Journal publications | Invited talks | Book chapters | Conferences, workshops, seminars

Journal publications

  1. 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 |pdf]

  2. 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 |pdf]

  3. 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 |pdf]

  4. 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 | pdf]

  5. 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). [pdf]

  6. 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 | pdf ]

  7. 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 | pdf ]

  8. 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 | pdf ]

  9. 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, 135-137 (2010). [PubMed | pdf]

  10. 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 | pdf]

  11. 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 | pdf]

  12. Claverie J.-M., Ogata H.
    Ten good reasons not to exclude giruses from the evolutionary picture.
    Nat. Rev. Microbiol., 7, 615 (2009). [PubMed |pdf]

  13. 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 |pdf]

  14. 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 | pdf]

  15. 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 | pdf]

  16. Ogata H., Claverie J.-M.
    How to infect a Mimivirus.
    Science, 321, 1305-1306 (2008). [PubMed | pdf]

  17. Monier A., Claverie J.-M., Ogata H.
    Taxonomic distribution of large DNA viruses in the sea.
    Genome Biol., 9, R106 (2008) [PubMed | Open access | pdf]

  18. 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 | Open access | pdf]

  19. 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 | pdf]

  20. Monier A., Claverie J.-M., Ogata H.
    Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses.
    BMC Genomics, 8, 456 (2007). [PubMed | Open access | pdf]

  21. 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 | pdf]

  22. Ogata H., Claverie J.-M.
    Unique genes in giant viruses: regular substitution pattern and anomalously short size.
    Genome Res., 17, 1353-1361 (2007). [PubMed | Open access| pdf]

  23. 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 | Open access]

  24. 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 | pdf]

  25. 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 | pdf]

  26. 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 | Open access]

  27. 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 | pdf]

  28. 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 |pdf]

  29. 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 | pdf | Open access]

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

  31. 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]

  32. 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]

  33. 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 |pdf]

  34. 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 | pdf | Open access]

  35. 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 | pdf]

  36. 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) [pdf | Free access]

  37. 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 | pdf]

  38. Ogata H., Suhre, K., Claverie J.-M.
    Discovery of protein-coding palindromic repeats in Wolbachia.
    Trends Microbiol., 13, 253-255 (2005). [PubMed | pdf]

  39. Ogata H., Raoult, D., Claverie J.-M.
    A new example of viral intein in Mimivirus.
    Virol. J., 2, 8 (2005). [PubMed | pdf | Open access]

  40. 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 | pdf | Open access]

  41. Renesto P., Ogata H., Audic S., Claverie J.-M., Raoult D.
    Some lessons from Rickettsia genomics. FEMS Microbiol. Rev., 29, 99-117 (2005). [PubMed |pdf]

  42. 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 | pdf]

  43. 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 | pdf]

  44. 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 | pdf | supplement]

  45. 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 |pdf | supplement]

  46. 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 | pdf]

  47. 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 | pdf]

  48. 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 | pdf | supplement]

  49. Claverie J.-M., Ogata H.
    The insertion of palindromic repeats in the evolution of proteins.
    Trends Biochemical Sci., 28, 75-80 (2003). [PubMed | pdf]

  50. 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 | pdf]

  51. 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]

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

  53. 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 | pdf | supplement]

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

  55. 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 | pdf | supplement]

  56. 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 | pdf]

  57. 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 | pdf]

  58. 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 | pdf]

  59. Kawashima S., Ogata H., Kanehisa M.
    AAindex: amino acid index database.
    Nucleic Acids Res., 27, 368-369 (1999). [PubMed | pdf]

  60. 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 | pdf]

  61. Ogata H., Goto S., Fujibuchi W., Kanehisa M.
    Computation with the KEGG pathway database.
    BioSystems, 47, 119-128 (1998). [PubMed | abstract | html]

  62. 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 | abstract | pdf]

  63. 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, 3, 683-694 (1997). [PubMed | abstract | pdf]

  64. 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). [abstract | pdf | ps]

  65. 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 | abstract | pdf | html | data]

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

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

  68. 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 | abstract | pdf | ps]

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


Invited talks

  1. 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)

  2. 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)

  3. 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)

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

  5. 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)

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

  7. 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)

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

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

  10. 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)

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

  12. 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)

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

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

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

  16. 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)

  17. 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).

  18. Ogata H.
    Mechanisms of genome evolution in Rickettsia.
    International Summer School - From Genome to Life, (2002). [abstract]

  19. Ogata H.
    Unexpected selfish DNA in protein coding regions of Rickettsia.
    4th Annual Conference on Computational Genomics (TIGR), (2000).

  20. 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). [abstract]

  21. Ogata H., Kanehisa M.
    A graph theoretical approach for comparative analysis of genomic structures and biochemical pathways.
    Glaxo Wellcome Symposium on Bioinformatics '98, (1998). [abstract]

  22. Ogata H.
    The new age of bioinformatics.
    A tutuorial at Communications Research Laboratory, Ministry of Posts & Telecommunications, Kobe(1997). [in Japanese]


Book chapters

  1. 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). [link]

  2. 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 | pdf]

  3. 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).

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

  5. 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]


Conferences, workshops, seminars

  1. Ogata H.
    Giant viruses in marine environments.
    Tara Japan Tour (Feb 11-19; 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)

  2. 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)

  3. 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)

  4. 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.)

  5. 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.)

  6. 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.)

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

  8. 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 Jamboee (June 17-18, 2009, Woods Hole Oceanographic Institute, Oral presentation June 18 by von Dassow P.)

  9. 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.)

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

  11. 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 Jamboee (October 15-17, 2008, DOE-JGI Walnut Creek California, Oral presentation October 15 by von Dassow P.)

  12. 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)

  13. 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.)

  14. 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.)

  15. 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.)

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

  17. 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)

  18. 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)

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

  20. 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)

  21. 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)

  22. 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)

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

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

  25. 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)

  26. 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)

  27. 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.)

  28. 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)

  29. 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)

  30. 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)

  31. 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). [abstract]

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

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

  34. 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). [abstract]

  35. Ogata H., Fujibuchi W., Kanehisa M.
    Detection of co-regulated genes by comparative analysis of microbial genomes.
    Genome Informatics Workshop 1998, 304-305 (1998). [pdf | ps]

  36. 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). [pdf]

  37. 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). [pdf]

  38. 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). [pdf]

  39. 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). [abstract | pdf]

  40. 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). [abstract]

  41. 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). [in Japanese]

  42. 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). [abstract]

  43. 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). [abstract]

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

  45. 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). [abstract | pdf | ps]

  46. 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). [in Japanese]

  47. 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). [in Japanese]

  48. 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). [abstract]

  49. 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). [abstract]

  50. 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). [in Japanese]

  51. Ogata H., Fujibuchi W., Kanehisa M.
    Statistical features identified from comparison of homologous introns.
    Genome Informatics Workshop 1995, 96-97, (1995). [abstract | pdf | ps]

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

  53. Tomii K., Ogata H., Kanehisa M.
    Cluster analysis of amino acid indices.
    Annual Meeting of the Biophysical Society of Japan, (1994). [in Japanese]

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

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


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