Research Topics
| K NakaiSummaryAffiliation: University of Tokyo Country: Japan Publications
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Detail Information
Publications
Profiling ascidian promoters as the primordial type of vertebrate promoterKohji Okamura
Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan
BMC Genomics 12:S7. 2011..However, the limited annotation of these genes has impeded the large-scale analysis of their promoters...- Positional variations among heterogeneous nucleosome maps give dynamical information on chromatinYoshiaki Tanaka
Department of Medical Genome Sciences, University of Tokyo, Minato ku, Japan
Chromosoma 119:391-404. 2010..Furthermore, the associations with gene function and histone modification were also discussed here... - PrognoScan: a new database for meta-analysis of the prognostic value of genesHideaki Mizuno
Pharmaceutical Technology Department, Kamakura Research Laboratories, Chugai Pharmaceutical Co Ltd, Kamakura, Kanagawa, Japan
BMC Med Genomics 2:18. 2009..The database is publicly accessible at http://gibk21.bse.kyutech.ac.jp/PrognoScan/index.html... - Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)Shoba Ranganathan
Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
BMC Genomics 11:S1. 2010..27 - Dec. 2, 2011 at Kuala Lumpur, Malaysia... - Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairsHirokazu Chiba
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
BMC Genomics 9:152. 2008..A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial... - Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regionsKatsuhiko Murakami
Integrated Database Group, Japan Biological Information Research Center JBIRC, Japan Biological Informatics Consortium, Aomi 2 41, Koto ku, Tokyo, 135 0064, Japan
BMC Genomics 9:112. 2008..It is essential in modern biology to understand how transcriptional regulatory regions are composed of cis-elements, yet we have limited knowledge of, for example, the combinational uses of these elements and their positional distribution... - Effects of Alu elements on global nucleosome positioning in the human genomeYoshiaki Tanaka
Department of Medical Genome Sciences, University of Tokyo, Minato ku, Japan
BMC Genomics 11:309. 2010..As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still unclear whether this feature can be observed in the whole genomes of all eukaryotes... - A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patternsSung Joon Park
Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
BMC Bioinformatics 12:S50. 2011..In it, the role of several core transcription factors (TFs), such as Oct4, Sox2 and Nanog, has been intensively investigated, details of their involvement in the genome-wide gene regulation are still not well clarified... - Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolutionKohji Okamura
Human Genome Centre, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato Ward, Tokyo 108 8639, Japan
BMC Bioinformatics 11:S2. 2010..However, DNA methylation patterns and levels in vertebrates and invertebrates have not been analyzed in the same way... - Genome informatics for data-driven biologyKenta Nakai
Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
Genome Biol 3:REPORTS4010. 2002 
[Tell me about algorithms in bioinformatics, Dr. Ochanomizu]Kenta Nakai
Tanpakushitsu Kakusan Koso 47:1332-6. 2002- Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related speciesG Terai
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
Genome Biol 2:RESEARCH0048. 2001..To overcome this problem, we used conserved information from three closely related species: Bacillus subtilis, B. halodurans and B. stearothermophilus... - DBTSS provides a tissue specific dynamic view of Transcription Start SitesRiu Yamashita
Frontier Research Initiative, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
Nucleic Acids Res 38:D98-104. 2010..Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated. DBTSS can be accessed at http://dbtss.hgc.jp/... - DBTSS: database of transcription start sites, progress report 2008Hiroyuki Wakaguri
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
Nucleic Acids Res 36:D97-101. 2008..With the expanded dataset and the enhanced functionalities, DBTSS provides a unique platform that enables in-depth transcriptome analyses. DBTSS is accessible at http://dbtss.hgc.jp/... - DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomicsYuko Makita
Human Genome Center, The Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Nucleic Acids Res 32:D75-7. 2004.... - Computational prediction of subcellular localizationKenta Nakai
Laboratory of Functional Analysis in silico, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
Methods Mol Biol 390:429-66. 2007..In this chapter we discuss these issues and close with an example illustrating the use of the WoLF PSORT web server for localization prediction... - Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regionsToshiyuki Okumura
Mitsui Knowledge Industry Co Ltd, University of Tokyo, Japan
Nucleic Acids Res 35:W227-31. 2007..thaliana) or to public motif databases (JASPAR or DBTBS) in order to find similar motifs. Melina II is a client/server system developed by using Adobe (Macromedia) Flash and is accessible over the web at http://melina.hgc.jp... - Functional prediction of B. subtilis genes from their regulatory sequencesT Yada
Japan Science and Technology, Corporation, Tokyo, Japan
Proc Int Conf Intell Syst Mol Biol 5:354-7. 1997..Furthermore, we predicted the sigma-dependencies for each of 1415 candidate genes in the genome. Our prediction results are experimentally testable and seem useful for the post-sequencing project... - [Transcriptome analyses and transcriptome databases]Yutaka Suzuki
Tanpakushitsu Kakusan Koso 49:1859-65. 2004 - A novel strategy to search conserved transcription factor binding sites among coexpressing genes in humanYosuke Hatanaka
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
Genome Inform 20:212-21. 2008..We also applied basket method analysis for seeking combinatorial activities of those conserved TFBSs... - DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAsYutaka Suzuki
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
Nucleic Acids Res 30:328-31. 2002.... - DBTSS, DataBase of Transcriptional Start Sites: progress report 2004Yutaka Suzuki
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
Nucleic Acids Res 32:D78-81. 2004.... - Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regionsYutaka Suzuki
Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
Genome Res 14:1711-8. 2004.... - An O(N2) algorithm for discovering optimal Boolean pattern pairsHideo Bannai
Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
IEEE/ACM Trans Comput Biol Bioinform 1:159-70. 2004.... - Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificityRiu Yamashita
Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokane-dai Minato-ku, Tokyo 108-8639, Japan
Gene 350:129-36. 2005.... - Extensive feature detection of N-terminal protein sorting signalsHideo Bannai
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
Bioinformatics 18:298-305. 2002..RESULTS: We have succeeded in finding rules whose prediction accuracies come close to that of TargetP, while still retaining a very simple and interpretable form. We also discuss and interpret the discovered rules... - Large-scale collection and characterization of promoters of human and mouse genesYutaka Suzuki
Human Genome Center, The Institute of Medical Science, The University of Tokyo 4 6 1 Shirokanedai, Tokyo, 108 8639, Japan
In Silico Biol 4:429-44. 2004..All the data were deposited and made available through a database for comparative studies, DBTSS... - DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation informationNicolas Sierro
Human Genome Center, The Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, Japan
Nucleic Acids Res 36:D93-6. 2008..DBTBS can be accessed at: http://dbtbs.hgc.jp... - Review: prediction of in vivo fates of proteins in the era of genomics and proteomicsK Nakai
Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, 108-8639, Japan
J Struct Biol 134:103-16. 2001..The prediction of in vivo fates of proteins will be useful for characterizing newly identified candidate genes in a genome or for interpreting multiple spots in proteome analyses... - Using simple rules on presence and positioning of motifs for promoter structure modeling and tissue-specific expression predictionAlexis Vandenbon
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
Genome Inform 21:188-99. 2008..We believe our model can help to increase our understanding about transcription factor cooperation and transcription initiation... - Intrinsic promoter activities of primary DNA sequences in the human genomeYuta Sakakibara
Graduate School of Frontier Sciences, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
DNA Res 14:71-7. 2007.... - Modeling tissue-specific structural patterns in human and mouse promotersAlexis Vandenbon
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
Nucleic Acids Res 38:17-25. 2010..Together, these results illustrate the validity of our models, but also indicate that the promoter structures for some tissues are easier to model than those of others... - DBTGR: a database of tunicate promoters and their regulatory elementsNicolas Sierro
Human Genome Center, The Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
Nucleic Acids Res 34:D552-5. 2006..At the time of writing, information about 184 promoters, containing 73 identified binding sites and >2000 newly predicted binding sites is available. This database is accessible at http://dbtgr.hgc.jp... - Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide dataM J L de Hoon
Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato ku, Tokyo, Japan
Bioinformatics 20:i101-8. 2004..We provide the corresponding RNA polymerase binding sites to enable a straightforward experimental verification of these predictions... - Melina: motif extraction from promoter regions of potentially co-regulated genesNatalia Poluliakh
Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Bioinformatics 19:423-4. 2003..It is also useful to optimize the sensitivity of software with a series of different parameter settings. AVAILABILITY: Melina is available at http://www.hgc.ims.u-tokyo.ac.jp/Melina/... - Pseudocounts for transcription factor binding sitesKeishin Nishida
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562, Japan
Nucleic Acids Res 37:939-44. 2009..As a simple representative, we suggest the value of 0.8 for practical uses... - Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristicsRiu Yamashita
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
Nucleic Acids Res 36:3707-15. 2008.... - Retrotransposition as a source of new promotersKohji Okamura
Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan
Mol Biol Evol 25:1231-8. 2008..This propensity could confer retrotransposability to promoters per se. Accordingly, the retrotransposability can explain the genesis of some alternative promoters... - DBTSS: DataBase of Human Transcription Start Sites, progress report 2006Riu Yamashita
Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Nucleic Acids Res 34:D86-9. 2006..Third, DBTSS provides detailed sequence comparisons of user-specified TSSs. Finally, we have added TSS information for zebrafish, malaria and schyzon (a red algae model organism). DBTSS is accessible at http://dbtss.hgc.jp... - Gangliosides GD1b, GT1b, and GQ1b suppress the growth of human melanoma by inhibiting interleukin-8 production: the inhibition of adenylate cyclaseN Kanda
Department of Dermatology, Teikyo University, School of Medicine, Tokyo, Japan
J Invest Dermatol 117:284-93. 2001..The data indicate that GD1b, GT1b, and GQ1b may suppress the growth of melanoma by inhibiting interleukin-8 production via the inhibition of adenylate cyclase... - Assessment of prediction accuracy of protein function from protein--protein interaction dataH Hishigaki
Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo 108-8639, Japan
Yeast 18:523-31. 2001..7%, 63.6% and 52.7%, respectively. The prediction accuracy rises for proteins with more than three binding partners and thus we present the open prediction results for 16 such proteins... - Markov chain-based promoter structure modeling for tissue-specific expression pattern predictionAlexis Vandenbon
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
DNA Res 15:3-11. 2008..This model can be useful for finding promising candidate genes for wet-lab experiments and for increasing our understanding of transcriptional regulation... - Prediction of transcriptional terminators in Bacillus subtilis and related speciesMichiel J L de Hoon
Human Genome Center, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo, Japan
PLoS Comput Biol 1:e25. 2005..Genome-wide predictions of Rho-independent terminators for the 57 Firmicutes are available in the Supporting Information section... - Small open reading frames in 5' untranslated regions of mRnasRiu Yamashita
Laboratory of Genome Database, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
C R Biol 326:987-91. 2003..They require attention for further analysis to identify their biological role... - An assessment of prediction algorithms for nucleosome positioningYoshiaki Tanaka
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
Genome Inform 23:169-78. 2009..The oligomers commonly enriched in all five eukaryotes were only CA/TG and AC/GT. Thus, to achieve relatively high performance for a species, it is desirable to prepare the training data from the same species... - Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genesKatsuki Tsuritani
Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minatoku, Tokyo 108 8639, Japan
Genome Res 17:1005-14. 2007..Taken together, our data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution... - Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signalsMitsuteru Nakao
Human Genome Center, Institute of Medical Science, University of Tokyo Tokyo, Japan
Nucleic Acids Res 33:2355-63. 2005..Our study sheds new light on the enrichment of the human proteome through alternative splicing and related events. Our database of alternative protein isoforms is available through the internet... 
Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysisNicolas Sierro
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
Gene 430:44-9. 2009..intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently...- WoLF PSORT: protein localization predictorPaul Horton
Computational Biology Research Center, AIST, Tokyo, Japan
Nucleic Acids Res 35:W585-7. 2007..Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org... - Diverse DNA methylation statuses at alternative promoters of human genes in various tissuesJieun Cheong
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan
DNA Res 13:155-67. 2006..DNA methylation appears to play a significant role in differential usage of alternative promoters and may be related to functional diversification between CpG-island-containing promoters and CpG-island-less promoters... - Integrative annotation of 21,037 human genes validated by full-length cDNA clonesTadashi Imanishi
Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
PLoS Biol 2:e162. 2004..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology... - Complete sequencing and characterization of 21,243 full-length human cDNAsToshio Ota
Helix Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan
Nat Genet 36:40-5. 2004..About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs... - ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in ArabidopsisTakeshi Obayashi
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B 14 Nagatsuta cho, Midori ku, Yokohama 226 8501, Japan
Nucleic Acids Res 35:D863-9. 2007..ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks... - The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcriptsChisato Yamasaki
Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
Nucleic Acids Res 36:D793-9. 2008.... - PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteriaJennifer L Gardy
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
Nucleic Acids Res 31:3613-7. 2003..This dataset, the largest of its kind, is freely available, along with the PSORT-B source code (under GNU General Public License)... - Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of infectionKoshiro Miura
Department of Microbiology and Immunology, Yamaguchi University School of Medicine, 1 1 1 Minami kogushi, Ube, Yamaguchi 755 8505, Japan
DNA Res 15:83-91. 2008..It suggests that besides sigma(28), there are certain up-regulatory mechanisms at the late stage, which may be involved in the chlamydial morphological change and thus pathogenesis... - Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cellsIzuho Hatada
Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3 39 15 Showa Machi, Maebashi 371 8512, Japan
J Hum Genet 53:185-91. 2008..We found a genome-wide demethylation of genes. This suggests demethylation rather than methylation is important in neural differentiation... - Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genesKouichi Kimura
Life Science Research Laboratory, Central Research Laboratory, Hitachi, Ltd, Kokubunji, Tokyo, 185-8601, Japan
Genome Res 16:55-65. 2006..Our findings suggest that use of alternate promoters and consequent alternative use of first exons should play a pivotal role in generating the complexity required for the highly elaborated molecular systems in humans... - Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissuesKikuya Kato
Osaka Medical Center for Cancer and Cardiovascular Diseases, 1 3 2 Nakamichi, Higashinari ku, Osaka 537 8511, Japan
Nucleic Acids Res 33:D533-6. 2005..Data for other cancers such as lung and thyroid cancers will be added in the near future. The URL of CGED is http://cged.hgc.jp...