Tokyo Waterfront, Tokyo; Oral presentation by 金子博人]

  2. 宮崎うらら, Delmont T., 遠藤 寿., Blanc-Mathieu R., 緒方博之
    海洋巨大ウイルスにおける新規補助代謝遺伝子の探索.
    環境ウイルス研究集会 [November 2, 2019, Uji Campus, Kyoto University; Oral presentation by 宮崎うらら]

  3. Meng L., Endo H., Blanc-Mathieu R., Ogata H.
    NCLDV host prediction with marker gene co-occurrence analysis in marine metagenomes.
    環境ウイルス研究集会 [November 2, 2019, Uji Campus, Kyoto University; Oral presentation by Meng L.]

  4. 吉田亘騎, 武村政春, 遠藤 寿., Blanc-Mathieu R., 緒方博之
    京都府南部水系からの新規マルセイユウイルス株の分離と今後の比較ゲノム解析.
    環境ウイルス研究集会 [November 2, 2019, Uji Campus, Kyoto University; Oral presentation by 吉田亘騎]

  5. Prodinger F., Endo H., Takano Y., Li Y., Tominaga K., Isozaki T., Blanc-Mathieu R., Gotoh Y., Nagasaki Keizo., Yoshida T., Ogata H. Exploring community changes of bloom forming eukaryotic phytoplankton and Megaviridae in Uranouchi Inlet, Japan.
    環境ウイルス研究集会 [November 2, 2019, Uji Campus, Kyoto University; Oral presentation by Prodinger F.]

  6. 富永賢人, 山本圭吾, 緒方博之, 左子芳彦, 吉田天士
    大阪湾での経時的動態観測で探る海洋微生物-ウイルス群集相互作用.
    環境ウイルス研究集会 [November 2, 2019, Uji Campus, Kyoto University; Oral presentation by 富永賢人]

  7. 金子博人, Blanc-Mathieu R., 遠藤寿, 緒方博之
    真核生物プランクトンに感染するウイルスと沈降粒子による炭素輸送の効率との地球規模での関連
    環境ウイルス研究集会 [November 2, 2019, Uji Campus, Kyoto University; Oral presentation by 金子博人]

  8. Endo H., Li Y., Blanc-Mathieu R., Ogata H.
    Global biogeography of giant viruses highlights their interplay with eukaryotic community.
    日本海洋学会2019年秋季大会 [September 25-29, 2019, Toyama International Conference Center; Oral presentation on September 26 by Endo. H.]

  9. Kaneko H., Blanc-Mathieu R., Endo H., Ogata H. The abundance profile of eukaryotic plankton viruses could predict global ocean carbon export efficiency.
    第8回 生命医薬情報連合大会(IIBMP) [September 9 ? 11, 2019, Tokyo Institute of Technology; Oral presentation on September 10 by Kaneko H.]

  10. 岡崎友輔, 西村陽介, 吉田天士, 緒方博之, 中野伸一
    メタゲノム解析でひも解く淡水湖のファージの多様性と生態.
    日本微生物生態学会 第33回大会 [September 10-13, 2019, Yamanashi University, Oral presentation on September 11, by 岡崎友輔]

  11. Blanc-Mathieu R., Dahle H., Ogata H., Sandaa R.-H.
    A persistent algal virus with an unprecedented amount of metabolic genes.
    日本微生物生態学会 第33回大会 [September 10-13, 2019, Yamanashi University, Oral presentation on September 11, by Blanc-Mathieu R.]

  12. 富永賢人, 緒方博之, 吉田天士
    未分離の海洋性Bacteroidetes門細菌感染ウイルスの生物情報学的探索.
    日本微生物生態学会 第33回大会 [September 10-13, 2019, Yamanashi University, Oral presentation on September 11, by 富永賢人]

  13. 礒崎達大, 富永賢人, 山本圭吾, 左子芳彦, 緒方博之, 吉田天士
    シアノウイルス-宿主相互作用解明に向けた海洋シアノバクテリアの高純度分手法の確立.
    日本微生物生態学会 第33回大会 [September 10-13, 2019, Yamanashi University, Oral presentation on September 11, by 礒崎達大]

  14. Prodinger F., Endo H., Li Y., Tominaga K., Isozaki T., Gotoh Y., Yoshida T., Ogata H.
    Linking seasonal dynamics of Megaviridae and bloom forming eukaryotic phytoplankton in Uranouchi inlet, Japan.
    日本微生物生態学会 第33回大会 [September 10-13, 2019, Yamanashi University, Oral presentation on September 11, by Prodinger F.]

  15. Ogata H. Prediction of viruses enhancing the biological carbon pump.
    Neo-Virology Informatics Workshop [August 29, 2019, JAMSTEC Tokyo Office; Oral presentation]

  16. Kaneko H., Blanc-Mathieu R., Endo H., Ogata H.
    Analysis of Tara Oceans omics data reveals eukaryotic plankton viruses related to carbon export flux and efficiency.
    19th Annual International Workshop on Bioinformatics and Systems Biology [July 14-17, 2019, Kyoto University; Oral presentation on July 15 by Kaneko H.]

  17. Prodinger F., Endo H., Li Y., Tominaga K., Tatsuhiro I., Gotoh Y., Yoshida T., Ogata H.
    Seasonal dynamics of a proposed group of giant viruses and bloom forming eukaryotic phytoplankton.
    19th Annual International Workshop on Bioinformatics and Systems Biology [July 14-17, 2019, Kyoto University; Oral presentation on July 17 by Prodinger F.]

  18. Endo H., Li Y., Blanc-Mathieu R., Ogata H.
    Global distribution of nucleocytoplasmic large DNA viruses in the Ocean.
    ASLO 2019 Aquatic Sciences Meeting [February 23-March 2, 2019, San Juan, Puerto Rico; Oral presentation on February 25 by Endo H.]

  19. 黒西愛, Blanc-Mathieu R., 遠藤寿, 五斗進, 緒方博之.
    配列類似性に基づいたウイルスゲノム自動分類法.
    環境ウイルス研究集会 [October 27, 2018, Kyoto University; Oral and poster presentation by 黒西愛]

  20. Kaneko H., Blanc-Mathieu R., Endo H., Ogata H.
    Regression analysis using global ocean metagenomes revealed the contribution of eukaryotic viruses to carbon export.
    Workshop on Environmental Viruses [October 27, 2018, Kyoto University; Oral and poster presentation by Kaneko H.]

  21. Blanc-Mathieu R., Dahle H., Brandt D., Ogata H., Sandaa R.-A.
    Prymnesium kappa Virus RF01: A deep branching Mimiviridae encoding a large number of metabolic genes.
    Workshop on Environmental Viruses [October 27, 2018, Kyoto University; Oral and poster presentation by Blanc-Mathieu R.]

  22. 吉川元貴, Blanc-Mathieu R., 望月智弘, Chihong Song, 村田和義, 緒方博之, 武村政春
    アカントアメーバに感染する新規ウイルスMedusavirus のゲノム解析.
    環境ウイルス研究集会 [October 27, 2018, Kyoto University; Oral and poster presentation by 吉川元貴]

  23. Yoshikawa G., Blanc-Mathieu R., Song C., Mochizuki T., Murata K., Ogata H., Takemura M.
    Genomic characterization of Medusavirus, a new giant virus infecting Acanthamoeba.
    International Workshop on Bioinformatics and Systems Biology (IBSB) [July 16-18, 2018, Boston University; Oral presentation on July 18 and poster presentation on July 17 by Yoshikawa G.]

  24. Kuronishi M., Blanc-Mathieu R., Endo H., Goto S., Ogata H.
    Development of viral genome classification method based on sequence similarity.
    International Workshop on Bioinformatics and Systems Biology 2018 [July 16-18, 2018, Boston; Oral and Poster presentation July 17 by Kuronishi M.]

  25. Blanc-Mathieu R., Kaneko H., Velazquez R.H., Endo H., Ogata H.
    Viruses of the eukaryotic plankton: insight into their diversity, host range and role in carbon export.
    2018 JSME annual meeting & 10th ASME [July 11-13, 2018, Convention Center, Okinawa, Japan; Oral presentation on July 12th by Blanc-Mathieu. R].

  26. Ogata H., Yoshikawa G., Chihong S., Blanc-Mathieu R., Mochizuki T., Murata K., Takemura M.
    A giant virus from a freshwater environment with a full set of histone genes.
    9th Aquatic Virus Workshop (June 17-21, 2018, Lincoln, USA, Oral presentation by Ogata H., June 18).

  27. Sandaa R.-A., Lawrence J., Blanc-Mathieu R., Dahle H., Steen I.H., Ogata H.
    Reluctant affaires -- algal virus-haptophyte relatioship in the ocean.
    9th Aquatic Virus Workshop (June 17-21, 2018, Lincoln, USA, Oral presentation by Sandaa R.-A.., June 21).

  28. Sandaa R.-A., Lawrence J., Blanc-Mathieu R., Dahle H., Steen I.H., Ogata H.
    Diversity of marine prymnesioviruses and their strategies for stable co-existence with their phytoplankton hosts.
    EMBO Workshop Viruses of Microbes 2018 (July 9-13, Wroclaw, Poland, Oral presentation by Sandaa R.-A., July 12).

  29. Blanc-Mathieu R., Kaneko H., Velazquez R.H., Endo H., Ogata H.
    Eukaryotic viruses in Tara Oceans samples: Insight into their diversity and role in carbon export.
    Rinkai Hackathon 2018 (June 10-13, 2018, Fukuyama Castle and Mukaishima Marine Biological Laboratory, Hiroshima University; invited lecture on June 10th by Blanc-Mathieu R.)

  30. 金子博人, Blanc-Mathieu R., 遠藤寿, 緒方博之
    Network analysis reveals the relationship between eukaryotic viruses and the biological carbon pump.
    第12回日本ゲノム微生物学会年会 (March 5-7, 2018, Katsura Campus, Kyoto University; Oral presentation with poster on March 7 by 金子博人)

  31. Blanc-Mathieu R., 金子博人, Velazquez R.H., 遠藤寿, 緒方博之
    Actors of the biological pump: are viruses involved in the process?
    第12回日本ゲノム微生物学会年会 (March 5-7, 2018, Katsura Campus, Kyoto University; Oral presentation on March 7 by Blanc-Mathieu R.)

  32. Blanc-Mathieu R., Li Y., Kaneko H., Endo H., Ogata H.
    Diversity and biogeography of marine giruses and their association with the biological carbon pump.
    The 3rd Ringberg Symposium on Giant Virus Biology (November 19-22, Ringberg Castle, Germany, oral presentation by Ogata H. on November 21)

  33. 武村政春, Song C., 望月智弘, 吉川元貴, Blanc-Mathieu R., 緒方博之, 村田和義
    温泉の底質泥から分離した新規巨大ウイルスについて.
    環境微生物系学会合同大会2017 (August 29-31, 2017, Tohoku University, Oral presentation Aug. 31 by Takemura M.)

  34. 吉川元貴, Blanc-Mathieu R., 望月智弘, Song C., 村田和義, 緒方博之, 武村 政春
    巨大ウイルス群NCLDVに属する新規ウイルスOVのゲノム解析.
    環境微生物系学会合同大会2017 (August 29-31, 2017, Tohoku University, Oral presentation Aug. 31 by Yoshikawa G.)

  35. 吉川 元貴, Romain Blanc-Mathieu, 緒方博之, 山田隆
    カンキツかいよう病菌に感染するファージXacN1 のゲノム解析.
    2017年度日本微生物生態学会環境ウイルス研究部会 (August 28, 2017, Tohoku University, Oral presentation by Yoshikawa G.)

  36. 黒西愛, Romain Blanc-Mathieu, 五斗進, 緒方博之
    ウイルス分類体系のゲノム類似性指標による評価.
    2017年度日本微生物生態学会環境ウイルス研究部会 (August 28, 2017, Tohoku University, Oral presentation by Kuronishi M.)

  37. Li Y., Hingamp P., Watai H., Blanc-Mathieu R., Yoshida T., Ogata H.
    Characterizing the diversity of Megaviridae.
    2017年度日本微生物生態学会環境ウイルス研究部会 (August 28, 2017, Tohoku University, Oral presentation by Li Y.)

  38. Li Y., Hingamp P., Watai H., Blanc-Mathieu R., Yoshida T., Ogata H.
    Comparison of giant virus diversity across ecosystem.
    17th International Workshop on Bioinformatics and Systems Biology (IBSB 17) (July 23-28, 2017, Berlin; Oral and poster presentation July 24 by Li Y.)

  39. Ogata H.
    Extreme diversity, high abundance and activities of giant viruses in the sea.
    The 39th Annual Meeting of the Molecular Biology Society of Japan (Nov 30 - Dec 2, 2016, Yokohama, Oral presentation Dec 2).

  40. 緒方博之
    アメーバウイルス研究がもたらしたンパクト.
    日本微生物生態学会年会 (Oct 22-25, 2016, 横須賀, Oral presentation Oct 24).

  41. 西村陽介, 吉田天士, 緒方博之, 五斗進
    環境ウイルスゲノムの自動分類法.
    ファージ・環境ウイルス研究会合同シンポジウム (Oct 21-22, 2016, JAMSTEC横浜本部, Oral presentation 西村陽介 Oct 22).

  42. 綿井博康, 西村陽介, 五斗進, 緒方博之, 左子芳彦, 吉田天士
    Diversity of the Bacteroidetes viruses through analysis of 48 new genera.
    ファージ・環境ウイルス研究会合同シンポジウム (Oct 21-22, 2016, JAMSTEC横浜本部, Oral presentation 綿井博康 Oct 22).

  43. Yoshikawa G., Blanc-Mathieu R., Ogata H.
    Global meta-transcriptomic analysis of nucleo-cytoplasmic large DNA viruses in the sea.
    16th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 16) (Aug 7-10, 2016, Tokyo, Oral presentation by Yoshikawa G. Aug 10)

  44. Nishiyama H., Goto S., Nagai T., Okazaki Y., Sakurai T., Ogata H.
    The effect of Lipacreon and Elental on mouse gut microbiota.
    16th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 16) (Aug 7-10, 2016, Tokyo, Oral presentation by Nishiyama H. Aug 9)

  45. Mihara T., Nishimura Y., Nishiyama H., Goto S., Ogata H.
    Virus-host database: a manually curated resource for viral host prediction.
    8th Aquatic Virus Workshop (July 10-13, 2016, Plymouth, UK, Oral presentation by Ogata H., July 13).

  46. Shimizu Y., Ogata H., Goto S.
    Relating the reaction types and phylogeny of type III polyketide synthases.
    Informatics in Biology, Medicine and Pharmacology 2015 (October 29-31, 2015, Uji, Oral presentation by Shimizu Y., October 29).

  47. Nishimura Y., Watai W., Honda T., Omae K., Mihara T., Hingamp P., Yamamoto K., Sako Y., Yoshida T., Goto S., Ogata H.
    Revealing complete genomes from metagenomes: a case study for viruses in the ocean.
    Informatics in Biology, Medicine and Pharmacology 2015 (October 29-31, 2015, Uji, Oral presentation by Nishimura Y., October 29).

  48. Mihara T., Koyano H., Goto S., Ogata H.
    Diversity of marine giant DNA viruses.
    International Workshop on Bioinformatics and Systems Biology 2015 (July 19-22, 2015, Boston University, Oral presentation by Mihara T., July 20, Poaster July 21).

  49. 綿井博康, 本田貴史, 山本圭吾, 緒方博之, 五斗進, 西村陽介, 左子芳彦, 吉田天士
    次世代シーケンサーを用いた未知の海洋細菌―ウイルス感染系の推定
    日本水産学会春季大会 (March 27-31, 2015, 東京海洋大学品川キャンパス, Oral presentation by Watai, Mar 29)

  50. 緒方博之
    巨大ウイルスは海洋生態系進化の原動力である
    第37回日本分子生物学会年会 (Nov 25-27, 2014, Yokohama, Oral and Poster presentation Nov 25)

  51. 緒方博之
    ウイルスは生命か?−巨大ウイルスを中心に−
    平成26年第二回化学研究所イブニングセミナー (Nov 12, ICR, Oral presentation)

  52. Shimizu Y., Tokimatsu T., Goto S., Ogata H.
    Exploring Polyketide Synthases from Huge Metagenomic Samples.
    14th International Workshop on Bioinformatics and Systems Biology (IBSB) (July 20-25, 2014, Oral presentation by Shimizu Y.)

  53. Ogata H., Villar E., Grimsley N., Hingamp P.
    Quantifying large DNA viruses in marine ecosystems.
    Ocean Science Meeting 2014, Session 075 (A holistic approach to marine eco-systems biology, major results and perspectives for research and education, organized by Lars S., Bowler C., Boss E., de Vargas C., Ogata H.) (Feb 23-28 Hawaii Convention Center, USA, Oral presentation, Feb 25 2014)

  54. Ogata H.
    Richness of NCLDV genes.
    Tara-Oceans Biodiversity Workshop, ENS, Paris (July 4-5, 2013, Paris, Presentation by C. de Vargas, July 5)

  55. Hingamp, P., Bowler C., Ogata H.
    Eco-system biology and modeling (WP5 of OCEANOMICS).
    OCEANOMICS Kick-off meeting, UPMC, Paris (Mar 19, 2013, Paris, Oral presentation, Mar 19)

  56. Ogata H.
    The big viruses in marine environments.
    Seminar at Nakai laboratory, Tokyo Univ., Tokyo (Feb 12, 2013, Tokyo, Oral presentation, Feb 12)

  57. Villar E., Ogata H., Hingamp P.
    A reference database for viruses and its application for the analysis of TARA-OCEANS metagenomic datasets from 3 Mediterranean stations.
    MicroB3 workshop: Exploring Ecosystems Biology WP6 (Dec 6-7, 2012; Istanbul, Turykey; Oral presentaion by Villar E.)

  58. Ogata H.
    Giant viruses in marine environments.
    Tara Japan Tour (Feb 11-19 2012; JAMSTEC, Yokosuka, Feb-13; Kyoto Univ., Kyoto, Feb-14; National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, Hiroshima, Feb-17; Oral presentaions)

  59. Ogata H., Yoshida T., Ray J., Sandaa R.-A., Bratbak G., Nagasaki K., Claverie J.-M.
    Diversity of DNA informational proteins originating from viruses.
    Aquatic Virus Workshop 6 (October 30-November 3, 2011, Texel, The Netherlands, Oral presentaion, Nov. 2)

  60. Nagasaki K., Tomaru Y., Nakayama N., Yoshida T., Ogata H., Claverie J.-M.
    Relationship between algae and their viruses - from the viewpoint of genomics.
    Symposium of National Bio-Resource Project 'Algae', pp. 14-15 (2011) (January 29, 2011, Tokyo, Oral presentation by Nagasaki K.) (in Japanese)

  61. Mahe F., Audic S., Christen R., Claverie J.-M., Ogata H., Dolan J., Edvardsen B., Kooistra W., Massana R., Pawlowski J., Richards T., Stoeck T., de Vargas C.
    Exploring the biodiversity of the world largest ecosystem: BioMarKs project first results and bioinformatics challenges.
    JOBIM 2010 (2010) (Sept 7-9, Montpellier, presented by Mahe F.)

  62. Nagasaki K., Toyoda K., Nakayama N., Ogata H., Claverie J.-M.
    The ocean is a treasury of strange viruses.
    International Symposium on Marine Genomics 2009 (December 17, 2009, Okinawa, Japan, Oral presentation by Nagasaki K.)

  63. Nagasaki K., Tomaru Y., Nakayama N., Toyoda K., Takao Y., Ogata H.
    The frontier of the study of dinoflagellate-infecting viruses.
    The 25-th conference of the Japanese Society of Microbial Ecology (November 21-23, 2009, Hiroshima, Japan, Oral presentation by Nagasaki K.)

  64. Ogata H., Monier A., Pagarete A., Claverie J.-M.
    Horizontal gene transfer between Emiliania huxleyi and viruses (II).
    Emiliania huxleyi Jamboree (June 17-18, 2009, Woods Hole Oceanographic Institute, Oral presentation June 17)

  65. von Dassow P., Ogata H., Audic S., Da Silva C., Probert I., Claverie J.-M., Wincker P., de Vargas, P.
    How the life cycle impacts transcriptome and genome contents in Emiliania huxleyi.
    Emiliania huxleyi Jamboree (June 17-18, 2009, Woods Hole Oceanographic Institute, Oral presentation June 18 by von Dassow P.)

  66. von Dassow P. Ogata H., Probert I., Wincker P., Da Silva C., Audic S., Claverie J.-M., de Vargas C.
    Unveiling the hidden life of a very visible phytoplankton: deep transcriptomic comparison of 1N and 2N life phases of Emiliania huxleyi.
    ASLO Aquatic Sciences Meeting 2009 (January 25-30, 2009, Nice, Poster presentation by von Dassow P.)

  67. Monier A., Ogata H., Claverie J.-M.
    Horizontal gene transfer between Emiliania huxleyi and viruses.
    Emiliania huxleyi Jamboree (October 15-17, 2008, DOE-JGI Walnut Creek California, Oral presentation October 15)

  68. von Dassow P., Ogata H., Probert I., Audic S., Claverie J.-M., Wincker P., Da Silva C., de Vargas, P.
    Transcriptomic comparison of 1N and 2N phases of Emiliania huxleyi.
    Emiliania huxleyi Jamboree (October 15-17, 2008, DOE-JGI Walnut Creek California, Oral presentation October 15 by von Dassow P.)

  69. Ogata H., Monier A., Claverie J.-M.
    Distribution of giant viruses in marine environments.
    The 13th France-Japan Oceanography Symposium (September 8-10, 2008, Marseille, France, Oral presentation September 10)

  70. Claverie J.-M., Monier A., Abergel C., Ogata H.
    Mimivirus and Mimiviridae: towards a new family of microalgae viruses.
    The 5th Aquatic Virus Workshop (July 6-11, 2008, Vancouver, Canada, Oral presentation July 8 by Claverie J.-M.)

  71. Takashima Y., Yoshida T., Yoshida M., Ogata H., Hiroishi S., Nagasaki K.
    Transcription of the phycobilisome degradation gene in cyanophage MA-LMM01 infecting Microcystis aeruginosa.
    The 5th Aquatic Virus Workshop (July 6-11, 2008, Vancouver, Canada, Oral presentation July 9 by Takashima Y.)

  72. Hosoda N., Yoshida T., Kurokawa Y., Takashima Y., Ogata H., Nagasaki K., Hiroishi S.
    Genetic and biochemical characterization of the lytic enzymes from cyanophage MA-LMM01 infecting Microcystis aeruginosa
    The 5th Aquatic Virus Workshop (July 6-11, 2008, Vancouver, Canada, Oral presentation July 9 by Hosoda N.)

  73. Ogata H.
    Giant viruses are old and ubiquitous.
    Seminaire MAGAMA (February 28, 2008, Marseille)

  74. Ogata H., Monier A., Claverie J.-M.
    Bioinformatics and evolutionary analysis of NCLDVs.
    Genomics and Ecology of Aquatic Viruses (February 11-13, 2008, Banyuls-sur-Mer, Oral presentation)

  75. Yoshida T., Nagasaki K., Takashima Y., Shirai Y., Tomaru Y., Takao Y., Sakamoto S., Hiroishi S., Ogata H.
    The genome of the freshwater cyanophage Ma-LMM01 infecting toxic Microcystis aeruginosa.
    Genomics and Ecology of Aquatic Viruses (February 11-13, 2008, Banyuls-sur-Mer, Oral presentation)

  76. Ogata H.
    Surprising discoveries from genomics of intracellular parasites.
    Seminar at The Institute for Bioinformatics (October 25, 2007, Munich, Oral presentation)

  77. Takashima Y., Yoshida T., Yoshida M., Hosoda N., Ogata H., Hiroishi S., Nagasaki K.
    Temporal gene transcription of cyanophage Ma-LMM01 during infection of a toxic cyanobacterium Microcystis aeruginosa.
    The 7th International Conference on Toxic Cyanobacteria (August 5-10, 2007, Rio das Pedras, Brazil, Oral presentation by Takashima)

  78. Ogata H.
    Comparative genomics of large DNA viruses.
    Seminar at l'Universite d'Aix Marseille I (June 11, 2007, Marseille)

  79. Ogata H., Monier A., Claverie J.-M.
    Analyses comparatives et quantitatives des genomes viraux.
    RAVIE (January 25-26, 2007, Aubiere, Oral presentation Jan. 25)

  80. Monier A., Claverie J.-M., Ogata H.
    Alien genes in viruses: biased biological roles and variable frequencies.
    10th Evolutionary Biology Meeting at Marseille (Sept. 20-22, 2006, Marseille, Oral presentation Sept. 20 by Adam Monier)

  81. Ogata H.
    Le genome de Rickettsia bellii - le role d'amibe dans l'evolution de pathogenes intracellulaires.
    IFR-48 seminar (April 22, 2006, Marseille, Oral presentation)

  82. Ogata H., Koch I., Heiner M., Claverie J.-M.
    An approach to generate testable hypotheses in microbiology.
    5th International Conference on Systems Biology (Oct. 9-13, 2004, Heidelberg, Oral presentation October 12.)

  83. Ogata H., Claverie J.-M.
    A new database towards rational design of culture conditions of obligate parasites.
    VIème Cogrès de la SFM (May 11, 2004, Bordeaux)

  84. Moinier D., Ogata H., Audic S.
    Outils bio-informatiques pour la protéomique - Comparaison TheGPM/Xcalibur Sequest - Gelprint: génération de gels 2D in-silico.
    Journée technique du Réseau National Genopole, "Quelle informatique et bioinformatique pour la protéomique ?", (June 1, 2004, Grenoble)

  85. Ogata H., Abergel C., Audic S., Enault F, Notredame C., Suhre K., Claverie J.-M.
    Rickettsia and Tropheryma: Lessons from small bacterial genomes.
    CBRC, (December 22, 2003, Tokyo, Japan)

  86. Ogata H., Monchois V., Audic S., Coutard B., Byrne D., Fournier P.-E., Renesto P., Raoult D., Abergel C., Claverie J.-M.
    Protein coding palindromes in Rickettsia: A unique mechanism to create novel protein sequences
    Molecular Evolution - International conference jointly organized by ISME and SMBE, (2002).

  87. Ogata H., Audic S., Claverie J.-M.
    Selfish DNA parasitizing protein-coding genes of Rickettsia.
    Journées Évolution Biologique, (2001).

  88. Benkahla A., Ogata H., Alimi P., Audic S., Poirot O., Abergel C., Claverie J.-M.
    Comparison of whole becterial genomes.
    International Congress of Molecular Infectiology 2000, (2000).

  89. Ogata H., Kanehisa M.
    Analysis of the metabolic pathways by the similar cluster searching method.
    Annual Meeting of the Molecular Biology Society of Japan, (1997).

  90. Bono H., Ogata H., Goto S., Kanehisa M.
    Genome scale prediction of enzyme genes utilizing the knowledge of metabolic interactions.
    Genome Informatics Workshop 1996, 252-253 (1996).

  91. Ogata H., Kanehisa M.
    Analyses of metabolic pathways - function and evolution based on classification of enzymes.
    Annual Meeting of the Biophysical Society of Japan, (1996).

  92. Bono H., Goto S., Ogata H., Kanehisa M.
    Systematic prediction of enzyme genes by the metabolic pathway database.
    Recent Advance in Genome Biology of Micro-organisms (10/27-29, 1996).

  93. Tomii K., Ogata H., Kanehisa M.
    Cluster analysis of amino acid indices.
    Annual Meeting of the Biophysical Society of Japan, (1994).

  94. Ogata H., Akiyama Y., Kanehisa M.
    A molecular modeling technique for RNA stem-loop structure.
    Annual Meeting of the Biophysical Society of Japan, (1994).

  95. Ogata H., Kanehisa M.
    A computer modeling method for the three-dimensional structure of RNA.
    Annual Meeting of the Biophysical Society of Japan, (1993).

Poster presentations (Conferences, workshops)

  1. 伴広輝, Romain Blanc-Mathieu, 桑田晃, 佐藤晋也, 吉川伸哉, 一宮睦雄, 緒方博之
    パルマ藻・珪藻の祖先的形質の解明に向けた比較ゲノム解析.
    日本微生物生態学会 第33回大会 [September 10-13, 2019, Yamanashi University, Poster presentation on September 12, by 伴広輝]

  2. Miyazaki U., Delmont T., Endo H., Blanc-Mathieu R., Ogata H.
    A Preliminary Metagenomic Study towards Discovering Novel Auxiliary Metabolic Genes in Marine Large Viruses.
    19th Annual International Workshop on Bioinformatics and Systems Biology [July 14-17, 2019, Kyoto University; Poster presentation on July 15,17 by Miyazaki U.]

  3. Ban H., Blanc-Mathieu R., Kuwata A., Yoshikawa S., Sato S., Ichinomiya M., Ogata H.
    Looking for ancestral genomic features in Parmales algae: the sister group of diatoms.
    19th Annual International Workshop on Bioinformatics and Systems Biology [July 14-17, 2019, Kyoto University; Poster presentation on July 15,17 by Ban H.]

  4. Kato Y., Nishiyama H., Endo H., Ogata H.
    Dissecting the association between gut microbiota and diseases through co-occurrence network analysis.
    第41回日本分子生物学会年会 [November 28-30, 2018, Yokohama; Poster presentation November 29 by Kato Y.]

  5. 青木啓太, 吉川元気, Blanc-Mathieu R., 緒方博之, 武村政春
    真核生物と同じ5種類のヒストン遺伝子を持つ新規巨大ウイルスAcanthamoeba castellanii medusavirusの解析.
    第41回日本分子生物学会年会 [November 28-30, 2018, Yokohama; Poster presentation November 28 by Aoki K.]

  6. Prodinger F., Yanze L., Morimoto D., Omae K., Tominaga K., Gotoh Y., Takano Y., Nagasaki K., Hingamp P., Endo H., Yoshida T., Ogata H.
    Optimization of a metabarcoding method for a major group of giant viruses in the environment.
    Workshop on Environmental Viruses [October 27, 2018, Kyoto University; Oral and poster presentation by Prodinger F.]

  7. Okazaki Y., Nishimura Y., Ogata H., Yoshida T., Nakano S.
    Comprehensive viromics uncovered the diverse viral community in a deep freshwater lake.
    17th International Symposium on Microbial Ecology (August 12-17, 2018, Leipzig, Germany, Poster presentation by Okazaki Y.)

  8. Kaneko H., Blanc-Mathieu R., Endo H., Ogata H.
    Using global metagenomes to unravel the role of viruses in carbon export.
    2018 JSME annual meeting & 10th ASME [July 11-13, 2018, Convention Center, Okinawa, Japan; Poster presentation on July 12th by Kaneko. H]

  9. Castillo Y.M., Mangot J.-F., Benites F., Ogata H., Kuronishi M, Logares R., Massana R., Sebastian M., Vaque D.
    Single cell genomics for the detection of viral signatures in uncultured marine Stramenopiles.
    EMBO Workshop Viruses of Microbes 2018 [July 9-13, 2018, Wroclow, Poland; Poster presentation by Castillo Y.M.]

  10. 金子博人, Blanc-Mathieu R., 遠藤寿, 緒方博之
    Relationship between marine eukaryotic viruses and the global carbon export: network and regression analysis.
    新学術領域「ネオウイルス学」第4回領域班会議 [April 14, 2018, Geisei, Kochi; Poster presentation by 金子博人]

  11. Blanc-Mathieu R., Kaneko H., Yoshikawa G., Endo H., Ogata H.
    Uncovering the diversity of marine large DNA viruses infecting protists and fingering out the ones involved in carbon export.
    2018 DOE JGI User Meeting [March 13-16, San Francisco, USA; Poster presentation on March 14 by Blanc-Mathieu R.]
  12. 李岩沢, Hingamp H., 綿井博康, Blanc-Mathieu R., 吉田天士, 緒方博之
    Assessing the diversity of the Megaviridae giant viruses based on DNA polymerase gene.
    第12回日本ゲノム微生物学会年会 [March 5-7, 2018, Katsura Campus, Kyoto University; Poster presentation on March 5 by 李岩沢]

  13. 吉川元貴, Blanc-Mathieu R., 望?智弘, Song C., 村田和義, 緒方博之, 武村政春
    NCLDVに属する新規巨大ウイルスAcanthamoeba castellanii medusavirusのゲノム解析
    第12回日本ゲノム微生物学会年会 [March 5-7, 2018, Katsura Campus, Kyoto University; Poster presentation on March 5 by 吉川元貴]

  14. 荒巻拓哉, Blanc-Mathieu R., 遠藤寿, 五斗進, 金久實, 緒方博之
    隠れマルコフモデルによるホモロジー検索に基づくタンパク質機能推定法
    第12回日本ゲノム微生物学会年会 [March 5-7, 2018, Katsura Campus, Kyoto University; Poster presentation on March 6 by 荒巻拓哉]

    西山拓輝, 永井知行, 櫻井俊治, 緒方博之
    膵酵素補充療法が腸内細菌叢に及ぼす影響の評価
    第12回日本ゲノム微生物学会年会 [March 5-7, 2018, Katsura Campus, Kyoto University; Poster presentation with short talk on March 6 by 西山拓輝]

    Prodinger F., 李岩沢, 森本大地, 大前公保, 富永賢人, Hingamp P., 吉田天士, 後藤康宏, 緒方博之
    Optimization of a DNA barcode method for a giant virus family.
    第12回日本ゲノム微生物学会年会 [March 5-7, 2018, Katsura Campus, Kyoto University; Poster presentation with short talk on March 6 by Prodinger F.]

    黒西愛, Blanc-Mathieu R.,遠藤寿, 五斗進, 緒方博之
    配列類似性に基づいたウイルスゲノム分類方法の開発
    第12回日本ゲノム微生物学会年会 [March 5-7, 2018, Katsura Campus, Kyoto University; Poster presentation with short talk on March 7 by 黒西愛]

  15. Kaneko H., Blanc-Mathieu R., Endo H., Ogata H.
    Relationship between viruses and biological carbon pump revealed by Tara Oceans omics data.
    International Workshop on Microbes in Hostile Environments (December 4, 2017, Uji Campus, Kyoto University; Poster presentation by Kaneko H.)

  16. Sandaa R.-A., Johannessen T., Lawrence J., Ogata H., Blanc-Mathieu R.
    Diversity of novel viruses infecting haptophytes.
    The 3rd Ringberg Symposium on Giant Virus Biology (November 19-22, 2017, Ringberg Castle, Germany, poster presentation by Sandaa R.-A. on November 20)

  17. Takemura M., Yoshikawa G., Song C., Mochizuki T., Blanc-Mathieu R., Murata K., Ogata H.
    温泉の底質泥から分離した新規巨大ウイルスは新たなNVLDVファミリーを形成する.
    第65回日本ウイルス学会学術集会 [October 24-26, 2017, Osaka International Convention Center; Poster presentation October 25 by Takemura M.]

  18. Aramaki T., Blanc-Mathieu R., Endo H., Goto S., Kanehisa M., Ogata H.
    Protein function annotation by hidden Markov model.
    第6回生命医薬情報学連合大会(IIBMP2017) [September 27-29, 2017, Hokkaido University; Poster presentation September 27 by Aramaki T.]

  19. Blanc-Mathieu R., Endo H., Kaneko H., Yoshikawa G., Ogata H.
    Biogeography of nucleocytoplasmic large DNA viruses in the ocean.
    第6回生命医薬情報学連合大会(IIBMP2017) [September 27-29, 2017, Hokkaido University; Poster presentation September 27 by Endo H.]

  20. 李岩沢, Hingamp P., 綿井博康, Blanc-Mathieu R., 吉田天士, 緒方博之
    Species diversity of the giant virus family Megaviridae.
    環境微生物系学会合同大会2017 (August 29-31, 2017, Tohoku University, Poster presentation Aug. 29 by Li Y.)

  21. 黒西愛, Tuan Watie binti Tuan Mat, Nurshahira binti Yusuf, Romain Blanc-Mathieu, 五斗進, 緒方博之
    ウイルス分類体系はゲノム類似性を反映しているか?
    環境微生物系学会合同大会2017 (August 29-31, 2017, Tohoku University, Poster presentation Aug. 30 by Kuronishi M.)

  22. Kaneko H., Blanc-Mathieu R., Endo H., Ogata H.
    Analysis of the correlation between eukaryotic viruses and the carbon export using ocean microbiome metagenome.
    第54回生命科学夏の学校 (September 1-3, 2017, Takashima, Shiga, Poster presentation Sept 3 by Kaneko H.)

  23. Li Y., Watai H., Yoshida T., Ogata H.
    Characterizing the diversity of giant viruses in Osaka Bay.
    Advanced Genome Science International Symposium: The Start of New Genomics. (Jan 10 - 11, 2017, Tokyo, Poster presentation by Li Y., Jan 10)

  24. Nishiyama H., Goto S., Nagai T., Okazaki Y., Sakurai T., Ogata, H.
    Investigation of gut microbiota alternation by elemental diet and pancrelipase.
    第39回日本分子生物学会年会 (Nov 30 & Dec 1-2, 2016, Yokohama; Poster presentation on Dec 2 by Nishiyama H.)

  25. Li Y., Watai H., Hingamp P., Yoshida T., Ogata H.
    Amplicon analysis of Megaviridae DNA polymerase gene.
    The 116th ICR Annual Symposium (Dec 2, 2016, Kyoto University; Poster presentation by Li Y.)

  26. 西村陽介, 吉田天士, 緒方博之, 五斗進
    あなたのウイルスゲノムを分類します.
    日本微生物生態学会年会 (Oct 22-25, 2016, 横須賀, Poster presentation 西村陽介 Oct 23-24).

  27. 吉川元貴, Blanc-Mathieu R., 緒方博之, 山田隆
    カンキツかいよう病菌に感染する大型ファージXacN1のゲノム解析による特徴づけ.
    日本微生物生態学会年会 (Oct 22-25, 2016, 横須賀, Poster presentation 吉川元貴 Oct 23-24).

  28. 綿井博康, 西村陽介, 山本圭吾, 五斗進, 緒方博之, 左子芳彦, 吉田天士
    genomic-OTUを用いたメタゲノム解析による海洋ウイルスの季節変動.
    日本微生物生態学会年会 (Oct 22-25, 2016, 横須賀, Poster presentation 綿井博康 Oct 23-24).

  29. Nishiyama H., Goto S., Nagai T., Okazaki Y., Sakurai T., Ogata H.
    Mouse gut microbiota composition is altered by elemental diet and pancrelipase treatment.
    日本微生物生態学会年会 (Oct 22-25, 横須賀, Poster presentation by Nishiyama H. Oct 23-24).

  30. Blanc-Mathieu R., Yoshikawa G., Ogata H.
    Pan-ocean meta-transcriptomic analysis of nucleo-cytoplasmic large DNA viruses.
    ファージ・環境ウイルス研究会合同シンポジウム (Oct 21-22, 2016, JAMSTEC横浜本部, Poster presentation by Blanc-Mathieu R. Oct 21).

  31. 吉川元貴, Blanc-Mathieu R., 緒方博之, 山田隆
    多数のtRNAをコードする大型ファージXacN1のゲノム解析.
    ファージ・環境ウイルス研究会合同シンポジウム (Oct 21-22, 2016, JAMSTEC横浜本部, Poster presentation by 吉川元貴 Oct 21).

  32. Yoshikawa G., Blanc-Mathieu R., Ogata H., Yamada T.
    A preliminary characterization of the genome of XacN1, a giant phage infecting the citrus canker agent Xanthomonas citri.
    Informatics in Biology, Medicine and Pharmacology 2016 (Sept 29 - Oct 1, 2016, Odaiba, Poster presentation by Yoshikawa G., Sept 29).

  33. Nishiyama H., Goto S., Nagai T., Okazaki Y., Sakurai T., Ogata H.
    Investigation of mouse gut microbiota affected by Elental and Lipacreon.
    Informatics in Biology, Medicine and Pharmacology 2016 (Sept 29 - Oct 1, 2016, Odaiba, Poster presentation by Nishiyama H., Sept 29).

  34. Blanc-Mathieu R., Ogata H.
    Ancient DNA repair genes from the virus world.
    Extremophiles 2016 (Sept 12-16, 2016, Kyoto University, Poster presentation by Blanc-Mathieu R., Sept 13).

  35. 西村陽介, 綿井博康, 本田貴史, 三原知子, 大前公保, Blanc-Mathieu R., 山本圭吾, 左子芳彦, 五斗進, 緒方博之, 吉田天士
    完全ゲノムから定量化した海洋ウイルスの多様性とその宿主予測.
    水圏微生物研究フォーラム(Aug 9-10, 2016,東京大学大気海洋研究所, Poster presentation 西村陽介 Aug 9)

  36. 綿井博康, 西村陽介, 山本圭吾, 五斗進, 緒方博之, 左子芳彦, 吉田 天士
    Seasonal dynamics of marine viral communities in Japanese coastal area revealed by genomic OTUs analysis.
    水圏微生物研究フォーラム(Aug 9-10, 2016,東京大学大気海洋研究所, Poster presentation 綿井博康 Aug 9)

  37. 綿井博康, 本田貴史, 山本圭吾, 西村陽介, 五斗進, 緒方博之, 左子芳彦, 吉田天士
    完全長ゲノムに基づく海洋ウイルスの定量的動態解析とその宿主微生物の推定.
    日本海洋学会2016年度春季大会(Mar 14-18, 2016,東京大学本郷キャンパス, Poster presentation March 12-14)

  38. Nishiyama H., Aoyama T., Ogata H.
    Utilization of ChIP-Seq data to characterize Arabidopsis thaliana ARR1 binding sites.
    Institute for Chemical Research International Symposium 2016 - Research Network Based on ICR MOU - (March, 7-8, 2016, Uji; Poster presentation on March 7 by Nishiyama H.)

  39. Ogata H., Mihara T., Nishimura Y., Blanc-Mathieu R., Goto S.
    GenomeNet's services for metagenomics studies.
    A New Age of Discovery for Aquatic Microeukaryotes (Jan 26-29, EMBL Heidelberg, Germany, Poster presentation by Ogata H. Jan 27).

  40. Nishiyama H., Ogata H., Aoyama T.
    Characterization of Arabidopsis thaliana ARR1 binding sites based on ChIP-Seq data.
    京都大学化学研究所第115回研究発表会 (Dec. 11, 2015, Uji; Poster presentation by Nishiyama H.)

  41. Mihara T., Koyano H., Hingamp P., Goto S., Ogata H.
    Assessing the diversity of the Megaviridae giant viruses based on RNA polymerase beta genes.
    Informatics in Biology, Medicine and Pharmacology 2015 (October 29-31, 2015, Uji, Poster and highlight track presentation by Mihara T., October 30).

  42. Mihara T., Nishimura Y., Uehara H., Hingamp P., Goto S., Ogata H.
    A GenomeNet resource for virus-host interaction network analyses.
    Annual meeting of Japanese Society of Microbial Ecology, 2015 (October 17-20, 2015, Tsuchiura, Poster presentation by Mihara T.,October 18-19).

  43. Nishimura Y., Mihara T., Yoshida T., Hingamp P., Ogata H., Goto S.
    A viral proteomic tree server and its application to a marine metagenomic study.
    Annual meeting of Japanese Society of Microbial Ecology, 2015 (October 17-20, 2015, Tsuchiura, Poster presentation by Nishimura Y.,October 18-19).

  44. Watai H., Nishimura Y., Mihara T., Honda T, Yamamoto K, Hingamp P., Goto S., Ogata H., Sako Y, Yoshida T.
    Metagenomic analysis of viral communities in Osaka bay, Japan.
    Annual meeting of Japanese Society of Microbial Ecology, 2015 (October 17-20, 2015, Tsuchiura, Poster presentation by Watai H.,October 18-19).

  45. 西村陽介, 綿井博康, 本田貴史, 三原知子, 山本圭吾, 左子芳彦, 吉田天士, 五斗進, 緒方博之
    メタオミクスによる海洋ウイルスと微生物群集の継時的観測
    NGS現場の会 (July 1-3, 2015, つくば国際会議場, Poster presentation by Nishimura Y., July 2-3)

  46. 西村陽介, 本田貴史, 綿井博康, 左子芳彦, 五斗進, 吉田天古, 緒方博之
    次世代配列解析による海洋ウイルスと宿主の相互作用の解析
    生命情報科学若手の会 第6回研究会 (Oct 29-30, 2014, CDB, Kobe, Poster presentation by Nishimura Y.)

  47. Mihara T., Goto S., Ogata H.
    Why do some viruses encode amino acid biosynthetic genes?
    Informatics in Biology, Medicine and Pharmocology 2014 (Oct 2-4, 2014, Sendai, Poster presentation by Mihara T., Oct 2)

  48. Goto S., Tokimatsu T., Moriya Y., Ogata H.
    Tools to Interpret Large Genomic and Metagenomic Data using KEGG Databases.
    14th International Workshop on Bioinformatics and Systems Biology (IBSB) (July 20-25, 2014, Poster presentation by Goto S.)

  49. Ogata H., Audic S., Cossart P., Weissenbach J., Claverie J.-M., Raoult D.
    Rickettsia conorii complete genome sequencing: Preliminary survey.
    Genomes 2000, (2000).

  50. Ogata H., Fujibuchi W., Kanehisa M.
    Detection of co-regulated genes by comparative analysis of microbial genomes.
    Genome Informatics Workshop 1998, 304-305 (1998).

  51. Kawashima S., Ogata H., Kanehisa M.
    Extracting regulatory signals from the upstream region of co-expressed genes derived from DNA microarray experiments.
    Genome Informatics Workshop 1998, 306-307 (1998).

  52. Fujibuchi W., Ogata H., Matsuda H., Kanehisa M.
    Automatic detection of gene clusters by P-quasi complete linkage grouping.
    Genome Informatics Workshop 1998, 300-301 (1998).

  53. Goto S., Shiraishi K., Okamoto K., Ishida H., Asanuma S., Bono H., Ogata H., Fujibuchi W., Kanehisa M.
    Constructing and annotating GENES database in KEGG.
    Genome Informatics Workshop 1998, 226-227 (1998).

  54. Goto S., Sato, K., Ogata H., Fujibuchi W., Kanehisa M.
    Reconstruction and prediction of biochemical pathways from genomic sequences using KEGG.
    Meeting on Genome Mapping, Sequencing & Biology, Cold Spring Harbor Laboratory, (1998).

  55. Ogata H., Bono H., Goto S., Fujibuchi W., Kanehisa M.
    Correlation between the chromosomal location of enzyme genes and the organization of metabolic pathways.
    Meeting on Genome Mapping & Sequencing, Cold Spring Harbor Laboratory, (1997).

  56. Bono H., Ogata H., Goto S., Fujibuchi W., Kanehisa M.
    Gene function identification system based on the metabolic pathway database.
    Meeting on Genome Mapping & Sequencing, Cold Spring Harbor Laboratory, (1997).

  57. Goto S., Bono H., Ogata H., Fujibuchi W., Sato K., Nishioka T., Kanehisa M.
    Metabolism and genome: Computation of metabolic pathways based on genome informatics.
    Annual Meeting of the Biophysical Society of Japan, (1996).

  58. Ogata H., Fujibuchi W., Kanehisa M.
    Size distribution and evolutionary rate of intron revealed by comparison of different mammalian species.
    Progress in biophysics & molecular biology, 65, suppl.1 p.75 (1996).

  59. Kawashima S, Hattori M., Ogata H., Fujibuchi W., Kanehisa, M.
    Analysis of the interaction between transcription factors and DNAs by free-energy decomposition.
    Annual Meeting of the Molecular Biology Society of Japan, (1996).

  60. Ogata H., Fujibuchi W., Kanehisa M.
    Statistical features identified from comparison of homologous introns.
    Genome Informatics Workshop 1995, 96-97, (1995).

  61. Ogata H., Fujibuchi W., Kanehisa M.
    Substitution rates in noncoding regions in mammalian genes.
    Annual Meeting of the Biophysical Society of Japan, (1995).

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