DDBJ staff Oral presentation (2006)

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  • Abe T, Sugawara H, Kanaya S, Ikemura T. Sequences from Almost All Prokaryotic, Eukaryotic, and Viral Genomes Available Could be Classified According to Genomes on a Large-Scale Self-Organizing Map Constructed with the Earth Simulator. Journal of the Earth Simulator. 2006 Oct 6; 17-23.
  • Abe T, Sugawara H, Kanaya S, Kinouchi M, Ikemura T. Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene. 2006 Jan 3;365:27-34.
  • Choy KW, Wang CC, Ogura A, Lau TK, Rogers MS, Ikeo K, Gojobori T, Tang LY, Lam DS, Chung TK, Pang CP. Molecular characterization of the developmental gene in eyes: through data-mining on integrated transcriptome databases. Clin Biochem. 2006 Mar;39(3):224-30.
  • Choy KW, Wang CC, Ogura A, Lau TK, Rogers MS, Ikeo K, Gojobori T, Lam DS, Pang CP. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. Physiol Genomics. 2006 Mar 13;25(1):9-15.
  • Cochrane G, Bates K, Apweiler R, Tateno Y, Mashima J, Kosuge T, Mizrachi IK, Schafer S, Fetchko M. Evidence standards in experimental and inferential INSDC Third Party Annotation data. OMICS. 2006 Summer;10(2):105-13.
  • Fukuchi S, Homma K, Minezaki Y, Nishikawa K. Intrinsically disordered loops inserted into the structural domains of human proteins. J Mol Biol. 2006 Jan 27;355(4):845-57.
  • Hanada K, Gojobori T, Li WH. Radical amino acid change versus positive selection in the evolution of viral envelope proteins. Gene. 2006 Dec 30;385:83-8. Hanada K, Tanaka Y, Mizokami M, Gojobori T, Alter HJ. A reduction in selective immune pressure during the course of chronic hepatitis C correlates with diminished biochemical evidence of hepatic inflammation. Virology. 2006 Dec 14; [Epub ahead of print]
  • Haruki M, Saito Y, Ota M, Nishikawa K, Kanaya S. Stabilization of E. coli Ribonuclease HI by the 'stability profile of mutant protein' (SPMP)-inspired random and non-random mutagenesis. J Biotechnol. 2006 Jul 25;124(3):512-22.
  • Homma K, Fukuchi S, Nakamura Y, Gojobori T, Nishikawa K. Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in Eight Species of {gamma}-Proteobacteria. 1: Mol Biol Evol. 2006 Dec 21; [Epub ahead of print]
  • Kinjo AR, Nishikawa K. CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. BMC Bioinformatics. 2006 Sep 5;7:401
  • Kobayashi N, Watanabe M, Kijimoto T, Fujimura K, Nakazawa M, Ikeo K, Kohara Y, Gojobori T, Okada N. magp4 gene may contribute to the diversification of cichlid morphs and their speciation. Gene. 2006 May 24;373:126-33.
  • Kosuge T, Abe T, Okido T, Tanaka N, Hirahata M, Maruyama Y, Mashima J, Tomiki A, Kurokawa M, Himeno R, Fukuchi S, Miyazaki S, Gojobori T, Tateno Y, Sugawara H. Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of New Genes: Gene Trek in Prokaryote Space (GTPS). DNA Res. 2006 Dec 13; [Epub ahead of print]
  • Makino T, Gojobori T. The evolutionary rate of a protein is influenced by features of the interacting partners. Mol Biol Evol. 2006 Apr;23(4):784-9.
  • Makino T, Suzuki Y, Gojobori T. Differential evolutionary rates of duplicated genes in protein interaction network. Gene. 2006 Dec 30;385:57-63.
  • Minezaki Y, Homma K, Kinjo AR, Nishikawa K. Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. J Mol Biol. 2006 Jun 16;359(4):1137-49.
  • Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, Field D. Concept of sample in OMICS technology. OMICS. 2006 Summer;10(2):127-37.
  • Niimi T, Sahara K, Oshima H, Yasukochi Y, Ikeo K, Traut W. Molecular cloning and chromosomal localization of the Bombyx Sex-lethal gene. Genome. 2006 Mar;49(3):263-8.
  • Noda AO, Ikeo K, Gojobori T. Comparative genome analyses of nervous system-specific genes. Gene. 2006 Jan 3;365:130-6.
  • Ogasawara O, Otsuji M, Watanabe K, Iizuka T, Tamura T, Hishiki T, Kawamoto S, Okubo K. BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D628-31.
  • Ohta T, Kawabata T, Nishikawa K, Tani A, Kimbara K, Kawai F. Analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from Sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants. Appl Environ Microbiol. 2006 Jun;72(6):4388-96.
  • Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T. The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D741-4.
  • Okubo K, Sugawara H, Gojobori T, Tateno Y. DDBJ in preparation for overview of research activities behind data submissions. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D6-9.
  • Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res. 2006 Jan 5;34(1):1-9.
  • Sakabe E, Tanaka N, Shimozono N, Gojobori T, Fujiwara S. Effects of U0126 and fibroblast growth factor on gene expression profile in Ciona intestinalis embryos as revealed by microarray analysis. Dev Growth Differ. 2006 Aug;48(6):391-400.
  • Sakai H, Koyanagi KO, Imanishi T, Itoh T, Gojobori T. Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes. Gene. 2006 Nov 18; [Epub ahead of print]
  • Shiina T, Ota M, Shimizu S, Katsuyama Y, Hashimoto N, Takasu M, Anzai T, Kulski JK, Kikkawa E,Naruse T, Kimura N, Yanagiya K, Watanabe A, Hosomichi K, Kohara S, Iwamoto C, Umehara Y, Meyer A, Wanner V, Sano K, Macquin C, Ikeo K, Tokunaga K, Gojobori T, Inoko H, Bahram S. Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity. Genetics. 2006 Jul;173(3):1555-70.
  • Suzuki Y. Ancient positive selection on CD155 as a possible cause for susceptibility to poliovirus infection in simians. Gene. 2006 May 24;373:16-22.
  • Suzuki Y. Natural selection on the influenza virus genome. Mol Biol Evol. 2006 Oct;23(10):1902-11.
  • Suzuki Y. Statistical properties of the methods for detecting positively selected amino acid sites. Gene. 2006 Jan 3;365:125-9.
  • Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T. Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res. 2006;34(14):3917-28.
  • Tanaka N, Abe T, Miyazaki S, Sugawara H. A Useful Bioinformatics Suite for Retrieving and Analyzing Microbial Genome Data (G-InforBIO). Journal of Computer Aided Chemistry. 2006;7:87-93.
  • Tanaka N, Abe T, Miyazaki S, Sugawara H. G-InforBIO: integrated system for microbial genomics. BMC Bioinformatics. 2006 Aug 4;7:368.
  • Tanaka T, Ikeo K, Gojobori T. Evolution of metabolic networks by gain and loss of enzymatic reaction in eukaryotes. Gene. 2006 Jan 3;365:88-94.
  • Traut W, Niimi T, Ikeo K, Sahara K. Phylogeny of the sex-determining gene Sex-lethal in insects. Genome. 2006 Mar;49(3):254-62.
  • Wang HY, Chien HC, Osada N, Hashimoto K, Sugano S, Gojobori T, Chou CK, Tsai SF, Wu CI, Shen CK. Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates. PLoS Biol. 2006 Dec 26;5(2):e13 [Epub ahead of print]
  • Yamasaki C, Kawashima H, Todokoro F, Imamizu Y, Ogawa M, Tanino M, Itoh T, Gojobori T, Imanishi T. TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W345-9.
  • Yoshida K, Fujisawa T, Hwang JS, Ikeo K, Gojobori T. Degeneration after sexual differentiation in hydra and its relevance to the evolution of aging. Gene. 2006 Dec 30;385:64-70.
  • Yura K, Shionyu M, Hagino K, Hijikata A, Hirashima Y, Nakahara T, Eguchi T, Shinoda K, Yamaguchi A, Takahashi K, Itoh T, Imanishi T, Gojobori T, Go M. Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene. 2006 Oct 1;380(2):63-71.

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