Hideya Kawaji

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. pmc The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
    Toshiaki Katayama
    Database Center for Life Science, Research Organization of Information and Systems, 2 11 16, Yayoi, Bunkyo ku, Tokyo, 113 0032, Japan
    J Biomed Semantics 4:6. 2013
  2. pmc Alternate transcription of the Toll-like receptor signaling cascade
    Christine A Wells
    Eskitis Institute for Cell and Molecular Therapies, School of Biological and Biomedical Sciences, Griffith University, Brisbane 4111, Australia
    Genome Biol 7:R10. 2006
  3. pmc The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho Tsurumi ku Yokohama, Kanagawa, 230 0045 Japan
    Genome Biol 10:R40. 2009
  4. pmc SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    BMC Bioinformatics 10:133. 2009
  5. pmc Hidden layers of human small RNAs
    Hideya Kawaji
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    BMC Genomics 9:157. 2008
  6. pmc Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama City, Kanagawa 230 0045, Japan
    Nucleic Acids Res 39:D856-60. 2011
  7. pmc FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
    Jessica Severin
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho Tsurumi ku Yokohama, Kanagawa, 230 0045 Japan
    Genome Biol 10:R39. 2009
  8. pmc CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis
    Hideya Kawaji
    NTT Software Corporation, Teisan Kannai Building 209, Yamashita cho Naka ku, Yokohama, Kanagawa, 231 8551, Japan
    Nucleic Acids Res 34:D632-6. 2006
  9. doi request reprint The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
    Harukazu Suzuki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    Nat Genet 41:553-62. 2009
  10. pmc Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer
    Masayoshi Itoh
    Omics Science Center, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, Japan
    PLoS ONE 7:e30809. 2012

Detail Information

Publications30

  1. pmc The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
    Toshiaki Katayama
    Database Center for Life Science, Research Organization of Information and Systems, 2 11 16, Yayoi, Bunkyo ku, Tokyo, 113 0032, Japan
    J Biomed Semantics 4:6. 2013
    ....
  2. pmc Alternate transcription of the Toll-like receptor signaling cascade
    Christine A Wells
    Eskitis Institute for Cell and Molecular Therapies, School of Biological and Biomedical Sciences, Griffith University, Brisbane 4111, Australia
    Genome Biol 7:R10. 2006
    ..Functional annotation of variant proteins was assessed in light of inflammatory signaling in mouse primary macrophages, and the expression of each variant transcript was assessed by splicing arrays...
  3. pmc The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho Tsurumi ku Yokohama, Kanagawa, 230 0045 Japan
    Genome Biol 10:R40. 2009
    ..In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource...
  4. pmc SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    BMC Bioinformatics 10:133. 2009
    ..While the format provides an explicit framework to describe experiments, increase of experimental steps makes it less obvious to understand the content of the SDRF files...
  5. pmc Hidden layers of human small RNAs
    Hideya Kawaji
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    BMC Genomics 9:157. 2008
    ....
  6. pmc Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama City, Kanagawa 230 0045, Japan
    Nucleic Acids Res 39:D856-60. 2011
    ..gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial release...
  7. pmc FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
    Jessica Severin
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho Tsurumi ku Yokohama, Kanagawa, 230 0045 Japan
    Genome Biol 10:R39. 2009
    ..This is an important resource for gene regulation in acute myeloid leukemia, monocyte/macrophage differentiation and human transcriptional networks...
  8. pmc CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis
    Hideya Kawaji
    NTT Software Corporation, Teisan Kannai Building 209, Yamashita cho Naka ku, Yokohama, Kanagawa, 231 8551, Japan
    Nucleic Acids Res 34:D632-6. 2006
    ..Now access is free for all users through the World Wide Web at http://fantom3.gsc.riken.jp/...
  9. doi request reprint The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
    Harukazu Suzuki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    Nat Genet 41:553-62. 2009
    ....
  10. pmc Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer
    Masayoshi Itoh
    Omics Science Center, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, Japan
    PLoS ONE 7:e30809. 2012
    ..Despite significant simplifications in the CAGE protocol, it has until now been a labour intensive protocol...
  11. doi request reprint Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing
    Mitsuoki Kawano
    RIKEN Omics Science Center, Yokohama, Japan
    Biotechniques 49:751-5. 2010
    ..This method improves the sequencing yield and efficiency, while simplifying library construction, and makes it easier to perform large-scale small RNA analysis under multiple conditions with next-generation sequencers...
  12. pmc Unamplified cap analysis of gene expression on a single-molecule sequencer
    Mutsumi Kanamori-Katayama
    Omics Science Center, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Japan
    Genome Res 21:1150-9. 2011
    ..Finally, although the majority of tags are 5' associated, we also observe a low level of signal on exons that is useful for defining gene structures...
  13. pmc Dynamic usage of transcription start sites within core promoters
    Hideya Kawaji
    NTT Software Corporation, 209 Yamashita cho Nakak ku, Yokohama, Kanagawa, 231 8551, Japan
    Genome Biol 7:R118. 2006
    ..We previously characterized the static structures of transcription start site usage within promoters at the base pair level, based on large-scale sequencing of transcript 5' ends...
  14. ncbi request reprint Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis
    Takeya Kasukawa
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    Genomics 84:913-21. 2004
    ..RTPSs of human, mouse, and rat have been produced by this method and used for validation. Their comprehensiveness and quality are discussed by comparison with other clustering approaches. The RTPSs are available at ...
  15. pmc Redefinition of the human mast cell transcriptome by deep-CAGE sequencing
    Efthymios Motakis
    RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
    Blood 123:e58-67. 2014
    ..This rich data set reveals that our knowledge of human MCs is still limited, but with this resource, novel functional programs of MCs may soon be discovered...
  16. pmc Pseudo-messenger RNA: phantoms of the transcriptome
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    PLoS Genet 2:e23. 2006
    ..Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level...
  17. pmc Novel small noncoding RNAs in mouse spermatozoa, zygotes and early embryos
    Mitsuoki Kawano
    RIKEN Omics Science Center, Yokohama, Kanagawa, Japan
    PLoS ONE 7:e44542. 2012
    ..These findings offer a new perspective regarding a possibly important role for gamete-specific small RNAs in early embryogenesis...
  18. pmc Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
    Michiel J L de Hoon
    Omics Science Center, RIKEN Yokohama Institute, Tsurumi, Yokohama 230 0045, Japan
    Genome Res 20:257-64. 2010
    ..Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In contrast to previous reports, our analysis suggests that RNA editing in mature miRNAs is rare in animals...
  19. pmc Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
    Hideya Kawaji
    RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351 0198, Japan
    Genome Res 24:708-17. 2014
    ..This study provides a perspective on the performance of these platforms, which will be a baseline in the design of further experiments to tackle complex transcriptomes uncovered in a wide range of cell types. ..
  20. ncbi request reprint Genome-wide analysis of mammalian promoter architecture and evolution
    Piero Carninci
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nat Genet 38:626-35. 2006
    ..These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them...
  21. pmc The RIKEN integrated database of mammals
    Hiroshi Masuya
    RIKEN BioResource Center, Tsukuba, Japan
    Nucleic Acids Res 39:D861-70. 2011
    ....
  22. pmc Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells
    Erik Arner
    RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan Department of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Huddinge, Sweden RIKEN Omics Science Center, Yokohama, Kanagawa, Japan
    PLoS ONE 9:e80274. 2014
    ..Whether there is a causal relationship between adipose overexpression of ceruloplasmin and cancer development in obesity cannot be answered by these cross-sectional comparisons. ..
  23. pmc Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
    Toshiyuki Shiraki
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Proc Natl Acad Sci U S A 100:15776-81. 2003
    ..The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression...
  24. ncbi request reprint Genome annotation
    Hideya Kawaji
    Functional RNA Research Program, Frontier Research System, RIKEN Wako Institute, Wako, Saitama, Japan
    Methods Mol Biol 452:125-39. 2008
    ..This chapter describes steps to obtain publicly available genome annotations or construct new annotations based on your own analyses, as well as an overview of the types of available genome annotations and corresponding resources...
  25. pmc Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells
    Yoshinari Ando
    RIKEN Omics Science Center, Yokohama, Kanagawa, Japan
    PLoS ONE 6:e23385. 2011
    ..Additional characterization of the NUP153-DICER1 association suggests NUP153 plays a crucial role in the nuclear localization of the DICER1 protein...
  26. pmc Exploration of small RNAs
    Hideya Kawaji
    RIKEN Frontier Research System, Wako, Saitama, Japan
    PLoS Genet 4:e22. 2008
    ..Here, we review recent progress in novel small RNA exploration, including discovered small RNA species, their pathways, and devised technologies...
  27. pmc Mouse proteome analysis
    Alexander Kanapin
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Genome Res 13:1335-44. 2003
    ..The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins..
  28. pmc Exploration of novel motifs derived from mouse cDNA sequences
    Hideya Kawaji
    Department of Informatics and Mathematical Science, Graduate School of Engineering Science, Osaka University, Toyonaka 560 8531, Japan
    Genome Res 12:367-78. 2002
    ....
  29. ncbi request reprint [Computational predictions of transcription factor binding sites]
    Hideya Kawaji
    Tanpakushitsu Kakusan Koso 49:2877-81. 2004
  30. ncbi request reprint Graph-based clustering for finding distant relationships in a large set of protein sequences
    Hideya Kawaji
    Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1 3 Machikaneyama, Toyonaka, Osaka 560 8531, Japan
    Bioinformatics 20:243-52. 2004
    ..However, it is still not easy to cluster distantly-related proteins, which have only regional similarity among their sequences. It is therefore necessary to develop an algorithm for clustering such distantly-related proteins...