農業生物先端ゲノム研究センター

ゲノムインフォマティックスユニット


  1. Sakai H, Naito K, Ogiso-Tanaka E, Takahashi Y, Iseki K, Muto C, Satou K, Teruya K, Shiroma A, Shimoji M, Hirano T, Itoh T, Tomooka N (2015) The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome Scientific Reports DOI: 10.1038/srep16780
  2. Numa H, Itoh T (2014) MEGANTE: A web-based system for integrated plant genome annotation Plant and Cell Physiology 55(1):e2
  3. Sakai H, Kanamori H, Arai-Kichise Y, Shibata-Hatta M, Ebana K, Oono Y, Kurita K, Fujisawa H, Katagiri S, Mukai Y, Hamada M, Itoh T, Matsumoto T, Katayose Y, Wakasa K, Yano M, Wu J (2014) Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice DNA Research 21(4):397-405
  4. The International Wheat Genome Sequencing Consortium (IWGSC) (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome Science 345(6194):1251788
  5. Tanaka T, Kobayashi F, Joshi G.P, Onuki R, Sakai H, Kanamori H, Wu J, ŠimkováH, Nasuda S, Endo TR, Hayakawa K, Doležel J, Ogihara Y, Itoh T, Matsumoto T, Handa H (2014) Next-generation survey sequencing and the molecular organization of wheat chromosome 6B DNA Research 21(2):103-114
  6. Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data Rice 6:4
  7. Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang C, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T (2013) Rice Annotation Project Database (RAP-DB): An integrative and interactive database for rice genomics Plant and Cell Physiology 54(2):e6
  8. Kawahara Y, Oono Y, Kanamori H, Matsumoto T, Itoh T, Minami E (2012) Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction PLoS ONE 7(11):e49423
  9. Rice WRKY Working Group (2012) Nomenclature report on rice WRKY's - Conflict regarding gene names and its solution Rice 5:3
  10. The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome Nature 491:711-716
  11. Yang C, Kawahara Y, Mizuno H, Wu J, Matsumoto T, Itoh T (2012) Independent domestication of Asian rice followed by gene flow from japonica to indica Molecular Biology and Evolution 29(5):1471-1479
  12. Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, Fujii N, Hori K, Itoh T, Sato K (2011) Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries Plant Physiology 156(1):20-28
  13. Mayer K.F.X, Martis M, Hedley P.E, Simkova H, Liu H, Morris J.A, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubalakova M, Suchankova P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Dolezel J, Waugh R, Stein N (2011) Unlocking the barley genome by chromosomal and comparative genomics The Plant Cell 23(4):1249-1263
  14. Oono Y, Kawahara Y, Kanamori H, Mizuno H, Yamagata H, Yamamoto M, Hosokawa S, Ikawa H, Akahane I, Zhu Z, Wu J, Itoh T, Matsumoto T (2011) mRNA-seq reveals a comprehensive transcriptome profile of rice under phosphate stress Rice 4(2):50-65
  15. Sakai H, Ikawa H, Tanaka T, Numa H, Minami H, Fujisawa M, Shibata M, Kurita K, Kikuta A, Hamada M, Kanamori H, Namiki N, Wu J, Itoh T, Matsumoto T, Sasaki T (2011) Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis The Plant Journal 66(5):796-805
  16. Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut B.S (2011) Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes Genome Biology and Evolution 3:1357-1368
  17. Amano N, Tanaka T, Numa H, Sakai H, Itoh T (2010) Efficient plant gene identification based on interspecies mapping of full-length cDNAs DNA Research 17(5):271-279
  18. Mizuno H, Kawahara Y, Sakai H, Kanamori H, Wakimoto H, Yamagata H, Oono Y, Wu J, Ikawa H, Itoh T, Matsumoto T (2010) Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.) BMC Genomics 11:683
  19. Sakai H, Itoh T (2010) Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis BMC Genomics 11:121
  20. Numa H, Nishimura M, Tanaka T, Kanamori H, Yang C, Matsumoto T, Nagamura Y, Itoh T (2009) Genome-wide validation of Magnaporthe grisea gene structures based on transcription evidence FEBS Letters 583(4):797-800
  21. Tanaka T, Koyanagi K.O, Itoh T (2009) Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis Plant Physiology 149(3):1316-1324
  22. Rice Annotation Project (2008) The Rice Annotation Project Database (RAP-DB): 2008 update Nucleic Acids Research 36:D1028-D1033
  23. Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio B.A, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, de Oliveira AC, 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 W.R, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, 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 N.K, Smith-White B, Takeda J-I, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi A.K, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana Genome Research 17(2):175-183

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