Published Papers

• 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

• 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. in press.

• 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)
  PDF

• 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

• 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

• 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

• 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

• 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

• 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.
  " 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, 358-365 (2004)
  PubMed

• Toyoda T, Mochizuki Y, Konagaya A.
  GSCOPE: A Clipped Fisheye Viewer for Biomolecular Network Graphs.
  Bioinformatics 19, 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, 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