Takashi Gojobori

Summary

Affiliation: National Institute of Genetics
Country: Japan

Publications

  1. pmc Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
  2. pmc Systems medicine and integrated care to combat chronic noncommunicable diseases
    Jean Bousquet
    Department of Respiratory Diseases, Arnaud de Villeneuve Hospital, CHU Montpellier, INSERM CESP U1018, Villejuif, France
    Genome Med 3:43. 2011
  3. pmc Binary classification of protein molecules into intrinsically disordered and ordered segments
    Satoshi Fukuchi
    Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411 8540, Japan
    BMC Struct Biol 11:29. 2011
  4. pmc Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors
    Satoshi Fukuchi
    Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka, Japan
    BMC Struct Biol 9:26. 2009
  5. pmc Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus
    Roberto A Barrero
    Centre for Comparative Genomics, Murdoch University, WA, Australia
    BMC Genomics 12:328. 2011
  6. pmc The evolutionary position of nematodes
    Jaime E Blair
    Astrobiology Research Center and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Evol Biol 2:7. 2002
  7. pmc Optimized ancestral state reconstruction using Sankoff parsimony
    Jose C Clemente
    Center for Information Biology and DNA Databank of Japan, National Institute of Genetics, Yata 1111, Mishima, Japan
    BMC Bioinformatics 10:51. 2009
  8. pmc CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies
    Yoji Nakamura
    Immunotherapy Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo, Nagaizumi cho, Sunto gun, Shizuoka, 411 8777, Japan
    BMC Bioinformatics 11:398. 2010
  9. pmc Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
    Akihiro Matsuya
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, Tokyo, Japan
    Nucleic Acids Res 36:D787-92. 2008
  10. pmc A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing
    Makoto K Shimada
    Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2 42 Aomi Koto ku, Tokyo135 0064, Japan
    BMC Evol Biol 10:122. 2010

Collaborators

Detail Information

Publications27

  1. pmc Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi 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...
  2. pmc Systems medicine and integrated care to combat chronic noncommunicable diseases
    Jean Bousquet
    Department of Respiratory Diseases, Arnaud de Villeneuve Hospital, CHU Montpellier, INSERM CESP U1018, Villejuif, France
    Genome Med 3:43. 2011
    ..This systems medicine strategy, which will take a holistic approach to disease, is designed to allow the results to be used globally, taking into account the needs and specificities of local economies and health systems...
  3. pmc Binary classification of protein molecules into intrinsically disordered and ordered segments
    Satoshi Fukuchi
    Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411 8540, Japan
    BMC Struct Biol 11:29. 2011
    ..As ID regions can be inferred from amino acid sequences, a method that combines SD and ID region assignments can determine the fractions of SDs and ID regions in any proteome...
  4. pmc Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors
    Satoshi Fukuchi
    Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka, Japan
    BMC Struct Biol 9:26. 2009
    ..In this report, we exploit the generally higher sequence divergence in ID regions than in structural regions to completely divide proteins into structural domains and ID regions...
  5. pmc Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus
    Roberto A Barrero
    Centre for Comparative Genomics, Murdoch University, WA, Australia
    BMC Genomics 12:328. 2011
    ..microplus...
  6. pmc The evolutionary position of nematodes
    Jaime E Blair
    Astrobiology Research Center and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Evol Biol 2:7. 2002
    ..Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes...
  7. pmc Optimized ancestral state reconstruction using Sankoff parsimony
    Jose C Clemente
    Center for Information Biology and DNA Databank of Japan, National Institute of Genetics, Yata 1111, Mishima, Japan
    BMC Bioinformatics 10:51. 2009
    ..Although optimizations exist to reduce the computations in the number of taxa, the original algorithm takes time O(n(2)) in the number of states, making it impractical for large values of n...
  8. pmc CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies
    Yoji Nakamura
    Immunotherapy Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo, Nagaizumi cho, Sunto gun, Shizuoka, 411 8777, Japan
    BMC Bioinformatics 11:398. 2010
    ..Therefore, we developed an integrated database of IG/TR data reported in cancer studies (the Cancer-related Immunological Gene Database [CIG-DB])...
  9. pmc Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
    Akihiro Matsuya
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, Tokyo, Japan
    Nucleic Acids Res 36:D787-92. 2008
    ..We expect the Evola to serve as a comprehensive and reliable database to be utilized in comparative analyses for obtaining new knowledge about human genes. Evola is available at http://www.h-invitational.jp/evola/...
  10. pmc A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing
    Makoto K Shimada
    Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2 42 Aomi Koto ku, Tokyo135 0064, Japan
    BMC Evol Biol 10:122. 2010
    ..We therefore surveyed validated SNPs in the database dbSNP located at splice dinucleotides of all human genes that are defined by the H-Invitational Database...
  11. pmc Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs
    Jun Ichi Takeda
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio IT Research, Building Aomi 2 42, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 34:3917-28. 2006
    ....
  12. pmc H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational
    Jun Ichi Takeda
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio IT Research, Building Aomi 2 42, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 35:D104-9. 2007
    ..H-DBAS is accessible at http://jbirc.jbic.or.jp/h-dbas/...
  13. pmc Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs
    Jun Ichi Takeda
    Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio IT Research Building, Aomi 2 42, Koto ku, Tokyo, Japan
    Nucleic Acids Res 36:6386-95. 2008
    ..This suggests that non-conserved exons in the CDSs of transcripts cause functional constraint. These findings should enhance our understanding of the relationship between AS and species specificity of human genes...
  14. pmc VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts
    Makoto K Shimada
    Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Japan Biological Informatics Consortium, Hitachi Software Engineering Co, Ltd, Tokyo, Japan
    Nucleic Acids Res 37:D810-5. 2009
    ..We expect that VarySysDB will yield useful information on polymorphisms affecting gene expression and phenotypes. VarySysDB is available at http://h-invitational.jp/varygene/...
  15. ncbi request reprint Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome
    Ryuichi Sakate
    Japan Biological Information Research Center, Japan Biological Informatics Consortium AIST Bio IT Research Bldg 7F, 2 42 Aomi, Koto ku, Tokyo, 135 0064, Japan
    Gene 399:1-10. 2007
    ....
  16. pmc TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
    Chisato Yamasaki
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Waterfront Bio IT Research Building, 2 42 Aomi, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 34:W345-9. 2006
    ..TACT is freely available at http://www.jbirc.aist.go.jp/tact/...
  17. pmc H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery
    Jun Ichi Takeda
    Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2 4 7, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 41:D915-9. 2013
    ..We propose that H-InvDB is an important resource for finding novel candidate targets for medical care and drug development...
  18. pmc Distribution and effects of nonsense polymorphisms in human genes
    Yumi Yamaguchi-Kabata
    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS ONE 3:e3393. 2008
    ..In particular, little is known about the distribution of nonsense polymorphisms in human genes despite their drastic effects on gene products...
  19. pmc Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions
    Katsuhiko 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...
  20. ncbi request reprint Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes
    Hiroaki Sakai
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio IT Research Bldg 7F, 2 42 Aomi, Tokyo, Japan
    Gene 389:196-203. 2007
    ..Our results indicate that the generation of processed pseudogenes was not wholly futile but instead has been an indispensable resource, driving dynamic evolution of the mammalian genomes...
  21. pmc Prediction of protein-destabilizing polymorphisms by manual curation with protein structure
    Craig Alan Gough
    Integrated Database Group, Japan Biological Information Research Center, Tokyo, Japan
    PLoS ONE 7:e50445. 2012
    ..Our approach would be useful in identifying potentially aggregation-inducing polymorphisms that may have pathological effects...
  22. ncbi request reprint Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB)
    Chisato Yamasaki
    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Waterfront Bio IT Research Building, 2 42 Aomi, Koto ku, Tokyo 135 0064, Japan
    Gene 364:99-107. 2005
    ..This unique integrative platform for conducting in silico data-mining represents a substantial contribution to resources required for the exploration of human biology and pathology...
  23. ncbi request reprint Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: a molecular dynamics study
    Craig A Gough
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio IT Research Building, 2 42 Aomi, Koto ku, Tokyo 135 0064, Japan
    Proteins 66:69-86. 2007
    ..The methods described here have potential for identifying correlated motions responsible for other long-range effects of deleterious mutations...
  24. ncbi request reprint A web tool for comparative genomics: G-compass
    Yasuyuki Fujii
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio IT Research Building 7F, 2 42, Aomi, Koto ku, Tokyo, Japan
    Gene 364:45-52. 2005
    ..G-compass is publicly accessible on the WWW at http://www.jbirc.aist.go.jp/g-compass/...
  25. ncbi request reprint Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs
    Naoki Osada
    Division of Genetic Resources, National Institute of Infectious Diseases, Tokyo, Japan
    Mol Biol Evol 22:1976-82. 2005
    ..The results imply that positive selection increased K5UTR and structural alteration rate of a certain fraction of genes as well as Ka. We found that both positive and negative selection can act on the 5'UTR sequences...
  26. pmc Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes
    So Nakagawa
    Department of Systems Biology, School of Biomedical Science, Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Yushima, Tokyo, Japan
    Nucleic Acids Res 36:861-71. 2008
    ....
  27. pmc Novel algorithm for automated genotyping of microsatellites
    Toshiko Matsumoto
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, Tokyo, Japan
    Nucleic Acids Res 32:6069-77. 2004
    ..Our algorithm is crucial for a high-throughput genotyping system for microsatellite markers by reducing manual editing and human errors...