Riu Yamashita

yamashita_850

HP : http://www.hgc.jp/~ryamasi/Japanese/index.html

  • Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lﾃｼtteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics. 2014 Feb 5;5(1):5.
  • Okuyama K, Ikawa T, Gentner B, Hozumi K, Harnprasopwat R, Lu J, Yamashita R, Ha D, Toyoshima T, Chanda B, Kawamata T, Yokoyama K, Wang S, Ando K, Lodish HF, Tojo A, Kawamoto H, Kotani A. MicroRNA-126-mediated control of cell fate in B-cell myeloid progenitors as a potential alternative to transcriptional factors. Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13410-5.
  • Ozawa M, Sakatani M, Yao J, Shanker S, Yu F, Yamashita R, Wakabayashi S, Nakai K, Dobbs KB, Sudano MJ, Farmerie WG, Hansen PJ. Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst. BMC Dev Biol. 2012 Nov 6;12:33.
  • Ohkura N, Hamaguchi M, Morikawa H, Sugimura K, Tanaka A, Ito Y, Osaki M, Tanaka Y, Yamashita R, Nakano N, Huehn J, Fehling HJ, Sparwasser T, Nakai K, Sakaguchi S. T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development. Immunity. 2012 Nov 16;37(5):785-99
  • Morita S, Takahashi RU, Yamashita R, Toyoda A, Horii T, Kimura M, Fujiyama A, Nakai K, Tajima S, Matoba R, Ochiya T, Hatada I. Genome-Wide Analysis of DNA Methylation and Expression of MicroRNAs in Breast Cancer Cells. Int J Mol Sci. 2012;13(7):8259-72.
  • Katayama T. et al, The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics. 2011 Aug 2;2:4.
  • Yamashita R., Sugano S., Suzuki Y. and Nakai K. DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res, 40(1), D150-4, Jan 2012.
  • Yamashita R., Sathira N.P., Kanai A., Tanimoto K., Arauchi T., Tanaka Y., Hashimoto S., Sugano S., Nakai K. and Suzuki Y. Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res, 21(5), 775-89, May 2011.
  • Okamura K., Yamashita R., Takimoto N., Nishitsuji K., Suzuki Y., Kusakabe G., T. and Nakai K. Profiling ascidian promoters as the primordial type of vertebrate promoter. BMC Genomics, 12(Suppl 3), S7, Nov 30 2011.
  • Ohshima D., Qin J., Konno H., Hirosawa A., Shiraishi T., Yanai H., Shimo Y., Shinzawa M., Akiyama N., Yamashita R., Nakai K., Akiyama T. and Inoue J. RANK signaling induces interferon-stimulated genes in the fetal thymic stroma. Biochem Biophys Res Commun, 408(4), 530-6, May 20 2011.
  • Katayama T., Wilkinson M.D., Vos R., Kawashima T., Kawashima S., Nakao M., Yamamoto Y., Chun H.W., Yamaguchi A., Kawano S., Aerts J., Aoki-Kinoshita K.F., Arakawa K., Aranda B., Bonnal R.J., Fernandez J.M., Fujisawa T., Gordon P.M., Goto N., Haider S., Harris T., Hatakeyama T., Ho I., Itoh M., Kasprzyk A., Kido N., Kim Y.J., Kinjo A.R., Konishi F., Kovarskaya Y., von Kuster G., Labarga A., Limviphuvadh V., McCarthy L., Nakamura Y., Nam Y., Nishida K., Nishimura K., Nishizawa T., Ogishima S., Oinn T., Okamoto S., Okuda S., Ono K., Oshita K., Park K.J., Putnam N., Senger M., Severin J., Shigemoto Y., Sugawara H., Taylor J., Trelles O., Yamasaki C., Yamashita R., Satoh N. and Takagi T. The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics, 2, 4, 2011.
  • Irie T., Park S.J., Yamashita R., Seki M., Yada T., Sugano S., Nakai K. and Suzuki Y. Predicting promoter activities of primary human DNA sequences. Nucleic Acids Res, 39(11), e75, Jun 2011.
  • Yamashita R., Wakaguri H., Sugano S., Suzuki Y. and Nakai K. DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Res, 38(Database issue), D98-104, Jan 2010.
  • Tanaka Y., Yamashita R., Suzuki Y. and Nakai K. Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics, 11, 309, 2010.
  • Sathira N., Yamashita R., Tanimoto K., Kanai A., Arauchi T., Kanematsu S., Nakai K., Suzuki Y. and Sugano S. Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer. DNA Res, 17(3), 169-83, Jun 2010.
  • Tsuchihara K., Suzuki Y., Wakaguri H., Irie T., Tanimoto K., Hashimoto S., Matsushima K., Mizushima-Sugano J., Yamashita R., Nakai K., Bentley D., Esumi H. and Sugano S. Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res, 37(7), 2249-63, Apr 2009.
  • Sierro N., Li S., Suzuki Y., Yamashita R. and Nakai K. Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis. Gene, 430(1-2), 44-9, Feb 1 2009.
  • Yamashita R., Suzuki Y., Takeuchi N., Wakaguri H., Ueda T., Sugano S. and Nakai K. Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. Nucleic Acids Res, 36(11), 3707-15, Jun 2008.
  • Wakaguri H., Yamashita R., Suzuki Y., Sugano S. and Nakai K. DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res, 36(Database issue), D97-101, Jan 2008.
  • Hatada I., Morita S., Kimura M., Horii T., Yamashita R. and Nakai K. Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells. J Hum Genet, 53(2), 185-91, 2008.
  • Chiba H., Yamashita R., Kinoshita K. and Nakai K. Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. BMC Genomics, 9, 152, 2008.
  • Tsuritani K., Irie T., Yamashita R., Sakakibara Y., Wakaguri H., Kanai A., Mizushima-Sugano J., Sugano S., Nakai K. and Suzuki Y. Distinct class of putative “non-conserved” promoters in humans: comparative studies of alternative promoters of human and mouse genes. Genome Res, 17(7), 1005-14, Jul 2007.
  • Sakakibara Y., Irie T., Suzuki Y., Yamashita R., Wakaguri H., Kanai A., Chiba J., Takagi T., Mizushima-Sugano J., Hashimoto S., Nakai K. and Sugano S. Intrinsic promoter activities of primary DNA sequences in the human genome. DNA Res, 14(2), 71-7, Apr 2007.
  • Okumura T., Makiguchi H., Makita Y., Yamashita R. and Nakai K. Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Res, 35(Web Server issue), W227-31, Jul 2007.
  • Yamashita R., Suzuki Y., Wakaguri H., Tsuritani K., Nakai K. and Sugano S. DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res, 34(Database issue), D86-9, Jan 1 2006.
  • Sierro N., Kusakabe T., Park K.J., Yamashita R., Kinoshita K. and Nakai K. DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res, 34(Database issue), D552-5, Jan 1 2006.
  • Kimura K., Wakamatsu A., Suzuki Y., Ota T., Nishikawa T., Yamashita R., Yamamoto J., Sekine M., Tsuritani K., Wakaguri H., Ishii S., Sugiyama T., Saito K., Isono Y., Irie R., Kushida N., Yoneyama T., Otsuka R., Kanda K., Yokoi T., Kondo H., Wagatsuma M., Murakawa K., Ishida S., Ishibashi T., Takahashi-Fujii A., Tanase T., Nagai K., Kikuchi H., Nakai K., Isogai T. and Sugano S. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res, 16(1), 55-65, Jan 2006.
  • Cheong J., Yamada Y., Yamashita R., Irie T., Kanai A., Wakaguri H., Nakai K., Ito T., Saito I., Sugano S. and Suzuki Y. Diverse DNA methylation statuses at alternative promoters of human genes in various tissues. DNA Res, 13(4), 155-67, Aug 31 2006.
  • Yamashita R., Suzuki Y., Sugano S. and Nakai K. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene, 350(2), 129-36, May 9 2005.
  • Kato K., Yamashita R., Matoba R., Monden M., Noguchi S., Takagi T. and Nakai K. Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res, 33(Database issue), D533-6, Jan 1 2005.
  • Suzuki Y., Yamashita R., Sugano S. and Nakai K. DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res, 32(Database issue), D78-81, Jan 1 2004.
  • Suzuki Y., Yamashita R., Shirota M., Sakakibara Y., Chiba J., Mizushima-Sugano J., Nakai K. and Sugano S. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Genome Res, 14(9), 1711-8, Sep 2004.
  • Suzuki Y., Yamashita R., Shirota M., Sakakibara Y., Chiba J., Mizushima-Sugano J., Kel A.E., Arakawa T., Carninci P., Kawai J., Hayashizaki Y., Takagi T., Nakai K. and Sugano S. Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biol, 4(4), 429-44, 2004.
  • Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S., Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Ohara O., Isogai T. and Sugano S. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet, 36(1), 40-5, Jan 2004.
  • Yamashita R., Suzuki Y., Nakai K. and Sugano S. Small open reading frames in 5′ untranslated regions of mRnas. C R Biol, 326(10-11), 987-91, Oct-Nov 2003.
  • Muro S., Takemasa I., Oba S., Matoba R., Ueno N., Maruyama C., Yamashita R., Sekimoto M., Yamamoto H., Nakamori S., Monden M., Ishii S. and Kato K. Identification of expressed genes linked to malignancy of human colorectal carcinoma by parametric clustering of quantitative expression data. Genome Biol, 4(3), R21, 2003.
  • Suzuki Y., Yamashita R., Nakai K. and Sugano S. DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res, 30(1), 328-31, Jan 1 2002.
  • Sugano S., Suzuki Y., Yamashita R., and Nakai K. Oligo-capped cDNAs for promoter identification and annotation. International Congress Series. International Congress Series 1246, 233-239, Dec 2002.
  • Yamashita R., Matsubara K. and Kato K. A comprehensive collection of mouse zinc finger motifs compiled by molecular indexing. Gene, 274(1-2), 101-10, Aug 22 2001.