» Oral presentation

Published article & presentation

2011(NEW)
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood T, Bateman A, Blake J, Bult C, Cherry M, Chisholm R, Cochrane G, Cook C, Eppig J, Galperin M, Gentleman R, Goble C, Gojobori T, Hancock J, Howe D, Imanishi T, Landsman D, Kelso J, Lewis S, Mizrachi I, Orchard S, Ouellette F, Ranganathan S, Richardson L, Rocca-Serra P, Schofield P, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel P, White O, and Yamasaki C on behalf of the BioDBCore working group (2011) Towards BioDBcore: a community-defined information specification for biological databases. Database: baq027. [PubMed] [NAR]
Taniya T, Tanaka S, Yamaguchi-Kabata Y, Hanaoka H, Maekawa H, Yamasaki C, Barrero R, Lenhard B, Datta MW, Shimoyama M, Imanishi T, and Gojobori T (2011) A prioritization analysis of disease association by data-mining of functional annotation of human genes. Genomics (in press). [PubMed] [Genomics]
Hara Y, and Imanishi T (2011) Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes. BMC Evolutionary Biology 11: 308. [PubMed] [BMC Evol Biol]
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications Journal of Biomedical Semantics 2011, 2:4 doi:10.1186/2041-1480-2-4 Published: 2 August 2011　http://www.jbiomedsem.com/content/2/1/4/abstract
2010(NEW)
Shimada MK, Hayakawa Y, Takeda J, Gojobori T and Imanishi T (2010) A comprehensive survey of human polymorphisms on conserved splice dinucleotides and its evolutionary relationship with alternative splicing. BMC Evolutionary Biology 10: 122.[PubMed][BMC Evol Biol]
Endo T, Ueno K, Yonezawa K, Mineta K, Hotta K, Satou Y, Yamada L, Ogasawara M, Takahashi H, Nakajima A, Nakachi M, Nomura M, Yaguchi J, Sasakura Y, Yamasaki C, Sera M, Yoshizawa A, Imanishi T, Taniguchi H, and Inaba K (2010) CIPRO 2.5: Ciona intestinalis Protein Database, a unique integrated repository of large-scale omics data, bioinformatic analyses, and curated annotation, with user rating and reviewing functionality. Nucleic Acids Research (Database Issue): D807-D814 (gkq1144).[PubMed] [NAR]
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood T, Bateman A, Blake J, Bult C, Cherry M, Chisholm R, Cochrane G, Cook C, Eppig J, Galperin M, Gentleman R, Goble C, Gojobori T, Hancock J, Howe D, Imanishi T, Landsman D, Kelso J, Lewis S, Mizrachi I, Orchard S, Ouellette F, Ranganathan S, Richardson L, Rocca-Serra P, Schofield P, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel P, White O, and Yamasaki C on behalf of the BioDBCore working group (2010) Towards BioDBcore: a community-defined information specification for biological databases. Database: baq027.
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood T, Bateman A, Blake J, Bult C, Cherry M, Chisholm R, Cochrane G, Cook C, Eppig J, Galperin M, Gentleman R, Goble C, Gojobori T, Hancock J, Howe D, Imanishi T, Landsman D, Kelso J, Lewis S, Mizrachi I, Orchard S, Ouellette F, Ranganathan S, Richardson L, Rocca-Serra P, Schofield P, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel P, White O, and Yamasaki C on behalf of the BioDBCore working group (2010) Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research (Database Issue): D7-D10.[PubMed] [NAR]
2009
Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A, Imanishi T, and Gojobori T (2009) H-InvDB in 2009, extended database and data mining resources for human genes and transcripts. Nucleic Acids Research 38 (Database Issue): D626-D632. [PubMed] [NAR]
Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, and Sugano S (2009) H-DBAS: Human-transcriptome DataBase for Alternative Splicing, update 2010. Nucleic Acids Research 38 (Database Issue): D86-D90. [PubMed] [NAR]
Kawahara Y, Sakate R, Matsuya A, Murakami K, Sato Y, Zhang H, Gojobori T, Itoh T, and Imanishi T (2009) G-compass: a web-based comparative genome browser between human and other vertebrate species. Bioinformatics. [PubMed] [Bioinformatics]
Imanishi T and Nakaoka H (2009) Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. Nucleic Acids Research 37 (Web Server Issue): W17-W22 (gkp355). [PubMed] [NAR]
Jin L, Kryukov K, Suzuki Y, Imanishi T, Ikeo K, and Gojobori T (2009) The evolutionary study of small RNA-directed gene silencing pathways by investigating Rnase III enzymes. Gene 435: 1-8. [PubMed] [Gene]
Shimada MK, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, and Gojobori T (2009) VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. Nucleic Acids Research 37 (Database Issue): D810-D815. [PubMed] [NAR]
2008
Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T, and Imanishi T (2008) Low conservation and species-specific evolution of alternative splicing in humans and mice analysed with comparative genomics using well-annotated full-length cDNAs. NUCLEIC ACIDS RESEARCH. [PubMed] [NAR]
Yamaguchi Y, Shimada M, Hayakawa Y, Minoshima S, Chakraborty R, Gojobori T, and Imanishi T(2008) Distribution and effects of nonsense polymorphisms in human genes. PLoS ONE 3(10): e3393. doi:10.1371/journal.pone.0003393 [PLoS ONE]
Shimizu K, Nagaoka E, Okada Y, Takeuchi Y, Harihara S, Omoto K, Imanishi T, Kim W, Shin D-J, Hao L, and Jin F(2008) Characteristics of the beta-Globin Gene Cluster Haplotypes of Three Han Chinese Populations at Beijing, Xi'an, and Kunming as Compared with Those of Other Asian Populations. BIOCHEMICAL GENETICS46(9-10):566-582. [PubMed][Biochem Genet]
Nakagawa S, Niimura Y, Gojobori T, Tanaka H, and Miura K.(2008) Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. NUCLEIC ACIDS RESEARCH 36(3): 861-871 [PubMed] [NAR]
Matsuya A, Sakate R, Kawahara Y, Koyanagi KO, Sato Y, Fujii Y, Endo T, Ota S, Ikeo K, Suzuki Y, Hanada K, Iwama H, Makalowski W, Saitou N, Hiraki AT, Jin L, Kaneko Y, Kanno M, Murakami K, Noda A, Saichi N, Sanbonmatsu R, Suzuki M, Takeda J, Tanaka M, Yamasaki C, Gojobori T, Imanishi T, and Itoh T (2008) Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Nucleic Acids Research 36 (Database Issue): D787-D792. [PubMed] [NAR]
The Rice Annotation Project* (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research 36 (Database Issue): D1028-D1033. [PubMed] [NAR]

*Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei F, Hsing Y, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Shimizu Y, Sakata K, Haberer G, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An G, OOta S, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Piegu B, Panaud O, and Echeverria M.
Genome Information Integration Project and H-Invitational 2* (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research 36 (Database Issue): D793-D799. [PubMed] [NAR]

*Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo M, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares M, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, and Gojobori T.
Koyanagi KO, Imanishi T, and Gojobori T (2008) Bi-directional gene pairs in the human genome. In "Encyclopedia of Life Sciences," John Wiley & Sons
Murakami K, Imanishi T, Gojobori T, and Nakai K (2008) Two different classes of co-occurring motif-pairs found by a novel visualization method in human promoter regions. BMC Genomics 9: 112. [PubMed] [BMC Genomics]
2007
Sakate R, Suto Y, Imanishi T, Tanoue T, Hida M, Hayasaka I, Kusuda J, Gojobori T, Hashimoto K, and Hirai M (2007) Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome. Gene 399(1): 1-10. [PubMed]
Kawahara Y, and Imanishi T (2007) A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group. BMC Evolutionary Biology 7: 9. [PubMed] [BMC Evol Biol]
Gough C, Gojobori T, and Imanishi T (2007) Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: A molecular dynamics study. Proteins: Structure, Function, and Bioinformatics 66(1): 69-86. [Proteins] [PubMed]
Takeda J, Suzuki Y, Nakao M, Kuroda T, Sugano S, Gojobori T, and Imanishi T (2007) H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Nucleic Acids Research 35(Database Issue) D104-D109.
The Rice Annotation Project* (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research 17: 175-183.


*Itoh T, Tanaka T, Barrero R, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing Y, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Costa de Oliveira A, OOta S, Osato N, Palmer L, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, and Sasaki T.
Sakai H, Koyanagi KO, Imanishi T, Itoh T, and Gojobori T (2007) Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes.Gene 389(2):196-203 [Gene] [PubMed]
2006
Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T and Imanishi T (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. NUCLEIC ACIDS RESEARCH 34(14): 3917-3928.
Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, and Sasaki T (2006) The Rice Annotation Project Database (RAP-DB): Hub for Oryza sativa ssp. japonica genome information. NUCLEIC ACIDS RESEARCH 34(Database Issue): D741-D744.
Yamasaki C, Kawashima H, Todokoro F, Imamizu Y, Ogawa M, Tanino M, Itoh T, Gojobori T, and Imanishi T (2006) TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB. Nucleic Acids Research 34(Web Server Issue): W345-349.
Yura K, Shionyu M, Hagino K, Hijikata A, Hirashima Y, Nakahara T, Eguchi T, Shinoda K, Yamaguchi A, Takahashi K, Itoh T, Imanishi T, Gojobori T, and Go M (2006) Alternative splicing in human transcriptome: functional and structural influence on proteins. GENE 380(2):63-71.
2005
Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza SJ, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, and Okubo K (2005) The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv Integrative Display of Human Gene Expression across Disparate Technologies and Platforms. Nucleic Acids Research 33: D567-D572. [PubMed] [NAR]
Ogasawara M, Imanishi T, Moriwaki K, Gaudieri S, Tsuda H, Hashimoto H, Shiroishi T, Gojobori T, and Koide T. (2005) Length variation of CAG/CAA triplet repeats in 50 genes among 16 inbred mouse strains. Gene 349: 107-119. [PubMed]
Takemura T, Ekwalanga M, Bikandou B, Ido E, Yamaguchi Y, Ohkura S, Harada H, Takehisa J, Ichimura H, Parra H J, Nende M, Mubwo E, Sepole M, Hayami M and Miura T (2005) A novel SIV from black mangabey (Lophocebus aterrimus) in Democratic Republic of Congo. JOURNAL OF GENERAL VIROLOGY 86(7):1967-1971.
Koyanagi KO, Hagiwara M, Itoh T, Gojobori T, and Imanishi T (2005) Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system. Gene 353(2): 169-176.
Chiusano, M L, Gojobori T, Toraldo, G (2005) A C++ computational environment for biomolecular sequence management. Computational Management Science 2(3):165-180.
Tamiya G, Shinya M, Imanishi T, Ikuta T, Makino S, Okamoto K, Furugaki K, Matsumoto T, Mano S, Ando S, Nozaki Y, Yukawa W, Nakashige R, Yamaguchi D, Ishibashi H, Yonekura M, Nakami Y, Takayama S, Endo T, Saruwatari T, Yagura M, Yoshikawa Y, Fujimoto K, Oka A, Chiku S, Linsen SE, Giphart MJ, Kulski JK, Fukazawa T, Hashimoto H, Kimura M, Hoshina Y, Suzuki Y, Hotta T, Mochida J, Minezaki T, Komai K, Shiozawa S, Taniguchi A, Yamanaka H, Kamatani N, Gojobori T, Bahram S, and Inoko H (2005) Whole genome association study of rheumatoid arthritis using 27,039 microsatellites. Human Molecular Genetics 14(16):2305-2321.
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800.
Fujii Y., Itoh T., Sakate R., Koyanagi K.O., Matsuya A., Habara T., Yamaguchi K., Kaneko Y., Gojobori T. and Imanishi T. (2005) A web tool for comparative genomics: G-compass. Gene 364: 45-52.
Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi-Kabata Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, and Gojobori T (2005) Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational Database (H-InvDB). Gene 364: 99-107.
Chun HW, Tsuruoka Y, Kim JD, Shiba R, Nagata N, Hishiki T, and Tsujii J (2005) Extraction of gene-disease relations from medline using domain dictionaries and machine learning. Pacific Symposium on Biocomputing 11:4-15.
2004
Mano S, Yasuda N, Katoh T, Tounai K, Inoko H, Imanishi T, Tamiya G, and Gojobori T (2004) Notes on the maximum likelihood estimation of haplotype frequencies. Annals of Human Genetics 68: 257-264.
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, and Sugano S (2004) Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biology 2: 856-875.
Nakamura Y, Itoh T, Matsuda H. and Gojobori, T (2004) Biased biological functions of horizontally transferred genes on 324,653 open reading frames of 116 prokaryotic complete genomes. Nature Genetics 36:760-766
Matsumoto T, Yukawa W, Nozaki Y, Nakashige R, Shinya M, Makino S, Yagura M, Ikuta T, Imanishi T, Inoko H, Tamiya G, and Gojobori T. (2004) Novel algorithm for automated genotyping of microsatellites. Nucleic Acids Research 32: 6069-77. [PubMed] [NAR]
Iwama H, and Gojobori T (2004) Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101(49):17156-61
Shimizu K, Marubayashi A, Tokimasa K, Harihara S, Omoto K, Imanishi T, Hao L, and Jin F. (2004) Characteristic beta-globin gene cluster haplotypes of Evenkis and Oroqens in north China. Hum Biol. 76: 765-78.[PubMed]
2003
Anzai T, Shiina T, Kimura N, Yanagiya K, Kohara S, Shigenari A, Yamagata T, Kulski JK, Naruse TK, Fujimori Y, Fukuzumi Y, Yamazaki M, Tashiro H, Iwamoto C, Umehara Y, Imanishi T, Meyer A, Ikeo K, Gojobori T, Bahram S, and Inoko H (2003) Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci USA 100(13): 7708-7713.
Yamaguchi-Kabata Y, Yamashita M, Ohkura S, Hayami M. and Miura T (2004) Linkage of amino acid variation and evolution of human immunodeficiency virus type1 gp120 envelope glycoprotein (subtype B) linked with usage of the second receptor J. Mol. Evol. 58: 333-340.
2002
Katoh T, Mano S, Ikuta T, Munkhbat B, Tounai K, Ando H, Munkhtuvshin N, Imanishi T, Inoko H, and Tamiya G (2002) Genetic isolates in East Asia: a study of linkage disequilibrium in the X chromosome. Amer J Hum Genet 71: 395-400.
2001
Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi F, Saitou N, Sugawara H, and Gojobori T (2002) DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Research 30: 27-30.
» Published article & presentation

Oral presentation

2005
Yamasaki C, Koyanagi K, Fujii Y, Itoh T, Barrero R A, Tamura T, Yamaguchi Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T and Gojobori T (2005) Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational Database (H-InvDB). HGM2005
Taniya T, Tanaka S, Hanaoka S, Maekawa H, Imanishi T, Gojobori T (2005) Priority ANalysis for Disease Association (PANDA) System HGM2005
Fujii Y, Itoh T, Sakate R, Matsuya A, Koyanagi K, Habara T, Yamaguchi K, Kaneko Y, Imanishi T, Gojobori T (2005) G-compass: A Web Tool for Comparative Genomics Analysis HGM2005
Gojobori T (2005) The H-Invitational dataset and online database HUGO Gene Nomenclature Committee
2004
Barero R, Auffray C, Suzuki Y, Dubchak I, Wilming L, Sugano S, Imanishi T, Gojobori T, Jia L (2004) Discovery and annotation of non-protein coding human RNAs HGM2004
Fujii Y, Imanishi T, Itoh T, Koyanagi K, Barero R, Tamura T, Yamaguchi Y, Tanino M, Yamasaki C, Takeda J, Gough C, Hilton P, Sakai H, Tanaka S, Nomura N, Sugano S, Gojobori T (2004) H-Invitational Database : Integrative human cDNA annotation database HGM2004
Itoh T, Oota S, Takahashi A, Hanada K, Sakate R, Koyanagi K, Kaneko Y, Suzuki Y, Matsuya A, Imanishi T, Makalowski W, Endo T, Ikeo K, Hirai M, Saitou N, Gojobori T (2004) Identification of orthologs between humans and model organisms by curation of molecular phylogenetic trees HGM2004
Sakai H, Fujii Y, Koyanagi K, Itoh T, Imanishi T, Gojobori T (2004) MAPPING OF 113,196 HUMAN MRNA SEQUENCES TO THE COMPLETE HUMAN GENOME 2004 Cold Spring Harbor Meeting on The Biology of Genomes
Fujii Y, Imanishi T, Itoh T, Koyanagi K, Roberto Barrero, Tamura T, Yamaguchi Y, Tanino M, Yamasaki C, Takeda J, Gough C, Hilton P, Sakai H, Tanaka S, Nomura N, Sugano S, Gojobori T (2004) H-Invitational Database : Integrative human cDNA annotation database 2004 Cold Spring Harbor Meeting on The Biology of Genomes
Gojobori T (2004) Activities of Human Full-length cDNA Annotation Project and H-Invitational Database First ISN Special Neurochemistry Conference
Makalowski W, Gojobori T (2004) Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones 29th FEBS Congress
Gough C, Imanishi T, Gojobori T (2004) Molecular Dynamics Simulations of the BRCT Region of BRCA1 Reveal Long-Range Effects of Mutations on a Protein-Protein Interaction Site ISMB/ECCB 2004
Nagata N, Hishiki T, Yamaguchi Y, Yoshida T, Imanishi T, Gojobori T (2004) Cataloguing of Disease-Associated Genetic and Environmental Factors by a Text-mining Approach ISMB/ECCB 2004/dd>
Imanishi T (2004) H-Invitational Database - A New Human Gene Annotation Database ISMB/ECCB 2004
Imanishi T　(2004)　Human cDNA Analysis and Annotation International Lectures on Bioinformatics and Genomics
Gojobori T (2004)　New Developments of Human Full-length cDNA Annotation Invitational (H-Invitational) Data Base. International Conference on Bioinformatics and Computational Biology
Yamasaki C, Koyanagi K, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T (2004) H-Invitational Database (H-InvDB): Integrated Database of the Human Transcriptome BITS2004"Beyond the Identification of Transcribed Sequences: Functional, Expression and Evolutionary Analysis"14th International Workshop
Fujii Y, Itoh T, Sakate R, Matsuya A, Koyanagi K, Habara T, Yamaguchi K, Kaneko Y, Imanishi T, Gojobori T (2004) G-compass: A Web Tool for Comparative Genomics Analysis BITS2004"Beyond the Identification of Transcribed Sequences: Functional, Expression and Evolutionary Analysis"14th International Workshop
Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza S, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, Ookubo K (2004) The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv Integrative Display of Human Gene Expression across Disparate Technologies and Platforms BITS2004"Beyond the Identification of Transcribed Sequences: Functional, Expression and Evolutionary Analysis"14th International Workshop
Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza S, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, Ookubo K (2004) The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv Integrative Display of Human Gene Expression across Disparate Technologies and Platforms 5th HUGO Pacific Meeting & 6th Asia-Pacific Conference on Human Genetics
Shiba R, Nagata N, Imanishi T (2004) Merging Biological Databases to Construct a Human Gene Dictionary 5th HUGO Pacific Meeting & 6th Asia-Pacific Conference on Human Genetics
Yamasaki C, Koyanagi K, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T (2004) H-Invitational Database (H-InvDB): Integrated Database of the Human Transcriptome 5th HUGO Pacific Meeting & 6th Asia-Pacific Conference on Human Genetics
Takeda J, Suzuki Y, Imanishi T, Gojobori T (2004) Towards comprehensive understandings of the functional diversification of human genes; functional annotation of the alternative splicing in H-Invitational 2 full-length cDNA dataset Alternate Transcript Diversity Symposium
Imanishi T (2004) Transcript Variants in H-InvDB, An Integrated Database for Human Transcriptome Alternate Transcript Diversity Symposium
Yamasaki C, Koyanagi K, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T (2004) H-Invitational Database (H-InvDB): Integrated Database of the Human Transcriptome The 13th Takeda Science Foundation Symposium on Bioscience
Taniya T, Tanaka S, Hanaoka S, Maekawa H, Imanishi T, Gojobori T (2004) Priority ANalysis for Disease Association (PANDA) System The 13th Takeda Science Foundation Symposium on Bioscience
Matsumoto T, Nozaki Y, Nakashige R, Shinya M, Yoshikawa Y, Mano S, Imanishi T, Inoko H, Tamiya G, and Gojobori T (2004) Investigating the Optimal Dataset Size for SNP Hunting The 15th International Conference on Genome Informatics [GIW2004]
Okido T, Shigemoto Y, Matsuo M, Koike T, Fukuchi S, Imanishi T, Miyazaki S, Tateno Y, and Gojobori T (2004) Construction of H-Invitational Database CIB-DDBJ Flat File Server The 15th International Conference on Genome Informatics [GIW2004]
2003
Imanishi T, Shikanai T, Nurimoto S, Sugisaki T (2003) A new method of finding functional sequence motifs and its application to human GC-rich genomic sequences. RECOMB 2003
Barero R, Koyanagi K, Tanino M, Gough G, Oka A, Yasuda N, Mano S, Takeda J, Yamasaki C, Takahashi A, Yamaguchi Y, Itoh T, Imanishi T, Gojobori T (2003) Efforts towards Construction of Integrated Database for Biological Information in JBIRC (Japan Biological Information Research Center) HGM2003
Itoh T (2003) EVOLUTIONARY STUDY OF AMINO ACID SUBSTITUTION PATTERNS AND NATURAL SELECTION IN ENDOSYMBIOTIC BACTERIA NIAST COE International Symposium
Sakai H, Koyanagi K, Itoh T, Imanishi T, Gojobori T (2003) Detection of processed pseudogenes based on cDNA mapping to the human genome The 14th International Conference on Genome Informatics [GIW2003]
Todokoro F, Itoh T, Yamasaki C, Kawashima H, Imanishi T, Gojobori T (2003) Improvement in the Accuracy of Gene Prediction in Human cDNA Sequences The 14th International Conference on Genome Informatics [GIW2003]
Kundu S, Hagiwara M, Koyanagi K, Imanishi T, Itoh T (2003) TTOP : A System for Phylogenetic Tree Editing and Evolutionary Annotation of Genes The 14th International Conference on Genome Informatics [GIW2003]
Koyanagi K, Hagiwara M, Itoh T, Imanishi T, Watanabe H, Gojobori T (2004) Biased organization of the closely located adjacent gene pairs in the human The 2nd NAIST Bio-COE International Symposium
Itoh T, Imanishi T, Gojobori T (2004) Integrated annotation database of 41,118 human full length cDNAs International Rice Genome Meeting 2004
Imanishi T (2004) An Integrated Database of Human Gene Annotations The Third Waterfront Symposium of Human Genome Science (WASH-3)
Gojobori T, Imanishi T (2004) Human full-length cDNA annotation invitational (H-Invitational)database and the future of the integrated databases JST-BIRD International Workshop
Imanishi T (2004) Human genome functional annotation The 3rd Japan-Korea Bioinformatics Training course
Takeda J, Itoh T, Imanishi T, Gojobori T (2004) Evolutionary Study of Amino Acid Substitution Patterns Associated with Accelerated Evolution in Endosymbiotic Bacteria The Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004)
Imanishi T, Hokari H, Tanino M, Takeda J, Sugisaki T, Nurimoto S (2004) An improved method of finding over-represented sequence motifs in sets of DNA sequences. The Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004)
2002
Okayama T, Imanishi T, Iizuka T, Fumoto M, Kawanishi Y, Nishinomiya N, Shigemoto Y, Mashima J, Okido T, Habara T, Sugawara H and Gojobori T (2002) Precise mapping of full-length cDNA sequences on the human genome. HGM2002
Koyanagi K, Hayakawa Y, Habara T, Tamura T, Gojobori T and Imanishi T (2002) EVALUATION OF THE ASSEMBLY OF HUMAN DRAFT SEQUENCES. Cold Spring Harbor Meeting "Genome Sequencing & Biology"
Itoh T (2002) Acceleration of genomic evolution in endocellular symbionts, Buchnera and a protist mitochondrion. Molecular Evolution: Evolution, Genomics, Bioinformatics
Itoh T (2002) Comparative studies of full-length cDNA sequences and construction of a fully-annotated database. Molecular Evolution: Evolution, Genomics, Bioinformatics
Barrero A R, Imanishi T, Yamaguchi Y, Itoh T and Gojobori T (2002) A novel actin-binding domain, ABD, inferred from a phylogenetic analysis of adenylyl cyclase-associated proteins. Molecular Evolution: Evolution, Genomics, Bioinformatics
Gojobori T (2002) Search for the evolutionary origin of the central nervous system by comparative functional genomics . Molecular Evolution: Evolution, Genomics, Bioinformatics
Anzai T, Shiina T, Kimura N, Yanagiya K, Kohara S, Shigenari A, Naruse T, Kulski J, Fujimori Y, Fukuzumi Y, Yamazaki M, Tashiro H, Iwamoto C, Umehara Y, Imanishi T, Ikeo K, Gojobori T, Inoko H (2002) Genomic diversity between Chimpanzee and Human within the entire MHC class-I region (1.8 Mb). 7th International workshop on MHC evolution
Oka A, Okamoto K, Makino S, Endo T, Hayashi H, Fujimoto K, Tokubo E, Takaki A, Nagatsuka Y, Imanishi T, Gojobori T, Tamiya G (2002) Comprehensive setting of 30,000 polymorphic microsatellite markers throughout human genome. ASHG 2002
Koyanagi K, Okiyama S, Hayakawa Y, Itoh T, Tamura T, Gojobori T, Imanishi T (2002) Evaluation Of The Assembly Of Human Draft Sequences. AIST Symposium 2002
Zhang H, Koyanagi K, Habara T, Mimiura Y, Tamura T, Imanishi T, Gojobori T (2002) BB-Plot：A tool for a demonstration of BLAST based sequence matches. AIST Symposium 2002
Mimiura Y, Matsumoto R, Tamura T, Imanish T, Gojobori T (2002) Development of Parallel Blast System for PC cluster. AIST Symposium 2002
Mano S, Yasuda N, Tamiya G, Inoko H, Gojobori T, Imanishi T (2002) Phase Space Structure of Haplotype Frequency Estimation by the EM Algorithm. AIST Symposium
Oka A, Okamoto K, Makino S, Ikuta T, Fujimoto K, Shinya M, Ishibashi H, Yonekura M, Nakami Y, Takayama S, Yagura M, Hayashi H, Yamaguchi D, Kuwabara H, Gojobori T, Tamiya G, Inoko H (2002) Comprehensive setting of 30,000 polymorphic microsatellite markers and the progress of genome-wide association study for complex diseases. AIST Symposium 2002
Imanishi T, Gojobori T (2002) Construction of Integrated Database of Human Genes. AIST Symposium 2002
2001
Hayakawa Y, Koyanagi K, Tamura T, Gojoubori T and Imanishi T （2001）gLdraw: A general tool for a comparison of chromosome maps. GIW 2001
Imanishi T, Koyanagi K, Habara T, Yamaguchi K and Gojoubori T(2002) Comparative genomics study of large genomic regions of human and mouse. Pacific Symposium on Biocomputing (PSB 2002)
Tanino T, Habara T, Imanishi T and Gojoubori T (2002) Integrated Database at JBIRC . Integrated Bioinformatics
Imanishi T (2002) Comparative genomic study of human and mouse major histocompatibility complex gene regions. The First Waterfront Symposium of Human Genome Science
Nurimoto S, Koyanagi K, Gojobori T and Imanishi T (2002) Auto-Gathering Efficient System for Biological databases −Bio-AGES−,The First Waterfront Symposium of Human Genome Science
Abe H, Habara T, Okiyama S, Koyanagi K, Gojobori T and Imanishi T (2002) galign : a program for megabase genomic sequence alignment. The First Waterfront Symposium of Human Genome Science
Hayakawa Y, Koyanagi K, Tanino M, Tamura T, Gojobori T and Imanishi T (2002) gLdraw: a general tool for a comparison of chromosome maps.The First Waterfront Symposium of Human Genome Science
Imanishi T, Hayakawa Y, Koyanagi K, Tanino M, Tamura T and Gojobori T (2002) Improvement of human genome sequences assembled by the human genome sequencing consortium. The First Waterfront Symposium of Human Genome Science
Kawashima H, Todokoro F, Koyanagi K, Habara T, Tanino M, Imanishi T, Itoh T and Gojobori T (2002) Towards construction of the complete human gene catalog based on full-length cDNA. The First Waterfront Symposium of Human Genome Science
Tanino M, Yamamoto N, Makita Y, Kawashima H, Kawamura T, Ikeo K, Imanishi T and Gojobori T (2002) SOUP: a management system for large-scale functional annotation The First Waterfront Symposium of Human Genome Science
Okiyama S, Koyanagi K, Tanino M, Hayakawa Y, Tamura T, Imanishi T and Gojobori T (2002) Mapping full-length cDNA sequences on the human genome. The First Waterfront Symposium of Human Genome Science
Koyanagi K, Habara T, Itoh T, Gojobori T, Imanishi T (2002) Molecular evolutionary genetics of full-length cDNA between humans and mice. The First Waterfront Symposium of Human Genome Science
Habara T, Yamaguchi K, Aono R, Okiyama S, Abe H, Koyanagi K, Tanino M, Gojobori T and Imanishi T (2002) CGAP: Comparative Genome Analysis Package. The First Waterfront Symposium of Human Genome Science
Zhang H, Koyanagi K, Habara T, Mimiura Y, Tamura T, Imanishi T and Gojobori T (2002) BB-Plot: A tool for a demonstration of blast based sequence matches. The First Waterfront Symposium of Human Genome Science
Mimiura Y, Matsumoto R, Tamura T, Imanishi T and Gojobori T (2002) Development of Parallel Blast System for PC cluster. The First Waterfront Symposium of Human Genome Science
Mano S, Yasuda N, Tamiya G, Inoko H, Gojobori T and Imanishi T (2002) Phase Space Structure of Haplotype Frequency Estimation by the EM Algorithm. The First Waterfront Symposium of Human Genome Science
Okamoto K, Makino S, Endo T, Hayashi H, Fujimoto K, Ikuta T, Tokubo E, Satou R, Takaki A, Nagatsuka Y, Imanishi T, Gojobori T, Oka A, Tamiya G, Inoko H (2002) Comprehensive setting of 30,000 polymorphic microsatellite markers throughout human genome. The First Waterfront Symposium of Human Genome Science
Niimura Y and Gojobori T (2002) In Silico Chromosome Staining: Reconstruction of Giemsa Bands from the Whole Human Genome Sequence. The First Waterfront Symposium of Human Genome Science
Iwama H and Gojobori T (2002) Comparison on Neurotransmitter Receptor Orthologue Gene Sets between Humans and Rodents.　The First Waterfront Symposium of Human Genome Science
Itoh T (2002) Acceleration of Genomic Evolution Revealed by Genome-wide Comparison of Endocellular Symbionts. The First Waterfront Symposium of Human Genome Science
Yamaguchi Y (2002) SEQUENCE VARIATION AND EVOLUTION OF HIV-1 GP120 WITH RESPECT TO USAGE OF THE SECOND RECEPTOR . 9th International Workshop on HIV Dynamics and Evolution
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