Published Papers

• Masuya H, Makita Y, Kobayashi N, Nishikata K, Yoshida Y, Mochizuki Y, Doi K, Takatsuki T, Waki K, Tanaka N, Ishii M, Matsushima A, Takahashi S, Hijikata A, Kozaki K, Furuichi T, Kawaji H, Wakana S, Nakamura Y, Yoshiki A, Murata T, Fukami-Kobayashi K, Mohan S, Ohara O, Hayashizaki Y, Mizoguchi R, Obata Y, Toyoda T.
  "The RIKEN integrated database of mammals."
  Nucleic Acids Res 39: D861-70 (2011)
  PubMed

• Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Shulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL.
  "MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data."
  Plant Physiol 155: 259-70 (2011)
  PubMed

• Hanada K, Sawada Y, Kuromori T, Klausnitzer R, Saito K, Toyoda T, Shinozaki K, Li WH, Hirai MY.
  "Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana."
  Mol Biol Evol 28: 377-82 (2011)
  PubMed

• Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH.
  "sORF finder: a program package to identify small open reading frames with high coding potential."
  Bioinformatics 26:399-400 (2010)
  PubMed

• Consortium IAI. Bastow R, Beynon J, Estelle M, Friesner J, Grotewold E, Lavagi I, Lindsey K, Meyers B, Provart N, Benfey P, Birney E, Braun P, Brendel V, Buell R, Caccamo M, Carrington J, Cherry M, Ecker J, Eppig J, Forster M, Gutiérrez R, Hilson P, Huala E, Katari M, Kersey P, Kudla J, Ma H, Matsui M, Matthews K, May S, Mayer K, Millar A, Millar H, Mjolsness E, Mockler T, Nikolau B, Nordborg M, Rawlings C, Schofield P, Schoof H, Schroeder JI, Sen TZ, Stanzione D, Town C, Toyoda T, Vision T, Walsh S, Wang X, Ware D, Weckwerth W, Yang W.
  "An international bioinformatics infrastructure to underpin the Arabidopsis community."
  Plant Cell 22:2530-6 (2010)
  PubMed

• Matsui A, Ishida J, Morosawa T, Okamoto M, Kim JM, Kurihara Y, Kawashima M, Tanaka M, To TK, Nakaminami K, Kaminuma E, Endo TA, Mochizuki Y, Kawaguchi S, Kobayashi N, Shinozaki K, Toyoda T, Seki M.
  "Arabidopsis tiling array analysis to identify the stress-responsive genes."
  Methods Mol Biol 639:141-55 (2010)
  PubMed

• Nakagami H, Sugiyama N, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K.
  "Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants."
  Plant Physiol 153:1161-74 (2010)
  PubMed

• Numa H, Kim JM, Matsui A, Kurihara Y, Morosawa T, Ishida J, Mochizuki Y, Kimura H, Shinozaki K, Toyoda T, Seki M, Yoshikawa M, Habu Y.
  "Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana."
  EMBO J 29:352-62(2010)
  PubMed

• Okamoto M, Tatematsu K, Matsui A, Morosawa T, Ishida J, Tanaka M, Endo TA, Mochizuki Y, Toyoda T, Kamiya Y, Shinozaki K, Nambara E, Seki M.
  "Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays."
  Plant J 62:39-51 (2010)
  PubMed

• Sharif J, Endo TA, Toyoda T, Koseki H.
  "Divergence of CpG island promoters: a consequence or cause of evolution?"
  Dev Growth Differ 52:545-54 (2010)
  PubMed

• Watarai H, Fujii S, Yamada D, Rybouchkin A, Sakata S, Nagata Y, Iida-Kobayashi M, Sekine-Kondo E, Shimizu K, Shozaki Y, Sharif J, Matsuda M, Mochiduki S, Hasegawa T, Kitahara G, Endo TA, Toyoda T, Ohara O, Harigaya K, Koseki H, Taniguchi M.
  "Murine induced pluripotent stem cells can be derived from and differentiate into natural killer T cells."
  J Clin Invest 120:2610-8 (2010)
  PubMed

• Hanada K, Kuromori T, Myouga F, Toyoda T, Li W, Shinozaki K.
  "Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis."
  Genome Biol Evol 1:409-14 (2009)
  PubMed

• Hanada K, Kuromori T, Myouga F, Toyoda T, Shinozaki K.
  "Increased expression and protein divergence in duplicate genes is associated with morphological diversification."
  PLoS Genet 5:e1000781 (2009)
  PubMed

• Hirabayashi Y, Suzki N, Tsuboi M, Endo TA, Toyoda T, Shinga J, Koseki H, Vidal M, Gotoh Y.
  "Polycomb limits the neurogenic competence of neural precursor cells to promote astrogenic fate transition."
  Neuron 63:600-13 (2009)
  PubMed

• Kurihara Y, Kaminuma E, Matsui A, Kawashima M, Tanaka M, Morosawa T, Ishida J, Mochizuki Y, Shinozaki K, Toyoda T, Seki M.
  "Transcriptome analyses revealed diverse expression changes in ago1 and hyl1 Arabidopsis mutants."
  Plant Cell Physiol 50:1715-20 (2009)
  PubMed

• Makita Y, Kobayashi N, Mochizuki Y, Yoshida Y, Asano S, Heida N, Deshpande M, Bhatia R, Matsushima A, Ishii M, Kawaguchi S, Iida K, Hanada K, Kuromori T, Seki M, Shinozaki K, Toyoda T.
  "PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants."
  Plant Cell Physiol 50:1249-59 (2009)
  PubMed

• Matsushima A, Kobayashi N, Mochizuki Y, Ishii M, Kawaguchi S, Endo TA, Umetsu R, Makita Y, Toyoda T.
  "OmicBrowse: a Flash-based high-performance graphics interface for genomic resources."
  Nucleic Acids Res 37:W57-62 (2009)
  PubMed

• Saeki Y, Endo T, Ide K, Nagashima T, Yumoto N, Toyoda T, Suzuki H, Hayashizaki Y, Sakaki Y, Okada-Hatakeyama M.
  "Ligand-specific sequential regulation of transcription factors for differentiation of MCF-7 cells."
  BMC Genomics 10:545 (2009)
  PubMed

• Yoshida Y, Makita Y, Heida N, Asano S, Matsushima A, Ishii M, Mochizuki Y, Masuya H, Wakana S, Kobayashi N, Toyoda T.
  "PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning."
  Nucleic Acids Res 37:W147-52 (2009)
  PubMed

• Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T, Tanaka M, Kaminuma E, Mochizuki Y, Matsushima A, Toyoda T, Shinozaki K, Seki M.
  "Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis."
  PNAS. (2008)
  

• Kaminuma E, Masuya H, Miura I, Motegi H, Takahashi K R, Nakazawa M, Matsui M, Gondo Y, Noda T, Shiroishi T, Wakana S, Toyoda T.
  "Objective evaluation measures of genetic marker selection in large-scale SNP genotyping."
  J Bioinform Comput Biol. 6(5), 905-917 (2008)
  PubMed

• Kaminuma E, Yoshizumi T, Wada T, Matsui M, Toyoda T.
  "Quantitative analysis of heterogeneous spatial distribution of Arabidopsis leaf trichomes using micro X-ray computed tomography."
  The Plant Journal 56(3), 470-482 (2008)
  PubMed

• Kim JM, To TK, Ishida J, Morosawa T, Kawashima M, Matsui A, Toyoda T, Kimura H, Shinozaki K, Seki M.
  "Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana."
  Plant Cell Physiol. 49(10), 1580-1588 (2008)
  PubMed

• Kurihara Y, Matsui A, Kawashima M, Kaminuma E, Ishida J, Morosawa T, Mochizuki Y, Kobayashi N, Toyoda T, Shinozaki K, Seki M.
  "Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis."
  Biochem Biophys Res Commun. 2008 Sep 19. [Epub ahead of print]
  PubMed

• Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, Endo TA, Okamoto M, Nambara E, Nakajima M, Kawashima M, Satou M, Kim JM, Kobayashi N, Toyoda T, Shinozaki K, Seki M.
  "Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array."
  Plant Cell Physiol. 49(8), 1135-1149 (2008)
  PubMed  Supplementary data

• Kobayashi N, Toyoda T.
  "Statistical Search on the Semantic Web."
  Bioinformatics. 24(7), 1002-1010 (2008)
  PDF  Supplementary data

• Endoh M, Endo T A, Endoh T, Fujimura Y, Ohara O, Toyoda T, Otte A P, Okano M, Brockdorff N, Vidal M, Koseki H .
  "Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity."
  Development. 135(8), 1513-1524 (2008)
  PubMed

• Nagashima T, Suzuki T, Kondo S, Kuroki Y, Takahashi K, Ide K, Hasegawa A, Toyoda T, Kojima T, Konagaya A, Suzuki H, Hayashizaki Y, Sakaki Y, Hatakeyama M.
  "Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in Heregulin-stimulated MCF-7 cells."
  PLoS ONE. 3(3), e1803 (2008)
  PubMed  PDF

• Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo TA, Shinga J, Mizutani-Koseki Y, Toyoda T, Okamura K, Tajima S, Mitsuya K, Okano M, Koseki H.
  "The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA."
  Nature. 450, 908-912 (2007)
  PubMed

• Masuya H, Yoshikawa S, Heida N, Toyoda T, Wakana S, Shiroishi T.
  "PhenoSITE: a web database integrating mouse phenotyping platform and the experimental procedures in mice."
  J Bioinform Comput Biol. 5(6), 1173-91 (2007)
  PubMed

• The Mouse Phenotype Database Integration Consortium
  "Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources."
  Mammalian Genome. 18(3), 157-163 (2007)
  PubMed

• Toyoda T, Mochizuki Y, Player K, Heida N, Sakaki Y.
  "OmicBrowse: a browser of multidimensional omics annotations."
  Bioinformatics 23, 524-526 (2006)
  PubMed  PDF

• Hasegawa Y, Seki M, Mochizuki Y, Heida N, Hirosawa K, Okamoto N, Sakurai T, Satou M, Akiyama K, Iida K, Lee K, Kanaya S, Demura T, Shinozaki K, Konagaya A, Toyoda T.
  "A flexible representation of omic knowledge for thorough analysis of microarray data."
  Plant Methods. 2, 5 (2006)
  PubMed  PDF

• Kaminuma E, Heida N, Yoshizumi T, Nakazawa M, Matsui M, Toyoda T.
  "In silico phenotypic screening method of mutants based on statistical modeling of genetically mixed samples."
  J Bioinform Comput Biol. 3(6), 1281-93 (2005)
  PubMed

• Toyoda T, Shinozaki K.
  " Tiling-array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models."
  The Plant Journal, 43(3), 611-621 (2005)
  PubMed  PDF

• Kaminuma E, Heida N, Tsumoto Y, Nakazawa M, Goto N, Konagaya A, Matsui M, Toyoda T.
  "Three-dimensional definition of leaf morphological traits of Arabidopsis in silico phenotypic analysis."
  J Bioinform Comput Biol, 3(2), 401-414 (2005)
  PubMed

• Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K.
  "RARTF: database and tools for complete sets of Arabidopsis transcription factors."
  DNA Res. 12(4), 247-256 (2005)
  PubMed  PDF

• Sakurai T, Satou M, Akiyama K, Iida K, Seki M, Kuromori T, Ito T, Konagaya A, Toyoda T, Shinozaki K.
  "RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome."
  Nucleic Acids Res. 33, Database issue D647-50
  PubMed  PDF

• Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K.
  " Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences."
  Nucleic Acids Res. 32(17), 5096-103 (2004)
  PubMed  PDF

• Toyoda T, Wada A.
  "Omic space: coordinate-based integration and analysis of genomic phenomic interactions."
  Bioinformatics 20(11), 1759-1765 (2004)
  PubMed  PDF

• Heida N, Hasegawa Y, Mochizuki Y, Hirosawa K, Konagaya A, Toyoda T.
  "TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks."
  Bioinformatics 20, i152-i160 (2004)
  PubMed  PDF

• Kaminuma E, Heida N, Tsumoto Y, Yamamoto N, Goto N, Okamoto N, Konagaya A, Matsui M, Toyoda T.
  "Automatic quantification of morphological traits via three-dimensional measurement of Arabidopsis."
  Plant J 38(2), 358-365 (2004)
  PubMed

• Toyoda T, Mochizuki Y, Konagaya A.
  GSCOPE: A Clipped Fisheye Viewer for Biomolecular Network Graphs.
  Bioinformatics 19(3), 437-438 (2003)
  PubMed  PDF

• Toyoda T, Konagaya A.
  "KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data."
  Bioinformatics 19(3), 433-434 (2003)
  PubMed  PDF

　

Presentation

• ISMB/ECCB2004

  　

Markup Languages

• The Omic Space Markup Language Version 1.1

osml.pdf (Feb 3, 2005. 146 KB)

• The Genetic Mapdata Markup Language Version 1.0

GMML_1.0.pdf (Aug 5, 2004. 388 KB)

　

Applications & Databases