H Toh

Summary

Affiliation: Biomolecular Engineering Research Institute
Country: Japan

Publications

  1. ncbi request reprint Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling
    Hiroyuki Toh
    Department of Bioinformatics, Biomolecular Engineering Research Institute 6 2 3, Furuedai, Suita, Osaka 565 0874, Japan
    Bioinformatics 18:287-97. 2002
  2. ncbi request reprint Homology modeling of human leptin/leptin receptor complex
    T Hiroike
    Biomolecular Engineering Research Institute, 6 2 3, Furuedai, Suita, 565 0874, Japan
    Biochem Biophys Res Commun 275:154-8. 2000
  3. ncbi request reprint Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm
    H Toh
    Biomolecular Engineering Research Institute, Osaka, Japan
    Comput Appl Biosci 13:387-96. 1997
  4. pmc Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus
    I K Cann
    Department of Molecular Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    J Bacteriol 183:2614-23. 2001
  5. ncbi request reprint Mutational analysis of the functional motifs of RuvB, an AAA+ class helicase and motor protein for holliday junction branch migration
    H Iwasaki
    Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565 0871, Japan
    Mol Microbiol 36:528-38. 2000
  6. ncbi request reprint Identification of new members of the GS ADP-forming family from the de novo purine biosynthesis pathway
    S Kanai
    Department of Bioinformatics, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka, 565 0874 Japan
    J Mol Evol 48:482-92. 1999
  7. ncbi request reprint Molecular evolution of the domain structures of protein disulfide isomerases
    S Kanai
    Department of Bioinfomatics, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka, 565 Japan
    J Mol Evol 47:200-10. 1998
  8. ncbi request reprint Three novel repetitive units of reelin
    H Ichihara
    Department of Bioinformatics, Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka 565-0874, Japan
    Brain Res Mol Brain Res 97:190-3. 2001
  9. pmc Functional interactions of a homolog of proliferating cell nuclear antigen with DNA polymerases in Archaea
    I K Cann
    Department of Molecular Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    J Bacteriol 181:6591-9. 1999
  10. ncbi request reprint Molecular evolution of the photolyase-blue-light photoreceptor family
    S Kanai
    Department of Bioinfomatics, Biomolecular Engineering Research Institute, 6 2 3, Furuedai, Suita, Osaka, 565 Japan
    J Mol Evol 45:535-48. 1997

Collaborators

Detail Information

Publications30

  1. ncbi request reprint Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling
    Hiroyuki Toh
    Department of Bioinformatics, Biomolecular Engineering Research Institute 6 2 3, Furuedai, Suita, Osaka 565 0874, Japan
    Bioinformatics 18:287-97. 2002
    ..Graphical Gaussian Modeling (GGM) is a widely utilized method to infer or test relationships among a plural of variables...
  2. ncbi request reprint Homology modeling of human leptin/leptin receptor complex
    T Hiroike
    Biomolecular Engineering Research Institute, 6 2 3, Furuedai, Suita, 565 0874, Japan
    Biochem Biophys Res Commun 275:154-8. 2000
    ..The observation suggests that the model is useful to lead the experimental study on the interaction between leptin and the receptor...
  3. ncbi request reprint Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm
    H Toh
    Biomolecular Engineering Research Institute, Osaka, Japan
    Comput Appl Biosci 13:387-96. 1997
    ..Finally, the double dynamic programming algorithm with full structural environments was applied to the residue pairs within the epsilon-suboptimal region to produce an improved alignment...
  4. pmc Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus
    I K Cann
    Department of Molecular Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    J Bacteriol 183:2614-23. 2001
    ..furiosus. We propose that PfuRFC is required for efficient loading of PfuPCNA and that the role of RFC in processive DNA synthesis is conserved in Archaea and Eucarya...
  5. ncbi request reprint Mutational analysis of the functional motifs of RuvB, an AAA+ class helicase and motor protein for holliday junction branch migration
    H Iwasaki
    Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565 0871, Japan
    Mol Microbiol 36:528-38. 2000
    ....
  6. ncbi request reprint Identification of new members of the GS ADP-forming family from the de novo purine biosynthesis pathway
    S Kanai
    Department of Bioinformatics, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka, 565 0874 Japan
    J Mol Evol 48:482-92. 1999
    ..Moreover, the analysis showed that archaeal GARS had diverged before the speciation between bacteria and eucarya...
  7. ncbi request reprint Molecular evolution of the domain structures of protein disulfide isomerases
    S Kanai
    Department of Bioinfomatics, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka, 565 Japan
    J Mol Evol 47:200-10. 1998
    ..The diverse domain structures of the members have been generated through domain duplications and deletions...
  8. ncbi request reprint Three novel repetitive units of reelin
    H Ichihara
    Department of Bioinformatics, Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka 565-0874, Japan
    Brain Res Mol Brain Res 97:190-3. 2001
    ..We found that the anti-Reelin antibodies' recognition region consists of three repetitive units. The correspondence of the repetitive units with the antigenicity is discussed...
  9. pmc Functional interactions of a homolog of proliferating cell nuclear antigen with DNA polymerases in Archaea
    I K Cann
    Department of Molecular Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    J Bacteriol 181:6591-9. 1999
    ..This is the first stage in elucidating the archaeal DNA replication mechanism...
  10. ncbi request reprint Molecular evolution of the photolyase-blue-light photoreceptor family
    S Kanai
    Department of Bioinfomatics, Biomolecular Engineering Research Institute, 6 2 3, Furuedai, Suita, Osaka, 565 Japan
    J Mol Evol 45:535-48. 1997
    ....
  11. ncbi request reprint Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold
    H Daiyasu
    Department of Bioinformatics, Biomolecular Engineering Research Institute, Osaka, Japan
    FEBS Lett 503:1-6. 2001
    ..In this minireview, the functional and structural varieties of the growing protein family are described...
  12. pmc Molecular cloning and characterization of human caspase-activated DNase
    N Mukae
    Department of Genetics, Osaka University Medical School, B 3, 2 2 Yamada oka, Suita, Osaka 565 0871, Japan
    Proc Natl Acad Sci U S A 95:9123-8. 1998
    ..Overexpression of CAD potentiated DNA fragmentation by apoptotic stimuli in these cell lines, indicating that CAD is responsible for the apoptotic DNA degradation...
  13. ncbi request reprint Binding of biliverdin, bilirubin, and thyroid hormones to lipocalin-type prostaglandin D synthase
    C T Beuckmann
    Osaka Bioscience Institute, Suita, Japan
    Biochemistry 38:8006-13. 1999
    ..These results show that prostaglandin D synthase binds small lipophilic ligands with a specificity distinct from that of other lipocalins...
  14. ncbi request reprint Molecular cloning and expression of the gene for serine hydroxymethyltransferase from an obligate methylotroph Hyphomicrobium methylovorum GM2
    A Miyata
    Department of Pharmacology, National Cardiovascular Center Research Institute, Osaka, Japan
    Eur J Biochem 212:745-50. 1993
    ..coli mutant ME5427 (glyA-). The transformed E. coli cells expressed SHMT, which was immunologically and enzymologically indistinguishable from the enzyme isolated from H. methylovorum GM2...
  15. ncbi request reprint Molecular evolution of biotin-dependent carboxylases
    H Toh
    Protein Engineering Research Institute, Osaka, Japan
    Eur J Biochem 215:687-96. 1993
    ..A repeated structure was found in biotin-carboxyl-carrier protein, and the secondary structure of the protein was predicted using the observed sequence similarity with a lipoic-acid-binding domain...
  16. ncbi request reprint Molecular evolution and zinc ion binding motif of leukotriene A4 hydrolase
    H Toh
    Protein Engineering Research Institute, Osaka, Japan
    Biochem Biophys Res Commun 171:216-21. 1990
    ..In agreement with the observation, LTA4 hydrolase is a zinc protein as determined by atomic absorption spectroscopy...
  17. pmc ASIAN: a web server for inferring a regulatory network framework from gene expression profiles
    Sachiyo Aburatani
    Laboratory of Biostatistics, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 33:W659-64. 2005
    ..Thus, the ASIAN (Automatic System for Inferring A Network) web server provides an initial basis for inferring regulatory relationships, in that the clustering serves as the first step toward identifying the gene function...
  18. ncbi request reprint Two novel genes expressed in Xenopus germ line: characteristic features of putative protein structures, their gene expression profiles and their possible roles in gametogenesis and embryogenesis
    Yasuko Ikema
    Department of Biological Science, Faculty of Science, Kumamoto University, Kurokami 2 39 1, Kumamoto, Japan
    Mol Reprod Dev 62:421-30. 2002
    ..The characteristic expression profile of Xtr and the protein structure similar to the Drosophila tudor protein suggested its possible role in the progression of meiosis and PGC differentiation...
  19. pmc ASH structure alignment package: sensitivity and selectivity in domain classification
    Daron M Standley
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita, Osaka, Japan
    BMC Bioinformatics 8:116. 2007
    ..The score is implemented in the ASH structure alignment package, for which the source code and a web service are freely available from the PDBj website http://www.pdbj.org/ASH/...
  20. ncbi request reprint Improvement in the accuracy of multiple sequence alignment program MAFFT
    Kazutaka Katoh
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Genome Inform 16:22-33. 2005
    ..The [GL]-INS-i options are applicable to aligning up to approximately 200 sequences, although not applicable to thousands of sequences because of time and space complexities...
  21. pmc GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures
    Daron M Standley
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita, Osaka 565 0871, Japan
    BMC Bioinformatics 6:221. 2005
    ..Initial alignments are generated by the program Local ASH, and can be supplemented by alignments from any other program...
  22. ncbi request reprint [Bioinformatics]
    Wataru Nemoto
    Nihon Yakurigaku Zasshi 125:159-64. 2005
  23. pmc MAFFT version 5: improvement in accuracy of multiple sequence alignment
    Kazutaka Katoh
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 33:511-8. 2005
    ..Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homologues collected from SwissProt using NCBI-BLAST...
  24. ncbi request reprint Prediction of interfaces for oligomerizations of G-protein coupled receptors
    Wataru Nemoto
    Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630 0101, Japan
    Proteins 58:644-60. 2005
    ..The benefits and the pitfalls of the new method will be discussed, based on the results of the applications...
  25. ncbi request reprint Detecting local structural similarity in proteins by maximizing number of equivalent residues
    Daron M Standley
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita, Osaka, Japan
    Proteins 57:381-91. 2004
    ..In addition, several structure-structure pairs that show only partial similarity are discussed, and results are compared to those from the LGA, SARF2, and ThreeCa programs...
  26. ncbi request reprint Identification of cryptochrome DASH from vertebrates
    Hiromi Daiyasu
    Bioinformatics Centre, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Genes Cells 9:479-95. 2004
    ..A phylogenetic analysis revealed that the seven candidates actually belong to the new type of cryptochrome subfamily. This is the first report of the CRY-DASH members from vertebrates and fungi...
  27. ncbi request reprint ASIAN: a website for network inference
    Sachiyo Aburatani
    Laboratory of Biostatistics, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Bioinformatics 20:2853-6. 2004
    ..One of the remarkable features of the website is its ability to infer a network, concomitant with hierarchical clustering and the following estimation of cluster boundaries. AVAILABILITY: http://eureka.ims.u-tokyo.ac.jp/asian..
  28. ncbi request reprint Identification of a new cryptochrome class. Structure, function, and evolution
    Ronald Brudler
    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Mol Cell 11:59-67. 2003
    ..Whole genome transcriptional profiling together with experimental confirmation of DNA binding indicated that Synechocystis cryptochrome DASH functions as a transcriptional repressor...
  29. ncbi request reprint [Extraction of information about protein interaction using evolutionary trace]
    Hisako Ichihara
    Tanpakushitsu Kakusan Koso 47:1863-9. 2002
  30. doi request reprint Recent developments in the MAFFT multiple sequence alignment program
    Kazutaka Katoh
    Digital Medicine Initiative, Kyushu University, Fukuoka 812 8582, Japan
    Brief Bioinform 9:286-98. 2008
    ..We review these and other techniques that MAFFT uses and suggest possible future directions of MSA software as a basis of comparative analyses. MAFFT is available at http://align.bmr.kyushu-u.ac.jp/mafft/software/...