Last updated:2011.8.4.

DDBJ staff publications (2008)

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


*Bold are CIB-DDBJ members.

  • Akihito, Fumihito A, Ikeda Y, Aizawa M, Makino T, Umehara Y, Kai Y, Nishimoto Y, Hasegawa M, Nakabo T, and Gojobori T. (2008) Evolution of Pacific Ocean and the Sea of Japan populations of the gobiid species, Pterogobius elapoides and Pterogobius zonoleucus, based on molecular and morphological analyses. Gene. 427: 7-18.

  • Blancher A, Bonhomme M, Crouau-Roy B, Terao K, Kitano T, and Saitou N. (2008) Mitochondrial DNA sequence phylogeny of four populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis). J. Hered. 99 (3): 254-264.

  • Calafell F, Roubinet F, Ramirez-Soriano A, Saitou N, Bertranpetit J, Blancher A. (2008) Evolutionary dynamics of the human ABO gene. Hum. Genet. 124: 123-135.

  • Collier N, Doan S, Kawazow A, Matsuda-Goodwin R, Tateno Y, Ngo Q-H, Dein D, Kawtrakul A, Takeuchi K, Shigematsu M, Taniguchi K. BioCaster: detecting public health rumors with a Web-based text mining system. Bioinformatics, published online on Oct. 15, 2008, 24: 2940-2941.

  • David CN, Ozbek S, Adamczyk P, Meier S, Pauly B, Chapman J, Hwang JS, Gojobori T, and Holstein TW. (2008) Evolution of complex structures: minicollagens shape the cnidarian nematocyst. Trends Genet. 24 (9): 431-438.

  • Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen M, Ashburner M, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, dePamphilis C, Edwards R, Faruque N, Feldman R, Glockner F O, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kyripides N, Leebens-Mack J, Lewis S E, Liste A, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Moxon R, Nelson K, Parkhill J, Sansone S-A Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, Wilson G, and Wipat A. (2008) Minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 26: 541-547.

  • Fukuchi S, Homma K, Sakamoto S, Sugawara H, Tateno Y, Gojobori T, and Nishikawa K. The GTOP database in 2009: updated content and novel features to expand and deepen insightsinto protein structures and functions. Nucleic Acids Res. Advance Accesspublished on Nov. 4 (2008).

  • Hotta K, Takahashi H, Satoh N, and Gojobori T. (2008) Brachyury-downstream gene sets in a chordate, Ciona intestinalis: Integrating notochord specification, morphogenesis and chordate evolution. Evo. & Dev. 10 (1): 37-51.

  • Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, and Yon Rhee S. (2008) Big data: The future of biocuration. Nature. 455 (7209): 47-50.

  • Hwang JS, Nagai S, Hayakawa S, Takaku Y, and Gojobori T. (2008) The Search for the Origin of Cnidarian Nematocysts in Dinoflagellates. Evolutionary Biology from Concept to Application, Pierre Pontarotti (ed), Chap. 8: 135-152.

  • Hwang JS, Takaku Y, Chapman J, Ikeo K, David CN, and Gojobori T. (2008) Cilium evolution: identification of a novel protein, nematocilin, in the mechanosensory cilium of Hydra nematocytes. Mol. Biol. Evol. 25 (9): 2009-2017.

  • Jin L, Kryukov K, Clemente J, Komiyama T, Suzuki Y, Imanishi T, Ikeo K, and Gojobori T. (2008) The evolutionary relationship between gene duplication and alternative splicing. Gene. 427: 19-31.

  • Kimura A, Ikeo K, Nonaka M. Evolutionary origin of the vertebrate blood complement and coagulation systems inferred from liver EST analysis of lamprey. Dev Comp Immunol. 2008 Aug. 27.

  • Koyanagi KO, Imanishi T, and Gojobori T. (2008) Bidirectional Gene Pairs in the Human Genome. Encyclopedia of Life Science (ELS).

  • Liu Y-H, Takahashi A, Kitano T, Koide T, Shiroishi T, Moriwaki K, and Saitou N. (2008) Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies. GGS. 83: 77-88.

  • Matsuya A, Sakate R, Kawahara Y, Koyanagi KO, Sato Y, Fujii Y, Yamasaki C, Habara T, Nakaoka H, Todokoro F, Yamaguchi K, Endo T, OOta S, Makalowski W, Ikeo K, Suzuki Y, Hanada K, Hashimoto K, Hirai M, Iwama H, Saitou N, Hiraki AT, Jin H, Kaneko Y, Kanno M, Murakami K, Noda AO, Saichi N, Sanbonmatsu R, Suzuki M, Takeda J, Tanaka M, Gojobori T, Imanishi T, and Itoh T. (2008) Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Nucleic Acids Res. 36: D787-792.

  • Meier S, Gehring C, MacPherson C, Kaur M, Maqungo M, Reuben S, Muyanga S, Shih M, Wei F, Wanchana S, Mauleon R, Radovanovic A, Bruskiewich R, Tanaka T, Mohanty B, Itoh T, Wing R, Gojobori T, Sasaki T, Swarup S, Hsing Y, and Bajic V. (2008) The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network. Rice. 1: 177-187.

  • Mineta K, Ikeo K, and Gojobori T. (2008) Gene Expression in the brain and central nervous system in planarians. Planaria: A Model for Drug Action and Abuse edited by Robert B. Raffa and Scott M. Rawls.

  • Murakami K, Imanishi T, Gojobori T, and Nakai K. (2008) Two different classes of co-occurring motif-pairs found by a novel visualization method in human promoter regions. BMC Genomics. 9 (112): 1-13.

  • Nagaoka S, Ohshima S, Honda H, Kawai Y, Kitazawa H, Tateno Y, Yamazaki Y, and Saito T. (2008) Identification of five phospho-beta-glycosidases from Lactobacillus gasseri ATCC33323T cultured in lactose medium. Biosci Biotech Biochem. 72: 1954-1957.

  • Nagayoshi S, Hayashi E, Abe G, Osato N, Asakawa K, Urasaki A, Horikawa K, Ikeo K, Takeda H, Kawakami K. (2008) Insertional mutagenesis by yhe Tol2 transposon-mediated enhancer trap approach generated mutations in two developmental genes: tcf7 and synembryn-like. Development. Jan; 135 (1): 159-169.

  • Nakagawa S, Niimura Y, Gojobori T, Tanaka H, and Miura K. (2008) Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nucleic Acids Res. 36 (3): 861-871.

  • Nemoto-Sasaki Y, Hayama K, Ohya H, Arata Y, Kato Kaneko M, Saitou N, Hirabayashi J, Kasai K. (2008) Caenorhabditis eleganc galectins LEC-1-LEC-11: Structural features and sugar-binding properties. Biochimica et Biophysica Acta. 1780: 1131-1142.

  • Ohyanagi H, Ikeo K, and Gojobori T. (2008) Eukaryotic nuclear structure explains the evolutionary rate difference of ribosome export factors. Gene. 421: 7-13.

  • Ohyanagi H, Ikeo K, and Gojobori T. (2008) The origin of nucleus: Rebuild from the prokaryotic ancestors of ribosome export factors. Gene. 423: 149-152.

  • Saitou N. (2008) Genetic Relationships of Human Populations in and around the Japanese Archipelago. In Matsumura S, Forster P, and Renfrew C. (eds.) "Simulations, genetics and human prehistory". McDonald Institute Monographs. Cambridge. 89-92.

  • Sakai H, Itoh T, and Gojobori T. (2008) Processed Pseudogenes and Their Functional Resurrection in the Human and Mouse Genomes. Encyclopedia of Life Science (ELS).

  • Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo N., Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, Shimogori T, and Okada N. (2008) Possible involvement of SINEs in mammalian-specific brain formation. PNAS. 105 (11): 4220-4225.

  • Shin-I T, Tanaka Y, Tateno Y, and Mizokami M. (2008) Development and public release of comprehensive Hepatitis virus database, Hepatol Res. 38: 234-243.

  • Sugawara H, Ikeo K, Fukuchi S, Gojobori T, and Tateno Y. DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res. Advance Access published on Oct. 16 (2008).

  • Sugawara H, Ogasawara O, Okubo K, Gojobori T, and Tateno Y. (2008) DDBJ with new system and face. Nucleic Acids Res. Jan; 36: D22-24.

  • Suzuki Y. (2008) False-positive results obtained from the branch-test of positive selection. Genes & Genetic Systems. 83: 331-338.

  • Suzuki Y. (2008) Phylogenetic window analysis for detecting chronological changes in natural selection. Open Evolution Journal. 2: 13-30.

  • Suzuki Y. (2008) Positive selection operates continuously on hemagglutininduring evolution of H3N2 human influenza A virus. Gene. 427: 111-116.

  • Tada M, Nagasima T, Udagawa T, Tachikawa M, and Sugawara H. (2008) Ab initio fragment molecular orbital (FMO) analysis of the structure of the phosphoinositide-binding peptide from gelsol. Journal of Molecular Structure: THEOCHEM Online publication complete: 14-JAN-2009 DOI information: 10. 1016/ j. theochem. 2008. 12. 003.

  • Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T, and Imanishi T. (2008) Low conservation and species-specific evolution of alternative splicing in humans and mice analysed with comparative genomics using well-annotated full-length cDNAs. Nucleic Acids Res. 36 (20): 6386-6395.

  • Tanaka T, Itoh T, Sasaki T, Gojobori T, Hsing Y, Han B, McCombie W, Apweiler R, Tyagi A, Haberer G, Bruskiewich R, Bureau T, Tatusova T, An G, Messing J, Christie K, Lieberherr D, Wing R, Meyers B, and Echeverria M. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36: D1028-1033.

  • Tateno Y. (2008) International collaboration among DDBJ, EMBL Bank and GenBank. Tanpakushitu Kouso Kakusan. 53: 182-189 (in Japanese).

  • Tateno Y, Fukami-Kobayashi K, and Inoko H. (2008) Evolution of MHC class I complex region with special reference to fragmentary LINE sequences. In: Quantum Bio-Informatics, pp412-426, Eds, L. Accardi, W. Freudenberg and M. Ohya, World Scientific Press, New Jersey.

  • Yamaguchi-Kabata Y, Shimada MK, Hayakawa Y, Minoshima S, Chakraborty R, Gojobori T, and Imanishi T. (2008) Distribution and effects of nonsense polymorphisms in human genes. PLos One. 3 (10): e3393.

* Some of the publications in Japanese are excluded.

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