Yoshihide Hayashizaki

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. ncbi request reprint [Genomic project network and the patents (discussion)]
    Yoshihide Hayashizaki
    Tanpakushitsu Kakusan Koso 49:3001-16. 2004
  2. ncbi request reprint Discovery of the "RNA continent" through a contrarian's research strategy
    Yoshihide Hayashizaki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    Genes Genet Syst 86:221-9. 2011
  3. ncbi request reprint [Genome network: the new researching style]
    Yoshihide Hayashizaki
    Tanpakushitsu Kakusan Koso 49:2617-9. 2004
  4. ncbi request reprint [Future views on genome network projects]
    Yoshihide Hayashizaki
    Tanpakushitsu Kakusan Koso 49:3017. 2004
  5. pmc Chromatin conformation signatures of cellular differentiation
    James Fraser
    Department of Biochemistry and McGill Cancer Center, McGill University, 3655 Promenade Sir William Osler, Montreal, H3G1Y6, Canada
    Genome Biol 10:R37. 2009
  6. pmc Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data
    Piotr J Balwierz
    Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, 4056 CH, Basel, Switzerland
    Genome Biol 10:R79. 2009
  7. pmc Towards defining the nuclear proteome
    J Lynn Fink
    ARC Centre of Excellence in Bioinformatics, The University of Queensland, St Lucia, Queensland, 4072, Australia
    Genome Biol 9:R15. 2008
  8. 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
  9. pmc Transcriptional features of genomic regulatory blocks
    Altuna Akalin
    Computational Biology Unit, Bergen Center for Computational Science, and Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
    Genome Biol 10:R38. 2009
  10. pmc Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases
    Alistair R R Forrest
    Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, Brisbane, QLD 4072, Australia
    Genome Biol 7:R5. 2006

Collaborators

Detail Information

Publications164 found, 100 shown here

  1. ncbi request reprint [Genomic project network and the patents (discussion)]
    Yoshihide Hayashizaki
    Tanpakushitsu Kakusan Koso 49:3001-16. 2004
  2. ncbi request reprint Discovery of the "RNA continent" through a contrarian's research strategy
    Yoshihide Hayashizaki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    Genes Genet Syst 86:221-9. 2011
    ..Omics is an approach that views the information controlling life as finite and seeks to assemble and analyze it as a whole. Here, I would like to present our transcriptome research while making reference to our unique research strategy...
  3. ncbi request reprint [Genome network: the new researching style]
    Yoshihide Hayashizaki
    Tanpakushitsu Kakusan Koso 49:2617-9. 2004
  4. ncbi request reprint [Future views on genome network projects]
    Yoshihide Hayashizaki
    Tanpakushitsu Kakusan Koso 49:3017. 2004
  5. pmc Chromatin conformation signatures of cellular differentiation
    James Fraser
    Department of Biochemistry and McGill Cancer Center, McGill University, 3655 Promenade Sir William Osler, Montreal, H3G1Y6, Canada
    Genome Biol 10:R37. 2009
    ..Genome-wide chromatin conformation signature identification might uniquely identify disease-associated states and represent an entirely novel class of human disease biomarkers...
  6. pmc Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data
    Piotr J Balwierz
    Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, 4056 CH, Basel, Switzerland
    Genome Biol 10:R79. 2009
    ....
  7. pmc Towards defining the nuclear proteome
    J Lynn Fink
    ARC Centre of Excellence in Bioinformatics, The University of Queensland, St Lucia, Queensland, 4072, Australia
    Genome Biol 9:R15. 2008
    ..The nucleus is a complex cellular organelle and accurately defining its protein content is essential before any systematic characterization can be considered...
  8. 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...
  9. pmc Transcriptional features of genomic regulatory blocks
    Altuna Akalin
    Computational Biology Unit, Bergen Center for Computational Science, and Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
    Genome Biol 10:R38. 2009
    ....
  10. pmc Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases
    Alistair R R Forrest
    Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, Brisbane, QLD 4072, Australia
    Genome Biol 7:R5. 2006
    ..We undertook a systematic study to catalog the variant transcripts of every protein kinase-like and phosphatase-like locus of mouse http://variant.imb.uq.edu.au...
  11. pmc Simplified ontologies allowing comparison of developmental mammalian gene expression
    Adele Kruger
    South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
    Genome Biol 8:R229. 2007
    ..We demonstrate the ontologies by identifying genes showing a bias for developmental brain expression in human and mouse...
  12. pmc Two-step cleavage of hairpin RNA with 5' overhangs by human DICER
    Yoshinari Ando
    RIKEN Omics Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    BMC Mol Biol 12:6. 2011
    ..On the other hand, production of mature miRNA from an endogenous hairpin RNA with 5' overhangs has also been reported, although the mechanism for this process is unknown...
  13. 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
    ....
  14. pmc Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation
    Sebastian Schmeier
    South African National Bioinformatics Institute, University of the Western Cape, Modderdam Road, Bellville, South Africa
    BMC Genomics 10:595. 2009
    ..We focus on getting insights into the transcriptional circuitry regulating miRNA genes expressed during monocytic differentiation...
  15. pmc Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    BMC Genet 6:23. 2005
    ..In the present study, we evaluated this transcript by using RT-PCR and compared the expression patterns of the sense and antisense transcripts by using quantitative RT-PCR (qRT-PCR)...
  16. pmc A novel replication-independent histone H2a gene in mouse
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    BMC Genet 6:10. 2005
    ..The proteins encoded by this transcript and the human H2afj mRNA isoform-2 have the highest amino acid similarity. In this paper, we characterize it from the expression pattern given by quantitative RT-PCR...
  17. pmc Development of a high-throughput method for the systematic identification of human proteins nuclear translocation potential
    Trinh Xuan Hoat
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    BMC Cell Biol 10:69. 2009
    ....
  18. pmc PhosphoregDB: the tissue and sub-cellular distribution of mammalian protein kinases and phosphatases
    Alistair R R Forrest
    The Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
    BMC Bioinformatics 7:82. 2006
    ....
  19. pmc Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes
    Manisha Brahmachary
    Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
    BMC Bioinformatics 7:S8. 2006
    ..For many AMPcgs the promoter elements and transcription factors that control their tissue cell-specific expression have yet to be fully identified and characterized...
  20. 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...
  21. pmc Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation
    Atsutaka Kubosaki
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Biol 10:R41. 2009
    ..EGR-1 has been thought to work as a modifier of monopoiesis, but the precise function of EGR-1 in monocytic differentiation has not been fully elucidated...
  22. ncbi request reprint Structural and functional differences of SWIRM domain subtypes
    Misao Yoneyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Mol Biol 369:222-38. 2007
    ..We also solved the structure of the SANT domain of MYSM1, and demonstrated that it bound DNA with a similar mode to that of the c-Myb DNA-binding domain...
  23. 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...
  24. ncbi request reprint Solution structure of the mouse enhancer of rudimentary protein reveals a novel fold
    Hua Li
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Yokohama, Tsurumi, 230 0045, Japan
    J Biomol NMR 32:329-34. 2005
  25. doi request reprint Gene expression during liver regeneration after partial hepatectomy in mice lacking type 1 tumor necrosis factor receptor
    Tetsuya Shimizu
    Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
    J Surg Res 152:178-88. 2009
    ..To investigate the function of tumor necrosis factor-alpha (TNF-alpha) during hepatocyte proliferation, we studied liver regeneration following partial hepatectomy in mice lacking type 1 TNF receptor (TNFR-1)...
  26. ncbi request reprint Effect of thiazole orange doubly labeled thymidine on DNA duplex formation
    Yasumasa Kimura
    RIKEN Omics Science Center OSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Yokohama, Kanagawa 230 0045, Japan
    Biochemistry 51:6056-67. 2012
    ..gsc.riken.jp/echo/thermodynamics/. It provides reliable thermodynamic data for using the unique features of ECHOs in fluorescence-based experiments...
  27. pmc Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3
    Naoya Tochio
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Protein Sci 15:2534-43. 2006
    ..This concave surface includes the highly conserved Glu-Leu-Lys-Leu motif at the C terminus, indicating that it is important for the function of the KA1 domain...
  28. ncbi request reprint The PDZ protein tax-interacting protein-1 inhibits beta-catenin transcriptional activity and growth of colorectal cancer cells
    Mutsumi Kanamori
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    J Biol Chem 278:38758-64. 2003
    ..These data suggest that TIP-1 may represent a novel regulatory element in the Wnt/beta-catenin signaling pathway...
  29. doi request reprint Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode
    Kanako Kuwasako
    Protein Research Group, Genomic Sciences Center, Yokohama Institute, RIKEN, Tsurumi ku, Yokohama 230 0045, Japan
    Biochemistry 47:6437-50. 2008
    ..An investigation of the chemical shift perturbation revealed similarity in the RNA recognition modes between the TIA-1 and U2AF65 RRMs...
  30. pmc Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi
    Taku Tanaka
    Division of Genomics, Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tusurumi Ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 32:2740-50. 2004
    ....
  31. pmc EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes
    Itoshi Nikaido
    Division of Genomic Information Resource Exploration, Science of Biological Supramolecular Systems, Yokohama City University, Graduate School of Integrated Science, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 32:D548-51. 2004
    ..gsc.riken.jp/EICODB/) and the DAS client software. These data and interfaces facilitate understanding of the mechanism of imprinting in mammalian inherited traits...
  32. doi request reprint Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode
    Hua Li
    Systems and Structural Biology Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 283:27165-78. 2008
    ..The extensive binding features of the PID domain of Fe65L1 with the cytoplasmic domain of APP provide a framework for further understanding of the function, trafficking, and processing of APP modulated by adapter proteins...
  33. pmc Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis
    Yasuhiro Tomaru
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Biol 10:R121. 2009
    ....
  34. 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...
  35. pmc FREP: a database of functional repeats in mouse cDNAs
    Takeshi Nagashima
    Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 32:D471-5. 2004
    ....
  36. doi request reprint The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells
    Atsutaka Kubosaki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Mol Immunol 47:2295-302. 2010
    ..We suggest that IRF8 and PU.1 can have both combined, and independent actions on different promoters in myeloid cells...
  37. pmc Comparative analysis of expression of histone H2a genes in mouse
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    BMC Genomics 6:108. 2005
    ..In addition, we compared histone H3 K9 acetylation levels in the promoter regions of H2a genes by ChIP (chromatin immunoprecipitation)--quantitative PCR (qPCR) analysis...
  38. 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/...
  39. ncbi request reprint Development of a spot reliability evaluation score for DNA microarrays
    Yonehiro Matsumura
    Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Gene 350:149-60. 2005
    ..This score was applied to approximately 1,500,000 points of the expression profile in the RIKEN Expression Array Database...
  40. ncbi request reprint Structure of the UNC5H2 death domain
    Noriko Handa
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Acta Crystallogr D Biol Crystallogr 62:1502-9. 2006
    ..In the death-domain dimer, residues in alpha3 and the 3(10)-helix preceding alpha3 and the residues in alpha4 make significant contacts, mainly by hydrophobic and van der Waals interactions...
  41. ncbi request reprint Crystal structure analysis of the PHD domain of the transcription co-activator Pygopus
    Yoshihiro Nakamura
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Mol Biol 370:80-92. 2007
    ..These results suggest that the Pygo1 PHD dimerization is functionally important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway...
  42. ncbi request reprint Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)
    Takeshi Maeda
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 279:13174-82. 2004
    ..On the other hand the tissue tumor marker MUC1 has a SEA domain belonging to another subfamily, and its GSVVV motif for proteolytic cleavage is located in the short loop connecting beta2 and beta3...
  43. pmc Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns
    Anton Kratz
    Keiko University, Graduate School of Media and Governance, Kanagawa, Japan
    BMC Genomics 11:257. 2010
    ..The promoter classes were analyzed for association with relevant genomic sequence features...
  44. pmc Ligand-specific sequential regulation of transcription factors for differentiation of MCF-7 cells
    Yuko Saeki
    Cellular Systems Modeling Team, Computational Systems Biology Research Group, Advanced Computational Sciences Department, RIKEN Advanced Science Institute, 1 7 22 Suehiro cho Tsurumi ku Yokohama, Kanagawa 230 0045, Japan
    BMC Genomics 10:545. 2009
    ....
  45. pmc Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
    Jasmina Ponjavic
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230 0045, Japan
    Genome Biol 7:R78. 2006
    ..The lack of precise transcription start site (TSS) locations linked with expression information has impeded genome-wide characterization of the interaction between TATA and the pre-initiation complex...
  46. pmc Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling
    Itoshi Nikaido
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku Yokohama, Kanagawa 230 0045, Japan
    Genome Res 13:1402-9. 2003
    ..These data provide a major resource for understanding the role of imprinting in mammalian inherited traits...
  47. pmc Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays
    Hidemasa Bono
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Res 13:1318-23. 2003
    ..In addition, 1926 clones (70%) of 2768 clones that were categorized as "unknown EST," and 1969 (58%) clones of 3388 clones that were categorized as "unclassifiable" were also shown to be reproducibly expressed...
  48. 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...
  49. pmc Large-scale clustering of CAGE tag expression data
    Kazuro Shimokawa
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    BMC Bioinformatics 8:161. 2007
    ..The standard hierarchical clustering algorithm, which gives us easily understandable graphical tree images, has difficulties in processing such huge amounts of TSS data and a better method to calculate and display the results is needed...
  50. ncbi request reprint Splicing bypasses 3' end formation signals to allow complex gene architectures
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Gene 403:188-93. 2007
    ..This bypassing mechanism permits nested and interleaved gene architectures, as well as fusion transcripts that combine exons from adjacent genes...
  51. pmc Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts
    Takahiro Suzuki
    Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    PLoS ONE 7:e33474. 2012
    ....
  52. pmc Genome-wide analysis of abnormal H3K9 acetylation in cloned mice
    Takahiro Suzuki
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    PLoS ONE 3:e1905. 2008
    ....
  53. pmc Rapid screening assay for KRAS mutations by the modified smart amplification process
    Kenji Tatsumi
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    J Mol Diagn 10:520-6. 2008
    ..The PNA-clamp SMAP-2 method is a rapid, simple, and highly sensitive detection assay for cancer mutations...
  54. ncbi request reprint Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell
    Hiromi Nishida
    Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Yokohama, Japan
    Chromosome Res 14:203-11. 2006
    ..Our results imply that the relative nucleosome depletion in the vicinity of TSS is not necessarily associated with active transcription, but with histone H3 K9 acetylation in promoter...
  55. ncbi request reprint Crystal structure of the RUN domain of the RAP2-interacting protein x
    Mutsuko Kukimoto-Niino
    RIKEN Genomic Sciences Center, Yokohama 230 0045, Japan
    J Biol Chem 281:31843-53. 2006
    ..In the crystal the putative Rap2 binding site of the RPIPx RUN domain interacts with the extended segment in a segment-swapping manner...
  56. pmc Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
    Morana Vitezic
    Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Nucleic Acids Res 38:8141-8. 2010
    ..We found a previously described composite motif for PU.1 and IRF8 that explains the overlapping set of transcriptional responses upon knockdown of either factor...
  57. ncbi request reprint Mammalian RNA polymerase II core promoters: insights from genome-wide studies
    Albin Sandelin
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nat Rev Genet 8:424-36. 2007
    ..A comprehensive survey of mammalian promoters is a major step towards describing and understanding transcriptional control networks...
  58. pmc Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells
    Misato Nakanishi
    Laboratory of Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 36:3443-54. 2008
    ..Finally, 36 transcriptional regulatory edges were validated by chromatin immunoprecipitation. These analyses enabled us to depict a part of the transcriptional regulatory cascades closely linked to ATRA-induced cell growth arrest...
  59. pmc Solution structure of the PWWP domain of the hepatoma-derived growth factor family
    Nobukazu Nameki
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Protein Sci 14:756-64. 2005
    ..These findings suggest that the PWWP domains of the HDGF family bind to some component of chromatin via the cavity...
  60. pmc Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi
    Yasuhiro Tomaru
    OMICS Sciences Center OSC, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Japan
    Nucleic Acids Res 37:1049-60. 2009
    ..The resultant significant edges enabled us to depict the inter-TRF TRN forming an apparent regulatory hierarchy of (FOXA1, RXRA) --> TCF1 --> (HNF4A, ONECUT1) --> (RORC, CEBPA) as the main streamline...
  61. pmc Optimization of turn-back primers in isothermal amplification
    Yasumasa Kimura
    RIKEN Omics Science Center OSC, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230 0045, Japan
    Nucleic Acids Res 39:e59. 2011
    ..Our computer script is freely available at: http://gerg.gsc.riken.jp/TP_optimization/...
  62. ncbi request reprint Discrimination of non-protein-coding transcripts from protein-coding mRNA
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Kanagawa, Japan
    RNA Biol 3:40-8. 2006
    ..Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts...
  63. pmc Evolutionary turnover of mammalian transcription start sites
    Martin C Frith
    Genome Exploration Research Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Genome Res 16:713-22. 2006
    ..These findings suggest that the signals encoding transcription start sites are highly flexible and evolvable, and have cautionary implications for the use of sequence-level conservation to detect gene regulatory elements...
  64. doi request reprint Identification of ZNF395 as a novel modulator of adipogenesis
    Ryota Hasegawa
    Omics Science Center OSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan Division of Genomic Information Resources, Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Exp Cell Res 319:68-76. 2013
    ..These loss and gain of function experiments firmly establish that ZNF395 coordinate the transcriptional regulatory pathway with PPARG2, which may be necessary for the genesis of adipocytes...
  65. doi request reprint CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication
    Atsutaka Kubosaki
    RIKEN Omics Science Center, 1 7 22 Suehiro cho, Yokohama, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 426:141-7. 2012
    ..Since the unmodified MoCEV did not undergo any DNA methylation during cell division, the results strongly suggest that somatic cells undergo hmC to mC specifically at the CpG sites during cell division...
  66. pmc One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RT-SmartAmp assay and its clinical validation
    Yuki Kawai
    Omics Science Center, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Japan
    PLoS ONE 7:e30236. 2012
    ..In Japan, infected patients accounted for 16% of the total population. The possibility of human-to-human transmission of highly pathogenic novel influenza viruses is becoming a fear for human health and society...
  67. 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...
  68. pmc LRRN4 and UPK3B are markers of primary mesothelial cells
    Mutsumi Kanamori-Katayama
    Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    PLoS ONE 6:e25391. 2011
    ..Once diagnosed there is a very poor prognosis with a median survival rate of 9 months. Considering this the development of early pre clinical diagnostic markers may help improve clinical outcomes...
  69. doi request reprint Sensitive detection of EGFR mutations using a competitive probe to suppress background in the SMart Amplification Process
    Yuki Kawai
    Genome Exploration Research Group Genome Network Project Core Group, Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Biologicals 36:234-8. 2008
    ..The CP approach is another tool enhancing the effectiveness and versatility of SMAP 2 assays, expanding its potential applications, and reinforcing its position as a highly effective technology for molecular diagnostics...
  70. pmc NMR solution structures of actin depolymerizing factor homology domains
    Alexander K Goroncy
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    Protein Sci 18:2384-92. 2009
    ..The G-actin binding site of the ADF-H domain of human HIP-55-drebrin-like protein is absent and distorted in mouse GMF beta and GMF gamma...
  71. 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...
  72. doi request reprint Analysis of gene expression profiles in fatal hepatic failure after hepatectomy in mice
    Hirochika Makino
    Department of Gastroenterological Surgery, Yokohama City University School Graduate of Medicine, Yokohama, Japan
    J Surg Res 169:36-43. 2011
    ..We developed 90%-hepatectomized mice that were the fatal model, and analyzed the gene expression profiles using a complementary DNA (cDNA) microarray to clarify the mechanisms of hepatic failure after excessive hepatectomy...
  73. 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 ...
  74. pmc The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition
    Takashi Nagata
    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Japan
    Nucleic Acids Res 36:4754-67. 2008
    ..These unique structural features in PARN RRM reveal a novel cap-binding mode, which is distinct from the nucleotide recognition mode of the canonical RRM domains...
  75. ncbi request reprint Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts
    Tomoko Hirozane-Kishikawa
    RIKEN Yokohama Institute, Yokohama, Japan
    Biotechniques 35:510-6, 518. 2003
    ..The proportion of full-length cDNAs and the gene discovery rate are high, and library diversity can be validated by in silico randomization...
  76. pmc The abundance of short proteins in the mammalian proteome
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    PLoS Genet 2:e52. 2006
    ..Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway...
  77. pmc Promoter architecture of mouse olfactory receptor genes
    Charles Plessy
    RIKEN Yokohama Institute, Omics Science Center, Yokohama, Kanagawa, Japan
    Genome Res 22:486-97. 2012
    ..Finally, we showed that a short genomic fragment flanking the major TSS of the OR gene Olfr160 (M72) can drive OSN-specific expression in transgenic mice...
  78. pmc A code for transcription initiation in mammalian genomes
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Genome Res 18:1-12. 2008
    ....
  79. ncbi request reprint Integrated analysis of the genome and the transcriptome by FANTOM
    Shintaro Katayama
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Brief Bioinform 5:249-58. 2004
    ..Categorised annotation, which refers to transcript grouping, not only helps naming of unknown transcripts, but will be the most utilised method for integration of the genome and the transcriptome from now on...
  80. pmc Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia
    Piero Carninci
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Res 13:1273-89. 2003
    ..Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete...
  81. 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...
  82. pmc NGSView: an extensible open source editor for next-generation sequencing data
    Erik Arner
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Bioinformatics 26:125-6. 2010
    ..NGSView is available under an open source license and can be extended through a well documented API. AVAILABILITY: http://ngsview.sourceforge.net..
  83. pmc Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes
    Hisashi Miura
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 37:778-92. 2009
    ..Finally, co-transfection reporter assays with various combinations of expression vectors for these HNF genes demonstrated the transcriptional activation of the CEBPA gene in a combinatorial manner by these TRFs...
  84. pmc Development and evaluation of an automated annotation pipeline and cDNA annotation system
    Takeya Kasukawa
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Res 13:1542-51. 2003
    ....
  85. pmc Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin
    Alexander Maxwell Burroughs
    Omics Science Center, RIKEN Yokohama Institute, Yokohama shi, Kanagawa, Japan
    RNA Biol 8:158-77. 2011
    ..Finally, we observe antisense miRNA transcripts are frequently present in low copy numbers across a range of diverse miRNA loci and these transcripts appear to associate with AGO proteins...
  86. doi request reprint Effects of the turn-back primer on intermediate product generation in isothermal DNA amplification
    Yuki Tanaka
    RIKEN Omics Science Center OSC, RIKEN Yokohama Institute, Yokohama, Japan
    Biotechniques 49:888-92. 2010
    ..Our results indicate that intermediate product creation is the rate-limiting step in TIA, and good TP design is advantageous for improving the intermediate production process...
  87. doi request reprint Tail variation of the folding primer affects the SmartAmp2 process differently
    Yasumasa Kimura
    Technology Development Unit, Omics Science Center OSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 383:455-9. 2009
    ..The above observations can be used to optimize the reaction and manipulate the reaction speed of SmartAmp2...
  88. ncbi request reprint CAGE: cap analysis of gene expression
    Rimantas Kodzius
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nat Methods 3:211-22. 2006
  89. ncbi request reprint Mapping of 19032 mouse cDNAs on mouse chromosomes
    Itaru Yamanaka
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama City, Kanagawa 230 0045, Japan
    J Struct Funct Genomics 2:23-8. 2002
    ..In the second approach, we related cDNAs to expressed sequence tags (EST) previously mapped in radiation hybrid experiments. We discuss improving the mapping by combining the 2 methods...
  90. 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...
  91. doi request reprint Detection of SNP by the isothermal smart amplification method
    Alexander Lezhava
    Genome Exploration Research Group, Genomic Sciences Center GSC, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, Japan
    Methods Mol Biol 578:437-51. 2009
    ..Furthermore, mutation detection and SNP genotypes can be obtained in as little as 30-40 min from sample preparation of raw blood or tissue specimens...
  92. pmc Role of survival motor neuron complex components in small nuclear ribonucleoprotein assembly
    Chihiro Ogawa
    RIKEN Omics Sciences Center, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Japan
    J Biol Chem 284:14609-17. 2009
    ..Taken together, these results indicate that snRNP is synthesized by harmonization of the SMN complex components...
  93. 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
    ....
  94. doi request reprint CC chemokine ligand 2 and leukemia inhibitory factor cooperatively promote pluripotency in mouse induced pluripotent cells
    Yuki Hasegawa
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, Japan
    Stem Cells 29:1196-205. 2011
    ..Overall, Ccl2 cooperatively activates the Stat3-pathway with LIF in feeder-free conditions to maintain pluripotency for ESCs/iPSCs...
  95. 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...
  96. pmc READ: RIKEN Expression Array Database
    Hidemasa Bono
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 30:211-3. 2002
    ..READ can be accessed at http://read.gsc.riken.go.jp/. READ also provides a search tool [READ integrates gene expression neighbor (RINGENE)] for genes with similarities in expression profiling...
  97. pmc CDS annotation in full-length cDNA sequence
    Masaaki Furuno
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Res 13:1478-87. 2003
    ....
  98. ncbi request reprint MaXML: mouse annotation XML
    Takeya Kasukawa
    Network Service Solution Business Group, Content Sharing Service Business Unit, NTT Software Corporation, Yokohama, Kanagawa, Japan
    In Silico Biol 4:7-15. 2004
    ..We have used the MaXML format to express mouse annotation data in FANTOM DB. We have also developed tools and systems utilizing these MaXML data, including a parser and a server to provide data on-the-fly...
  99. doi request reprint Isothermal single nucleotide polymorphism genotyping and direct PCR from whole blood using a novel whole-blood lysis buffer
    Sylvia T Victor
    Technology Development Unit, Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan
    Mol Diagn Ther 13:383-7. 2009
    ..Furthermore, pretreatment with SIL-B enables the PCR amplification of genomic material directly from whole blood...
  100. ncbi request reprint Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: causes of signal variation and false positive signals
    Daisuke Sasaki
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    Genomics 89:541-51. 2007
    ..It was also demonstrated that hybridization of full-length cDNA clones is an excellent method to investigate the characteristics of oligonucleotide tiling arrays...
  101. pmc Antisense transcripts with rice full-length cDNAs
    Naoki Osato
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center GSC, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, Japan 230 0045
    Genome Biol 5:R5. 2003
    ..The Rice Full-Length cDNA Sequencing Project has enabled computational searching of a large number of plant sense-antisense transcript pairs...