DDBJ staff publications (2004)

| 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 |


*Bold are CIB-DDBJ members.

  • Abe T, Ikemura T, Kanaya S, Kinouchi M, Sugawara H. (2004) Novel genome informatics for unveiling hidden signatures in genome sequences: self-organizing map (SOM) of oligonucleotide frequencies. Proceedings of Information-Based Induction Sciences. 94-99.
  • Abe T, Kanaya S, Kinouchi M, Ikemura T. (2004) Genome Informatics for Unveiling Hidden Genome Signatures. Proceedings of the Institute of Statistical Mathematics. 52:207-215.
  • Abe T, Kanaya S, Kinouchi M, Kosaka Y, Ikemura T. (2004) Novel bioinformatics for unveiling hidden characteristics in genome sequences and searching in silico for genetic signal sequences. The 8th World Multi-Conference on Systemics, Cybernetics and Informatics.
  • Alexopoulos H, Bottger A, Fischer S, Levin A, Wolf A, Fujisawa T, Hayakawa S, Gojobori T, Davies J, David C, Bacon J. (2004) Evolution of gap junctions: the missing link? Curr Biol. 14(20):R879-80.
  • Andrews TD, Gojobori T. (2004) Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen neisseria meningitidis. Genetics. 166(1):25-32.
  • Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N. (2004) Submission of microarray data to public repositories. PLoS Biol. 2:1276-1277, also Microbiology. 150:3522-3524 and Environ Health Perspect 112:A666-A667. Epub 2004 Jan 31.
  • Bellgard M, Ye J, Gojobori T, Appels R. (2004) The bioinformatics challenges is comparative analysis of cereal genomes - an overview. Funct Integr Genomics. 4(1):1-11. Epub 2004 Feb 10 .
  • Chiba H, Michibata H, Wakimoto K, Seishima M, Kawasaki S, Okubo K, Mitsui H, Torii H, Imai Y. (2004) Cloning of a gene for a novel epithelium-specific Cytosolic Phospholipase A2,cPLA2delta, induced in Psoriatic Skin. J Biol Chem. 279(13):12890-7. Epub 2004 Jan 06
  • Fukuchi S, Nishikawa K. (2004) Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res. 11(4), 219-231, 311-313.
  • Hanada K, Suzuki Y, Gojobori T. (2005) A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol. 21, 1074-80.
  • Hishiki T, Ogasawara O, Tsuruoka Y, Okubo K. (2004) Indexing anatomical concepts to OMIM Clinical Synopsis using the UMLS Metathesaurus. In Silico Biol. 4:31-54. Epub 2003 Dec 28.
  • Homma K, Kikuno RF, Nagase T, Ohara O, Nishikawa K. (2004) Alternative splice variants encoding unstable protein domains exist in the human brain. J Mol Bio. 343(5):1207-20.
  • Hwang JS, Kobayashi C, Agata K, Ikeo K, Gojobori T. (2004) Detection of apoptosis during planarian regeneration by the expression of apoptosis-related genes and TUNEL assay. Gene. 333:15-25.
  • Imanishi T, and another 151 authors including Suzuki Y, Fukuchi S, Barrero RA, Miyazaki S, Ikeo K, Nishikawa K, Sugawara H, Tateno Y, Okubo K, Gojobori T. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20.
  • Iwama H, Gojobori T. (2004) Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network. Proc Natl Acad Sci USA. 101(49):17156-61. Epub 2004 Nov 30.
  • Kadota M, Nishigaki R, Wang CC, Toda T, Shirayoshi Y, Inoue T, Gojobori T, Ikeo K, Rogers MS, Oshimura M. (2004) Containing a single human chromosome 21 in neuronal differentiation: an in vitro model of Down syndrome. Neuroscience. 129(2):325-35.
  • Kaimori J, Takenaka M, Okubo K.(2004) Quantification of Gene Expression in Mouse and Human Renal Proximal Tubules., Laser Capture Microdissection Methods and Protocols. In: Methods in Molecular Biology 293. Grame I. Murray and Stephanie Curran ed (Humana Press). 209-220.
  • Kashiwagi K, Fukami-Kobayashi K, Shiba K, Nishikawa K. (2004) Construction and characterization of chimeric proteins composed of type-1 and type-2 periplasmic binding proteins MglB and ArgT. Biosci Biotechnol Biochem. 68(4):808-813
  • Kawai Y, Ishii Y, Arakawa K, Uemura K, Saitoh B, Nishimura J, Kitazawa H, Yamazaki Y, Tateno Y, Itoh T, Saito T. (2004) Structural and functional differences in two cyclic bacteriocins with the same sequences produced by lactobacilli. Appl Environ Microbiol. 70(5):2906-2911.
  • Kinjo AR, Nishikawa K. (2004) Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. Bioinformatics. 20(16):2504-2508. Epub 2004 May 6.
  • Komiyama T, Ikeo K, Gojobori T. (2004) The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis. Gene. 333:91-99.
  • Komiyama T, Ikeo K, Tateno Y, Gojobori T. (2004) Japanese domesticated chickens have been derived from Shamo, traditional fighting cocks. Mol Phylogenet Evo. 33(1):16-21.
  • Mano S, Yasuda N, Katoh T, Tounai K, Inoko H, Imanishi T, Tamiya G, Gojobori T. (2004) Notes on the maximum likelihood estimation of haplotype frequescies. Ann Hum Genet. 68(Pt 3):257-64.
  • Matsumoto T, Yukawa W, Nozaki, Y, Nakashige R, Shinya M, Makino S, Yagura, M, Ikuta T, Imanishi T, Inoko H, Tamiya G, Gojobori T. (2004) Novel algorithm for automated genotyping of microsatelites. Nucleic Acids Res. 32(20):6069-77.
  • Michibata H, Chiba H, Wakimoto K, Seishima M, Kawasaki S, Okubo K, Mitsui H, Torii H, Imai Y. (2004) Identification and characterization of a novel component of the cornified envelope, cornifelin. Biochem Biophys Res Commun. 318(4):803-13.
  • Miyazaki S, Sugawara H, Ikeo K, Gojobori T, Tateno Y. (2004) DDBJ in the stream of various biological data. Nucleic Acids Res. 32(Database issue):D31-4.
  • Nakamura Y, Itoh T, Matsuda H, Gojobori T. (2004) Biased biological functions of horizontally transferred genes on 324,653 open reading frames of 116 prokaryotic complete genomes. Nat Genet. 36(7):760-6. Epub 2004 Jun 20.
  • Nishio H, Altaf-Ul-Amin M, Nakamura Y, Abe T, Kinouchi M, Ikemura T, Kobayashi K, Ogasawara N, Kanaya S. (2004) Gene Classification Based on Expression Profile Using BL-SOM: Suitability Assessment of Multivariate Gene Expression Data to Spherical and Plain SOM by N-Measure. The 8th World Multi-Conference on Systemics. Cybernetics and Informatics,
  • Nishio Y, Nakamura Y, Usuda Y, Sugimoto S, Matsui, K, Kawarabayashi Y, Kikuchi H, Gojobori T, Ikeo K. (2004) Evolutionary process of the amino acids biosynthesis in Corynebacterium at the whole genome level. Mol Biol Evol. 21(9):1683-91. Epub 2004 May 26.
  • Ogura A, Ikeo K, Gojobori T. (2004) Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human. Genome Res. 14(8):1555-61.
  • Sugawara H. (2004) Tsunami of data: Data resources and utilization. Kurtboke I. and Swings J. (ed.) Microbial Genetic Resources and Biodiscovery. 40-56/ National Library of Australia.
  • Sugawara H, Abe T, Tanaka N, Miyazaki S. (2004) Encounter of microbiology with the data science in the phase called post-genome sequencing. Soil microorganisms. 58(2):57-67.
  • Suzuki Y. (2004) Negative selection on neutralization epitopes of poliovirus surface proteins: implications for prediction of candidate epitopes for immunization. Gene. 328:127-133.
  • Suzuki Y. (2004) New methods for detecting positive selection at single amino acid sites. J Mol Evol. 59(1):11-9.
  • Suzuki Y, Nei M. (2004) False positive selection identified by ML-based methods: examples from the Sig1 gene of diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol Bio Evol. 21(5):914-921. Epub 2004 Mar 10.
  • Suzuki Y. (2004) Three-dimensional window analysis for detecting positive selection at structural regions of proteins. Mol Biol Evol. 21(12):2352-2359. Epub 2004 Sep 08.
  • Tateno Y, Saitou N, Okubo K, Sugawara H, Gojobori T. (2005) DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Res. 33: D25-D28.
  • Toyoda R, Kasai A, Sato S, Wada S, Saiga H, Ikeo K, Gojobori T, Numakunai T, Yamamoto H. (2004) Pigment cell lineage-specific expression activity of the ascidian tyrosinase-related gene. Gene. 332:61-69.
  • Wang CC, Kadota M, Nishigaki, Kazuki Y, Shirayoshi Y, Rogers MS, Gojobori T, Ikeo K, Oshimura M. (2004). Molecular hierarchy in neurons differentiated from mouse ES cells containing a single human chromosome 21. Biochem Biophys Res Commun. 314(2):335-50
  • Watanabe M, Kobayashi N, Shin-I T, Horiike T, Tateno Y, Kohara Y, Okada N. (2004) Extensive analysis of ORF sequences from two different cichlid species in Lake Victoria provides molecular evidence for a recent radiation event of the Victoria species flock Identity of EST sequences between Haplochromis chilotes and Haplochromis sp. "Redtailsheller". Gene. 343: 263-269.
  • Yokomine T, Shirohzu H, Purbowasito W, Toyoda A, Iwama H, Ikeo K, Hori T, Mizuno S, Tsudzuki M, Matsuda Y, Hattori M, Sakaki Y, Sasaki H. (2005). Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-Igf2-H19 region. Genome Res. 15(1):154-65. Epub 2004 Dec 08.

* Some of the publications in Japanese are excluded.

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