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Education
- Ph.D. ... Department of Anthropology, Graduate School of Science, University of Tokyo (1993)
- B.Sc. ... Department of Anthropology, Faculty of Science, University of Tokyo (1988)
Research Experience
- JSPS Postdoctoral Research Fellow (Univ. Tokyo) ... 1993-1994
- Assistant Professor, National Institute of Genetics ... 1994-2001
- Visiting Scholar, University of Washington ... 1998-1999
- Team Leader, Integrated Database Team, BIRC, AIST ... 2001-2008
- Team Leader, Integrated Database and Systems Biology Team, BIRC, AIST ... 2008-present
- Visiting Associate Professor, Tokyo Metropolitan University ... 2002-present
- Visiting Professor, Hokkaido University ... 2004-present
Recent Publications [2004-] (complete list is in preparation)
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. Ann Hum Genet. 68: 257-64. [PubMed] [AHG]
- 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. [PubMed] [PLoS Biology]
- 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]
- 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]
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(Database issue): D567-72. [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: 107-19. [PubMed] [Gene]
- 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: 169-176. [PubMed]
- Fujii Y, Itoh T, Sakate R, Koyanagi KO, 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. [PubMed]
- 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. [PubMed]
- 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: 2305-2321. [PubMed]
2006
- 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. [PubMed]
- 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-W349. [PubMed]
- 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: 63-71. [PubMed]
- 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: 3917-3928. [PubMed]
- Shimizu K, Tokimasa K, Takeuchi Y, Batsuuri J, Nyamkhishig S, Dashnyam B, Dashnyam S, Gereksaikhan T, Tanabe Y, Omoto K, Imanishi T, Harihara S, Hao L, and Jing F (2006) Frequencies of the β-globin gene cluster haplotypes of Khalkhs in Mongolia and Buryats in northeast China. Human Biology 78(6): 749-756. [PubMed]
2007
- 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. [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. [PubMed]
- 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. [PubMed] [Genome Res]
*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: 196-203. [PubMed] [Gene]
- 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]
- 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]
2008
- 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]
- Shimizu K, Nagaoka E, Okada Y, Takeuchi Y, Harihara S, Omoto K, Imanishi T, Kim W, Shin DJ, Hao L, and Jin F (2008) Characteristics of the β-globin gene cluster haplotypes of three Han Chinese populations at Beijing, Xi'an, and Kunming as compared with those of other Asian populations. Biochemical Genetics 46: 566-582. [PubMed] [Biochem Genet]
- Jin L, Kryukov K, Clemente JC, Komiyama T, Suzuki Y, Imanishi T, Ikeo K, and Gojobori T (2008) The evolutionary relationship between gene duplication and alternative splicing. Gene 427: 19-31. [PubMed] [Gene]
- Yamaguchi-Kabata Y, Shimada MK, 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. [PubMed] [PLoS One]
- 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: comparative genomics analysis using well-annotated full-length cDNAs. Nucleic Acids Research 36: 6386-6395. [PubMed] [NAR]
2009
- 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]
- 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]
- 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]
- 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 25: 3321-3322. [PubMed] [Bioinformatics]
- 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]
- 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]
2010
- 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 39 (Database Issue): D807-D814 (gkq1144). [PubMed] [NAR]
- Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; on behalf of the BioDBCore working group (2010) Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research 39 (Database Issue): D7-D10 (gkq1173). [PubMed] [NAR]
2011
- 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]
Links
[Organizations]
[Updated on October 12, 2011]
Tadashi Imanishi, Dr. Sci.
Integrated Database and Systems Biology Team (IDB), Leader
Biomedicinal Information Research Center (BIRC)
National Institute of Advanced Industrial Science and Technology (AIST)
AIST Waterfront Bio-IT Research Building,
Aomi 2-4-7, Koto-ku, Tokyo 135-0064, Japan
Tel. +81-3-3599-8800, Fax. +81-3-3599-8801
E-mail: t.imanishi [at] aist.go.jp
