DDBJ staff papers(1996-2008)

Bold are CIB-DDBJ members. Some of the publications in Japanese are excluded.

2008

  • 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.
  • Genome Information Integration Project And H-Invitation 2 (DDBJ からは、Okido T, Mashima J, Lee K-B, Nozaki A, Sakai K, Suzuki Y, Ikeo K, Saitou N, Sugawara H, Fukuchi S, Tateno Y, Gojobori T.) (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res., 2008, 36 Database issue: D793-D799.

2007

  • Dobashi Y, Suzuki S, Sugawara H, Ooi A (2007) Involvement of epidermal growth factor receptor and downstream molecules in bone and soft tissue tumors. Hum Pathol. June;38(6):914-25.
  • Field D, Garrity G, Gray T, Selengut J, Sterk P, Thomson N, Tatusova T, Cochrane G, Kottmann R, Lister A. L, Tateno Y, and Vaughan R (2007) eGenomics: Cataloguing our complete genome collection III, Comp and Func Genomics ID 47304
  • Fukami-Kobayashi K, Minezaki Y, Tateno Y and Nishikawa K (2007) A tree of life based on protein domain organizations Mol Biol Evol. 24: 1181 - 1189
  • Gough C, Gojobori T and Imanishi T (2007) Cancer-related Mutations in BRCA1-BRCT Cause Long-Range Structural Changes in Protein-Protein Binding Sites: A Molecular Dynamics Study. Proteins 66(1), 69-86.
  • Hanada K, Tanaka Y, Mizokami M, Gojobori T and Alter H J (2007). A reduction in selective immune pressure during the course of chronic hepatitis C correlates with diminished biochemical evidence of hepatic inflammation. Virology 361, 27-33.
  • Homma K, Fukuchi S, Nakamura Y, Gojobori T and Nishikawa K (2007). 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. Mol. Biol. Evol. 24(3), 805-813.
  • Honda H, Kataoka F, Nagaoka S, Kawai Y, Kitazawa K, Kimura N, Taketomo N, Yamazaki Y, Tateno Y and Saito T (2007) β-galactosidase, phospho-β-galactosidase and phospho-β- glucosidase activities of lactobacilli strains isolated from human faces, Lett Appl Microbiol. 45: 461-466
  • Hoshino H, Uchida T, Otsuki T, Kawamoto S, Okubo K, Takeichi M, and Chisaka O (2007) Cornichon-like Protein Facilitates Secretion of HB-EGF and Regulates Proper Development of Cranial Nerves. Molecular Biology of the Cell. Apr Vol.18 D1143-1152
  • Hotta K, Mitsuhara K, Takahashi H., Inaba K, Oka K, Gojobori T and Ikeo K (2007). A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva. Dev. Dyn. 236(7), 1790-1805.
  • The Rice Annotation Project: Ito, T, Ikeo K, Gojobori T et al. (2007). Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana. Genome Res. 17(2), 175-183.
  • Jung Shan H, Ohyanagi H, Hayakawa S, Osato N, Nishimiya-Fujisawa C, Ikeo K, David C, Fujisawa T and Gojobori T (2007). The evolutionary emergence of cell type specific genes inferred from the gene expression analysis of hydra. Proc. Natl. Acad. Sci. USA 104(37), 14735-14740.
  • Kotegawa H, Hidaka H, Kobayashi TC, Kikuchi D, Sugawara H, Sato H (2007) Connection between Charge Fluctuations and the Coherent Temperature in the Heavy-Fermion System SmOs4Sb12: A ;{121, 123}Sb NQR Study.Phys Rev Lett. Oct 12;99(15):156408.
  • Kubota R, Hanada K, Furukawa Y, Arimura K, Osame M, Gojobori T and Izumo S (2007) Genetic Stability of Human T Lymphotropic Virus Type I despite Antiviral Pressures by CTLs.. Journal of Immunol. 178(9), 5966-5972.
  • Landry CR, Castillo-Davis CI, Ogura A, Liu JS, and Hartl DL (2007) Systems-level analysis and evolution of the phototransduction network in Drosophila. PNAS 104,9, 3283-3288
  • Liu QX, Nakashima-Kamimura N, Ikeo K, Hirose S, and Gojobori T (2007). Compensatory Change of Interacting Amino Acids in the Coevolution of Transcriptional Coactivator MBF1 and TATA-Box Binding Protein TBP. Mol. Biol. Evol. 24(7), 1458-1463.
  • Makino T and Gojobori T (2007). Evolution of Protein-Protein Interaction Network. Gene and Protein Evolution. Ge-nome Dynamics Vol. 3, 13-29.
  • Hirahata M, Abe T, Tanaka N, Kuwana Y, Shigemoto Y, Miyazaki S, Suzuki Y, Sugawara H (2007) Genome Infor-mation Broker for Viruses (GIB-V): database for comparative analysis of virus genomes. Nucleic Acids Research 35:D339-D342.
  • Osato N, Suzuki Y, Ikeo K, and Gojobori T (2007). Transcriptional interferences in cis natural antisense transcripts of human and mouse. Genetics 176, 1299-1306.
  • Sakai H, Koyanagi KO, Imanishi T, Itoh T, and Gojobori T (2007). Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes. GENE 389(2), 196-203.
  • Sakamoto A, Iwabata K, Koshiyama A, Sugawara H, Yanai T, Kanak Y, Takeuchi R, Daikuhara Y, Takakusagi Y, Sakaguchi K (2007) Two X family DNA polymerases, lambda and mu, in meiotic tissues of the basidiomycete, Coprinus cinereus. Chromosoma. Dec;116(6):545-56.
  • Sakate R, Suto Y, Imanishi T, Tanoue T, Hida M, Hayasaka I, Kusuda J, Gojobori T, Hashimoto K and Hirai M (2007) Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the tran-scriptome.GENE 399(1), 1-10.
  • Semba H, Sugawara H, Otsuka M, Ueki A (2007) [Nocturnal epilepsy associated with sleep apnea syndrome] Nippon Naika Gakkai Zasshi. Apr 10;96(4):784-6.
  • Shin-I T, Tanaka Y, Tateno Y and Mizokami M (2007) Development and public release of comprehensive Hepatitis virus database, Hepatol Res. Sep 17.
  • Shiono Y, Sugawara H, Nazarova M, Murayama T, Takahashi K, Ikeda M (2007) Three lanostane triterpenoids, aeruginosols A, B and C, from the fruiting bodies of Stropharia aeruginosa.J Asian Nat Prod Res. Sep;9(6):531-5.
  • Sugawara H, Abe T, Gojobori T, and Tateno Y (2007) DDBJ working on evaluation and classification of bacterial genes in INSDC. Nucleic Acids Res. 35: D13-D15
  • Sugawara H, Iwata H, Souri M, Ichinose A (2007) Regulation of human protein Z gene expression by liver-enriched transcription factor HNF-4alpha and ubiquitous factor Sp1.J Thromb Haemost. Nov;5(11):2250-8.
  • Sugawara H, Ogasawara O, Okubo K, Gojobori T and Tateno Y (2007) DDBJ with new system and face. Nucleic Acids Res Oct 25
  • Suzuki Y (2007) Multiple transmissions of tick-borne encephalitis virus between Japan and Russia. Genes & Genetic Systems 82:187-195.
  • Suzuki Y (2007) Inferring natural selection operating on conservative and radical substitution at single amino acid sites. Genes & Genetic Systems 82:341-360.
  • Takeda JI, Suzuki Y, Nakao M, Kuroda T, Sugano S, Gojobori T and Imanishi T (2007). H-DBAS: Alternative Splic-ing Database of Completely Sequenced and Manually Annotated Full-length cDNAs Based on H-Invitational. Nu-cleic Acids Res. 35 (Database issue), D104-109
  • Tanaka N, Uchino M, Miyazaki S, Sugawara H (2007) Identification of discriminative characteristics for clusters from biologic data with InforBIO software.BMC Bioinformatics. Aug 2;8:281.
  • Tanaka Y, Hanada K, Hanabusa H, Kurbanov F, Gojobori T and Mizokami M (2007). Increasing genetic diversity of hepatitis C virus in hemophiliacs with human immunodeficiency virus coinfection. J. Gen. Virol. 88(Pt 9), 2513-2519.
  • Ushiyama M, Ikeda R, Sugawara H, Yoshida M, Mori K, Kangawa K, Inoue K, Yamada K, Miyata A (2007) Differen-tial intracellular signaling through PAC1 isoforms as a result of alternative splicing in the first extracellular domain and the third intracellular loop. Mol Pharmacol. Jul;72(1):103-11.
  • Wang HY, Chien HC, Osada N, Hashimoto K, Sugano S, Gojobori T, Chou CK, Tsai SF, Wu CI, and Shen CK (2007). Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates. PLoS Biology 5(2), e13.
  • Yamasaki A, Imada S, Higashimichi H, Fujiwara H, Saita T, Miyamachi T, Sekiyama A, Sugawara H, Kikuchi D, Sato H, Higashiya A, Yabashi M, Tamasaku K, Miwa D, Ishikawa T, Suga S (2007) Coexistence of strongly mixed-valence and heavy-fermion character in SmOs4Sb12 studied by soft- and hard-X-ray spectroscopy. Phys Rev Lett. Apr 13;98(15):156402.
  • Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Taka-bayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halli-gan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res. Jan;36(Database issue):D793-9.
  • You DJ, Fukuchi S, Nishikawa K, Koga Y, Takano K, Kanaya S (2007) Protein thermostabilization requires a fine-tuned placement of surface-charged residues. J Biochem. Oct;142(4):507-16.
  • Yuge K, Ikeo K and Gojobori T (2007) Evolutionary origin of sex-related genes in the mouse brain. Gene 406(1-2), 108-112.

2006

  • 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.

2005

  • Chiusano ML, Gojobori T, Toraldo G. A C++ computational environment for biomolecular sequence management. Computational Management Sciences. 2005 2(3): 165-80.
  • Fujii Y, Itoh T, Sakate R, Koyanagi KO, Matsuya A, Habara T, Yamaguchi K, Kaneko Y, Gojobori T, Imanishi T. A web tool for comparative genomics: G-compass. Gene. 2005 Dec 30;364C:45-52.
  • Fukami-Kobayashi K, Shiina T, Anzai T, Sano K, Yamazaki M, Inoko H, Tateno Y. Genomic evolution of MHC class I region in primates. Proc Natl Acad Sci U S A. 2005 Jun 28;102(26):9230-4.
  • Hanada K, Suzuki Y, Nakane T, Hirose O, Gojobori T. The origin and evolution of porcine reproductive and respiratory syndrome viruses. Mol Biol Evol. 2005 Apr;22(4):1024-31.
  • Hayashi H, Abe T, Sakamoto M, Ohara H, Ikemura T, Sakka K, Benno Y. Direct cloning of genes encoding novel xylanases from the human gut. Can J Microbiol. 2005 Mar;51(3):251-9.
  • International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005 Aug 11;436:793-800
  • Itoh K, Kawasaki S, Kawamoto S, Seishima M, Chiba H, Michibata H, Wakimoto K, Imai Y, Minesaki Y, Otsuji M, Okubo K. Identification of differentially expressed genes in psoriasis using expression profiling approaches. Exp Dermatol. 2005 Sep;14(9):667-74.
  • Kaimori JY, Takenaka M, Okubo K. Quantification of gene expression in mouse and human renal proximal tubules. Methods Mol Biol. 2005;293:209-19.
  • Kijimoto T, Watanabe M, Fujimura K, Nakazawa M, Murakami Y, Kuratani S, Kohara Y, Gojobori T, Okada N. cimp1, a novel astacin family metalloproteinase gene from East African cichlids, is differentially expressed between species during growth. Mol Biol Evol. 2005 Aug;22(8):1649-60
  • Kinjo AR, Horimoto K, Nishikawa K. Predicting absolute contact numbers of native protein structure from amino acid sequence. Proteins. 2005 Jan 1;58(1):158-65.
  • Kinjo AR, Nishikawa K. Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks. BIOPHYSICS. 2005, 1:67-74.
  • Kinjo AR, Nishikawa K. Recoverable one-dimensional encoding of three-dimensional protein structures. Bioinformatics. 2005 May 15;21(10):2167-70.
  • Koyanagi KO, Hagiwara M, Itoh T, Gojobori T, Imanishi T. Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system. Gene. 2005 Jul 4;353(2):169-76.
  • Matsumura Y, Shimokawa K, Hayashizaki Y, Ikeo K, Tateno Y, Kawai J. Development of a spot reliability evaluation score for DNA microarrays. Gene. 2005 May 9;350(2):149-60.
  • Minezaki Y, Homma K, Nishikawa K. Genome-Wide Survey of Transcription Factors in Prokaryotes Reveals Many Bacteria-Specific Families Not Found in Archaea. DNA Res. 2005,12(5): 269-80.
  • Nakao M, Barrero RA, Mukai Y, Motono C, Suwa M, Nakai K. Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals. Nucleic Acids Res. 2005 Apr 28;33(8):2355-63.
  • Nishio Y, Usuda Y, Gojobori T, Ikeo K. Comparative whole genome sequence analysis of corynebacteria. Bioinformatics of Genome Regulation and Structure II. 2005 121-9.
  • Ogasawara M, Imanishi T, Moriwaki K, Gaudieri S, Tsuda H, Hashimoto H, Shiroishi T, Gojobori T, Koide T. Length variation of CAG/CAA triplet repeats in 50 genes among 16 inbred mouse strains. Gene. 2005 Apr 11;349:107-19.
  • Ogura A, Ikeo K, Gojobori T. Estimation of ancestral gene set of bilaterian animals and its implication to dynamic change of gene content in bilaterian evolution. Gene. 2005 Jan 17;345(1):65-71.
  • Osada N, Hirata M, Tanuma R, Kusuda J, Hida M, Suzuki Y, Sugano S, Gojobori T, Shen CK, Wu CI, Hashimoto K. Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs. Mol Biol Evol. 2005 Oct;22(10):1976-82.
  • Saka K, Tadenuma M, Nakade S, Tanaka N, Sugawara H, Nishikawa K, Ichiyoshi N, Kitagawa M, Mori H, Ogasawara N, Nishimura A. A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studies. DNA Res. 2005 Feb 28;12(1):63-8.
  • Shirai T, Nakato A, Izutani N, Nagahisa K, Shioya S, Kimura E, Kawarabayasi Y, Yamagishi A, Gojobori T, Shimizu H. Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria. Metab Eng. 2005 Mar;7(2):59-69.
  • Tamiya G, Shinya M, Imanishi T, Ikuta T, Makino S, Okamoto K, Furugaki K, Matsumoto T, Mano S, Ando S, Nozaki Y, Yukawa W, Nakashige R, Yamaguchi D, Ishibashi H, Yonekura M, Nakami Y, Takayama S, Endo T, Saruwatari T, Yagura M, Yoshikawa Y, Fujimoto K, Oka A, Chiku S, Linsen SE, Giphart MJ, Kulski JK, Fukazawa T, Hashimoto H, Kimura M, Hoshina Y, Suzuki Y, Hotta T, Mochida J, Minezaki T, Komai K, Shiozawa S, Taniguchi A, Yamanaka H, Kamatani N, Gojobori T, Bahram S, Inoko H. Whole genome association study of rheumatoid arthritis using 27 039 microsatellites. Hum Mol Genet. 2005 Aug 15;14(16):2305-21.
  • Tanaka T, Tateno Y, Gojobori T. Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. Mol Biol Evol. 2005 Feb;22(2):243-50.
  • Tanaka Y, Hanada K, Orito E, Akahane Y, Chayama K, Yoshizawa H, Sata M, Ohta N, Miyakawa Y, Gojobori T, Mizokami M. Molecular evolutionary analyses implicate injection treatment for schistosomiasis in the initial hepatitis C epidemics in Japan. J Hepatol. 2005 Jan;42(1):47-53.
  • Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza SJ, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, Okubo K. The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D567-72.
  • Tateno Y, Saitou N, Okubo K, Sugawara H, Gojobori T. DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D25-8.
  • The FANTOM Consortium: Carninci P, Gojobori T and other 158 authors and Hume D.A. and Riken Genome Exploration Research Group and Genome Science Group. (Genome Network Project Core Group):Kai C., and other 31 authors and Hayashizaki Y. (2005). The transcriptional landscape of the mammalian genome. Science. 2005 Sep 2;309(5740):1559-63.
  • Uchiyama T, Abe T, Ikemura T, Watanabe K. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol. 2005 Jan;23(1):88-93.
  • Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi-Kabata Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T. Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene. 2005 Dec 30;364:99-107.
  • 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. Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-Igf2-H19 region. Genome Res. 2005 Jan;15(1):154-65.

2004

  • 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.

2003

  • Ando A, Kawata H, Shigenari A, Anzai T, Ota M, Katsuyama Y, Sada M, Goto R, Takeshima SN, Aida Y, Iwanaga T, Fujimura N,Suzuki Y, Gojobori T, Inoko H. (2003) Genetic polymorphism of the swine major histocompatibility complex (SLA) class I genes, SLA-1, -2 and -3. Immunogenetics. 55(9):583-93.
  • Anzai T, Shiina T, Kimura N, Yanagiya K, Kohara S, Shigenari A, Yamagata T, Kulski JK, Naruse TK, Fujimori Y, Fukuzumi Y, Yamazaki M, Tashiro H, Iwamoto C, Umehara Y, Imanishi T, Meyer A, Ikeo K, Gojobori T, Bahram S, Inoko H. (2003) Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci U S A. 100(13):7708-13.
  • Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31(13):3497-500.
  • Fukami-Kobayashi K, Tateno Y, Nishikawa K. (2003) Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol Biol Evol. 20(2):267-77.
  • Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K. (2003) Unique amino acid composition of proteins in halophilic bacteria. J Mol Biol. 327(2):347-57.
  • Hotta K, Takahashi H, Ueno N, Gojobori T. (2003) A genome-wide survey of the genes for planar polarity signaling or convergent extension-related genes in Ciona intestinalis and phylogenetic comparisons of evolutionary conserved signaling components. Gene. 317(1-2):165-85.
  • Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y. (2003) CIBEX: center for information biology gene expression database. C R Biol. 326(10-11):1079-82.
  • Ishibashi T, Nakazawa M, Ono H, Satoh N, Gojobori T, Fujiwara S. (2003) Microarray analysis of embryonic retinoic acid target genes in the ascidian Ciona intestinalis. Dev Growth Differ. 45(3):249-59.
  • Kaimori JY, Takenaka M, Nakajima H, Hamano T, Horio M, Sugaya T, Ito T, Hori M, Okubo K, Imai E. (2003) Induction of glia maturation factor-beta in proximal tubular cells leads to vulnerability to oxidative injury through the p38 pathway and changes in antioxidant enzyme activities. J Biol Chem. 278(35):33519-27. Epub 2003 Jun 05.
  • Kashiwagi K, Shiba K, Fukami-Kobayashi K, Noda T, Nishikawa K, Noguchi H. (2003) Characterization of folding pathways of the type-1 and type-2 periplasmic binding proteins MglB and ArgT. J Biochem. 133(3):371-6.
  • Kawasaki S, Kawamoto S, Yokoi N, Connon C, Minesaki Y, Kinoshita S, Okubo K. (2003) Up-regulated gene expression in the conjunctival epithelium of patients with Sjogren's syndrome. Exp Eye Res. 77(1):17-26.
  • Kinjo AR, Takada S. (2003) Competition between protein folding and aggregation with molecular chaperones in crowded solutions: insight from mesoscopic simulations. Biophys J. 85(6):3521-31.
  • Komiyama T, Ikeo K, Gojobori T. (2003) Where is the origin of the Japanese gamecocks? Gene. 317(1-2):195-202.
  • Mineta K, Nakazawa M, Cebria F, Ikeo K, Agata K, Gojobori T. (2003) Origin and evolutionary process of the CNS elucidated by comparative genomics analysis of planarian ESTs. Proc Natl Acad Sci U S A. 100(13):7666-71.
  • Miyazaki S, Sugawara H, Gojobori T, Tateno Y. (2003) DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res. 31(1):13-6.
  • Miyazaki S, Sugawara H, Ikeo K, Gojobori T, Tateno Y. (2003) Free in PMC DDBJ in the stream of various biological data. Nucleic Acids Res. 32 Database issue:D31-4.
  • Miyazaki S, Tateno Y. (2003) DNA Data Bank of Japan as an Indispensable Public Database. In: Populations and Genetics. Knoppers B.M. eds (Martinus Nijhoff Publishers). 115-121.
  • Nakamura K, Suzuki Y, Ikeo K, Ikeda Y, Sato E, Nguyen NT, Gojobori T, Mikami T, Miyazawa T. (2003) Phylogenetic analysis of Vietnamese isolates of feline immunodeficiency virus: genetic diversity of subtype C. Arch Virol. 148(4):783-91.
  • Nakamura Y, Nishio Y, Ikeo K, Gojobori T. (2003) The genome stability in Corynebacterium species due to lack of the recombinational repair system. Gene. 317(1-2):149-55.
  • Nakashima H, Fukuchi S, Nishikawa K. (2003) Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem. 133(4):507-13.
  • Nakazawa M, Cebria F, Mineta K, Ikeo K, Agata K, Gojobori T. (2003) Search for the evolutionary origin of a brain: planarian brain characterized by microarray. Mol Biol Evol. 20(5):784-91.
  • Niimura Y, Terabe M, Gojobori T, Miura K. (2003) Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes. Nucleic Acids Res. 31(17):5195-201.
  • Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K, Gojobori T. (2003) Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. Genome Res. 13(7):1572-9.
  • Ogasawara O, Kawamoto S, Okubo K. (2003) Zipf's law and human transcriptomes: an explanation with an evolutionary model. C R Biol. 326(10-11):1097-101.
  • Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N. (2003) Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol. 4(11):R74.
  • Ota K, Tateno Y, Gojobori T. (2003) Highly differentiated and conserved sex chromosome in fish species (Aulopus japonicus: Teleostei, Aulopidae). Gene. 317(1-2):187-93.
  • Ota M, Kinoshita K, Nishikawa K. (2003) Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J Mol Biol. 327(5):1053-64.
  • Pignatelli S, Dal Monte P, Rossini G, Chou S, Gojobori T, Hanada K, Guo JJ, Rawlinson W, Britt W, Mach M, Landini MP. (2003) Human cytomegalovirus glycoprotein N (gpUL73-gN) genomic variants: identification of a novel subgroup, geographical distribution and evidence of positive selective pressure. J Gen Virol. 84(Pt 3):647-55.
  • Shigemoto Y, Ymaguchi M, Miyzazaki S, Sugawara, H. (2003) Enhancement of the SOAP Server in DDBJ Web Services to Process Tsunami of Biological Data. Genome Informatics 14: 669-70.
  • Sugawara H, Gojobori T, Konno T, Shigemoto Y, Ymaguchi M. (2003) A Prototype of PubMed Central Japan. Genome Informatics 14: 671-2.
  • Sugawara H, Miyazaki S. (2003) AHMII: Agent to Help Microbial Information Integration. Nucleic Acids Res. 31(13):3727-8.
  • Sugawara H, Nakamura Y, Ikeo K, Miyazaki S, Gojobori T, Satou K, Konagaya A. (2003) Analysis of Horizontal Gene Transfer and Clustering of Microbial ORFs by Use of a GRID Environment. Genome Informatics 14: 567-8.
  • Suzuki Y, Gojobori T. (2003) Analysis of coding sequences. In The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. Salemi M, Vandamme A.-M. eds. (Cambridge University Press). 283-303.
  • Wakimoto K, Chiba H, Michibata H, Seishima M, Kawasaki S, Okubo K, Mitsui H, Torii H, Imai Y. (2003) A novel diacylglycerol acyltransferase (DGAT2) is decreased in human psoriatic skin and increased in diabetic mice. Biochem Biophys Res Commun. 310(2):296-302.
  • Yajima I, Endo K, Sato S, Toyoda R, Wada H, Shibahara S, Numakunai T, Ikeo K, Gojobori T, Goding CR, Yamamoto H. (2003) Cloning and functional analysis of ascidian Mitf in vivo: insights into the origin of vertebrate pigment cells. Mech Dev. 120(12):1489-504.

2002

  • Akashi H and Gojobori T. (2002) Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A, 99(6): 3695-3700.
  • Andres AM, Soldevila M, Saitou N, Volpini V, Calafell F, and Bertranpetit J. (2002) Understanding the dynamics of Spinocerebellar Ataxia 8 (SCA8) locus through a comparative genetic approach in humans and apes. Neuroscience Letters. 336: 143-146.
  • Blair JE, Ikeo K, Gojobori T and Hedges SB. (2002) The evolutionary position of nematodes. BMC Evol Biol. 2(1): 7.
  • Callaerts P, Lee PN, Hartmann B, Farfan C, Choy DW, Ikeo K, Fischbach KF, Gehring WJ, de Couet HG. (2002) HOX genes in the sepiolid squid Euprymna scolopes: implications for the evolution of complex body plans. Proc Natl Acad Sci U S A, 99(4): 2088-2093.
  • Cebria F, Kobayashi C, Umesono Y, Nakazawa M, Mineta K, Ikeo K, Gojobori T, Itoh M, Taira M, Alvarado A and Agata K. (2002) FGFR-related gene nou-darake restricts brain tissues to the head region of planarians. Nature, 419: 620-624.
  • Cebria F, Nakazawa M, Mineta K, Ikeo K, Gojobori T and Agata K. (2002) Dissecting planarian central nervous system regeneration by the expression of neural-specific genes. Develop. Dev Growth Differ, 44(2): 135-146.
  • Cebria F, Kudome T, Nakazawa M, Mineta K, Ikeo K, Gojobori T and Agata K. (2002) The expression of neural-specific genes reveals the structural and molecular complexity of the planarian central nervous system. Mech Dev, 116(1-2): 199-204.
  • Elmerot C, Arnason U, Gojobori T and Janke A. (2002) The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships. Gene, 295: 163-172.
  • Fantom Consortium (Okazaki Y, Gojobori T, et al.), Riken Genome Exploration Research Group Phase I & II Team, Mouse Genome Sequencing Consortium, Scientific management: Hayashizaki Y. (2002) Analysis of the Mouse Transcriptome based upon Functional Annotation of 60,770 full length cDNAs. Nature 420: 563-573.
  • Fujishima H, Nishimura A, Wachi M, Takagi H, Hirasawa T, Teraoka H, Nishimori K, Kawabata T, Nishikawa K and Nagai K. (2002) kdsA mutations affect FtsZ-ring formation in Escherichia coli K-12. Microbiology, 148: 103-112.
  • Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, Tsai S-F, Park H-S, Yaspo M-L Lehrach H, Chen Z, Fu G, Saitou N, Osoegawa K, de Jong PJ, Suto Y. Hattori M, and Sakaki Y. (2002) Construction and Analysis of a Human-Chimpanzee Comparative Clone Map. Science,. 295(5552): 131-134.
  • Fukami-Kobayashi K, Schrieber DR and Benner SA. (2002) Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J Mol Biol, 319(3): 729-743.
  • Fumoto M, Miyazaki S and Sugawara H. (2002) Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more. Nucleic Acids Res, 30(1): 66-68.
  • Homma K, Fukuchi S, Kawabata T, Ota M and Nishikawa K. (2002) A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome. Gene, 294: 25-33.
  • Isobe T, Yoshio M, Mizuno K, Lindahl KF, Koide T, Gaudieri S, Gojobori T and Shiroishi T. (2002) Molecular Characterization of the Pb Recoombination Hotspot in the Mouse Major Histocompatibility Complex Class II Region. Genomics, 80: 229-235.
  • Isogai Y, Ota M, Ishii A, Ishida M and Nishikawa K. (2002) Identification of amino acids involved in protein structural uniqueness: Implication for de novo protein design. Prot Engineer, 15: 555-560.
  • Iwama H and Gojobori T. (2002) Identification of Neurotransmitter Receptor Genes under Significantly Relaxed Selective Constraint by Orthologous Gene Comparisons between Humans and Rodents. Mol Biol Evol, 19(11): 1891-1901.
  • Katayama K, Shirato-Horikoshi H, Kojima S, Kageyama T, Oka T, Hoshino FB, Fukushi S, Shinohara M, Uchida K, Suzuki Y, Gojobori T and Takeda N. (2002) Phylogenetic analysis of the complete genome of 18 norwalk-like viruses. Virology, 299: 225-239
  • Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N and Nishikawa K. (2002) GTOP: A database of protein structures predicted from genome sequences. Nucl. Acids Res, 30: 294-298.
  • Kunihiro S, Kawanishi Y, Sano M, Naito K, Matsuura Y, Tateno Y, Gojobori T, Yamagata Y, Abe K and Machida M. (2002) A polymerase chain reaction-based method for cloning novel members of a gene family using a combination of degenerate and inhibitory primers. Gene, 289: 177-184.
  • Miyazaki S and Sugawara H. (2002) Networking of Biological Resource Centers: WDCM experiences. Data Science Journal, 1(2): 102-107.
  • Niimura Y and Gojobori T. (2002) In silico chromosome staining: reconstrustion of Giemsa bands from the whole human genome sequence. Proc Natl Acad Sci, 99(2): 797-802.
  • Nishikawa K. (2002) Editorial: Information concept in biology. Bioinformatics, 18: 649-651.
  • Ogawa K, Ishihara S, Saito Y, Mineta K, Nakazawa M, Ikeo K, Gojobori T, Watanabe K and Agata K. (2002) Induction of a noggin-like gene by ectopic DV interaction during planarian regeneration. Dev Biol, 250(1): 59-70.
  • Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murata M, Mori N, Takumi S, Ikeo K, Gojobori T, Murai R, Murai K, Matsuoka Y, Ohnishi Y, Tajiri H and TsunewakiK. (2002) Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol Genet Genomics, 266(5): 740-746.
  • Oota H, Kitano T, Jin ., Yuasa I, Wang L, Ueda S, Saitou N, and Stoneking M. (2002) Extreme mtDNA homogeneity in continental Asian populations. American Journal of Physical Anthropology. 118(2): 146-53.
  • Oota H, Saitou N, and Ueda S. (2002) A large-scale analysis of human mitochondrial DNA sequences with special reference to the population history of East Eurasian. Anthropological Science. 110(3): 293-312.
  • OOta S and Saitou N. (2002). NJML+P: A Hybrid Algorithm of The Maximum Likelihood and Neighbor-Joining Methods Using Parallel Computing. Proceedings of Genome Informatics. 13: 434-435.
  • Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Antonio BA, Gojobori T, et. al. (2002) The genome sequence and structure of rice chromosome 1. Nature 420: 312-316.
  • Sawada H, Kanaya S, Tsuda M, Suzuki F, Azegami K, and Saitou N. (2002) Phylogenomic study of OCTase genes in Pseudomonas syringae pathovars: Horizontal transfer of argK-tox cluster and evolutionary history of OCTase genes on their genomes. Journal of Molecular Evolution. 54: 437-457.
  • Sumiyama K, Saitou N, and Ueda S. (2002) Adaptive evolution of the IgA hinge region in primates. Molecular Biology and Evolution. 19(7): 1093-1099.
  • Tanaka Y, Hanada L, Mizokami M, Yeo A, Shih JW, Gojobori T and Alter HJ. (2002) A Comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades, Proc Natul Acad Sci, 99(24): 15584-15589.
  • Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi K, Saitou N, Sugawara H and Gojobori T. (2002) DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res, 30(1): 27-30.
  • Umetsu K, Iwabuchi N, Yuasa I, Saitou N, Clark PF, Boxshall G, Osawa M, Igarashi K. (2002) Complete mitochondrial DNA sequence of a tadpole shrimp (Triops cancriformis) and analysis of museum samples. Electrophoresis. 23: 4080-4084.
  • Yamaoka Y, Orito E, Mizokami M, Gutierrez O, Saitou N, Kodama T, Osato MS, Kim JG, Ramirez FC, Mahachai V, and Graham DY. (2002) Helicobacter pylori in North and South America before Columbus. FEBS Letter. 517: 180-184.

2001

  • Bellgard M, Schibeci D, Trifonov E, Gojobori T. (2001) Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. J. Mol. Evol. 53(4-5):465-8.
  • Cebria F, Nakazawa M, Mineta K, Ikeo K, Gojobori T, Agata K. (2001) Dissecting planarian central nervous system regeneration by the expression of neural-specific genes. Dev Growth Differ. 44(2):135-46.
  • Fukuchi S, Nishikawa K. (2001) Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria. J Mol Biol. 309(4):835-43.
  • Goto K, Miyazaki S, Sugawara H. (2001) Genome Information Broker for Data Retrieval and Comparative Analysis of Microbial Genomes. Journal of Japan Society of Information and Knowledge. 10(4):4-13.
  • Fukami-Kobayashi K, Nishikawa K. (2001) Parallel evolution at molecular level: Phylogenetic analysis of the LacI/GalR family repressors and their PBP homologues. Genes and Genetic Systems. 76:439.
  • International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
  • Kinjo AR, Kidera A, Nakamura H, Nishikawa K. (2001) Physicochemical evaluation of protein folds predicted by threading. Eur Biophys J. 30(1):1-10.
  • Kinjo AR, Nishikawa K. (2001) Comparison of energy components of proteins from thermophilic and mesophilic organisms. Eur. Biophys. J. 30:378-84.
  • Misu S, Iizuka T, Kawanishi Y, Fukami K, Saitou N. (2001) CAMUS DB for amino acid sequence data. Genome Informatics. 502-3.
  • Miyazaki S, Sugawara H. (2001) Visualization of features in the Flat File by use of DDBJ-XML. Currents in computational molecular biology. 249-50.
  • Nakashima H, Yamashita S, Nishikawa K. (2001) Directional gene distributions of two mycoplasma species exhibited in the nucleotide composition space. Res. Comm. In Biochem., Cell & Mol. Biol. 5:27-35.
  • Noguchi T, Ito M, Matsuda H, Akiyama Y, Nishikawa K. (2001) Prediction of protein secondary structure using the threading algorithm and local sequence similarity. Res. Comm. In Biochem., Cell & Mol. Biol. 5:115-31.
  • Osawa M, Yuasa I, Kitano T, Heinke J, Kaneko M, Saitou N, Umetsu K. (2001) Haplotype analysis of human alpha2-HS glycoprotein (fetuin). Annals of Human Genetics. 65(1):27-34.
  • Osawa S, Gojobori T. (2001) Preface. J. Mol. Evol. (Thomas Jukes special issue) 53(4-5):257.
  • Ota M, Isogai Y, Nishikawa K. (2001) Knowledge-based potential defined for a rotamer library to design protein sequences. Protein Eng. 14:557-64.
  • RIKEN Genome Exploration Research Group Phase II Team and FANTOM Consortium (Okazaki Y, Gojobori T, et al.), Genelal organizer: Y.Hayashizaki (2001) Functional anotation of a full-length mouse cDNA collection. Nature. 409(6821):685-90.
  • Sanders AR, Cao Q, Taylor J, Levin TE, Badner JA, Cravchik A, Comeron JM, Saitou N, Del Rosario A, Salvi DA, Walczyk KA, Mowry BJ, Levinson DF, Crowe RR, Silverman JM, Gejman PV. (2001) Genetic diversity of the human serotonin receptor 1B (HTR1B) gene. Genomics. 72(1):1-14.
  • Sato S, Tanaka M, Miura H, Ikeo K, Gojobori T, Takeuchi T, Yamamoto H (2001) Functional conservation of the promoter regions of vertebrate tyrosinase genes. J Investig Dermatol Symp Proc. 6(1):10-8.
  • Sato T, Terabe M, Watanabe H, Gojobori T, Hori-Takemoto C, Miura Ki. (2001) Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency. J Biochem. 129(6):851-60.
  • Suzuki Y, Gojobori T, Nei, N. (2001) ADAPTSITE:detecting natural selection at single amino acid sites. Bioinformatics. 17(7):660-1.
  • Suzuki Y, Gojobori T. (2001) Positively selected amino acid sites in the entire coding region of hepatitis C virus subtypes 1b. Gene. 276(1):83-7.
  • Suzuki Y, Wyndham A, Gojobori T. (2001) Virus Evolution. Handbook of statistical genetics, eds. D.J.Balding, M.Bishop, and C.Canning. John Wiley & Sons. 377-413.
  • Tanaka H, Chinami M, Mizushima T, Ogasawara K, Ota M, Tsukihara T, Yutani K. (2001) X-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus and its cys-free mutant. J. of Biochem. 130:107-18.
  • Tsunoyama K, Bellgard MI, Gojobori T. (2001) Intragenic variation of synonymous substitution rates is caused by nonrandom mutations at methylated CpG. J Mol Evol. 53(4-5):456-64.
  • Umetsu K, Tanaka M, Yuasa I, Saitou N, Naito E, Ago K, Nakayashiki N, Miyoshi A, Kashimura S, Watanabe G, Osawa M. (2001) Multiplex amplified product length polymorphism analysis to rapidly detect human mitochondrial DNA variations. Electrophoresis. 22:3533-8.
  • Yamamoto M, Lin X-H, Kominato Y, Hata Y, Noda R, Saitou N, Yamamoto F. (2001) Murine equivalent of the human histo-blood group ABO gene is a cis-AB gene and encodes a glycosyltransferase with both A and B transferase activity. Journal of Biological Chemmistry. 276(17):13701-8.
  • Yuasa I, Umetsu K, Ago K, Sun C-S, Pan I-H, Ishida T, Saitou N, Horai S. (2001) Population genetic studies on nine aboriginal ethnic groups of Taiwan. II. Serum protein systems. Anthropological Science. 109(4):257-73.

2000

  • Abola, E.E., Bairoch, A., Baker, W.C., Beck, S., Benson, D.A., Berman, H., Cameron, G., Cantor, C., Doubet, S., Hubbbard, T.J.P, Jones, T.A., Kleywegt, G.J. Kolaskar, A.S., Kuik, Van A., Lesk, A.M., Mews, H.-W., Neuhaus, D., Pfeiffer, F., TenEyck, L.F., Simpson, R.J., Stosser, G., Sussman, J.L., Tateno, Y., Tsugita, H., Ulrich, E.L., and Viegenthart, J.F.G. (2000) Quality control in data banks for molecular biology. BioEssays. 22:1024-1034.
  • Akihito, Iwata, A., Kobayashi, T., Ikeo, K., Imanishi, T., Ono, H., Umehazra, Y., Hamamatsu, C., Sugiyama, K., Ikeda, Y., Sakamoto, K., Fumihito, A., Ohno, S., and Gojobori, T. (2000) Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome B genes. Gene. 259(1-2):5-15.
  • Fukami-Kobayashi, K., Nishikawa, K. and Siddiqui, S.S. (2000) Expression and cDNA cloning of klp-12 gene encoding an ortholog of the chichen chromokinesin, mediatingchromosome segregation in Caenorhabditis elegans. J. Bio chem. Mol. Biol. 33:138-146.
  • Gaudieri, S., Dawkins, R.L., Habara, K., Kulski, J.K., and Gojobori, T. (2000) SNP profile within the human major histocompatibility complex reveals an extreme and interrupted level of nucleotide diversity. Genome Research. 10(10):1579-1586.
  • Gojobori, T. (2000) Susumu Ohno 1928-2000. GENE. 259(1-2):2-3.
  • Isogai, Y., Ishii, A., Fujisawa, T., Ota, M., and Nishikawa, K. (2000) Redesign ofartificial globins: Effects of residue replacements at hydrophobic sites onthe structural properties. Biochemistry. 39(19):5683-5690.
  • Isogai, Y., Ishii, A., Ishida, M., Mukai, M., Ota., M., Nishikawa, K., and Iizuka, T. (2000) Structural and functional properties of designed globins. Proc. Indian Acad. Sci. (Chem. Sci.) 112:215-221.
  • Kawabata, T., and Nishikawa, K. (2000) Protein structure comparison using the Markov transition matrix of evolution. PROTEINS. 41(1):108-122.
  • Kawabata, T., Arisaka, F., and Nishikawa, K. (2000) Structural/functional assignment of bacteriophage T4 unknown proteins by iterative database searches. GENE. 259(1-2):223-233.
  • Khan, M.L.A., Yusuf Ali, M., Siddiqui, Z.K., Shakir, M.A., Ohnishi, H., Nishikawa, K., and Siddiqui, S.S. (2000) C. elegans KLP-11/OSM-3/KAP-1:Orthologs of the sea urchin kinesin-II, and mouse KIF3A/KIFB/KAP3 kinesin complexes. DNA. Res. 7:121-125.
  • Kikuchi M., Misu S., Imanishi, T., and Saitou, N. (2000) CAMUS DB: Development of structural database for homology search. In Miyano S., Shamir R., and Takagi T. (eds.), "Currents in Computational Molecular Biology", Universal Academy Press, Tokyo, pp. 80-81.
  • Kitano, T., Noda, R., Sumiyama, K., Ferrell R. E., and Saitou, N. (2000) Gene diversity of chimpanzee ABO blood group elucidated from intron 6 sequences. Journal of Heredity. 91(3):211-214.
  • Kitano, T. and Saitou, N. (2000) Evolutionary history of the Rh blood group-related genes in vertebrates. Immunogenetics, 51(7) (published in online). Full text in Immunogenetics homepage
  • Miyazaki, S., Hashimoto, H., Shimada, A., Tateno, Y. and Sugawara, H. (2000) A new file format and tools for the large-scale data submission to DNA Data Bank of Japan (DDBJ), Currents in Computational Molecular Biology. 60-61.
  • Miyazaki, S., Mashima, J., Mizunuma, T., Sugawara, H., Tateno, Y., and Gojobori, T. (2000) Large-scale submission of mouse EST data and their handling at the DNA Data Bank of Japan (DDBJ)., "Proceedings of The 14th International Mouse Genome Conference", Tokyo.178.
  • Nakane, S., Shirabe, S., Moriuchi, R., MIzokami, A., Furuya, T., Nishiura, Y., Okazaki, S., Nakamura, N., Suzuki, Y., Nakamura, T., Katamine, S., and Gojobori, T. (2000) Comparative molecular analysis of HTLV-I proviral DNA in HTLV-I infected members of a family with a discordant HTLV-I associated myelopathy in monozygotic twins. Journal of Neuro Virology 6:275-283.
  • Nakamura Y., Gojobori T., and Ikemura T. (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucl. Acids Res. 28(1): 292.
  • Nakashima, H., and Nishikawa, K. (2000) The genomic DNA sequences of various species are distinctively distributed in nucleotide compostion space. Res. Comm. In Biochem, Cell & Mol. Biol. 4:25-45
  • Noda R., Kitano T., Takenaka O., and Saitou N. (2000) Evolution of the ABO blood group gene in Japanese macaque. Genes and Genetic Systems, 75(3):141-147.
  • Ogura, A., Imanishi, T., Ikeo, K., and Gojobori, T. (2000) Comparative genomics of mouse ESTs with particular reference to evolution of mammalian genomes. Proceedings of The 14th International Mouse Genome Conference, Tokyo.176.
  • Ota, K., Kobayashi, T., Ueno, K., and Gojobori, T. (2000) Evolution of heteromorphic sex chromosomes in the order Aulopiformes. GENE. 259(1-2):25-30.
  • Pineda, D., Gonzalez, J., Callaerts, P., Ikeo, K., Gehring, WJ., and Salo, E. (2000) Searching for the prototypic eye genetic network: Sine oculis is essential for eye regeneration in planarians. Proc Natl Acad Sci USA. 97(9):4525-4529.
  • Saitou N. (2000) Programs for constructing phylogenetic trees and networks of closely related sequences. In Iwatuki.K. (ed.), "IIAS International Symposium on Biodiversity", International Institute for Advanced Studies, Kyoto. 45-50.
  • Seki, M., Higashiyama, Y., Mizokami, A., Kadota, J.-I., Moriuchi, R., Kohno, S., Suziki, Y., Takahashi, K., Gojobori, T., and Katamine, S. (2000) Up-regulation of human T lymphotropic virus type 1 (HTLV-1) tax/rex mRNA in infected lung tissues. Clin Exp Immunol. 120(3):488-498.
  • Shimizu, N., and Gojobori, T. (2000) How can human and simian immunodeficiency viruses utilize chemokine receptors as their coreceptors? GENE. 259(1-2):199-205.
  • Sugawara, H. and Miyazaki, S. (2000) A workbench for the research and development of biological diversity, Currents in Computational Molecular Biology. 58-59.
  • Suzuki, Y.,Yamaguchi-Kabata, Y.,and Gojobori, T. (2000) Nucleotide substitution rates of HIV-1. AIDS Reviews. 2(1):39-47.
  • Tateno Y., Miyazaki S., Ota M., Sugawara H. and Gojobori T. (2000) DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res. 28 (1): 24-26.
  • Toyoda, R., Sato, S., Ikeo, K., Gojobori, T., Numakunai, T., Goding, CR., and Yamamoto, H. (2000) Pigment cell-specific expression of the tyrosinase gene in ascidians has a different regulatory mechanism from vertebrates. Gene. 259(1-2):159-170.
  • Wada, Y., Imanishi, T., and Gojobori, T. (2000) Estimating the number of mouse genes and the duplicated regions within the mouse genome. Proceedings of The 14th International Mouse Genome Conference, Tokyo. 24.
  • Wang L., Oota H., Saitou N., Jin F., Matsushita T., and Ueda S. (2000) Genetic structure of a!!2500-year-old human population in China and its spatiotemporal changes. Molecular Biology and Evolution, 17(9):1396-1400.
  • Yamaguchi-Kabata, Y., and Gojobori, T. (2000) Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J.Virology. 74(9):4335-4350.

1999

  • Baba T., Shiina T., Ando A., Imanishi T., Matsuno N., Skurai E., Nagao T., Tanaka K., Gojyobori T. and Inoko H. (1999) Isolation and characterization of a pig major histocompatibility complex (SLA) class II DNA cDNA clone. Immunogenetics. 49 (10): 915-917.
  • Bellgard M. I. and Gojobori T. (1999) Identification of a ribonuclease H gene in both Mycoplasma genitalium and Mycoplasma pneumoniae by a new method for exhaustive identification of ORFs in the complete genome sequences. FEBS Lett. 445: 6-8.
  • Bellgard M. I. and Gojobori T. (1999) Inferring the direction of evolutionary changes of genomic basecomposition. Trends Genet. 15 (7): 254-256.
  • Bellgard M. I. and Gojobori T. (1999) Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content. Gene. 238 (1): 33-37.
  • Bellgard M. I., Itoh T., Watanabe H., Imanishi T. and Gojobori T. (1999) Dynamic evolution of genomes and the concept of genome space. Ann N Y Acad Sci. 870: 293-300.
  • Fukami-Kobayashi K., Tateno Y. and Nishikawa K. (1999) Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history. J. Mol. Biol. 286: 279-290.
  • Gaudieri S., Dawkins R. L., Habara K., Kulski J. K., and Gojobori T. (1999) Nucleotide diversity within the human major histocompatibility complex: Function of hitch-hiking effect, duplications, indels and recombination. in 6th International workshop on MHC evolution. Hayama:186-200 Springer.
  • Gaudieri S., Kulski J. K., Dawkins R. L. and Gojobori T. (1999) Different evolutionary histories in two subgenomic regions of the major histocom patibility complex. Genome Res. 9 (6): 541-549.
  • Gaudieri S., Kulski J. K. , Dawkins R. L. and Gojobori T. (1999) Extensive nucleotide variability within a 370 kb sequence from the central region of the major histocompatibility complex. Gene. 238 (1): 157-161.
  • Gehring W. J. and Ikeo K. (1999) Pax 6: mastering eye morphogenesis and eye evolution. Trends Genet. 15 (9): 371-377.
  • Gojobori T. (1999) Evolution, in The Encyclopedia of Molecular Biology, T.E. Creighton, Editor. John Wiley & Sons: NY.
  • Gojobori T. (1999) Part VI. Introduction, in Molecular Starategies in Biological Evolution, L.H. Caporale, Editor. Ann N Y Acad Sci. : 292.
  • Gojobori T. (1999) Part VI. Summary, in Molecular Starategies in Biological Evolution, L.H. Caporale, Editor. Ann N Y Acad Sci. : 339-340.
  • Hatta Y., Ohashi J., Imanishi T., Kamiyama H., Iha M., Simabukuro T., Ogawa A., Tanaka H., Akaza T., Gojobori T., Juji T. and Tokunaga K. (1999) HLA genes and haplotypes in Ryukyuans suggest recent gene flow to the Okinawa Islands. Hum Biol. 71 (3): 353-365.
  • Hayasaka D., Suzuki Y., Kariwa H., Ivanov L., Volkov V., Demenev V., Mizutani T., Gojobori T. and Takashima I. (1999) Phylogenetic and virulence analysis of tick-borne encephalitis viruses from Japan and far-eastern Russia. J Gen Virol. 80 (12): 3127-3135.
  • Isogai Y., Ota M., Fujisawa T., Izuno H., Mukai M., Nakamura H., Iizuka T. and Nishikawa K. (1999) Design and synthesis of a globin fold. Biochemistry. 38 (23): 7431-7443.
  • Itoh T., Takemoto K., Mori H. and Gojobori T. (1999) Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16: 332-346.
  • Itoh T., Okayama T., Hashimoto H., Takeda J.-i., Davis R. W., Mori H. and Gojobori T. (1999) A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome sequences between two different substrains. FEBS Lett. 450: 72-76.
  • Jin F., Saitou N., Ishida T., Sun C-S., Pan I-H., Omoto K., and Horai S. (1999) Population genetic studies on nine aboriginal ethnic groups of Taiwan. I Red cell enzyme systems. Anthropological Science 107 (3): 229-246.
  • Jin F., Saitou N., and Omoto K. (1999) Population genetic studies on the Chinese. In Omoto K. (ed.),   "Interdisciplinary Perspectives on the Origin of Japanese", International Research Center for Japanese Studies, Kyoto, Japan 15-24.
  • Kaneko M., Kudo T., Iwasaki H., Ikehara Y., Nishihara S., Nakagawa S., Sasaki K., Shiina T., Inoko H., Saitou N., and Narimatsu H. (1999) alpha1-3-Fucosyltransferase IX (Fuc-TIX) is very highly conserved between human
    and mouse; molecular cloning, characterization and tissue distribution of human Fuc-TIX. FEBS Letters 452: 237-242.
  • Kaneko M., Kudo T., Iwasaki H., Shiina T., Inoko H., Kozaki T., Saitou N. and Narimatsu H. (1999) Assignment of the human alpha 1,3-fucosyltransferase IX (FUT9) gene to chromosome band 6q16 by in situ hybridization. Cytogenetics and Cell Genetics 86: 329-330.
  • Kawabata T., Ota M. and Nishikawa K. (1999) The protein mutant database. Nucl. Acids Res. 27: 355-357.
  • Kitano T. and Saitou N. (1999) Evolution of Rh blood group genes have experienced gene conversions and positive selection. Journal of Molecular Evolution 49 (5): 615-626.
  • Kobayashi K., Iwasaki M., Suzuki Y., Suzuki H., and Saitou N. (1999) An analysis of polymorphism for the ABO blood group genes in a Japanese population based on polymerase chain reaction. Anthropological Science 107(2): 109-121.
  • Luo C., Morishita T., Satou K., Tateno Y., Nakajima K. and Nobusawa E. (1999) Evolutionary pattern of influenza B viruses based on the HA and NS genes during 1940 to 1999: origin of the NS genes after 1997. Arch Virol. 144 (10): 1881-1891.
  • Miyazaki S. and Sugawara H. (1999) From linking to integration of biological databases, The International Joint Workshop for Studies on BIODIVERSITY (Species 2000, CODATA and Global Environment Tsukuba), Tsukuba.
  • Miyazaki S. and Sugawara H.,(1999) Reconstruction of large-scale phylogenetic trees: problems and solutions,6th International Congress on Amino Acids, 17 (1) :119.
  • Mizokami M., Imanishi T., Ikeo K., Suzuki Y., Orito E., Kumada T., Ueda R., Iino S., and Nakano T. (1999) Mutation patterns for two flaviviruses: hepatitis C virus and GB virus C/hepatitis G virus. FEBS Lett. 450 (3): 294-298.
  • Nagano N., Ota M. and Nishikawa K. (1999) Strong hydrophobic nature of cysteine residues in proteins. FEBS Lett. 1458 (1): 69-71.
  • Nakamura Y., Gojobori T., and Ikemura T. (1999) Codon usage tabulated from the international DNA sequence databases; its status 1999. Nucl. Acids Res. 27: 292.
  • Nishikawa K. (1999) Protein structure prediction The Encyclopedia of Molecular Biology (Ed., T.E. Creighton), John Wiley & Sons, Inc.
  • Ophir R., Itoh T., Graur D. and Gojobori T. (1999) A simple method for estimating the intensity of purifying selection in protein-coding genes. Mol. Biol. Evol. 16: 49-53.
  • OOta S. and Saitou N. (1999) Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol. Biol. Evol. 16 (6): 856-867.
  • Oota H., Saitou N., Kurosaki K., Pookajorn S., Ishida T, Matsushita T., and Ueda S. (1999) Ancient DNA: a New Strategy for Studying Population History. In Omoto K. (ed.), "Interdisciplinary Perspectives on the Origin of Japanese", International Research Center for Japanese Studies, Kyoto, Japan 25-41.
  • Oota H., Saitou N., Matsushita T. and Ueda S. (1999) Molecular genetic analysis of a 2,000-year old human population in China. American Journal of Human Genetics 64 (1): 250-258.
  • Ota M., Kawabata T., Kinjo A. R. and Nishikawa K. (1999) Cooperative approach for the protein fold recognition.
    Proteins. 37 (S3): 126-132.
  • Ota M. and Nishikawa K. (1999) Feasibility in the inverse protein folding protocol. Protein Sci. 8: 1001-1009.
  • Ren F., Hiroshi T., Okayama T. and Gojobori T. (1999) The application of model-based complexity inference method to molecular evolution analysis. Medinfo. 9 (1): 367-371.
  • Ren F., Tanaka H., Okayama T., and Gojobori T. (1999) Reconstructing molecular phylogenetic tree with multifurcation by using minimum complexity principle. DNA and Molecular Computing. : 1825-1828.
  • Robertson B., Myers G., Howard C., Brettin T., Bukh J., Gaschen B., Gojobori T., Maertens G., Mizokami M., Nainan O., Netesov S., Nishioka K., Shin i T., Simmonds P., Smith D., Stuyver L. and Weiner A. (1999) Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. International Committee on Virus Taxonomy. Arch Virol. 143 (12): 2493-2503.
  • Sato H., Koide T., Ishiguro S.-I., Tamai M., Saitou N. and Shiroishi T. (1999) The organization of the type I keratin genes in the mouse Krt1 domain. Genomics 56: 303-309.
  • Sato S., Toyoda R., Katsuyama Y., Saiga H., Numakunai T., Ikeo K., Gojobori T., Yajima I. and Yamamoto H. (1999) Related Articles Structure and developmental expression of the ascidian TRP gene: insights into the evolution of pigment cell-specific gene expression. Dev Dyn. 215 (3): 225-237.
  • Sawada H., Suzuki F., Matsuda I., and Saitou N. (1999) Phylogenetic analysis of Pseudomonas syringe pathovar suggests the horizontal gene transfer of argK and the evolutionary stability of hrp gene cluster. Journal of Molecular Evolution 49 (5): 627-644.
  • Shiina T., Oka A., Imanishi T., Hanzawa K., Gojobori T., Watanabe S. and Inoko H. (1999) Multiple class I loci expressed by the quail MHC. Immunogenetics 49: 456-460.
  • Shiina T., Shimizu C., Oka A., Teraoka Y., Imanishi T., Gojobori T., Hanzawa K., Watanabe S. and Inoko H. (1999) Gene organization of the quail major histocompatibility complex (MhcCoja) class I gene region. Immunogenetics 49: 384-394.
  • Sugawara H. and Miyazaki S. (1999) An information system for data integration and polyphasic analysis of microbes, Proceedings of 99th General Meeting of the American Society for Microbiology, Chicago
  • Sugawara H. and Miyazaki S. (1999) Evolution of genes, genomes and species, The International Joint Workshop for Studies on BIODIVERSITY (Species 2000, CODATA and Global Environment Tsukuba), Tsukuba.
  • Sugawara H. (1999) Links between microbial resources and gene sequences, IXth International Congress of Bacteriology & Applied Microbiology, Sydney
  • Sugawara H., Miyazaki S., Gojobori T. and Tateno Y. (1999) DNA Data Bank of Japan dealing with large-scale data submission. Nucl. Acids Res. 27: 25-28.
  • Suzuki Y. and Gojobori T. (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol. 16 (10):1315-1328.
  • Suzuki Y., Katayama K., Fukushi S., Kageyama T., Oya A., Okamura H., Tanaka Y., Mizokami M. and Gojobori T. (1999) Slow evolutionary rate of GB virus C/Hepatitis G virus. J. Mol. Evol. 48: 383-389.
  • Takano K., Ota M., Ogasahara K., Yamagata Y., Nishikawa K. and Yutani K. (1999) Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes. Protein Eng. 12 (8): 663-672.
  • Takezaki N. and Gojobori T. (1999) Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences. Mol. Bol. Evol. 16: 590-601.
  • Tanaka H., Ren F., Okayama T., and Gojobori T. (1999) Topology selection in unrooted molecular phylogenetic tree by minimum model-based complexity method. in Pacific Symposium on Biocomputing'99. Hawaii, USA.
  • Tazaki A., Gaudieri S., Ikeo K., Gojobori T., Watanabe K. and Agata K. (1999) Related Articles, Protein, Nucleotide Neural network in planarian revealed by an antibody against planarian synaptotagmin homologue. Biochem Biophys Res Commun. 260 (2): 426-432.
  • Watanabe M., Sumida N., Murakami S., Anzai H., Thompson C. J., Tateno Y. and Murakami T. (1999) A phosphate-induced gene which promotes Penicillium mediated bioconversion ofcis-propenylphosphonic acid to Fosfomycin. Applied and Environmental Microbiology 65: 1036-1044.
  • Yamazaki M., Tateno Y. and Inoko H. (1999) Genomic organization around the centromeric end of the HLA class I region: Large-scale sequence analysis. J. Mol. Evol. 48: 317-327.

1998

  • Horiuchi M., Yamaguchi Y., Gojobori T., Mochizuki M., Nagasawa H., Toyoda Y., Ishiguro N. and Shinagawa M. (1998) Differences in the evolutionary pattern of feline Panleukopenia virus and canine Parvovirus. Virology 249: 440-452.
  • Itagaki H., Ohno T., Miyazaki S., Sugawara H. et al (1998) Validation study on five cytotoxicity assays by JSAAE - V. Details of the crystal violet staining assays. Altern. Animal Test. EXperiment 5: 87-98.
  • Itagaki H., Ohno T., Miyazaki S., Sugawara H. et al (1998) Validation study on five cytotoxicity assays by JSAAE - VII. Details of the MTT assay. Altern. Animal Test. EXperiment 5: 119-130.
  • Katsuyama Y., Inoko H., Imanishi T., Mizuki N., Gojobori T. and Ota M. (1998) Genetic relationships among Japanese, Northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian and Italian populations based on allelic frequencies at four VNTR (D1S80, D4S43, C0L2A1, D17S5) and one STR (ACTBP2) loci. Human Heredity 48: 126-137.
  • Kitano T., Sumiyama K., Shiroishi T., and Saitou N. (1998) Conserved evolution of the Rh50 gene compared to its homologous Rh blood group gene. Biochemical and Biophysical Research Communications 249 (1): 78-85.
  • Mizuki N., Ohno S., Ando H., Sato T., Imanishi T., Gojobori T., Ishihara M., Goto K., Ota M., Geng Z., Geng L., Li G. and Inoko H. (1998) Major histocompatibility complex class II alleles in an Uygur population in the Silk Route of Northwest China. Tissue Antigens 51: 287-292.
  • Nakamura Y., Gojobori T. and Ikemura T. (1998). Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 26 (1): 334.
  • Nakashima H., Ota M., Nishikawa K. and Ooi T. (1998) Gene from nine genomes are separated into their organisms in the dinucleotide composition space. DNA Res. 5: 251-259.
  • Ohno T., Miyazaki S., Sugawara H. et al (1998) Validation study on five cytotoxicity assays by JSAAE - I. Overview of the study and analysis of variations of ED50 Values. Altern. Animal Test. EXperiment 5: 1-38.
  • Ohno T., Miyazaki S., Sugawara H. et al (1998) Validation study on five cytotoxicity assyas by JSAAE - VI. Details of the LDH release assay. Altern. Animal Test. EXperiment 5: 99-118.
  • Ohno T., Miyazaki S., Sugawara H. et al (1998) Validation study on five cytotoxicity assays by JSAAE - VIII. Details of the neutral red uptake assay. Altern. Animal Test. EXperiment 5: 131-145.
  • Okayama T., Tamura T., Gojobori T., Tateno Y., Ikeo K., Miyazaki S., Fukami-Kobayashi K. and Sugawara H. (1998). Formal design and implementation of an improved DDBJ DNA database with a new schema and objectoriented library. Bioinformatics 14 (6): 472-478.
  • Omori T., Saijo K., Kato M., Itagaki H., Hayashi M., Miyazaki S., Ohno T., Sugawara H., Teramoto N., Tanaka N., Wakuri S. and Yoshimura I. (1998) Validation study on five cytotoxicity assays by JSAAE - II. Statistical analysis. Altern. Animal Test. EXperiment 5: 39-58.
  • Omori T., Saijo K., Kato M., Itagaki H., Hayashi M., Miyazaki S., Ohno T., Sugawara H., Teramoto N., Tanaka N., Wakuri S. and Yoshimura I. (1998) Validation study on five cytotoxicity assays by JSAAE - III. Quality of collected data files. Altern. Animal Test. EXperiment 5: 59-73.
  • Perrire G. Gouy M. and Gojobori T. (1998) The non-reduntant Bacillus subtilis. (NRSub) databse: update 1998. Nucl. Acids Res. 26: 60-62.
  • Robertson B., Myers G., Howard C., Brettin T., Bukh J., Gaschen B., Gojobori T, Maertens G., Mizokami M., Nainan O., Netesov S., Nishioka K., Shin-i T., Simmonds P., Smith D., Stuyver L. and Weiner A. (1998) Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: Proposals for standardization. Arch. Virol. 143: 2493-2503.
  • Saitou N. (1998) Patterns in Evolution - The New Molecular View -. (Roger Lewin, Scientific American Library, New York, 1987). Anthropological Science 106 (2): 193-195.
  • Satou K., Miyazaki S. and Ohya M. (1998) Analysis of HIV by entropy evolution rate. Amino Acids 14: 343-352.
  • Sugawara H. (1998) International nucleotide sequence database. Experimental Medicine 16: 30-37.
  • Sugawara H. and Miyazaki S. (1998) Towards the Aisa-Pacific Bioinformatics Network. In Pacific Symposium on Biocomputing '98. (eds.) Altman, R. B., Dunker A. K., Hunter, L. and Klein, T. E. (Hawaii). 759-764.
  • Sugawara H., Miyazaki S., Gojobori T. and Tateno Y. (1999) DNA Data Bank of Japan dealing with large-scale data submission. Nucl. Acids Res. 27: 25-28.
  • Suzuki Y. and Gojobori T. (1998) The origin and evolution of human T-Cell lymphotrophic virus type I and II. Virus Genes 16: 69-84.
  • Suzuki Y., Gojobori T. and Nakagomi O. (1998) Intragenic recombinations in rotaviruses. FEBS Lett. 427: 183-187.
  • Tanaka N., Miyazaki S., Sugawara H. et al (1998) Validation study on five cytotoxicity assays by JSAAE - IV. Details of the colony formation assay. Altern. Animal Test. EXperiment 5: 74-86.
  • Tanaka Y., Mizokami M., Orito E., Ohba K., Kato T., Kondo Y., Mboudjeka I., Zekeng L., Kaptue L., Rikandou B., MPele P., Takahisa J., Hayami M., Suzuki Y. and Gojohori T. (1998) African origin of GB virus c/ hepatitis G virus. FEBS Lett. 423: 143-148.
  • Tateno Y., Fukami-Kobayashi K., Miyazaki S., Sugawara H. and Gojobori T. (1998). DNA Data Bank of Japan at work on genome sequence data. Nucleic Acids Res. 26 (1): 16-20.
  • Tsunoyama K. and Gojobori T. (1998) Evolution of nicotinic acetylcholine receptor subunits. Mol. Biol. Evol. 15: 518-527.

1997

  • Endo T., Imanishi T., Gojobori T. and Inoko H. (1997) Evolutionary significance of intra-genome duplications on human chromosomes. Gene 205: 19-27.
  • Futatsuki T., Kawanishi Y., Naito K., Miyazaki S. and Sugawara H. (1997) Efficient Computation of Sequence Analysis in a Vector-Parallel Computer for the Study of Molecular Evolution. In Genome Informatics 1997. Universal Academy Press (Tokyo). 264-265.
  • Goto K., Yamamoto H., Tamura T., Okayama T., Koike T., Miyazaki S., Mori H., Gojobori T. and Sugawara H. (1997) Visualization of Sequence and Biological Data in DNA Data Bank of Japan: Genome Information Broker and the Enhancement of SAKURA. In Genome Informatics 1997. Universal Academy Press (Tokyo). 236-237.
  • Gready J.E., Ranganathan S., Schofield P.R., Matsuo Y. and Nishikawa K. (1997) Predicted structure of the extracellular region of ligand-gated ion-channel receptors shows SH2-like and SH3-like domains forming the ligand binding site. Prot. Sci. 6: 983-998.
  • Ito M., Matsuo Y. and Nishikawa K. (1997) Prediction of protein secondary structure using the 3D-1D compatibility algorithm. CABIOS 13: 415-423.
  • Khan M.L.A., Gogonea C.B., Siddiqui Z.K., Ali M.Y., Kikuno R., Nishikawa K. and Siddiqui S.S. (1997) Molecular cloning and expression of the Caenorhabditis elegans klp-3, an ortholog of C terminus motor kinesins Kar3 and ncd. J. Mol. Biol. 270: 627-639.
  • Kitano T., Matsuoka N., and Saitou N. (1997) The phylogenetic relationship of the genus Oncorhynchus species inferred from nuclear and mitochondrial markers. Genes and Genetic Systems 72 (1): 25-34.
  • Kurihara T., Sakuma M. and Gojobori T. (1997) Molecular evolution of myelin proteolipid protein. Biochemical and Biophysical Research Communications. 237: 559-561.
  • Miyazaki S., Shimura J., Hirose S., Sanokawa R., Tsurui H., Wakiya M., Sugawara H. and Shirai T. (1997) Is structural flexibility of antigen-binding loops involved in the affinity maturation of anti-DNA antibodies? International Immunology 9: 771-777.
  • Mizokami M., Orito E., Ohba K., Ikeo K., Lau J.Y.N. and Gojobori T. (1997) Constrained evolution of hepatitis B virus with overlapping genes. Journal of Molecular Evolution (Special Issue) 44 (1): 83-90.
  • Mizuki N., Ohno S., Ando H., Sato T., Imanishi T., Gojobori T., Ishihara M., Ota M., Geng Z., Geng L., Li G., Kimura M. and Inoko H. (1997) Major histocompatibility complex class II allelles in Kazak and Han populations in the Silk Route of northwestern China. Tissue Antigens 50: 527-534.
  • Nakamura Y., Tateno Y. and Gojobori T. (1997) Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Research 25: 244-245.
  • Nakashima H., Nishikawa K. and Ooi T. (1997) Differences in dinucleotide frequencies of human, yeast, and E. coli genes. DNA Res. 4: 185-192.
  • Okamoto Y., Shiosaki K., Eda Y., Tokiyoshi S., Yamaguchi Y., Gojobori T., Hachimori T., Yamazaki S. and Honda M. (1997) Father-to-mother-to-infant transmission of HIV-1: clonally transmitted isolate of infant mutates more rapidly than that of the mother and rapidly loses reactivity with neutralizing antibody. Microbiol Immunol 41: 131-138.
  • OOta S. and Saitou N. (1997) Reconstruction of maximum likelihood phylogenetic trees in parallel enviromnent using logic programming. In Miyano S. and Takagi T. (eds.), Genome Informatics 1997, Universal Academy Press, Tokyo 326-327.
  • Omoto K. and Saitou N. (1997) Genetic origins of the Japanese: A partial support for the "dual structure hypothesis". American Journal of Physical Anthropology 102 (4): 437-446.
  • Ota M. and Nishikawa K. (1997) Assessment of the pseudo-energy potential by the best-five test: a new use of the three-dimensional profiles of proteins. Prot. Eng. 10: 339-351.
  • Ota M., Isogai Y. and Nishikawa K. (1997) Structural requirement of highly-conserved residues in globins. FEBS Lett. 415: 129-133.
  • Saitou N. and Yamamoto F.-I. (1997) Evolution of primate ABO blood group genes and their homologous genes. Molecular Biology and Evolution 14 (4): 399-411.
  • Sato S., Masuya H., Numakunai T., Satoh N., Ikeo K., Gojobori T., Tamura K., Ide H., Takeuchi T. and Yamamoto H. (1997) Ascidian tyrosinase gene: Its unique structure and expression in the developing brain. Developmental Dynamics 208: 363-374.
  • Sumikawa H., Fukuhara K., Suzuki E., Matsuo Y. and Nishikawa K. (1997) Tertiary structural models for human interleukin-6 and evaluation by a sequence-structure compatibility method and NMR experimental information. FEBS Lett. 404: 234-240.
  • Suyama M., Matsuo Y. and Nishikawa K. (1997) Comparison of protein structures using 3D profile alignment. J. Mol. Evol. 44 (Suppl. 1): S163-S173.
  • Suzuki Y. and Gojobori T. (1997) The origin and evolution of ebola and marburg viruses. Mol. Biol. Evol. 14: 800-806.
  • Perriere G., Moszer I., and Gojobori T. (1997) The NRSub database: update 1997. Nucleic Acids Reseach 25: 53-56.
  • Tanaka H., Ren F., Okayama T. and Gojobori T. (1997) Inference of molecular phylogenetic tree based on minimum model-based complexity method. In Proceedings of Fifth international conference on intelligent systems for molecular biology. ISMB 97, Halkidiki, Greece / American Association for Artificial Intelligence. 319-328.
  • Tateno Y. and Gojobori T. (1997) DNA Data Bank of Japan in the age of information biology. Nucleic Acids Reseach 25: 14-17.
  • Tateno, Y., Ikeo K., Imanishi T., Watanabe H., Endo T., Yamaguchi Y., Suzuki Y., Takahashi K., Tsunoyama K., Kawai M., Kawanishi Y., Naitou K. and Gojobori T. (1997) Evolutionary motif and its biological and structural significance. Journal of Molecular Evolution (Special Issue) 44 (1): 38-43.
  • Tenzen T., Yamagata T., Fukagawa T., Sugaya K., Ando A., Inoko H., Gojobori T., Fujiyama A., Okumura K. and Ikemura T. (1997) Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex. Mol. Cel. Biol. 17: 4043-4050.
  • Watanabe H., Gojobori T. and Miura K. (1997) Bacterial features in the genome of Methanococcus Jannaschii in terms of gene composition and biased base composition in ORFs and their surrounding regions. Gene 205: 7-18.
  • Watanabe H., Itoh T., Mori H. and Gojobori T. (1997) Genome plasticity as a paradigm of eubacteria evolution. Journal of Molecular Evolution 44 (1): 57-64.
  • Yamaguchi Y. and Gojobori T. (1997) Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc. Natl. Acad. Sci. U.S.A. 94: 1264-1269.

1996

  • Bannai M., Tokunaga K., Imanishi T., Harihara S., Fujisawa K., Juji T. and Omoto K. (1996) HLA class II alleles in Ainu living in Hidaka district, Hokkaido, northern Japan. American Journal of Physical Anthropology 101: 1-9.
  • Endo T., Ikeo K., and Gojobori T. (1996) Large-scale search for genes on which positive selection may operate. Molecular Biology and Evolution 13: 685-690.
  • Fukagawa T., Nakamura Y., Okumura K., Ando A., Inoko H., Saitou N., and Ikemura T. (1996) Human pseudoautosomal boundary-like sequences: expression, and involvement in evolutionary formation of the present-day pseudoautosomal boundary of human sex chromosome. Human Molecular Genetics 5 (1): 23-32.
  • Fukami-Kobayashi K., Nosaka M., Nakazawa A. and Go M. (1996) Ancient divergence of long and short isoforms of adenylate kinase: molecular evolution of the nucleoside monophosphate kinase family. FEBS Lett. 385: 214-220.
  • Fumihito A., Miyake T., Takada M., Shingu R., Endo T., Gojobori T., Kondo N. and Ohno S. (1996) Monophyletic origin and unique dispersal patterns of domestic fowls. Proceedings of National Academy of Sciences U.S.A. 93: 6792-6795.
  • Gojobori T. and Tateno Y. (1996) DNA database and its applications to the study of molecular evolution. BIOJAPAN '96: Symposium Proceedings: 355-359.
  • Imanishi T. and Gojobori T. (1996) Diversity in human MHC genes among ethnic groups worldwide. In Tajima K. and Sonoda S. (eds.), Ethnoepidemiology of Cancer. Gann Monograph on Cancer Research No. 44, Japan Scientific Societies Press, Tokyo / CRC Press, Boca Raton: 89-96.
  • Imanishi T. (1996) DNA polymorphisms shared among different loci of the major histocompatibility complex genes. In Nei M. and Takahata N. (eds.), Current Topics on MolecularEvolution, Proceedings of the U.S.-Japan Workshop, Institute of Molecular Evolutionary Genetics, Penn. State University: 89-95.
  • Kitakami H., Mori Y., Tateno Y. and Gojobori T. (1996) A biological taxonomy database system on World Wide Web. In Computer Science and Biology, Proceedings of the German Conference on Bioinformatics (GCB'96), Univ. of Leipzig. 244-246.
  • Koike T., Okayama T., Ishii J., Mizunuma M., Tamura T., Tateno Y., Sugawara H., Nishikawa K., Imanishi T., Fukami-Kobayashi K., Ikeo K. and Gojobori T. (1996) Development of New DDBJ DNA Sequence Database with Data Annotation Tool Yamato II. In Akutsu T. et al. (eds.), Genome Informatics, University Academy Press, Tokyo: 157-165.
  • Lin L., Tokunaga K., Tanaka H., Nakajima F., Imanishi T., Kashiwase K., Bannai M., Mizuno S., Akaza T., Tadokoro K., Shibata Y. and Juji T. (1996) Further molecular diversity in the HLA-B15 group. Tisue Antigens. 47: 265-274.
  • Ling L., Shimura J., Sugawara H. and Tsugita A (1996) Epitope data bank. In Dubois J.-E. and Gershon E. (eds.), The Information Revolution: Impact on Science and Technology, Springer, Berlin. 249-254.
  • Matsuo Y., Yamada A., Tsukamoto K., Tamura H., Ikezawa H., Nakamura H. and Nishikawa K. (1996) A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I.
    Protein Science. 5: 2459-2467
  • Miyzaki S., Sugawara H. and Ohya, M. (1996) The efficiency of entropy evolution rate for contruction of phylogenetic trees. Genes and Genetic Systems. 71: 323-327.
  • Miyazaki S. and Sugawara H. (1996) The construction of phylogenetic tree from the large scale data of gene sequences, In Ebisuzaki T. (ed.), High Performance Computing in RIKEN 1996, vol. 1, Universal Academy Press, Japan. 209.
  • Mizokami M., Gojobori T., Ohba K., Ikeo K., Orito E. and Lau J. Y. N. (1996) Hepatitis C virus type 7, 8 and 9 should be classified as type 6 subtypes. J. Hepatol. 24: 622-624.
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