Company Overview

Publications

Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M, Kawashima K, Minami C, Muraki A, Nakazaki N, Takahashi C, Nakayama S, Kishida Y, Kohara M, Yamada M, Tsuruoka H, Sasamoto S, Tabata S, Aizu T, Toyoda A, Shin-I T, Minakuchi Y, Kohara Y, Fujiyama A, Tsuchimoto S, Kajiyama S, Makigano E, Ohmido N, Shibagaki N, Cartagena JA, Wada N, Kohinata T, Atefeh A, Yuasa S, Matsunaga S, Fukui K. : "Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L." DNA research : an international journal for rapid publication of reports on genes and genomes. 18(1):65-76(2011)

Katsuma S, Kang W, Shin-I T, Ohishi K, Kadota K, Kohara Y, Shimada T. : "Mass identification of transcriptional units expressed from the Bombyx mori nucleopolyhedrovirus genome." The Journal of general virology. 92(Pt 1):200-3(2011)

Aoki K, Yano K, Suzuki A, Kawamura S, Sakurai N, Suda K, Kurabayashi A, Suzuki T, Tsugane T, Watanabe M, Ooga K, Torii M, Narita T, Shin-I T, Kohara Y, Yamamoto N, Takahashi H, Watanabe Y, Egusa M, Kodama M, Ichinose Y, Kikuchi M, Fukushima S, Okabe A, Arie T, Sato Y, Yazawa K, Satoh S, Omura T, Ezura H, Shibata D. : "Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics." BMC genomics. 11:210(2010)

Mukaide M, Tanaka Y, Shin-I T, Yuen MF, Kurbanov F, Yokosuka O, Sata M, Karino Y, Yamada G, Sakaguchi K, Orito E, Inoue M, Baqai S, Lai CL, Mizokami M. : "Mechanism of entecavir resistance of hepatitis B virus with viral breakthrough as determined by long-term clinical assessment and molecular docking simulation." Antimicrobial agents and chemotherapy. 54(2):882-9(2010)

Manickavelu A, Kawaura K, Oishi K, Shin-I T, Kohara Y, Yahiaoui N, Keller B, Suzuki A, Yano K, Ogihara Y. : "Comparative gene expression analysis of susceptible and resistant near-isogenic lines in common wheat infected by Puccinia triticina." DNA research : an international journal for rapid publication of reports on genes and genomes. 17(4):211-22(2010)

Tanino M, Matoba R, Nakamura S, Kameda H, Amano K, Okayama T, Nagasawa H, Suzuki K, Matsubara K, Takeuchi T. (2009) "Prediction of efficacy of anti-TNF biologic agent, infliximab, for rheumatoid arthritis patients using a comprehensive transcriptome analysis of white blood cells." Biochem Biophys Res Commun. 2009 Sep 18;387(2):261-5.

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Bjorkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hornquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schonbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegner J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y. (2009) "The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line." Nat Genet. 2009 May;41(5):553-62.

Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K. (2009) "BodyParts3D: 3D structure database for anatomical concepts." Nucleic Acids Res. 37(Database issue):D782-5.

Hashimoto H, Miyamoto R, Watanabe N, Shiba D, Ozato K, Inoue C, Kubo Y, Koga A, Jindo T, Narita T, Naruse K, Ohishi K, Nogata K, Shin-I T, Asakawa S, Shimizu N, Miyamoto T, Mochizuki T, Yokoyama T, Hori H, Takeda H, Kohara Y, Wakamatsu Y. : "Polycystic kidney disease in the medaka (Oryzias latipes) pc mutant caused by a mutation in the Gli-Similar3 (glis3) gene." PloS one. 4(7):e6299(2009)

Sato K, Shin-I T, Seki M, Shinozaki K, Yoshida H, Takeda K, Yamazaki Y, Conte M, Kohara Y. : "Development of 5006 full-length CDNAs in barley: a tool for accessing cereal genomics resources." DNA research : an international journal for rapid publication of reports on genes and genomes. 16(2):81-9(2009)

Genome Information Integration Project And H-Invitational 2, 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 Mde F, 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 MB, 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, Gojobori T. (2008) "The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts." Nucleic Acids Res. 36(Database issue):D793-9.

Yu JK, Wang MC, Shin-I T, Kohara Y, Holland LZ, Satoh N, Satou Y. : "A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae." Development genes and evolution. 218(11-12):723-7(2008)

Xia Q, Wang J, Zhou Z, Li R, Fan W, Cheng D, Cheng T, Qin J, Duana J, Xu H, Li Q, Li N, Wang M, Dai F, Liu C, Lin Y, Zhao P, Zhang H, Liu S, Zha X, Li C, Zhao A, Pan M, Pan G, Shen Y, Gao Z, Wang Z, Wang G, Wu Z, Hou Y, Chai C, Yu Q, He N, Zhang Z, Li S, Yang H, Lu C, Wang J, Xiang Z, Mita K, Kasahara M, Nakatani Y, Yamamoto K, Abe H, Ahsan B, Daimoni T, Doi K, Fujii T, Fujiwara H, Fujiyama A, Futahashi R, Hashimotol S, Ishibashi J, Iwami M, Kadono-Okuda K, Kanamori H, Kataoka H, Katsuma S, Kawaoka S, Kawasaki H, Kohara Y, Kozaki T, Kuroshu RM, Kuwazaki S, Matsushima K, Minami H, Nagayasu Y, Nakagawa T, Narukawa J, Nohata J, Ohishi K, Ono Y, Osanai-Futahashi M, Ozaki K, Qu W, Roller L, Sasaki S, Sasaki T, Seino A, Shimomura M, Shimomura M, Shin-I T, Shinoda T, Shiotsuki T, Suetsugu Y, Sugano S, Suwa M, Suzuki Y, Takiya S, Tamura T, Tanaka H, Tanaka Y, Touhara K, Yamada T, Yamakawa M, Yamanaka N, Yoshikawa H, Zhong YS, Shimada T, Morishita S. : "The genome of a lepidopteran model insect, the silkworm Bombyx mori." Insect biochemistry and molecular biology. 38(12):1036-45(2008)

Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiテゥrrez EL, Dubchak I, Garcia-Fernテ?dez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS. : "The amphioxus genome and the evolution of the chordate karyotype." Nature. 453(7198):1064-71(2008)

Shin-I T, Tanaka Y, Tateno Y, Mizokami M. : "Development and public release of a comprehensive hepatitis virus database." Hepatology research : the official journal of the Japan Society of Hepatology. 38(3):234-43(2008)

Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL. : "The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants." Science (New York, N.Y.). 319(5859):64-9(2008)

Ahsan B, Kobayashi D, Yamada T, Kasahara M, Sasaki S, Saito TL, Nagayasu Y, Doi K, Nakatani Y, Qu W, Jindo T, Shimada A, Naruse K, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Kohara Y, Morishita S. : "UTGB/medaka: genomic resource database for medaka biology." Nucleic acids research. 36(Database issue):D747-52(2008)

Gyoja F, Satou Y, Shin-I T, Kohara Y, Swalla BJ, Satoh N. : "Analysis of large scale expression sequenced tags (ESTs) from the anural ascidian, Molgula tectiformis." Developmental biology. 307(2):460-82(2007)

Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y, Jindo T, Kobayashi D, Shimada A, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Morishita S, Kohara Y. : "The medaka draft genome and insights into vertebrate genome evolution." Nature. 447(7145):714-9(2007)

Yamato KT, Ishizaki K, Fujisawa M, Okada S, Nakayama S, Fujishita M, Bando H, Yodoya K, Hayashi K, Bando T, Hasumi A, Nishio T, Sakata R, Yamamoto M, Yamaki A, Kajikawa M, Yamano T, Nishide T, Choi SH, Shimizu-Ueda Y, Hanajiri T, Sakaida M, Kono K, Takenaka M, Yamaoka S, Kuriyama C, Kohzu Y, Nishida H, Brennicke A, Shin-I T, Kohara Y, Kohchi T, Fukuzawa H, Ohyama K. : "Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system." Proceedings of the National Academy of Sciences of the United States of America. 104(15):6472-7(2007)

Yu JK, Satou Y, Holland ND, Shin-I T, Kohara Y, Satoh N, Bronner-Fraser M, Holland LZ. : "Axial patterning in cephalochordates and the evolution of the organizer." Nature. 445(7128):613-7(2007)

Ogasawara O, Otsuji M, Watanabe K, Iizuka T, Tamura T, Hishiki T, Kawamoto S, Okubo K.(2006) "BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression." Nucleic Acids Res. 34(Database issue):D628-31.

Kuiken C, Combet C, Bukh J, Shin-I T, Deleage G, Mizokami M, Richardson R, Sablon E, Yusim K, Pawlotsky JM, Simmonds P. : "A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes." Hepatology (Baltimore, Md.). 44(5):1355-61(2006)

Mochida K, Kawaura K, Shimosaka E, Kawakami N, Shin-I T, Kohara Y, Yamazaki Y, Ogihara Y. : "Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat." Molecular genetics and genomics : MGG. 276(3):304-12(2006)

Kuiken C, Mizokami M, Deleage G, Yusim K, Penin F, Shin-I T, Charavay C, Tao N, Crisan D, Grando D, Dalwani A, Geourjon C, Agrawal A, Combet C. : "Hepatitis C databases, principles and utility to researchers." Hepatology (Baltimore, Md.). 43(5):1157-65(2006)

Terasaki H, Murakami R, Yasuhiko Y, Shin-I T, Kohara Y, Saga Y, Takeda H. : "Transgenic analysis of the medaka mesp-b enhancer in somitogenesis." Development, growth & differentiation. 48(3):153-68(2006)

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.

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.

Hishiki T, Tamura T, Oyama H. (2005) "GenoCache: a Genomics and Cancer Chemoprevention portal" AMIA Annu Symp Proc. 2005:980.

Simmonds P, Bukh J, Combet C, Delテゥage G, Enomoto N, Feinstone S, Halfon P, Inchauspテゥ G, Kuiken C, Maertens G, Mizokami M, Murphy DG, Okamoto H, Pawlotsky JM, Penin F, Sablon E, Shin-I T, Stuyver LJ, Thiel HJ, Viazov S, Weiner AJ, Widell A. : "Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes." Hepatology (Baltimore, Md.). 42(4):962-73(2005)

Suzuki T, Shin-I T, Fujiyama A, Kohara Y, Kasahara M. : "Hagfish leukocytes express a paired receptor family with a variable domain resembling those of antigen receptors." Journal of immunology (Baltimore, Md. : 1950). 174(5):2885-91(2005)

田村卓郎, 池尾一穂, 五條堀孝.: "統合データベース(1): ゲノムネットワークプロジェクトにおける統合データベース", 蛋白質核酸酵素, 49: 2916-20(2004)

岡山利次, 池尾一穂, 五條堀孝; "統合データベース(2): データからみたインフォマティックス", 蛋白質核酸酵素, 49: 2921-27(2004)

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.

Watanabe M, Kobayashi N, Shin-I T, Horiike T, Tateno Y, Kohara Y, Okada N. : "Extensive analysis of ORF sequences from two different cichlid species in Lake Victoria provides molecular evidence for a recent radiation event of the Victoria species flock: identity of EST sequences between Haplochromis chilotes and Haplochromis sp. "Redtailsheller"." Gene. 343(2):263-9(2004)

Kawahara Y, Matsuo T, Nozawa M, Shin-I T, Kohara Y, Aigaki T. : "Comparative sequence analysis of a gene-dense region among closely related species of Drosophila melanogaster." Genes & genetic systems. 79(6):351-9(2004)

Suzuki T, Shin-I T, Kohara Y, Kasahara M. : "Transcriptome analysis of hagfish leukocytes: a framework for understanding the immune system of jawless fishes." Developmental and comparative immunology. 28(10):993-1003(2004)

Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, Kamiya A, Shinozaki K, Carninci P, Hayashizaki Y, Shin-I T, Kohara Y, Yamazaki Y. : "Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags." Genes & genetic systems. 79(4):227-32(2004)

Nozaki H, Matsuzaki M, Misumi O, Kuroiwa H, Hasegawa M, Higashiyama T, Shin-I T, Kohara Y, Ogasawara N, Kuroiwa T. : "Cyanobacterial genes transmitted to the nucleus before divergence of red algae in the Chromista." Journal of molecular evolution. 59(1):103-13(2004)

Kimura T, Jindo T, Narita T, Naruse K, Kobayashi D, Shin-I T, Kitagawa T, Sakaguchi T, Mitani H, Shima A, Kohara Y, Takeda H. : "Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics." Mechanisms of development. 121(7-8):915-32(2004)

Katogi R, Nakatani Y, Shin-I T, Kohara Y, Inohaya K, Kudo A. : "Large-scale analysis of the genes involved in fin regeneration and blastema formation in the medaka, Oryzias latipes." Mechanisms of development. 121(7-8):861-72(2004)

Maruyama S, Misumi O, Ishii Y, Asakawa S, Shimizu A, Sasaki T, Matsuzaki M, Shin-I T, Nozaki H, Kohara Y, Shimizu N, Kuroiwa T. : "The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae." DNA research : an international journal for rapid publication of reports on genes and genomes. 11(2):83-91(2004)

Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T. : "Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D." Nature. 428(6983):653-7(2004)

Mita K, Kasahara M, Sasaki S, Nagayasu Y, Yamada T, Kanamori H, Namiki N, Kitagawa M, Yamashita H, Yasukochi Y, Kadono-Okuda K, Yamamoto K, Ajimura M, Ravikumar G, Shimomura M, Nagamura Y, Shin-I T, Abe H, Shimada T, Morishita S, Sasaki T. : "The genome sequence of silkworm, Bombyx mori." DNA research : an international journal for rapid publication of reports on genes and genomes. 11(1):27-35(2004)

Ikeo, K., Ishi-i, J., Tamura, T., Gojobori, T., Tateno, Y.: "CIBEX: center for information biology gene expression database." C R Biol., 326: 1079-1082(2003)

Nishiyama T, Fujita T, Shin-I T, Seki M, Nishide H, Uchiyama I, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K, Kohara Y, Hasebe M. : "Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution." Proceedings of the National Academy of Sciences of the United States of America. 100(13):8007-12(2003)

Ohta N, Matsuzaki M, Misumi O, Miyagishima SY, Nozaki H, Tanaka K, Shin-I T, Kohara Y, Kuroiwa T. : "Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae." DNA research : an international journal for rapid publication of reports on genes and genomes. 10(2):67-77(2003)

Nozaki H, Matsuzaki M, Takahara M, Misumi O, Kuroiwa H, Hasegawa M, Shin-I T, Kohara Y, Ogasawara N, Kuroiwa T. : "The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids." Journal of molecular evolution. 56(4):485-97(2003)

Ogihara Y, Mochida K, Nemoto Y, Murai K, Yamazaki Y, Shin-I T, Kohara Y. "Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags." Plant J. 33(6):1001-11(2003)

Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS.: "The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins." Science. 13;298(5601):2157-67(2002)

Inaba K, Padma P, Satouh Y, Shin-I T, Kohara Y, Satoh N, Satou Y.: "EST analysis of gene expression in testis of the ascidian Ciona intestinalis." Mol Reprod Dev. 62(4):431-45(2002)

田村卓郎, 大久保公策: "遺伝子の発現地図-ゲノムとプロテオームの間", 蛋白質核酸酵素, 47: 906-913(2002)