Research Topics
Genomes and GenesSpecies | Hideya KawajiSummaryAffiliation: RIKEN Brain Science Institute Country: Japan Publications
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Detail Information
Publications
Alternate transcription of the Toll-like receptor signaling cascadeChristine 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...- Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulationHideya 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... - The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulationHideya 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... - SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processesHideya 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... - Hidden layers of human small RNAsHideya 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.... - FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactionsJessica 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... - CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysisHideya 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/... 
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell lineHarukazu Suzuki
RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
Nat Genet 41:553-62. 2009....- Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencerMasayoshi 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... - Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencingMitsuoki 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... - Dynamic usage of transcription start sites within core promotersHideya 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... - Unamplified cap analysis of gene expression on a single-molecule sequencerMutsumi 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... - Pseudo-messenger RNA: phantoms of the transcriptomeMartin 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... 
Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysisTakeya 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 ...- Genome-wide analysis of mammalian promoter architecture and evolutionPiero 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... - Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing librariesMichiel 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... - Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usageToshiyuki 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... - The RIKEN integrated database of mammalsHiroshi Masuya
RIKEN BioResource Center, Tsukuba, Japan
Nucleic Acids Res 39:D861-70. 2011.... - Genome annotationHideya 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... - Nuclear pore complex protein mediated nuclear localization of dicer protein in human cellsYoshinari 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... - Exploration of small RNAsHideya 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... - Novel small noncoding RNAs in mouse spermatozoa, zygotes and early embryosMitsuoki 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... - Mouse proteome analysisAlexander 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.. - Exploration of novel motifs derived from mouse cDNA sequencesHideya Kawaji
Department of Informatics and Mathematical Science, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
Genome Res 12:367-78. 2002.... - [Computational predictions of transcription factor binding sites]Hideya Kawaji
Tanpakushitsu Kakusan Koso 49:2877-81. 2004 - Graph-based clustering for finding distant relationships in a large set of protein sequencesHideya 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..AVAILABILITY: The complete result of our algorithm for all the human proteins in SWISS-PROT and TrEMBL, and other supplementary information are available at http://motif.ics.es.osaka-u.ac.jp/Ncut-KL/..