List of Publications

Preprints

• • Zhang R., Mayer L., Hikida H., Shichino Y., Mito M., Willemsen A., Iwasaki S., Ogata H. Giant virus creates subcellular environment to overcome codon-tRNA mismatch. bioRxiv, doi: https://doi.org/10.1101/2024.10.07.616867 (2024). — preprint
  • Endo H., Yamagishi Y., Nguyen T.T., Ogata H.. Extracellular rRNA profiling reveals the sinking and cell lysis dynamics of marine microeukaryotes. bioRxiv, doi: https://doi.org/10.1101/2024.05.31.596594 (2024). — preprint
  • Fang Y., Meng L., Xia J., Gotoh Y., Hayashi T., Nagasaki K., Endo H., Okazaki Y., Ogata H. Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity. bioRxiv, doi: https://doi.org/10.1101/2024.07.08.602415 (2024). — preprint
  • Chen J., Ogata H., Hikida H. Sputnik virophage disrupts the transcriptional regulation of its host giant virus. bioRxiv, doi: https://doi.org/10.1101/2024.08.09.607287 (2024). — preprint
  • Okazaki Y, Nishikawa Y, Wagatsuma R, Takeyama H, Nakano S. Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus–host pairing of freshwater bacteria. bioRxiv, doi:10.1101/2024.07.24.604879 (2024). — preprint

2024

• Yang Q., Yang Y., Xia J., Fukuda H., Okazaki Y., Nagata T., Ogata H., Endo H.Taxon-specific contributions of microeukaryotes to biological carbon pump in the Oyashio region. ISME Commun., ycae136 (2024) [Link]
• Zhang L., Meng L., Fang Y., Ogata H., Okazaki Y. Spatiotemporal dynamics revealed the dark water community of giant virus from a deep freshwater lake. ISME J., wrae182 (2024). [PubMed]
• Wu J., Meng L., Gaïa M., Okazaki Y., Hikida H., Ogata H. Gene transfer among viruses substantially contributes to gene gain of giant viruses. Mol. Biol. Evol. 41, msae161 (2024). [PubMed] [Link]
• Kijima S., Hikida H., Delmont T.O., Gaïa M., Ogata H. Complex genomes of early nucleocytoviruses revealed by ancient origins of viral aminoacyl-tRNA synthetases. Mol. Biol. Evol. 41, msae149 (2024). [PubMed] [Link]
• Zhao H., Meng L., Hikida H., Ogata H. Eukaryotic genomic data uncover an extensive host range of mirusviruses. Curr. Biol. 34, 2633-2643.e3 (2024). [PubMed] [Link]
• Ban H., Endo H., The EukBank Team, Kuwata A., Ogata H. Global distribution and diversity of marine Parmales. Microbes Environ., 39, ME23093 (2024). [Link]
• Nishimura Y., Yamada K., Okazaki Y., Ogata H. DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics. Microbes Environ., 39, ME23061 (2024). [Link]

2023

• Zhao H., Zhang R., Wu J., Meng L., Okazaki Y., Hikida H., Ogata H. A 1.5 Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis. Virus Evol., 9, vead064 (2023). [PubMed] [Link]
• Meng L., Delmont T.O., Gaïa M., Pelletier E., Fernandez-Guerra A., Chaffron S., Neches R.Y., Wu J., Kaneko H., Endo H., Ogata H. Genomic adaptation of giant viruses in polar oceans. Nat. Commun., 14, 6233 (2023). [PubMed] [Link]
• Kaneko H., Endo H., Henry H., Berney C., Mahé F., Poulain J., Labadie K., Beluche O., El Hourany R., Tara Oceans Coordinators, Chaffron S., Wincker P., Nakamura R., Karp-Boss L., Boss E., Bowler C., de Vargas C., Tomii K., Ogata H. Predicting global distributions of eukaryotic plankton communities from satellite data. ISME Commun., 3, 101 (2023). [PubMed] [Link]
• Hikida H., Okazaki Y., Zhang R., Nguyen T.T., Ogata H. A rapid genome-wide analysis of isolated giant viruses only using MinION sequencing. Environ. Microbiol., 25, 2621-2635 (2023). [PubMed]
• Ban H., Sato S., Yoshikawa S., Yamada K., Nakamura Y., Ichinomiya M., Sato N., Blanc-Mathieu R., Endo H., Kuwata A., Ogata H. Genome analysis of Parmales, a sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun. Biol., 6, 697 (2023). [PubMed] [Link]
• Rigonato J., Budinich M., Murillo A.A., Brandao M.C., Pierella Karlusich J.J., Soviadan Y.D., Gregory A.C., Endo H., Kokoszka F., Vik D., Henry H., Fremont P., Labadie K., Zayed A.A., Dimier C., Picheral M., Searson S., Poulain J., Kandels S., Pesant S., Karsenti E., The Tara Oceans coordinators, Bork P., Bowler C., de Vargas C., Eveillard D., Gehlen M., Iudicone D., Lombard F., Ogata H., Stemmann L., Sullivan M.B., Sunagawa S., Wincker P., Chaffron S., Jaillon O. Ocean-wide comparisons of mesopelagic planktonic community structures. ISME Commun., 3, 83 (2023). [PubMed] [Link]
• Zhang R., Takemura M., Murata K., Ogata H. Create a new family (“Mamonoviridae”), a genus (“Medusavirus”), and two species (“Medusavirus medusae” and “Medusavirus sthenus”) in the phylum Nucleocytoviricota. ICTV Taxonomic Proposal (2023). [ICTV Taxon Details]
• Fujita H., Ushio M., Suzuki K., Abe SM., Yamamichi M., Okazaki Y., Canarini A., Hayashi I., Fukushima K., Fukuda S., Kiers T., Toju H. Facilitative interaction networks in experimental microbial community dynamics. Frontiers in Microbiology, 14, 1153952 [PubMed]
• Tanabe Y., Yamaguchi H., Yoshida M., Kai A., Okazaki Y. Characterization of a bloom-associated alphaproteobacterial lineage, ‘Candidatus Phycosocius’: Insights into freshwater algal-bacterial interactions. ISME Commn., 3, 20 (2023). [PubMed]
• Gaïa M., Meng L., Pelletier E., Forterre P., Vanni C., Fernandez-Guerra A., Jaillon O., Wincker P., Ogata H., Krupovic M., Delmont, T.O. Mirusviruses link herpesviruses to giant viruses. Nature, 616, 783-789 (2023). [PubMed]
• Okazaki Y., Nguyen T.T., Nishihara A., Endo H., Ogata H., Nakano S., Tamaki H. A fast and easy method to co-extract DNA and RNA from an environmental microbial sample. Microbes Environ., 38, ME22102 (2023). [PubMed] [OA]
• Zhang R., Takemura M., Murata K., Ogata H. “Mamonoviridae”, a proposed new family of the phylum Nucleocytoviricota. Arch. Virol., 168, 80 (2023). [PubMed]
• Tominaga K., Ogawa-Haruki N.,  Nishimura Y., Watai H., Yamamoto K., Ogata H., Yoshida T. Prevalence of viral frequency-dependent infection in coastal marine prokaryotes revealed using monthly time series virome analysis. mSystems, 8, e0093122 (2023). [PubMed]

• Endo H, Umezawa Y, Takeda S, Suzuki K. Haptophyte communities along the Kuroshio Current reveal their geographical sources and ecological traits. Mol. Ecol., 31, 110-123 (2023). [PubMed]

2022

• Liu C., Song J., Ogata H., Akutsu T. MSNet-4mC: Learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. Bioinformatics, 38, 5160-5167 (2022). [PubMed]
• Okazaki Y., Nakano S., Toyoda A., Tamaki H. Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes. mSystems, 7, e00433-22 (2022). [PubMed]
• Richter D.J., Watteaux R., Vannier T., Leconte J., Frémont P., Reygondeau G., Maillet N., Henry N., Benoit G., Da Silva O., Delmont T.O., Fernàndez-Guerra A., Suweis S., Narci R., Berney C., Eveillard D., Gavory F., Guidi L., Labadie K., Mahieu E., Poulain J., Romac S., Roux S., Dimier C., Kandels S., Picheral M., Searson S., Tara Oceans Coordinators, Pesant S., Aury J.-M., Brum J.R., Lemaitre C., Pelletier E., Bork P., Sunagawa S., Lombard F., Karp-Boss L., Bowler C., Sullivan M.B., Karsenti E., Mariadassou M., Probert I., Peterlongo P., Wincker P., de Vargas C., Ribera d’Alcalà M., Iudicone D., Jaillon O. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife, 11, e78129 (2022). [PubMed]
• Chiriac M.C., Bulzu P.A., Andrei A.S., Okazaki Y., Nakano S., Haber M., Kavagutti V.S., Layoun P., Ghai R., Salcher M.M. Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR. Microbiome, 10, 84 (2022). [PubMed]
• Watari M., Kato M., Blanc-Mathieu R., Tsuge T., Ogata H., Aoyama T. Functional Differentiation among the Arabidopsis Phosphatidylinositol 4-Phosphate 5-Kinase Genes PIP5K1, PIP5K2 and PIP5K3. Plant Cell Physiol., 63, 635-648 (2022). [PubMed]
• Vernette C., Lecubin J., Sánchez P., Tara Oceans Coordinators, Sunagawa S., Delmont T.O., Acinas S.G., Pelletier E., Hingamp P., Lescot M. The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucleic Acids Res., 50, W516-W526 (2022). [PubMed]
• Delmont T.O., Gaïa M., Hinsinger D.D., Fremont P., Vanni C., Fernandez-Guerra A., Eren A.M., Kourlaiev A., d’Agata L., Clayssen Q., Villar E., Labadie K., Cruaud C.,  Poulain J., Da Silva C., Wessner M., Noel B., Aury J.-M., Tara Oceans Coordinators, de Vargas C., Bowler C., Karsenti E., Pelletier E., Wincker P., Jaillon O. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genomics, 2, 100123 (2022). [PubMed] [OA] [preprint]
• Xia J., Kameyama S., Prodinger F., Yoshida T., Cho K.-H., Jung J., Kang S.-H., Yang E.-J., Ogata H., Endo H. Tight association between microbial eukaryote and giant virus communities in the Arctic Ocean. Limnol. Oceanogr., 67, 1343-1356 (2022). [Journal]
• Dominguez-Huerta G., Zayed A.A., Wainaina J.M., Guo J., Tian F., Pratama A.A., Bolduc B., Mohssen M., Zablocki O., Pelletier E., Delage E., Alberti A., Aury J.-M., Carradec Q., da Silva C., Labadie K., Poulain J., Tara Oceans Coordinators, Bowler C., Eveillard D., Guidi L., Karsenti E., Kuhn J.H., Ogata H., Wincker P., Culley A., Chaffron S., Sullivan M.B. Diversity and ecological footprint of Global Ocean RNA viruses. Science, 376, 1202-1208 (2022). [PubMed]
• Zayed A.A., Wainaina J.M., Dominguez-Huerta G., Pelletier E., Guo J., Mohssen M., Tian F., Pratama A.A., Bolduc B., Zablocki O., Cronin D., Solden L., Delage E., Alberti A., Aury J.-M., Carradec Q., da Silva C., Labadie K., Poulain J., Ruscheweyh H.-J., Salazar G., Shatoff E, Tara Oceans Coordinators, Bundschuh R., Fredrick K., Kubatko L.S., Chaffron S., Culley A.I., Sunagawa S., Kuhn J.H., Wincker P., Sullivan M.B. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. Science, 376, 156-162 (2022). [PubMed]
• Da Cunha V., Gaïa M., Ogata H., Jaillon O., Delmont T.O., Forterre P. Giant viruses encode actin-related proteins. Mol. Biol. Evol., 39, msac022 (2022). [PubMed]
• Sakurai T., De Velasco M.A., Sakai K., Nagai T., Nishiyama H., Hashimoto K., Uemura H., Kawakami H., Nakagawa K., Ogata H., Nishio K., Kudo M. Integrative analysis of gut microbiome and host transcriptomes reveals associations between treatment outcomes and immunotherapy-induced colitis. Mol. Oncol., 16, 1493-1507 (2022). [PubMed]
• Prodinger F., Endo H., Takano Y., Li Y., Tominaga K., Isozaki T., Blanc-Mathieu R., Gotoh Y., Hayashi T., Taniguchi E., Nagasaki K., Yoshida T., Ogata H. Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Imitevirales, and prokaryotes in a coastal ecosystem. FEMS Microbiol. Ecol., 97, fiab167 (2022). [PubMed] [Link]

2021

• Royo-Llonch M., Sánchez P., Ruiz-González C., Salazar G., Pedrós-Alió C., Sebastián M., Labadie K., Paoli L., Ibarbalz F.M., Zinger L., Churcheward B., Tara Oceans Coordinators, Chaffron S., Eveillard D., Karsenti E., Sunagawa S., Wincker P., Karp-Boss L., Bowler C., Acinas S.G. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. Nat. Microbiol., 6, 1561-1574 (2021). [PubMed]
• Sandaa R.-A., Saltvedt M.R., Dahle H., Wang H., Våge S., Blanc-Mathieu R., Steen I.H., Grimsley N., Edvardsen B., Ogata H., Lawrence J. Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence. Biol. Rev. Camb. Philos. Soc.,  97, 179-194 (2021). [PubMed] [Free-access]
• Shiozaki T., Hashihama F., Endo H., Ijichi M., Takeda M., Makabe A., Fujiwara A., Noshino S., Harada N. Assimilation and oxidation of urea-derived nitrogen in the summer Arctic Ocean. Limnol. Oceanogr., 66, 4159-4170 (2021). [Journal]
• Zhang R., Endo H., Takemura M., Ogata H. RNA Sequencing of medusavirus suggests remodeling of the host nuclear environment at an early infection stage. Microbiol. Spectr., 9, e0006421 (2021). [PubMed]
• Cheung S, Zehr JP, Xia X, Tsurumoto C, Endo H., Nakaoka S., Mark W., Suzuki K., Liu H. Gamma4: a genetically versatile Gammaproteobacterial nifH phylotype that is widely distributed in the North Pacific Ocean. Environ. Microbiol., 23, 4246-4259 (2021). [PubMed]
• Chaffron S., Delage E., Budinich M., Vintache D., Henry N., Nef C., Ardyna M., Zayed A.A., Junger P.C., Galand P.E., Lovejoy C., Murray A., Sarmento H., Tara Oceans coordinators, Acinas S., Babin M., Iudicone D., Jaillon O., Karsenti E., Wincker P., Karp-Boss L., Sullivan M.B., Bowler C., de Vargas C., Eveillard D. Environmental vulnerability of the global ocean plankton community interactome. Sci. Adv., 7, eabg1921 (2021). [PubMed]
• C. Brandão M.C., Benedetti F., Martini S., Soviadan Y.D., Irisson J.-O., Romagnan J.-B., Elineau A., Desnos C., Jalabert L., Freire A.S., Picheral M., Guidi L., Gorsky G., Bowler C., Karp-Boss L., Henry N., de Vargas C., Sullivan M.B., Tara Oceans Consortium Coordinators, Stemmann L., Lombard F. Macroscale patterns of oceanic zooplankton composition and size structure. Sci. Rep. 11, 15714 (2021). [PubMed] [Link]
• Acinas S.G., Sánchez P., Salazar G., Cornejo-Castillo F.M., Sebastián M., Logares R., Sunagawa S., Hingamp P., Ogata H., Lima-Mendez G., Roux S., González J.M., Arrieta J.M., Alam I.S., Kamau A., Bowler C., Raes J., Pesant S., Bork P., Agustí S., Gojobori T., Bajic V., Vaqué D., Sullivan M.B., Pedrós-Alió C., Massana R., Duarte C.M., Gasol J.M. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun. Biol., 4, 604 (2021). [PubMed]
• Kijima S., Delmont T.O., Miyazaki U., Gaïa M., Endo H., Ogata H. Discovery of viral myosin genes with complex evolutionary history within plankton. Front. Microbiol. 12, 683294 (2021). [PubMed] [Open Access]
• Yoshikawa G., Miyazaki K., Ogata H., Miyazaki M. The evolution of Rag gene enhancers and transcription factor E and Id proteins in the adaptive immune system. Int. J. Mol. Sci., 22, 5888 (2021). [PubMed]
• Meng L., Endo H., Blanc-Mathieu R., Hernández-Velázquez R., Kaneko H., Ogata H. Quantitative assessment of NCLDV–host interactions predicted by co-occurrence analyses. mSphere, 6, e01298-20 (2021). [PubMed]
• Ogawa S., Shimidzu H., Fukuda K., Tsunekawa N., Hirano T., Sato F., Yura K., Hasunuma T., Ochi K., Yamamoto M., Sakamoto W., Hashimoto K., Ogata H., Kanao T., Nemoto M., Inagaki K., Tamura T. Multiple mutations in RNA polymerase beta-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory. Biosci. Biotechnol. Biochem., 85, 1275-1282 (2021). [PubMed]
• Blanc-Mathieu R., Dahle H., Hofgaard A., Brandt D., Ban H., Kalinowski J., Ogata H., Sandaa R.-A. A persistent giant algal virus, with a unique morphology, encodes an unprecedented number of genes involved in energy metabolism. J. Virol., 95, e02446-20 (2021). [PubMed]
• Kawasaki T., Endo H., Ogata H., Chatchawankanphanich O., Yamada T. The complete genomic sequence of the novel myovirus RP13 infecting Ralstonia solanacearum, the causative agent of bacterial wilt. Arch. Virol., 166, 651-654 (2021). [PubMed] [Free Article View]
• Yoshida K., Zhang R., Garcia K., Endo H., Gotoh Y., Hayashi T., Takemura M., Ogata H. Draft genome sequence of medusavirus stheno, a new member of “Medusaviridae” isolated from the Tatakai River of Uji, Japan. Microbiol. Resour. Announc., 10, e01323-20 (2021). [PubMed]

2020

• Kaneko H., Blanc-Mathieu R., Endo H., Chaffron S., Delmont T.O., Gaïa M., Henry N., Hernández-Velázquez R., Nguyen C.H., Mamitsuka H., Forterre P., Jaillon O., de Vargas C., Sullivan M.B., Suttle C.A., Guidi L., Ogata H. Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. iScience, 24, 102002 (2020). [PubMed] [Free Article View]
• Sakurai T., Nishiyama H., Sakai K., De Velasco M.A., Nagai T., Komeda Y., Kashida H., Okada A., Kawai I., Nishio K., Ogata H., Kudo M. Mucosal microbiota and gene expression are associated with long-term remission after discontinuation of adalimumab in ulcerative colitis. Sci. Rep., 10, 19186 (2020). [PubMed]
• Nishiyama H., Endo H., Blanc-Mathieu R., Ogata H. Ecological structuring of temperate bacteriophages in the inflammatory bowel disease-affected gut. Microorganisms, 8, E1663 (2020). [PubMed]
• Endo H., Blanc-Mathieu R., Li Y., Salazar G, Henry N., Labadie K., de Vargas C., Sullivan M.B., Bowler C., Wincker P., Karp-Boss L., Sunagawa S., Ogata H. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nat. Ecol. Evol., 4, 1639-1649 (2020). [Preprint] [PubMed] [Free Article View]
• Cheung S., Nitanai R., Tsurumoto C., Endo H., Nakaoka S., Cheah W., Lorda J.F., Xia Z., Liu H., Suzuki K. Physical forcing controls the basin-scale occurrence of nitrogen-fixing organisms in the North Pacific Ocean. Global Biogeochem. Cy., 34, e2019GB006452 (2020). [Journal]
• Miyazaki K., Watanabe H., Yoshikawa G., Chen K., Hidaka R., Aitani Y., Osawa K., Takeda R., Ochi Y., Tani-ichi S., Uehata T., Takeuchi O., Ikuta K., Ogawa S., Kondoh G., Lin Y.C., Ogata H., Miyazaki M. The transcription factor E2A activates multiple enhancers that drive Rag expression in developing T and B cells. Sci. Immunol., 5, eabb1455 (2020). [PubMed]
• Sandaa R.-T., Dahle H., Brussaard C.P.D., Ogata H., Blanc-Mathieu R. Algal viruses belonging to a subgroup within the Mimiviridae family. Reference Module in Life Sciences, doi: 10.1016/B978-0-12-809633-8.21318-6 (2020). [Link]
• 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., 18, 428-445 (2020). [PubMed]
• Tominaga K., Morimoto D., Nishimura Y., Ogata H., Yoshida T. In silico prediction of virus-host interactions for marine Bacteroidetes with the use of metagenome-assembled genomes. Front. Microbiol., 11, 738 (2020). [PubMed]
• 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]
• 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]
• 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]
• 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, 36, 2251-2252 (2020). [PubMed]

2019

• Ibarbalz F.M., Henry N., Brandão M.C., Martini S., Busseni G., Byrne H., Coelho L.P., Endo H., Gasol J.M., Gregory A.C, Mahé F., Rigonato J., Royo-Llonch M., Salazar G., Sanz-Sáez 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]
• 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., Sánchez 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]
• 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]
• Castillo Y.M., Mangot J.-F., Benites F., Logares R., Kuronishi M., Ogata H., Jaillon O., Massana R., Sebastián M., Vaqué D. Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics. Mol. Ecol. 28, 4272-4289 (2019). [PubMed]
• 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]
• 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]
• Endo H, Suzuki K. Spatial variations in community structure of haptophytes across the Kuroshio front in the Tokara Strait. In: Kuroshio Current: Physical, Biogeochemical and Ecosystem Dynamics (eds.Nagai T, Saito H, Suzuki K, and Takahashi M), AGU Geophysical Monograph Series, AGU-Wiley, doi.org/10.1002/9781119428428.ch13 (2019).
• Gregory A.C., Zayed A.A., Conceição-Neto N., Temperton B., Bolduc B., Alberti A., Ardyna M., Arkhipova K., Carmichael M., Cruaud C., Dimier C., Domínguez-Huerta G.,　Ferland J., Kandels S., Liu Y., Marec C., Pesant S., Picheral M., Pisarev S., Poulain J., Tremblay J.É., 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]
• 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]
• Yan D, Endo H, Suzuki K. Increased temperature benefits growth and photosynthetic performance of the sea ice diatom Nitzschia cf. neglecta (Bacillariophyceae) isolated from Lake Saroma, Hokkaido, Japan. J. Phycol., 55(3), 700–713 (2019). [PubMed]
• Xia X, Cheung, S, Endo H, Suzuki K, Liu H. Latitudinal and vertical variations of Synechococcus assemblage composition along 170°W transect from the South Pacific to the Arctic Ocean. Microb. Ecol., 77, 333–342 (2019). [PubMed]
• 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]
• 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). [Open Access]
• 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]

2018

• 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]
• 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, 496 (2018). [PubMed]
• 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]
• Ogata H. Habitat alterations by viruses: strategies by Tupanviruses and others. Microbes Environ, 33, 117-119 (2018). [PubMed]
• 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]
• 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]
• 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]
• 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]
• 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 (2018). [PubMed]
• 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 (2018). [PubMed]
• Nishiyama, H., Nagai, T., Kudo, M., Okazaki, Y., Azuma, Y., Watanabe, T., Susumu, G., Ogata, H., and Sakurai, T. Supplementation of pancreatic digestive enzymes alters the composition of intestinal microbiota in mice. Biochem. Biophys. Res. Commun., 495, 273-279 (2018). [PubMed]

2017

• 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 (2017). [PubMed]
• 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 (2017). [Open Access] [PubMed]
• Blanc-Mathieu, R., Krasovec, M., Hebrard, M., Yau, S., Desgranges, E., Martin, J., Schackwitz, W., Kuo, A., Salin, G., Donnadieu, C., Desdevises, Y., Sanchez-Ferandin, S., Moreau, H., Rivals, E., Grigoriev, I.V., Grimsley, N., Eyre-Walker, A., Piganeau, G. Population genomics of picophytoplankton unveils novel chromosome hypervariability. Sci. Adv., 3, e1700239 (2017). [PubMed]
• Blanc-Mathieu, R., Perfus-Barbeoch, L., Aury, J.M., Da Rocha, M., Gouzy, J., Sallet, E., Martin-Jimenez, C., Bailly-Bechet, M., Castagnone-Sereno, P., Flot, J.F., Kozlowski, D.K., Cazareth, J., Couloux, A., Da Silva, C., Guy, J., Kim-Jo, Y.J., Rancurel, C., Schiex, T., Abad, P., Wincker, P., Danchin, E.G.J. Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLoS Genet., 13, e1006777 (2017). [PubMed]
• Nishimura, Y., Yoshida, T., Kuronishi, M., Uehara, H., Ogata, H., Goto, S. ViPTree: the viral proteomic tree server. Bioinformatics, 33, 2379-2380 (2017). [PubMed]
• Shimizu, Y., Ogata, H., Goto, S. Discriminating the reaction types of plant type III polyketide synthases. Bioinformatics, 33, 1937-1943 (2017). [PubMed]
• 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, e00459-16 (2017). [PubMed]
• Shimizu, Y., Ogata, H., Goto, S. Type III polyketide synthases: functional classification and phylogenomics. ChemBioChem, 18, 50-65 (2017). [PubMed]
• Okuda, S., Watanabe, Y., Moriya, Y., Kawano, S., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S., Ishihama, Y. jPOSTrepo: an international standard data repository for proteomes. Nucleic Acids Res., 45, D1107-D1111 (2017). [PubMed]

2016

• 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). [PubMed]
• Takami, H., Taniguchi, T., Arai, W., Takemoto, K., Moriya, Y., Goto, S. An automated system for evaluation of the potential functionome: MAPLE version 2.1.0. DNA Res., 23, 467-475 (2016). [PubMed]
• Kotera, M., Goto, S. Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis. Biophysics and Physicobiology, 13, 195-205 (2016). [J-STAGE]
• 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, fiw129, (2016). [PubMed]
• 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. Virology Reports, 6, 61-73 (2016). [open access]
• 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. Two Asian jumbo phages, phiRSL2 and phiRSF1, infect Ralstonia solanacearum and show common features of phiKZ-related phages. Virology, 494, 56-66 (2016). [PubMed]
• Blanc-Mathieu, R., Ogata, H. DNA repair genes in the Megavirales pangenome. Curr. Opin. Microbiol., 31, 94-100 (2016). [PubMed]
• Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., Ogata, H. Linking virus genomes with host taxonomy. Viruses, 8, 66 (2016). [PubMed] [open access]
• Moriya, Y., Yamada, T., Okuda, S., Nakagawa, Z., Kotera, M., Tokimatsu, T., Kanehisa, M., Goto, S. Identification of enzyme genes using chemical structure alignments of substrate-product pairs. J. Chem. Inf. Model., 56, 510-516 (2016). [PubMed]
• Guidi, L., Chaffron, S., Bittner, L., Eveillard, D., Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J., Coelho, L.P., Espinoza, J.C., Malviya, S., Sunagawa, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Poulain, J., Searson, S., Tara Oceans Consortium Coordinators, Stemmann, L., Not, F., Hingamp, P., Speich, S., Follows, M., Karp-Boss, L., Boss, E., Ogata, H., Pesant, S., Weissenbach, J., Wincker, P., Acinas, S.G., Bork, P., de Vargas, C., Iudicone, D., Sullivan, M.B., Raes, J., Karsenti, E., Bowler, C., Gorsky, G. Plankton networks driving carbon export in the oligotrophic ocean. Nature, 532, 465-470 (2016). [PubMed]
• Lescot, M., Hingamp, P., Kojima, K.K., Villar, E., Romac, S., Veluchamy, A., Boccara, M., Jaillon, O., Iudicone, D., Bowler, C., Wincker, P., Claverie, J.-M., Ogata, H Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ISME J., 10, 1134-1146 (2016). [PubMed]
• 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, 10, 1134-1146 (2016). [PubMed]

2015

• 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]
• 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 (2015). [PubMed]
• 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, 979-89 (2015). [PubMed]
• 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), pp. 147-160 (2015). [Publisher]
• 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]
• 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 (2015). [PubMed] [see Cover]
• Suzuki, M., Nakabayashi, R., Ogata, Y., Sakurai, N., Tokimatsu, T., Goto, S., Suzuki, M., Jasinski, M., Martinoia, E., Otagaki, S., Matsumoto, S., Saito, K., Shiratake, K. Multi omics in grape berry skin revealed specific induction of stilbene synthetic pathway by UV-C irradiation. Plant Physiol, 168, 47-59 (2015). [PubMed]
• 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]
• 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]
• 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]
• 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]
• 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]
• 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]
• 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]
• 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, 1365-1377 (2015). [PubMed]

2014

• 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]
• 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]
• Kotera, M., Nishimura, Y., Nakagawa, Z., Muto, A., Moriya, Y., Okamoto, S., Kawashima, S., Katayama, T., Tokimatsu, T., Kanehisa, M., Goto, S. PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list. J. Bioinform. Comput. Biol. 12, 1442001 (2014).
• 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]
• Jin, Z., Kotera, M., Goto, S. Virus proteins similar to human proteins as possible disturbance on human pathways. Syst. Synth. Biol. 8, 283-295 (2014).
• Kotera, M., Tabei, Y., Yamanishi, Y., Muto, A., Moriya, Y., Tokimatsu, T., Goto, S. Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. Bioinformatics 30, i165-i174 (2014). [PubMed]
• Yamanishi, Y., Kotera, M., Moriya, Y., Sawada, R., Kanehisa, M., Goto, S. DINIES: drug-target interaction network inference engine based on supervised analysis. Nucleic Acids Res. 42, W39-W45 (2014). [PubMed]
• Mizutani, S., Noro, Y., Kotera, M., Goto, S. Pharmacoepidemiological characterization of drug-induced adverse reaction clusters towards understanding of their mechanisms. Comput. Biol. Chem. 50, 50-59 (2014). [PubMed]
• Kotera, M., Goto, S., Kanehisa, M. Predictive genomic and metabolic analysis for the standardization of enzyme data. Perspectives in Science 1, 24-32 (2014). [ScienceDirect]
• Ingale, A. G., Goto, S. Prediction of CTL epitope, in silico modeling and functional analysis of cytolethal distending toxin (CDT) protein of Campylobacter jejuni. BMC Res. Notes 7, 92 (2014). [PubMed]
• Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., Tanabe, M. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199-D205 (2014). [PubMed]

2013

• Kotera, M., Tabei, Y., Yamanishi, Y., Moriya, Y., Tokimatsu, T., Kanehisa, M., and Goto, S.; KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst. Biol. 7(S6), S2 (2013).
• Iwata, H., Mizutani, S., Tabei, Y., Kotera, M., Goto, S., and Yamanishi, Y.; Inferring protein domains associated with drug side effects based on drug-target interaction network. BMC Syst. Biol. 7(S6), S18 (2013).
• Kotera, M., Tabei, Y., Yamanishi, Y., Tokimatsu, T., and Goto, S.; Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. Bioinformatics 29, i135-i144 (2013). [PubMed] [PDF]
• Kirwan, G. M., Hancock, T., Hassell, K., Niere, J. O., Nugegoda, D., Goto, S., and Adams, M. J; Nuclear magnetic resonance metabonomic profiling using tO2PLS. Anal. Chim. Acta 781, 33-40 (2013). [PubMed]
• Muto, A., Kotera, M., Tokimatsu, T., Nakagawa, Z., Goto, S., and Kanehisa, M.; Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J. Chem. Inf. Model. 53, 613-622 (2013). [PubMed]
• Nakaya, A., Katayama, T., Itoh, M., Hiranuka, K., Kawashima, S., Moriya, Y., Okuda, S., Tanaka, M., Tokimatsu, T., Yamanishi, Y., Yoshizawa, A. C., Kanehisa, M., and Goto, S.; KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res. 41, D353-D357 (2013). [PubMed] [PDF]
• Frost, K., Johansson, E., Shanks, R., Goto, S., Kirwan, G. M.; Thermoplastic starch films: DOE and O2PLS methodology for optimization and increased understanding of polymer processing. Polymer Testing 32, 343-352 (2013). [DOI]

2012

• Yamanishi, Y., Pauwels, E., and Kotera, M.; Drug side-effect prediction based on the integration of chemical and biological spaces. J. Chem. Inf. Model. 52, 3284-3292 (2012). [PubMed]
• Takami, H., Taniguchi, T., Moriya, Y., Kuwahara, T., Kanehisa, M., and Goto, S.; Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics 13, 699 (2012). [PubMed] [BMC]
• Godel, C., Kumar, S., Koutsovoulos, G., Ludin, P., Nilsson, D., Comandatore, F., Wrobel, N., Thompson, M., Schmid, C. D., Goto, S., Bringaud, F., Wolstenholme, A., Bandi, C., Epe, C., Kaminsky, R., Blaxter, M., and Mäser, P.; The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targers. FASEB J. 26, 4650-4661 (2012). [PubMed]
• Kirwan, G. M., Johansson, E., Kleemann, R., Verheij, E. R., Wheelock, A. M., Goto, S., Trygg, J., and Wheelock, C. E.; Building Multivariate Systems Biology Models. Anal. Chem. 84, 7064-7071 (2012). [PubMed]
• Takarabe, M., Kotera, M., Nishimura, Y., Goto, S., and Yamanishi, Y.; Drug target prediction using adversed event report systems: a pharmacogenomic approach. Bioinformatics 28, i611-i618 (2012). [PubMed]
• Mizutani, S., Pauwels, E., Stoven, V., Goto, S., and Yamanishi, Y.; Relating drug-protein interaction network with drug side-effects. Bioinformatics 28, i522-i528 (2012). [PubMed]
• Kotera, M., Moriya, Y., Tokimatsu, T., Kanehisa, M., and Goto, S.; KEGG and GenomeNet, new developments, metagenomic analysis. In “Encyclopedia of Metagenomics” (Nelson, K. E., ed.), Springer (2012). [SpringerReference]
• Diez, D., Goto, S., Fahy, J. V., Erle, D. J., Woodruff, P. G., Wheelock, A. M., and Wheelock, C. E.; Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics. BMC Med. Genomics 5, 27 (2012). [PubMed] [BMC]
• Kotera, M., Yamanishi, Y., Moriya, Y., Kanehisa, M., and Goto, S.; GENIES: gene network inference engine based on supervised analysis. Nucleic Acids Res. 40, W162-W167 (2012). [PubMed] [pdf]
• Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., and Tanabe, M.; KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res. 40, D109-114 (2012). [PubMed] [pdf]
• Kotera, M., Hirakawa, M., Tokimatsu, T., Goto, S., and Kanehisa, M.; The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol. Biol. 802, 19-39 (2012). [PubMed]
• Onuki, R., Yamada, R., Yamaguchi, R., Kanehisa, M., and Shibuya, T.; Population model-based inter-diplotype similarity measure for accurate diplotype clustering. J. Comput. Biol. 19, 55-67 (2012). [PubMed]

2011

• Takarabe, M., Shigemizu, D., Kotera, M., Goto, S., and Kanehisa, M.; Network-based analysis and characterization of adverse drug-drug interactions. J. Chem. Inf. Model. 51, 2977-2985 (2011). [PubMed]
• Kotera, M., Tokimatsu, T., Kanehisa, M., and Goto, S.; MUCHA: multiple chemical alignment algorithm to obtain building block substructures of orphan metabolites. BMC Bioinformatics 12, S1 (2011). [PubMed]
• Yamada, T., Letunic, I., Okuda, S., Kanehisa, M., and Bork, P.; iPath2.0: interactive pathway explorer. Nucleic Acids Res. 39, W412-W415 (2011). [PubMed]
• Kirwan, G. M., Diez, D., Haeggstrom, J. Z., Goto, S., and Wheelock, C. E.; Systems biology approaches for investigating the relationships between lipids and cardiovascular disease. Curr. Cardiovasc. Risk Rep. 5, 52-61 (2011).
• Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; KEGG and GenomeNet resources for predicting protein function from omics data including KEGG PLANT resource. In “Protein Function Prediction for Omics Era” (Kihara, D., ed.), pp. 271-288, Springer (2011).
• Sakurai, N,. Ara, T., Ogata, Y., Sano, R., Ohno, T., Sugiyama, K., Hiruta, A., Yamazaki, K., Yano, K., Aoki, K., Aharoni, A., Hamada, K., Yokoyama, K., Kawamura, S., Otsuka, H., Tokimatsu, T., Kanehisa, M., Suzuki, H., Saito, K., and Shibata, D.; KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res. 39, D677-D684 (2011). [PubMed] [pdf]

2010

• Takigawa, I., Hashimoto, K., Shiga, M., Kanehisa, M., and Mamitsuka, H.; Mining patterns from glycan structures. In “Proceedings of the International Beilstein Symposium on Glyco-Bioinformatics” (Hicks, M.G. and Kettner, C.), pp. 13-24, Beilstein-Institut (2010).
• Erguner, B., Hattori, M., Goto, S., and Kanehisa, M.; Characterizing common substructures of ligands for GPCR protein subfamilies. Genome Informatics 24, 31-41 (2010). [PubMed]
• Kotera, M., Kobayashi, T., Hattori, M., Tokimatsu, T., Goto, S., Mihara, H., and Kanehisa, M.; Comprehensive genomic analysis of sulfur-relay pathway genes. Genome Informatics 24, 104-115 (2010). [PubMed]
• Mizutani, S., Tanaka, M., Wheelock, C., Kanehisa, M., and Goto, S.; Phylogenetic analysis of lipid mediator GPCRs. Genome Informatics 24, 116-126 (2010). [PubMed]
• Nishimura, Y., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; Genome-wide analysis of plant UGT family based on sequence and substrate information. Genome Informatics 24, 127-138 (2010). [PubMed]
• Tamura, T., Yamanishi, Y., Tanabe, M., Goto, S., Kanehisa, M., Horimoto, K., and Akutsu, T.; Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer. Genome Informatics 24, 193-203 (2010). [PubMed]
• Sato, T., Yamanishi, Y., Kanehisa, M., Horimoto, K., and Toh, H.; Improvement of the mirrortree method by extracting evolutionary information. In “Sequence and Genome Analysis: Methods and Applications” (Zhao, Z., ed.), iConcept Press (2010). [pdf]
• Yamanishi, Y., Kotera, M., Kanehisa, M., and Goto, S.; Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics 26, i246-i254 (2010). [PubMed] [pdf]
• Hattori, M., Tanaka, N., Kanehisa, M., and Goto, S.; SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acids Res. 38, W652-W656 (2010). [PubMed] [pdf]
• Moriya, Y., Shigemizu, D., Hattori, M., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 38, W138-W143 (2010). [PubMed] [pdf]
• Imada, M., Kawashima, S., Kanehisa, M., Takeuchi, T., and Asai, T.; Characterization of alpha-phosphoglucomutase isozymes from Toxoplasma gondii. Parasitol. Int. 59, 206-210 (2010). [PubMed]
• Diez, D., Wheelock, A.M., Goto, S., Haeggstrom, J.Z., Paulsson-Berne, G., Hansson, G.K., Hedin, U., Gabrielsen, A., and Wheelock, C.E.; The use of network analyses for elucidating mechanisms in cardiovascular disease. Mol. Biosyst. 6, 289-304 (2010). [PubMed]
• Diez, D., Hayes, N., Joannin, N., Normark, J., Kanehisa, M., Wahlgren, M., Wheelock, C.E., and Goto, S.; varDB: a database of antigenic variant sequences — current status and future prospects. Acta Trop. 14, 144-151 (2010). [PubMed]
• Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010). [PubMed] [pdf]

2009

• Aoki-Kinoshita, K.F. and Kanehisia, M.; Bioinformatics analysis of glycan structures from a genomic perspective. In “Bioinformatics for Glycobiology and Glycomics: an Introduction” (von der Lieth, C.-W., Luetteke, T., and Frank, M., eds.), pp. 125-141 (2009).
• Hayes, C.N., Diez, D., Joannin, N., Kanehisa, M., Wahlgren, M., Wheelock, C. E., and Goto, S.; Tools for investigating mechanisms of antigenic variation: new extensions to varDB. Genome Informatics 23, 46-59 (2009). [PubMed] [pdf]
• Onuki, R., Shibuya, T., and Kanehisa, M.; New kernel methods for phenotype prediction from genotype data. Genome Informatics 22, 132-141 (2009). [PubMed] [pdf]
• Takarabe, M., Shigemizu, D., Kotera, M., Goto, S., and Kanehisa, M.; Characterization and classification of adverse drug interactions. Genome Informatics 22, 167-175 (2009). [PubMed] [pdf]
• Tanaka, M., Moriya, Y., Goto, S., and Kanehisa, M.; Analysis of a lipid biosynthesis protein family and phospholipid structural variations. Genome Informatics 22, 191-201 (2009). [PubMed] [pdf]
• Hashimoto, K. and Kanehisa, M.; KEGG GLYCAN for integrated analysis of pathways, genes, and glycan structures. In “Handbook of Glycomics” (Cummings, R.D. and Pierce, J.M., eds.), pp. 197-210, Academic Press (2009).
• Kanehisa, M., Limviphuvadh, V., and Tanabe, M.; Knowledge based analysis of protein interaction networks in neurodegenerative diseases. In “Neuroproteomics” (Alzate, O., ed.), pp. 147-162, CRC Press (2009). [PubMed]
• Wheelock, C.E., Goto, S., Yetukuri, L., D’Alexandri, F.L., Klukas, C., Schreiber, F., and Oresic, M.; Bioinformatics strategies for the analysis of lipids. Methods Mol. Biol. 580, 339-368 (2009). [PubMed]
• Folkersen, L., Diez, D., Wheelock, C.E., Haeggstrom, J.Z., Goto, S., Eriksson, P., and Gabrielsen, A.; GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome. Bioinformatics 25, 1978-1979 (2009). [PubMed] [pdf]
• Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., and Kanehisa, M.; E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics 25, i79-i86 (2009). [PubMed] [pdf]
• Wheelock, C.E., Wheelock, A.M., Kawashima, S., Diez, D., Kanehisa, M., van Erk, M., Kleemann, R., Haeggstrom, J.Z., and Goto, S.; Systems biology approaches and pathway tools for investigating cardiovascular disease. Mol. Biosyst. 5, 588-602 (2009). [PubMed]
• Kawashima, T., Kawashima, S., Tanaka, C., Murai, M., Yoneda, M., Putnum, N.H., Rokhsar, D.S., Kanehisa, M., Satoh, N., and Wada H.; Domain shuffling and the evolution of vertebrates. Genome Res. 19, 1393-1403 (2009). [PubMed] [pdf]
• Shigemizu, D., Araki, M., Okuda, S., Goto, S., and Kanehisa, M.; Extraction and analysis of chemical modification patterns in drug development. J. Chem. Inf. Model. 49, 1122-1129 (2009). [PubMed]
• Hashimoto, K., Tokimatsu, T., Kawano, S., Yoshizawa, A.C., Okuda, S., Goto, S., and Kanehisa, M.; Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr. Res. 344, 881-887 (2009). [PubMed]
• Aoki-Kinoshita, K.F. and Kanehisa, M.; Using KEGG in the transition from genomics to chemical genomics. In “Bioinformatics for Systems Biology” (Krawetz, S., ed.), pp.429-445, Humana Press (2009).
• Hirakawa, M., Nishihara, H., Kanehisa, M., and Okada, N.; Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes. Gene 441, 100-110 (2009). [PubMed]

2008

• Shimizu, Y., Hattori, M., Goto, S., and Kanehisa, M.; Generalized reaction patterns for prediction of unknown enzymatic reactions. Genome Informatics 20, 149-158 (2008). [PubMed] [pdf]
• Takarabe, M., Okuda, S., Itoh, M., Tokimatsu, T., Goto, S., and Kanehisa, M.; Network analysis of adverse drug interactions. Genome Informatics 20, 252-259 (2008). [PubMed] [pdf]
• Hayes, C.N., Diez, D., Joannin, N., Honda, W., Kanehisa, M., Wahlgren, M., Wheelock, C.E., and Goto, S.; varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics 24, 2564-2565 (2008). [PubMed] [pdf]
• Hashimoto, K. and Kanehisa, M.; KEGG GLYCAN for integrated analysis of pathways, genes, and structures. In “Experimental Glycoscience” (Taniguchi, N., Suzuki, A., Ito, Y., Narimatsu, H., Kawasaki, T., and Hase, S., eds.), pp. 441-444, Springer (2008).
• Hashimoto, K., Takigawa, I., Shiga, M., Kanehisa, M., and Mamitsuka, H.; Mining significant tree patterns in carbohydrate sugar chains. Bioinformatics 24, i167-i173 (2008). [PubMed] [pdf]
• Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., and Kanehisa, M.; Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics 24, i232-i240 (2008). [PubMed] [pdf]
• Aoki-Kinoshita, K.F. and Kanehisa, M.; Systems approach to metabolism. In “Wiley Encyclopedia of Chemical Biology” (Begley, T.P., ed.) wecb589 (2008).
• Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S., and Kanehisa, M.; KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res. 36, W423-W426 (2008). [PubMed] [pdf]
• Kojima, K.K. and Kanehisa, M.; Systematic survey for novel types of prokaryotic retroelements based on gene neighborhood and protein architecture. Mol. Biol. Evol. 25, 1395-1404 (2008). [PubMed] [pdf]
• Hashimoto, K., Aoki-Kinoshita, K.F., Ueda, N., Kanehisa, M., and Mamitsuka, H.; A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology. ACM TKDD, Volume 2, Issue 1, Article No. 6 (2008). [abstract]
• Letunic, I., Yamada, T., Kanehisa, M., and Bork P.; iPath: interactive exploration of biochemical pathways and networks. Trends Biochem. Sci. 33, 101-103 (2008). [PubMed]
• Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.; KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2008). [PubMed] [pdf]
• Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., and Kanehisa, M.; AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202-D205 (2008). [PubMed] [pdf]
• Hashimoto, K., Yoshizawa, A.C., Okuda, S., Kuma, K., Goto, S., and Kanehisa, M.; The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J. Lipid Res. 49, 183-191 (2008). [PubMed] [pdf] [see Cover]

2007

• Huang, J., Honda, W., and Kanehisa, M.; Predicting B cell epitope residues with network topology based amino acid indices. Genome Informatics 19, 40-49 (2007). [PubMed] [pdf]
• Kawashima, S., Kawashima, T., Putnam, N.H., Rokhsar, D.S., Wada, H., and Kanehisa, M.; Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes. Genome Informatics 19, 50-60 (2007). [PubMed] [pdf]
• Huang, J., Kawashima, S., and Kanehisa, M.; New amino acid indices based on residue network topology. Genome Informatics 18, 152-161 (2007). [PubMed] [pdf]
• Suga, A., Yamanishi, Y., Hashimoto, K., Goto, S., and Kanehisa, M.; An improved scoring scheme for predicting glycan structures from gene expressison data. Genome Informatics 18, 237-246 (2007). [PubMed] [pdf]
• Muto, A., Hattori, M., and Kanehisa, M.; Analysis of common substructures of metabolic compounds within the different organism groups. Genome Informatics 18, 299-307 (2007). [PubMed] [pdf]
• Kadowaki, T., Wheelock, C.E., Adachi, T., Kudo, T., Okamoto, S., Tanaka, N., Tonomura, K., Tsujimoto, G., Mamitsuka, H., Goto, S., and Kanehisa, M.; Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis. Environ. Sci. Technol. 41, 7997-8003 (2007). [PubMed]
• Aoki-Kinoshita, K.F. and Kanehisa, M.; Gene annotation and pathway mapping in KEGG. In “Comparative Genomics Volume 2” (Bergman, N.H., ed.), Humana Press, Methods Mol. Biol. 396, 71-92 (2007). [PubMed]
• Masoudi-Nejad, A., Goto, S., Endo, T.R., and Kanehisa, M.; KEGG bioinformatics resource for plant genomics research. In “Plant Bioinformatics” (Edwards, D., ed.), Humana Press, Methods Mol. Biol. 406, 437-458 (2007). [PubMed]
• Fujita, M., Mihara, H., Goto, S., Esaki, N., and Kanehisa, M.; Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach. BMC Bioinformatics 8, 225 (2007). [PubMed] [pdf]
• Schwartz, J.-M., Gaugain, C., Nacher, J.C., de Daruvar, A., and Kanehisa, M.; Observing metabolic functions at the genome scale. Genome Biol. 8, R123 (2007). [PubMed] [pdf]
• Itoh, M., Nacher, J.C., Kuma, K.I., Goto, S., and Kanehisa, M.; Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. Genome Biol. 8, R121 (2007). [PubMed] [pdf]
• Limviphuvadh, V., Tanaka, S., Goto, S., Ueda, K., and Kanehisa, M.; The commonality of protein interaction networks determined in Neurodegenerative disorders (NDDs). Bioinformatics 23, 2129-2138 (2007). [PubMed] [pdf]
• Hu, Z., Ng, D.M., Yamada, T., Chen, C., Kawashima, S., Mellor, J., Linghu, B., Kanehisa, M., Stuart, J.M., and Delisi, C.; VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res. 35, W625-W632 (2007). [PubMed] [pdf]
• Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A., and Kanehisa, M.; KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007). [PubMed] [pdf]
• Oh, M., Yamada, T., Hattori, M., Goto, S., and Kanehisa, M.; Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J. Chem. Inf. Model. 47, 1702-1712 (2007). [PubMed]
• Hu, Z., Mellor, J., Wu, J., Kanehisa, M., Stuart, J.M., and DeLisi, C.; Toward scalable multidimensional maps of the cell. Nat. Biotech. 25, 547-554 (2007). [PubMed]
• Masoudi-Nejad, A., Goto, S., Jauregui, R., Ito, M., Kawashima, S., Moriya, Y., Endo, T.R., and Kanehisa, M.; EGENES: Transcriptome-based plant database of genes with metabolic pathway information and EST indices in KEGG. Plant Physiol. 144, 857-866 (2007). [PubMed] [pdf]
• Minowa, Y., Araki, M., and Kanehisa, M.; Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J. Mol. Biol. 368, 1500-1517 (2007). [PubMed]
• Yamanishi, Y., Mihara, H., Osaki, M., Muramatsu, H., Esaki, N., Sato, T., Hizukuri, Y., Goto, S., and Kanehisa, M.; Prediction of missing enzyme genes in bacterial metabolic network: a reconstruction of lysine degradation pathway of Pseudomonas aeruginosa. FEBS J. 274, 2262-2273 (2007). [PubMed]
• Okamoto, S., Yamanishi, Y., Ehira, S., Kawashima, S., Tonomura, K., and Kanehisa, M.; Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis. Proteomics 7, 900-909 (2007). [PubMed]
• Gutteridge, A., Kanehisa, M., and Goto, S.; Regulation of metabolic networks by small molecule metabolites. BMC Bioinformatics 8, 88 (2007). [PubMed] [pdf]
• Okuda, S., Kawashima, S., Kobayashi, K., Ogasawara, N., Kanehisa, M., and Goto, S.; Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics 8, 48 (2007). [PubMed] [pdf]
• Sugita, C., Ogata, K., Shikata, M., Jikuya, H., Takano, J., Furumichi, M., Kanehisa, M., Omata, T., Suiura, M., and Sugita, M.; Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: Gene content and organization. Photosynth. Res. 93, 55-67 (2007). [PubMed]

2006

• Aoki-Kinoshita, K.F. and Kanehisa, M.; Bioinformatics approaches in glycomics and drug discovery. Curr. Opin. Mol. Ther. 8, 514-520 (2006). [PubMed]
• Aoki-Kinoshita, K.F., Kanehisa, M., Kao, M.-Y., Li, X.-Y., and Wang, W.; A 6-approximation algorithm for computing smallest common AoN-supertree with application to the reconstruction of glycan trees. Lecture Notes in Computer Science 4288, 100-110 (2006). [abstract]
• Huang, J., Gutteridge, A., Honda, W., and Kanehisa, M.; MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics 7, 451 (2006). [PubMed] [pdf]
• Kadowaki, T., Wheelock, C.E., Hattori, M., Goto, S., and Kanehisa, M.; Structure-activity relationships and pathway analysis of biological degradation processes. J. Pesticide Sci. 31, 273-281 (2006). [abstract] [pdf]
• Hashimoto, K., Yoshizawa, A.C., Saito, K., Yamada, T., and Kanehisa, M.; The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes. Genome Informatics 17(1), 173-183 (2006). [PubMed] [pdf]
• Honda, W., Kawashima, S., and Kanehisa, M.; Metabolite antigens and pathway incompatibility. Genome Informatics 17(1), 184-194 (2006). [PubMed] [pdf]
• Tanaka, M., Yamada, T., Itoh, M., Okuda, S., Goto, S., and Kanehisa M.; Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes. Genome Informatics 17(1), 230-239 (2006). [PubMed] [pdf]
• Hashimoto, K., Aoki-Kinoshita, K., Ueda, N., Kanehisa, M., and Mamitsuka, H.; A new efficient probabilistic model for mining labeled ordered trees. ACM SIGKDD (2006). [abstract]
• Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., and Toh, H.; Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. Bioinformatics 22, 2488-2492 (2006). [PubMed] [pdf]
• Yoshizawa, A.C., Kawashima, S., Okuda, S., Fujita, M., Itoh, M., Moriya, Y., Hattori, M., and Kanehisa, M.; Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic. Traffic 7, 1104-1118 (2006). [PubMed] [pdf]
• Aoki-Kinoshita, K., Ueda, N., Mamitsuka, H., and Kanehisa, M.; ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. Bioinformatics 22, e25-e34 (2006). [PubMed] [pdf]
• Nacher, J., Schwartz, J.-M., Kanehisa, M., and Akutsu, T.; Identification of metabolic units induced by environmental signals. Bioinformatics 22, e375-e383 (2006). [PubMed] [pdf]
• Masoudi-Nejad, A., Tonomura, K., Kawashima, S., Moriya, Y., Suzuki, M., Itoh, M., Kanehisa, M., Endo, T., and Goto, S.; EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res. 34, W459-W462 (2006). [PubMed] [pdf]
• Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., and Kanehisa, M.; KEGG as a glycome informatics resource. Glycobiology 16, 63R-70R (2006). [PubMed] [pdf] [see Editorial]
• Schwartz, J.M. and Kanehisa, M.; Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 7, 186 (2006). [PubMed] [pdf]
• Yamada, T., Kanehisa, M., and Goto, S.; Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics 7, 130 (2006). [PubMed] [pdf]
• Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006). [PubMed] [pdf] [see Thomson]
• Okuda, S., Katayama, T., Kawashima, S., Goto, S., and Kanehisa, M.; ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res. 34, D358-D362 (2006). [PubMed] [pdf]
• Nacher, J.C., Ochiai, T., Yamada, T., Kanehisa, M., and Akutsu, T.; The role of log-normal dynamics in the evolution of biochemical pathways. BioSystems 83, 26-37 (2006). [PubMed]

2005

• Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M., and Miyano, S.; Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models. J. Bioinform. Comput. Biol. 3, 1295-1313 (2005). [PubMed]
• Aoki, K.F. and Kanehisa, M.; Using the KEGG Database Resource. In “Current Protocols in Bioinformatics”, Unit 1.12, Wiley (2005). [PubMed]
• Schwartz, J.M. and Kanehisa, M.; A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics 21, ii204-ii205 (2005). [PubMed] [pdf]
• Kawano, S., Hashimoto, K., Miyama, T., Goto, S., and Kanehisa, M.; Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics 21, 3976-3982 (2005). [PubMed] [pdf]
• Tamori, A., Yamanishi, Y., Kawashima, S., Kanehisa, M., Enomoto, M., Tanaka, H., Kubo, S., Shiomi, S., and Nishiguchi, S.; Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin. Cancer Res. 15, 5821-5826 (2005). [PubMed] [pdf]
• Noguchi, T., Ren, X.Q., Aoki, S., Igarashi, Y., Che, X.F., Nakajima, Y., Takahashi, H., Mitsuo, R., Tsujikawa, K., Sumizawa, T., Haraguchi, M., Kobayashi, M., Goto, S., Kanehisa, M., Aikou, T., Akiyama, S.I., and Furukawa, T.; MRP1 mutated in the L(0) region transports SN-38 but not leukotriene C(4) or estradiol-17 (beta-d-glucuronate). Biochem. Pharmacol. 70, 1056-1065 (2005). [PubMed]
• Okuda, S., Kawashima, S., Goto, S., and Kanehisa, M.; Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli. Genome Informatics 16(1), 116-124 (2005). [PubMed] [pdf]
• Yamada, T., Kawashima, S., Mamitsuka, H., Goto, S., and Kanehisa, M.; Comprehensive analysis and prediction of synthetic lethality using subcellular locations. Genome Informatics 16(1), 150-158 (2005). [PubMed] [pdf]
• Fujita, M. and Kanehisa, M.; Comparative analysis of DNA-binding proteins between thermophilic and mesophilic bacteria. Genome Informatics 16(1), 174-181 (2005). [PubMed] [pdf]
• Hashimoto, K., Kawano, S., Goto, S., Aoki-Kinoshita, K., Kawashima, M., and Kanehisa, M.; A global representation of the carbohydrate structures: a tool for the analysis of glycan. Genome Informatics 16(1), 214-222 (2005). [PubMed] [pdf]
• Honda, W., Kawashima, S., and Kanehisa, M.; Autoimmune diseases and peptide variations. Genome Informatics 16(1), 272-280 (2005). [PubMed] [pdf]
• Hizukuri, Y., Yamanishi, Y., Nakamura, O., Yagi, F., Goto, S., and Kanehisa, M.; Extraction of leukemia specific glycan motifs in human by computational glycomics. Carbohydr. Res. 340, 2270-2278 (2005). [PubMed]
• Sato, T., Yamanishi, Y., Kanehisa, M., and Toh, H.; The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21, 3482-3489 (2005). [PubMed] [pdf]
• Yamanishi, Y., Vert, J.-P., and Kanehisa, M.; Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics 21, i468-i477 (2005). [PubMed] [pdf]
• Osanai, T., Kanesaki, Y., Nakano, T., Takahashi, H., Kanehisa, M., Suzuki, I., Murata, N., and Tanaka, K.; Positive regulation of sugar catabolic pathways in the cyanobacterium Synechocystis sp. PCC 6803 by the group 2 sigma factor SigE. J. Biol. Chem. 280, 30653-30659 (2005). [PubMed] [pdf]
• Kucho, K., Okamoto, K., Tsuchiya, Y., Nomura, S., Nango, M., Kanehisa, M., and Ishiura, M.; Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J. Bacteriol. 187, 2190-2199 (2005). [PubMed] [pdf]
• Nacher, J.C., Ueda, N., Kanehisa, M., and Akutsu, T.; Flexible construction of hierarchical scale-free networks with general exponent. Phys. Rev. E 71, 036132 (2005). [PubMed]
• Aoki, K.F., Mamitsuka, H., Akutsu, T., and Kanehisa, M.; A score matrix to reveal the hidden links in glycans. Bioinformatics 21, 1457-1463 (2005). [PubMed] [pdf]
• Itoh, M., Goto, S., Akutsu, T., and Kanehisa, M.; Fast and accurate database homology search using upper bounds of local alignment scores. Bioinformatics 21, 912-921 (2005). [PubMed] [pdf]
• Nacher, J.C., Yamada, T., Goto, S., Kanehisa, M., and Akutsu, T.; Two complementary representations of a scale-free network. Physica A, 349, 349-363 (2005). [abstract]

2004

• Nacher, J.C., Ueda, N., Yamada, T., Kanehisa, M., and Akutsu, T.; Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics 5, 207 (2004). [PubMed] [pdf]
• Nikitin, F., Rance, B., Itoh, M., Kanehisa, M., and Lisacek, F.; Using protein motif combinations to update KEGG pathway maps and orthologue tables. Genome Informatics 15(2), 266-275 (2004). [PubMed] [pdf]
• Kotera, M., Okuno, Y., Hattori, M., Goto, S., and Kanehisa, M.; Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc. 126, 16487-16498 (2004). [PubMed]
• Igarashi, Y., Aoki, K.F., Mamitsuka, H., Kuma, K., and Kanehisa, M.; The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes. Mol. Biol. Evol. 21, 2149-2160 (2004). [PubMed] [pdf]
• Yamanishi, Y., Vert, J.-P., and Kanehisa, M.; Heterogeneous data comparison and gene selection with kernel canonical correlation analysis. In “Kernel Methods in Computational Biology” (Scholkopf, B., Tsuda, K., and Vert, J.-P., eds.), pp. 209-230, MIT Press (2004).
• Aoki, K.F., Ueda, N., Yamaguchi, A., Kanehisa, M., Akutsu, T., and Mamitsuka, H.; Application of a new probabilistic model for recognizing complex patterns in glycans. Bioinformatics 20, i6-i14 (2004). [PubMed] [pdf]
• Yamanishi, Y., Vert, J.-P., and Kanehisa, M.; Protein network inference from multiple genomic data: a supervised approach. Bioinformatics 20, i363-i370 (2004). [PubMed] [pdf]
• Aoki, K.F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S., and Kanehisa, M.; KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32, W267-W272 (2004). [PubMed] [pdf]
• Aoki, K.F., Ueda, N., Yamaguchi, A., Akutsu, T., Kanehisa, M., and Mamitsuka, H.; Managing and analyzing carbohydrate data. ACM SIGMOD Record, Vol. 33, No. 2, pp. 33-38 (2004) [abstract] [pdf]
• Hizukuri, Y., Yamanishi, Y., Hashimoto, K., and Kanehisa, M.; Extraction of species-specific glycan substructures. Genome Informatics 15(1), 69-81 (2004). [PubMed] [pdf]
• Itoh, M., Akutsu, T., and Kanehisa, M.; Clustering of database sequences for fast homology search using upper bounds on alignment score. Genome Informatics 15(1), 93-104 (2004). [PubMed] [pdf]
• Yamada, T., Goto, S., and Kanehisa, M.; Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Informatics 15(1), 249-258 (2004). [PubMed] [pdf]
• Levchenko, M.E., Poroikov, M., and Kanehisa, M.; G-protein coupled receptors and and their endogenous ligand in the human genome. Biomeditsinskaya Khimiya (Biomedical Chemistry) 50, 149-158 (2004). [PubMed]
• Imanishi, T, et al.; Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biol. 2, e162 (2004). [PubMed] [pdf]
• Kobayashi, M., Ishizuka, T., Katayama, M., Kanehisa, M., Bhattacharyya-Pakrasi, M., Pakrasi, H.B., and Ikeuchi, M.; Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol. 45, 290-299 (2004). [PubMed]
• Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M.; The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-D280 (2004). [PubMed] [pdf]

2003

• Aoki, K.F., Yamaguchi, A., Okuno, Y., Akutsu, T., Ueda, N., Kanehisa, M., and Mamitsuka, H.; Efficient tree-matching methods for accurate carbohydrate database queries. Genome Informatics 14, 134-143 (2003). [PubMed] [pdf]
• Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M.; Heuristics for chemical compound matching. Genome Informatics 14, 144-153 (2003). [PubMed] [pdf]
• Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M.; Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc. 125, 11853-11865 (2003). [PubMed]
• Vert, J.-P. and Kanehisa, M.; Extracting active pathways from gene expression data. Bioinformatics 19, ii238-ii234 (2003). [PubMed] [pdf]
• Park, K.-J. and Kanehisa, M.; Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics 19, 1656-1663 (2003). [PubMed] [pdf] [see Thomson]
• Yamanishi, Y., Vert, J.-P., Nakaya, A., and Kanehisa, M.; Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. Bioinformatics 19, i323-i330 (2003). [PubMed] [pdf]
• Vert, J.-P. and Kanehisa, M.; Graph-driven features extraction from microarray data using diffusion kernels and kernel CCA. Advances in Neural Information Processing Systems 15 (Becker, S., Thrun, S., and Obermayer, K., eds.), pp. 1425-1432, MIT Press, Cambridge, MA (2003).
• Kanehisa, M. and Bork, P.; Bioinformatics in the post-sequence era. Nature Genetics 33, 305-310 (2003). [PubMed] [pdf]
• Hihara, Y., Sonoike, K., Kanehisa, M., and Ikeuchi, M.; DNA microarray analysis of redox responsive genes in the genome of the cyanobacterium Synechocystis sp. PCC 6803. J. Bacteriol. 185, 1719-1725 (2003). [PubMed] [pdf]
• Brudler, R., Hitomi, K., Daiyasu, H., Toh, H., Kucho, K., Ishiura, M., Kanehisa, M., Roberts, V.A., Todo, T., Tainer, J.A., and Getzoff, E.D.; Identification of a new cryptochrome class: structure, function and evolution. Mol. Cell 11, 59-67 (2003). [PubMed]

2002

• Yamanishi, Y., Itoh, M., and Kanehisa, M.; Extraction of organism groups from phylogenetic profiles using independent component analysis. Genome Informatics 13, 61-70 (2002). [PubMed] [pdf]
• Kanehisa, M.; The KEGG database. Novartis Found. Symp. 247, 91-101 (2002). [PubMed]
• Yamaguchi, K., Suzuki, I., Yamamoto, H., Lyukevich, A., Bodrova, I., Los, D.A., Piven, I., Zinchenko, V., Kanehisa, M., and Murata, N.; A two-component Mn(2+)-sensing system negatively regulates expression of the mntCAB operon in Synechocystis. Plant Cell 14, 2901-2913 (2002). [PubMed] [pdf]
• Yoshimura, H., Yanagisawa, S., Kanehisa, M., and Ohmori, M.; Screening for the target gene of cyanobacterrial cAMP receptor protein SYCRP1. Mol. Microbiol. 43, 843-853 (2002). [PubMed] [pdf]
• Yoshikawa, T., Watanabe, A., Ishitsuka, Y., Nakaya, A., and Nakatani, N.; Identification of multiple genetic loci linked to the propensity for “behavioral despair” in mice. Genome Res. 12, 357-366 (2002). [PubMed] [pdf]
• Kanehisa, M. and Goto, S.; KEGG for computational genomics. In “Current Topics in Computational Molecular Biology” (Jiang, T., Xu, Y., and Zhang, M.Q., eds.), pp. 301-315, MIT-Press, Cambridge, MA (2002).
• Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.; The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002). [PubMed] [pdf]
• Goto, S., Okuno, Y., Hattori, M., Nishioka, T., and Kanehisa, M.; LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30, 402-404 (2002). [PubMed] [pdf]
• Kawashima, T., Kawashima, S., Kohara, Y., Kanehisa, M., and Makabe, K.W.; Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags. Nucleic Acids Res. 30, 119-120 (2002). [PubMed] [pdf]

2001

• Ohmori, M., Ikeuchi, M., Sato, N., Wolk, P., Kaneko, T., Ogawa, T., Kanehisa, M., Goto, S., Kawashima, S., Okamoto, S. Yoshimura, H., Katoh, H., Fujisawa, T., Ehira, S., Kamei, A., Yoshihara, S., Narikawa, R., and Tabata, S.; Characterization of genes encoding multi-domain proteins in the genome of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. Strain PCC 7120. DNA Res. 8, 271-284 (2001). [PubMed] [pdf]
• Nakaya, A., Goto, S., and Kanehisa, M.; Extraction of correlated gene clusters by multiple graph comparison. Genome Informatics 12, 44-53 (2001). [PubMed] [pdf]
• Kanehisa, M.; Prediction of higher order functional networks from genomic data. Pharmacogenomics 2, 373-385 (2001). [PubMed]
• Kihara, D. and Kanehisa, M.; Prediction of membrane proteins in post-genomic era. Recent Res. Devel. Protein Eng. 1, 179-196 (2001).
• Makabe, K.W., Kawashima, T., Kawashima, S., Minokawa, T., Adachi, A., Kawamura, H., Ishikawa, H., Yasuda, R., Yamamoto, H., Kondoh, K., Arioka, S., Sasakura, Y., Kobayashi, A., Yagi, K., Shojima, K., Kondoh, Y., Kido, S., Tsujinami, M., Nishimura, N., Takahashi, M., Nakamura, T., Kanehisa, M., Ogasawara, M., Nishikata, T., and Nishida, H.; Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development. Development 128, 2555-2567 (2001). [PubMed] [pdf]
• Kuroda, M., Ohta, T., Uchiyama, I., Baba, T., Yuzawa, H., Kobayashi, I., Cui, L., Oguchi, A., Aoki, K., Nagai, Y., Lian, J., Ito, T., Kanamori, M., Matsumaru, H., Maruyama, A., Murakami, H., Hosoyama, A., Mizutani-Ui, Y., Takahashi, N.K., Sawano, T., Inoue, R., Kaito, C., Sekimizu, K., Hirakawa, H., Kuhara, S., Goto, S., Yabuzaki, J., Kanehisa, M., Yamashita, A., Oshima, S., Furuya, K., Yoshino, C., Shiba, T., Hattori, M., Ogasawara, N., Hayashi H., and Hiramatsu, K.; Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357, 1225-1240 (2001). [PubMed]
• Makabe, K.W., Kawashima, T., Kawashima, S., Sasakura, Y., Ishikawa, H., Kawamura, H., Kanehisa, M., Nishikata, T., and Nishida, H.; Maternal genetic information stored in fertilized eggs of the ascidian, Halocynthia roretzi. In “The Biology of Ascidians” (Sawada, H., Yokosawa, H., Lambert, C.C. eds.), pp.165-177, Springer-Verlag, Tokyo (2001).
• Suzuki, I., Kanesaki, Y., Mikami, K., Kanehisa, M., and Murata, N.; Cold-regulated genes under control of the cold sensor Hik33 in Synechocystis. Mol. Microbiol. 40, 235-244 (2001). [PubMed] [pdf]
• Hihara, Y., Kamei, A., Kanehisa, M., Kaplan, A., and Ikeuchi, M.; DNA microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell 13, 793-806 (2001). [PubMed] [pdf]

2000

• Ogata, H., Fujibuchi, W., Goto, S., and 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]
• Fujibuchi, W., Ogata, H., Matsuda, H., and 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]
• Kihara, D. and Kanehisa, M.; Tandem clusters of membrane proteins in complete genome sequences. Genome Res. 10, 731-743 (2000). [PubMed] [pdf]
• Kanehisa, M.; Pathway databases and higher order function. Adv. Protein Chem. 54, 381-408 (2000). [PubMed]
• Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [PubMed] [pdf]
• Kawashima, T., Kawashima, S., Kanehisa, M., Nishida, H., and Makabe, K.W.; MAGEST: MAboya Gene Expression patterns and Sequence Tags. Nucleic Acids Res. 28, 133-135 (2000). [PubMed] [pdf]
• Kawashima, S. and Kanehisa, M.; AAindex: Amino Acid index database. Nucleic Acids Res. 28, 374 (2000). [PubMed] [pdf]
• Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: chemical database for enzyme reactions. Nucleic Acids Res. 28, 380-382 (2000). [PubMed] [pdf]

1999

• Nakao, M., Bono, H., Kawashima, S., Kamiya, T., Sato, K., Goto, S., and Kanehisa, M.; Genome-scale gene expression analysis and pathway reconstruction in KEGG. Genome Informatics 10, 94-103 (1999). [PubMed] [pdf]
• Tomii, K. and Kanehisa, M.; Systematic detection of protein structural motifs. In “Pattern Discovery in Biomolecular Data” (Wang, J.T.L., Shapiro, B.A., and Shasha, D., eds.), pp.97-110, Oxford Univ. Press (1999)
• Kanehisa, M.; KEGG: From genes to biochemical pathways. In “Bioinformatics: Databases and Systems” (Letovsky, S., ed.), pp. 63-76, Kluwer Academic Publishers (1999).
• Wackett, L.P., Ellis, L.B.M., Speedie, S.M., Hershberger, C.D., Knackmuss, H.-J., Spormann, A.M., Walsh, C.T., Forney, L.J., Punch, W.F., Kazic, T., Kanehisa, M., and Berndt, D.J.; Predicting microbial biodegradation pathways. ASM News 65, 87-93 (1999).
• Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34 (1999). [PubMed] [pdf]
• Goto, S., Nishikoka, T., and Kanehisa, M.; LIGAND database for enzymes, compounds, and reactions. Nucleic Acids Res. 27, 377-379 (1999). [PubMed] [pdf]
• Kawashima, S., Ogata, H., and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 27, 368-369 (1999). [PubMed] [pdf]

1998

• Bono, H., Goto, S., Fujibuchi, W., Ogata, H., and Kanehisa, M.; Systematic prediction of orthologous units of genes in the complete genomes. Genome Informatics 9, 32-40 (1998). [PubMed] [pdf]
• Kanehisa, M.; Databases of Biological Information. In “Trends Guide to Bioinformatics” (Brenner, S. and Lewitter, F., eds.), pp. 24-26, Elsevier (1998).
• Tomii, K. and Kanehisa, M.; A comparative analysis of ABC transporters in the complete microbial genomes. Genome Res. 8, 1048-1059 (1998). [PubMed] [pdf]
• Kihara, D., Shimizu, T., and Kanehisa, M.; Prediction of membrane proteins based on classification of transmembrane segments. Protein Eng. 11, 961-970 (1998). [PubMed] [pdf]
• Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: Chemical database for enzyme reactions. Bioinformatics 14, 591-599 (1998). [PubMed] [pdf]
• Fujibuchi, W., Sato, K., Ogata, H., Goto, S., and Kanehisa, M.; KEGG and DBGET/LinkDB: Integration of biological relationships in divergenet molecular biology data. In “Knowledge Sharing Across Biological and Medical Knowledge Based Systems”, Technical Report WS-98-04, pp. 35-40, AAAI Press (1998).
• Ogata, H., Goto, S., Fujibuchi, W., and Kanehisa, M.; Computation with the KEGG pathway database. BioSystems 47, 119-128 (1998). [PubMed]
• Kanehisa, M.; Editorial: Grand challenges in bioinformatics. Bioinformatics 14, 309 (1998). [PubMed] [pdf]
• Kanehisa, M.; Books etc: Microbiology – on a plate. Trends Genet. 14, 165-166 (1998).
• Bono, H., Ogata, H., Goto, S., and Kanehisa, M.; Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res. 8, 203-210 (1998). [PubMed] [pdf]

1997

• Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an Integrated Database Retrieval System. Pacific Symposium on Biocomputing ’98, 683-694 (1997). [PubMed]
• Kanehisa, M.; Linking databases and organisms – GenomeNet resources in Japan. Trends Biochem. Sci. 22, 442-444 (1997). [PubMed]
• Kanehisa, M.; A database for post-genome analysis. Trends Genet. 13, 375-376 (1997). [PubMed]
• Fujibuchi, W. and Kanehisa, M.; Prediction of gene expression specificity by promoter sequence patterns. DNA Res. 4, 81-90 (1997). [PubMed] [pdf]
• Kanehisa, M. and Goto, S.; A systematic analysis of gene functions by the metabolic pathway database. In “Theoretical and Computational Methods in Genome Research” (Suhai, S., ed.), pp. 41-55, Plenum (1997).

1996

• Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K., and Kanehisa, M.; Organizing and computing metabolic pathway data in terms of binary relations. Pacific Symposium on Biocomputing ’97, 175-186 (1996). [PubMed]
• Ogata, H., Bono, H., Fujibuchi, W., Goto, S., and Kanehisa, M.; Analysis of binary relations and hierarchies of enzymes in the metabolic pathways. Genome Informatics 7, 128-136 (1996). [pdf]
• Kanehisa, M.; Toward pathway engineering: a new database of genetic and molecular pathways. Science & Technology Japan, No. 59, pp. 34-38 (1996).
• Ogiwara, A., Uchiyama, I., Takagi, T., and Kanehisa, M.; Construction and analysis of a profile library characterizing groups of structurally known proteins. Protein Sci. 5, 1991-1999 (1996). [PubMed] [pdf]
• Ogata, H., Fujibuchi, W., and Kanehisa, M.; The size differences among mammalian introns are due to the accumulation of small deletions. FEBS Lett. 390, 99-103 (1996). [PubMed]
• Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996). [PubMed] [pdf]

1995

• Ogata, H., Akiyama, Y., and Kanehisa, M.; A genetic algorithm based molecular modeling technique for RNA stem-loop structures. Nucleic Acids Res. 23, 419-426 (1995). [PubMed] [pdf]

1994

• Mizuno, M. and Kanehisa, M.; Distribution of base composition around the splice sites in different species. Genome Informatics 5, 130-137 (1994). [pdf]
• Mizuno, M. and Kanehisa, M.; Distribution profiles of GC content around the translation initiation site in different species. FEBS Lett. 352, 7-10 (1994). [PubMed]
• Uchiyama, I., Ogiwara, A., and Kanehisa, M.; A library of signature pentapeptides for the Protein Data Bank. In “Protein Structures by Distance Analysis” (Bohr, H. and Brunak, S., eds.), pp. 237-246, IOS Press (1994).
• Suzuki, T., Takagi, T., Kuhara, S., and Kanehisa, M.; Development of an integrated database for genome mapping and nucleotide sequences. Proc. 27th Hawaii Int. Conf. on System Sciences, Vol. 5, pp. 68-76 (1994).

1993

• Ohkubo, Z. and Kanehisa, M.; Characterization of spatially close peptide segments in proteins. Bull. Inst. Chem. Res., Kyoto Univ. 71, 327-337 (1993).
• Fujibuchi, W. and Kanehisa, M.; A method to extract functional motifs for transcriptional regulation in eukaryotic sequences. Bull. Inst. Chem. Res., Kyoto Univ. 71, 317-326 (1993).
• Ishikawa, M., Toya, T., Hoshida, M., Nitta, K., Ogiwara, A., and Kanehisa, M.; Multiple sequence alignment by parallel simulated annealing. Comput. Appl. Biosci. 9, 267-273 (1993). [PubMed]
• Matsuo, Y. and Kanehisa, M.; An approach to systematic detection of protein structural motifs. Comput. Appl. Biosci. 9, 153-159 (1993). [PubMed]

1992

• Nakai, K. and Kanehisa, M.; A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14, 897-911 (1992). [PubMed]
• Ogiwara, A., Uchiyama, I., Seto, Y., and Kanehisa, M.; Construction of a dictionary of sequence motifs that characterize groups of related proteins. Protein Eng. 5, 479-488 (1992). [PubMed]
• Horton, P.B. and Kanehisa, M.; An assessment of neural network and statistical approaches for prediction of E.coli promoter sites. Nucleic Acids Res. 20, 4331-4338 (1992). [PubMed] [pdf]

1991

• Iijima, T. and Kanehisa, M.; Analysis of DNA functional sites by information contents. Bull. Inst. Chem. Res., Kyoto Univ. 69, 226-233 (1991).
• Nakai, K. and Kanehisa, M.; Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins 11, 95-110 (1991). [PubMed] [pdf]

1990

• Seto, Y., Ikeuchi, Y., and Kanehisa, M.; Fragment peptide library for classification and functional prediction of proteins. Proteins 8, 341-351 (1990). [PubMed] [pdf]
• Seto, Y., Ikeuchi, Y., and Kanehisa, M.; Peptide sequence library for protein expert system. In “Protein Engineering” (Ikehara, M., ed.), pp. 311-313 (1990).

1989

• Kanehisa, M.; Databases: What’s There and What’s Needed. In “Biomolecular Data: A Resource in Transition” (Colwell, R.R., ed.), pp. 91-95, Oxford Univ. Press (1989).
• Seto, Y. and Kanehisa, M.; Repeat sequences of amino acids suggest the origin of protein. Bull. Inst. Chem. Res., Kyoto Univ. 66, 461-468 (1989).

1988

• Kanehisa, M. and Lesk, A.M.; The future of computational molecular biology. In “Computational Molecular Biology” (Lesk, A.M., ed.), pp. 223-224, Oxford Univ. Press (1988).
• Nakai, K. and Kanehisa, M.; Prediction of in-vivo modification sites of proteins from their primary structures. J. Biochem. 104, 693-699 (1988). [PubMed]
• Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988). [PubMed]
• Kanehisa, M.; A multivariate analysis method for discriminating protein secondary structural segments. Protein Eng. 2, 87-92 (1988). [PubMed]

1987

• Kanehisa, M.; Multivariate analysis of amino acid sequences for structural and functional predictions. In “Impact of Knowledge of Amino Acid Sequence Data on Biophysical Research — Proceedings of the 13th Taniguchi International Symposium on Biophysics” (Tsugita, A., ed.) pp. 75-80, Science Univ. of Tokyo (1987).
• Nishikawa, K., Nakashima, H., Kanehisa, M., and Ooi, T.; Detection of weak sequence homology of proteins for tertiary structure prediction. Protein Seq. Data Anal. 1, 107-116 (1987). [PubMed]

1986

• Kanehisa, M.; Prediction of protein structures by database analysis. In “Proceedings of the International Symposium on Computer Analysis for Life Science” (Kawabata, C. and Bishop, A.R., eds.), pp. 204-211, Ohmsha, Ltd., Tokyo (1986).
• Takagi, J.S., Tokushige, M., Shimura, Y., and Kanehisa, M.; L-Aspartate ammonia-lyase and fumarate hydratase share extensive sequence homology. Biochem. Biophys. Res. Commun. 138, 568-572 (1986). [PubMed]