Collection and Investigation into Basic Evolutionary Information by Orrsite Collaboration

• Project/Area Number: 16255006
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 海外学術
• Research Field: Evolutionary biology
• Research Institution: National Institute of Genetics
• Principal Investigator: TATENO Yoshio National Institute of Genetics, Center for Information Biology and DNA Data Bank of Japan, Professor (00202424)
• Co-Investigator(Kenkyū-buntansha): GOJOBORI Takashi National Institute of Genetics, Center for Information Biology and DNA Data Bank of Japan, Professor (50162136) ; SUGAWARA Hideaki National Institute of Genetics, Center for Information Biology and DNA Data Bank of Japan, Professor (80231372) ; SAITOU Naruya National Institute of Genetics, Department of Population Genetics, Professor (30192587) ; OKUBO Kosaku National Institute of Genetics, Center for Information Biology and DNA Data Bank of Japan, Professor (40233069) ; IKEO Kazuho National Institute of Genetics, Center for Information Biology and DNA Data Bank of Japan, Associate Professor (20249949) ; 西川 建 (西川 健) 国立遺伝学研究所, 生命情報・DDBJ研究センター, 教授 (10093288)
• Project Period (FY): 2004 – 2007
• Project Status: Completed (Fiscal Year 2007)
• Budget Amount: ¥29,900,000 (Direct Cost: ¥23,000,000、Indirect Cost: ¥6,900,000); Fiscal Year 2007: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000); Fiscal Year 2006: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000); Fiscal Year 2005: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000); Fiscal Year 2004: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
• Keywords: International visit / biological database / genome / annotation / evolutionary information / human genes / data standardization / DDBJ / UniProt / Annotation / マイクロアレイデータ / イネゲノム / ヒト発現遺伝子 / チンパンジー染色体 / 非タンパク質遺伝子 / 国際DNAデータバンク実務者会議

Research Abstract

In the term of the present grant from 2004 to 2007 we visited 67 universities and research institutes in 16 countries in total to fulfill our investigation purposes. Since we DDBJ organize the International Nucleotide Sequence Database Collaboration (INSDC) with GenBank in USA and EMBL Bank in Europe, our frequent visits to these two research organizations were crucial and fruitful, resulted in a steep increase in the number of published entries from 35 to 80 million sequences (or 40 to 82 billon bases) in the four years. The published entries include expressed sequences and the whole genome sequence with biological information for many species and thus indispensable for research in biology and related areas. We have also sewed specified databases such as GIB (bacterial genome database), GTOP (protein-structure prediction database) and CIBEX (gene expression database). These databases have been enriched in the contents and the number of users because of various international visits supported by the present grant.
Some of the international visits have also contributed to carrying out data annotations of human genes, rice genes and mouse genes. The results of the annotations have been published in their respective databases and journals. For example, we have shown that the total number of genes in the human genome is about 35, 000 that is much larger than previously estimated.
Recently, we participated in the international standardization of genome sequence data and published the guidelines for annotating genome sequences of eukaryotes, prokaryotes, viruses, plasmids and others.
The outcomes of the international visits have been published in internationally well-known academic journals such as Nature, Nature Biotechnology, Nature Genetics, Science, Proc. Natl. Acad. Sci. USA, Genome Research and Nucleic Acids Research (see the list of publications).

Research Products

• [Journal Article] The H-Invitational Database(H-InvDB),a comprehensive annotation resource for human genes and transcripts (2008)
  • Author(s): Yamasaki, C.
  • Journal Title: Nucleic Acids Res. 36
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] DDBJ with new system and face (2008)
  • Author(s): Sugawara H.
  • Journal Title: Nucleic Acids Research 36
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The Rice Annotation Project Database(RAP-DB):2008 update (2008)
  • Author(s): Tanaka, T.
  • Journal Title: Nucleic Acids Res. 36
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The minimum information about a genome sequence(MIGS)specification (2008)
  • Author(s): Dawn Field
  • Journal Title: Nature Biotechnology 26 Pages: 541-547
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The H-Invitational Database(H-InvDB), a comprehensive annotation resource for human genes and transcripts. (2008)
  • Author(s): Yamasaki, C.
  • Journal Title: Nucleic Acids Res. 36
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] DDBJ with new system and face (2008)
  • Author(s): Sugawara H.
  • Journal Title: Nucleic Acids Res. 36
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The Rice Annotation Project Database(RAP DB) : 2008 update. (2008)
  • Author(s): Tanaka, T.
  • Journal Title: Nucleic Acids Res. 36
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The minimum information about a genome sequence(MIGS) specification. (2008)
  • Author(s): Dawn Field
  • Journal Title: Nature Biotechnology 26 Pages: 541-547
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. (2008)
  • Author(s): Genome Information Integration Project and H-Invitational 2 Consortium: Yamasaki, C.
  • Journal Title: Nucleic Acids Res. 36(Databaseissue)
  • Peer Reviewed
• [Journal Article] The Rice Annotation Project Database (RAP-DB): 2008 update. (2008)
  • Author(s): Tanaka, T.
  • Journal Title: Nucleic Acids Res. 36(Databaseissue)
  • Peer Reviewed
• [Journal Article] Evola: Ortholog database of all human genes in H-lnvDB with manual curation of phylogenetic trees (2008)
  • Author(s): Matsuya, A.
  • Journal Title: Nucleic Acids Res. 36(Databaseissue)
  • Peer Reviewed
• [Journal Article] Development and public release of comprehensive Hepatitis virus database (2008)
  • Author(s): Shin-I, T.
  • Journal Title: Hepatol Res 38 Pages: 234-243
  • Peer Reviewed
• [Journal Article] H-DBAS:Alternative Splicing Database of Completely Sequenced and Manually Annotated Full-length cDNAs Based on H-Invitational (2007)
  • Author(s): Takeda, JI.
  • Journal Title: Nucleic Acids Res. 35
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Genome Information Broker for Viruses(GIB-V):database for comparative analysis of virus genomes (2007)
  • Author(s): Masaki Hirahata.
  • Journal Title: Nucleic Acids Research 35
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Identification of discriminative characteristics for clusters from biologic data with InforBIO software (2007)
  • Author(s): Tanaka N.
  • Journal Title: BMC Bioinformatics 8 Pages: 281-288
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] A tree of life based on protein domain organizations (2007)
  • Author(s): Fukami-Kobayashi K.
  • Journal Title: Mol.Biol.Evol. 24 Pages: 1181-1189
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] DDBJ working on evaluation and classification of bacterial genes in INSDC (2007)
  • Author(s): Sugawara, H.
  • Journal Title: Nucleic Acids Res. 35
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Curated Genome Annotation of Oryza sativa ssp.Japonica and Comparative Genome Analysis with Arabidopsis thaliana (2007)
  • Author(s): Ito, T.
  • Journal Title: Genome Res. 17 Pages: 175-183
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] H-DBAS : Alternative Splicing Database of Completely Sequenced and Manually Annotated Full-length cDNAs Based onH-Invitational. (2007)
  • Author(s): Takeda, JI.
  • Journal Title: Nucleic Acids Res. 35
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Genome Information Broker for Viruses(GIB-V) : database for comparative analysis of virus genomes. (2007)
  • Author(s): Masaki Hirahata.
  • Journal Title: Nucleic Acids Research 35
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Identification of discriminative characteristics for clusters from biologic data with InforBIO software. (2007)
  • Author(s): Tanaka N.
  • Journal Title: BMC Bioinformatics 8 Pages: 281-288
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A tree of life based on protein domain organizations. (2007)
  • Author(s): Fukami-Kobayashi K.
  • Journal Title: Mol. Biol. Evol. 24 Pages: 1181-1189
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] DDBJ working on evaluation and classification of bacterial genes in INSDC. (2007)
  • Author(s): Sugawara, H.
  • Journal Title: Nucleic Acids Res. 35
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana. (2007)
  • Author(s): Ito, T.
  • Journal Title: Genome Res. 17 Pages: 175-183
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The evolutionary emergence of cell type specific genes inferred from the gene expre ssion analysis of hydra. (2007)
  • Author(s): Jung Shan, H.
  • Journal Title: Proc. Natl. Acad. Sci. USA 104(37) Pages: 14735-14740
  • Peer Reviewed
• [Journal Article] Compensatory Change of Interacting Amino Acids in the Coevolution of Transcriptional Coactivator MBF1 and TATA-Box Binding Protein TBP. (2007)
  • Author(s): Liu, QX.
  • Journal Title: Mol. Biol. Evol. 24(7) Pages: 1458-1463
  • Peer Reviewed
• [Journal Article] Transcriptional interferences in cis natural antisense transcripts of human and mouse (2007)
  • Author(s): Osato, N.
  • Journal Title: Genetics 176 Pages: 1299-1306
  • Peer Reviewed
• [Journal Article] 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. (2007)
  • Author(s): Homma, K.
  • Journal Title: Mol. Biol. Evol. 24(3) Pages: 805-813
  • Peer Reviewed
• [Journal Article] H-DBAS: Alternative Splicing Database of Completely Sequenced and Manually Annotated Full-length cDNAs Based on H-Invitational. (2007)
  • Author(s): Takeda, JI.
  • Journal Title: Nucleic Acids Res. 35(Databaseissue)
  • Peer Reviewed
• [Journal Article] Genome Information Broker for Viruses(GIB-V): database for comparative analysis of virus genomes. (2007)
  • Author(s): Masaki Hirahata.
  • Journal Title: Nucleic Acids Research 35
  • Peer Reviewed
• [Journal Article] Identification of discriminative characteristics for clusters from biologic data with Infor BIO software. (2007)
  • Author(s): Tanaka N.
  • Journal Title: BMC Bioinformatics 8 Pages: 281-288
  • Peer Reviewed
• [Journal Article] Intrinsically disordered regions of human plasma membrane proteins preferentially occur in the cytoplasmic segment. (2007)
  • Author(s): Minezaki Y.
  • Journal Title: J.Mol. Biol. 368 Pages: 902-913
  • Peer Reviewed
• [Journal Article] A tree of life based on protein domain organizations. (2007)
  • Author(s): Fukami-Kobayashi K.
  • Journal Title: Mol. Biol. Evol. 24(5) Pages: 1181-1189
  • Peer Reviewed
• [Journal Article] Cornichon-like Protein Facilitates Secretion of HB-EGF and Regulates Proper Development of Cranial Nerves. (2007)
  • Author(s): Hoshino H.
  • Journal Title: Molecular Biology of the Cell 18
  • Peer Reviewed
• [Journal Article] DDBJ working on evaluation and classification of bacterial genes in lNSDC. (2007)
  • Author(s): Sugawara, H.
  • Journal Title: Nucleic Acids Res. 35
  • Peer Reviewed
• [Journal Article] Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana. (2007)
  • Author(s): The Rice Annotation Project: Ito, T.
  • Journal Title: Gonome Res. 17(2) Pages: 175-183
  • Peer Reviewed
• [Journal Article] Systems-level analysis and evolution of the phototransduction network in Drosophila. (2007)
  • Author(s): Landry CR.
  • Journal Title: PNAS 104,9 Pages: 3283-3288
  • Peer Reviewed
• [Journal Article] Tempo and mode of evolution of the Rh blood group genes before and after geneduplication. (2007)
  • Author(s): Kitano T.
  • Journal Title: Immunogenetics 59 Pages: 427-431
  • Peer Reviewed
• [Journal Article] Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana (2007)
  • Author(s): The Rice Annotation Project: Ito, T, Gojobori, T., et al.
  • Journal Title: Genome Res 17(2) Pages: 175-83
• [Journal Article] H-DBAS : Alternative Splicing Database of Completely Sequenced and Manually Annotated Full-length cDNAs Based on H-Invitational (2007)
  • Author(s): Takeda, JI, Suzuki, Y, Nakao, M, Kuroda, T, Sugano, S, Gojobori, T, Imanishi, T.
  • Journal Title: Nucleic Acids Res. 35(Database issue)
• [Journal Article] DDBJ Working on Evaluation and Classification of Bacterial Genes in INSDC (2007)
  • Author(s): Sugawara, H, Abe, T, Gojobori, T., Tateno, Y.
  • Journal Title: Nucleic Acids Res. 35(Database issue)
• [Journal Article] A series of ENU-induced single base substitutions in a long-range cis-element altering Sonic hedgehog expression in the developing mouse limb bud. (2007)
  • Author(s): Hiroshi Masuya, Hideki Sezutsu, Yoshiyuki Sakuraba, Tomoko Sagai, Masaki Hosoya, Hideki Kaneda, Ikuo Miura, Kimio Kobayashi, Kenta Sumiyama, Aya Shimizu, Junko Nagano, Haruka Yokoyama, satoko Kaneko, Noriko Sakurai, Yuka Okagaki, Tetsuo Noda, Shigeharu Wakana, Yoichi Gondo, Toshihiko Shiroishi.
  • Journal Title: Genomics 89(2) Pages: 207-14
• [Journal Article] Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway (2006)
  • Author(s): Kuroki Y.
  • Journal Title: Nature Genetics 38 Pages: 158-167
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] A SNP in the ABCC11 gene is the determinant of human earwax type (2006)
  • Author(s): Yoshiura K.
  • Journal Title: Nature Genetics 38 Pages: 324-330
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs (2006)
  • Author(s): J.Takeda.
  • Journal Title: Nucleic Acids Res. 34 Pages: 3917-3928
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The concept of sampling in OMICS technology (2006)
  • Author(s): Morrison, N.
  • Journal Title: OMICS 10 Pages: 127-137
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Evidence standards in experimental and inferential INSDC Third Party Annotation data (2006)
  • Author(s): Cochrane, G.
  • Journal Title: OMICS 10 Pages: 105-113
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] DDBJ in preparation for overview of research activities behind data submissions (2006)
  • Author(s): Okubo, K.
  • Journal Title: Nucleic Acids Res. 34
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The Rice Annotation Project Database(RAP-DB):Hub for Oryza sativa ssp.japonica genome information (2006)
  • Author(s): Ohyanagi, H.
  • Journal Title: Nucleic Acids Res. 34
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Exploration and grading of possible genes in 183 bacterial strains by a common fine protocol lead to new genes:Gene Trek in Prokaryote Space(GTPS) (2006)
  • Author(s): Takehide Kosuge
  • Journal Title: DNA Research 13 Pages: 245-254
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] BodyMap-Xs:anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression (2006)
  • Author(s): Ogasawara O
  • Journal Title: Nucleic Acids Res. 34
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. (2006)
  • Author(s): Kuroki Y.
  • Journal Title: Nature Genetics 38 Pages: 158-167
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A SNP in the ABCC11 gene is the determinant of human earwax type. (2006)
  • Author(s): Yoshiura K.
  • Journal Title: Nature Genetics 38 Pages: 324-330
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56, 419 completely sequenced and manually annotated full-length cDNAs. (2006)
  • Author(s): J. Takeda.
  • Journal Title: Nucleic Acids Res. 34 Pages: 3917-3928
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The concept of sampling in OMICS technology. (2006)
  • Author(s): Morrison, N.
  • Journal Title: OMICS 10 Pages: 127-137
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Evidence standards in experimental and inferential INSDC Third Party Annotation data. (2006)
  • Author(s): Cochrane, G.
  • Journal Title: OMICS 10 Pages: 105-113
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] DDBJ in preparation for overview of research activities behind data submissions. (2006)
  • Author(s): Okubo, K.
  • Journal Title: Nucleic Acids Res. 34
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The Rice Annotation Project Database(RAP-DB) : IIub for Oryza sativa ssp. japonica genome information. (2006)
  • Author(s): Ohyanagi, H.
  • Journal Title: Nucleic Acids Res. 34
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Exploration and grading of possible genes in 183 bacterial strains by a common fine protocol lead to new genes : Gene Trek in Prokaryote Space(GTPS) (2006)
  • Author(s): Kosuge T.
  • Journal Title: DNA Research 13 Pages: 245-254
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] BodyMap-Xs anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. (2006)
  • Author(s): Ogasawara O.
  • Journal Title: Nucleic Acids Res. 34
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Exploration and grading of possible genes in 183 bacterial strains by a common fine protocol lead to new genes : Gene Trek in Prokaryote space (GTPS) (2006)
  • Author(s): Takehide Kosuge, Takashi Abe, Toshihisa Okido, Naoto Tanaka, Masaki Hirahata, Yutaka Maruyama, Aki Tomiki, Motoyoshi Kurokawa, Ryutaro Himeno, Satoshi Fukuchi, Satoru Miyazaki, Takashi Gojobori, Yoshio Tateno, Hideaki Sugawara
  • Journal Title: DNA Research 13(6) Pages: 245-254
• [Journal Article] Alternative splicing in human transcriptome : functional and structural influence on proteins (2006)
  • Author(s): 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.
  • Journal Title: GENE 380 Pages: 63-71
• [Journal Article] Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs (2006)
  • Author(s): Takeda, JI, 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, Thicrry-Mieg, J, Thierry-Mieg, D, Wiemann, S, Nomura, N, Sugano, S, Gojobori, T, Imanishi, T.
  • Journal Title: Nucleic Acids Res. 34(14) Pages: 3917-3928
• [Journal Article] TACT : Transcriptome Auto-annotation Conducting Tool of H-InvDB (2006)
  • Author(s): Yamasaki, C, Kawashima, H, Todokoro, F, Imamizu, Y, Ogawa, M, Tanino, M, Itoh, T, Gojobori, T, Imanishi, T
  • Journal Title: Nucleic Acids Res. 34(Web Server issue)
• [Journal Article] Molecular characterization of the developmental gene in eyes : Through data-mining on integrated transcriptome databases (2006)
  • Author(s): Choy, KW, Wang, CC, Ogura, A, Lau, TK, Rogers, MS, Ikeo, K, Gojobori, T, Tang, LY, Lam, DS, Chung, TK, Pang, CP
  • Journal Title: Clin. Biochem. 34(Web Server issue) Pages: 224-230
• [Journal Article] Genomic annotation of 15,809 ESTs identified from pooled early gestation hman eyes (2006)
  • Author(s): Choy, KW, Wang, CC, Ogura, A, Lau, TK, Rogers, MS, Ikeo, K, Gojobori, T, Lam, DS, Pang, CP.
  • Journal Title: Physiol. Genomics 39(3) Pages: 9-15
• [Journal Article] The Rice Annotation Project Database(RAP-DB) : Hub for Oryza sativa ssp. japonica genome information. (2006)
  • Author(s): Ohyanagi, H, Tanaka, T, Sakai, H, Shigemoto, Y, Yamaguchi, K, Habara, T, Fujii, Y, Antonio, B, Nagamura, Y, Imanishi, T, Ikeo, K, Ito, T, Gojobori, T, Sakaki, T
  • Journal Title: Nucleic Acids Res. 25(1)
• [Journal Article] DDBJ in preparation for overview of research activities behind data submissions. (2006)
  • Author(s): Okubo, K, Sugawara, H, Gojobori, T, Tateno, Y.
  • Journal Title: Nucleic Acids Res. 34(Database issue)
• [Journal Article] Evolution metabolic networks by gain and loss of enzymatic in eukaryotes. (2006)
  • Author(s): Tanaka, T, Ikeo, K, Gojobori T.
  • Journal Title: GENE 365C Pages: 88-94
• [Journal Article] Natural selection on the influenza virus genome. (2006)
  • Author(s): Yoshiyuki Suzuki
  • Journal Title: Molecular Biology and Evolution 23 Pages: 1902-1911
• [Journal Article] Evidence standards in experimental and inferential INSDC Third Party Annotation data. (2006)
  • Author(s): Cochrane, G, Bates, K, Apweiler, R, Tateno, Y, Mashima, J, Kosuge, T, Mizrachi, I, Schafer, S, Fetchko, M.
  • Journal Title: OMICS 10 Pages: 105-113
• [Journal Article] The concept of sampling in 'omics technology. (2006)
  • Author(s): Morrison, N, Cochrane, G., Faruque, N., Tatusova, T., Tateno, Y., Hancock, D., Field, D.
  • Journal Title: OMICS 10 Pages: 127-137
• [Journal Article] Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. (2006)
  • Author(s): J.Takeda, Y.Suzuki, M.Nakao, R.A.Barrero, S, Sugano, S.Wiemann, T.gojobori, T.Imanishi et al.
  • Journal Title: Nucleic Acids Res. 34 Pages: 3917-3928
• [Journal Article] A SNP in the ABCC11 gene is the determinant of human earwax type. (2006)
  • Author(s): Yoshiura K., Kinoshita A., Ishida T., Ninokata A., Ishikawa T., Kaname T., Bnnai M., Tokunaga K., Sonoda S., Komaki R., Ihara M., Saenko V.A., Alipov G.K., Sekine I., Komatsu K., Takahashi H., Nakashima M., Sosonkina N., Mapendano C.K., Ghadami M., Nomura M., Liang D.S., Miwa N., Kim D.K., Garidkhuu A., Natsume N., Ohta T., Tomita H., Kaneko A., Kikuchi M., Russomando G., Hirayama K., Ishibashi M., Takahashi A., Saitou N., Murray J.C., Saito S., Nakamura Y., Niikawa N.
  • Journal Title: Nature Genetics 38(3), Pages: 324-330
• [Journal Article] Genomewide search of gene conversions in duplicated genes of mouse and rat. (2006)
  • Author(s): Ezawa K., OOta S., Saitou N.
  • Journal Title: Molecular Biology and Evolution 23(5) Pages: 927-940
• [Journal Article] Comparative analysis of chimpanzee and hman Y chromosomes unveils complex evolutionary pathway. (2006)
  • Author(s): Kuroki Y., Toyoda A., Noguchi H., Taylor T.D., Itoh T., Kim D.S., Kim D.W., Choi S.H., Kim I.C., Choi H.H., Kim Y.S., Satta Y., Saitou N., Yamada T., Morishita S., Hattori M., Sakaki Y., Park H.S., Fujiyama A.
  • Journal Title: Nature Genetics 38(2), Pages: 158-167
• [Journal Article] Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci. (2006)
  • Author(s): Li S.L, Yamamoto T, Yoshimoto T, Uchihi R., Mizutani M., Kurimoto Y., Tokunaga K., Jin F., Katsumata Y., Saitou N.
  • Journal Title: Human Genetics 118(6) Pages: 695-707
• [Journal Article] Escherichia coli K-12 : a cooperatively developed annotation snapshot-2005 (2006)
  • Author(s): Riley, M., Abe, T., Amaud, B.M., Berlyn, M., Blattner, R.F., Chaudhuri, R.R., Glasner, D.J., Horiuchi, T., Keseler, M.I., Kosuge, T., Mori, H., Perna, T.N., Plunkett, G., Rudd, E.K., Serres, H.M., Thomas, H.G., Thomson, R.H., Wishart, D., Wanner, L.B.
  • Journal Title: Nucleic Acids Research 34 Pages: 1-9
• [Journal Article] A large-scale Self-Organizing Map (SOM) unveils sequence characteristics of a wide range of eukaryote genomes (2006)
  • Author(s): Abe, T., Sugawara, H., Kanaya, K., Kinouchi, M., Ikemura, T.
  • Journal Title: Gene 365 Pages: 27-34
• [Journal Article] A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes (2006)
  • Author(s): Abe, T, Sugawara, H, Kanaya, S, Ikemura, T.
  • Journal Title: Polar Bioscience 20 Pages: 103-112
  • NAID: 110006199745
• [Journal Article] Intrinsically disordered loops inserted into the structural domains of human proteins. (2006)
  • Author(s): Fuuchi, S., Homma, K., Minezaki, Y., Nishikawa, K.
  • Journal Title: J. Mol. Biol. 355 Pages: 845-857
• [Journal Article] Analysis of amino acid residues involved in the catalysis of polyethylene glycol dehydrogenase from sphingomonas terrae using three-dimensional molecular modeling-based kinetic characterization of mutants. (2006)
  • Author(s): Ohta, T, Kawabata, T, Nishikawa, K, Tani, A, Kimbara, K, Kawai, F.
  • Journal Title: Appl. Environ. Microbiol. 72 Pages: 4388-4396
• [Journal Article] Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. (2006)
  • Author(s): Minezaki, Y., Homma, K., Kinjo, A.R., Nishikawa, K.
  • Journal Title: J. Mol. Biol. 359 Pages: 1137-1149
• [Journal Article] Stabilization of E. coli ribonuclease HI by the 'stability profile of mutant protein'(SPMP)-inspired random and non-random mutagenesis. (2006)
  • Author(s): Haruki, M., Saito, Y., Ota, M., Nishikawa, K., Kanaya, S.
  • Journal Title: J. Biotech. 124 Pages: 512-522
• [Journal Article] BodyMap-Xs : anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. (2006)
  • Author(s): Ogasawara O., Otsuji M., Watanabe K., Iizuka T., Tamura T., Hishiki T., Kawamoto S., Okubo K.
  • Journal Title: Nucleic Acids Res. 1;34(Database issue)
• [Journal Article] BodyMap-Xs : anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. (2006)
  • Author(s): Ogasawara O, Otsuji M, Watanabe K, Iizuka T, Tamura T, Hishiki T, Kawamoto S, Okubo K.
  • Journal Title: Nucleic Acids Res. 34
• [Journal Article] Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-lgf2-H19 region (2005)
  • Author(s): Yokomine T
  • Journal Title: Genome Res. 15 Pages: 154-165
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The map-based sequence of the rice genome (2005)
  • Author(s): Iwama, H.
  • Journal Title: Nature 436 Pages: 793-800
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The transcriptional landscape of the mammalian genome (2005)
  • Author(s): Carninci, P.
  • Journal Title: Science 309 Pages: 1559-1563
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Large-scale analysis of human alternative protein isoforms:pattern classification and correlation with subcellular localization signals (2005)
  • Author(s): Nakao M.
  • Journal Title: Nucleic Acids Res. 33 Pages: 2355-2363
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Genomic evolution of MHC class l region in primates (2005)
  • Author(s): Fukami-Kobayashi, K.
  • Journal Title: Proc Natl Acad Sci USA 102 Pages: 9230-9234
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Development of a spot evaluation score for DNA microarrays (2005)
  • Author(s): Matsumura, Y.
  • Journal Title: Gene 350 Pages: 149-160
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studiesc (2005)
  • Author(s): Saka, K.
  • Journal Title: DNA Res. 12 Pages: 63-68
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The Human Anatomic Gene Expression Library(H-ANGEL),the H-lnv integrative display of human gene expression across disparate technologies and platforms (2005)
  • Author(s): Tanino, M.
  • Journal Title: Nucleic Acids Res. 33
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] DDBJ in collaboration with mass-sequencing teams on annotation (2005)
  • Author(s): Tateno Y.
  • Journal Title: Nucleic Acids Research 33
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-lgf2-H19 region (2005)
  • Author(s): Yokomine T.
  • Journal Title: Genome Research 15 Pages: 154-65
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-Igf2-H19 region. (2005)
  • Author(s): Yokomine T.
  • Journal Title: Genome Res. 15 Pages: 154-165
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The map-based sequence of the rice genome. (2005)
  • Author(s): Iwama, H.
  • Journal Title: Nature 436 Pages: 793-800
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The transcriptional landscape of the mammalian genome. (2005)
  • Author(s): Carninci, P.
  • Journal Title: Science 30 Pages: 1559-1563
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Large-scale analysis of human alternative protein isoforms : pattern classification and correlation with subcellular localization signals. (2005)
  • Author(s): Nakao M
  • Journal Title: Nucleic Acids Res. 33 Pages: 2355-2363
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Genomic evolution of MHC class I region in primates. (2005)
  • Author(s): Fukami-Kobayashi, K.
  • Journal Title: Proc NatlAcad Sci USA 102 Pages: 9230-9234
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Development of a spot evaluation score for DNA microarrays. (2005)
  • Author(s): Matsumura, Y
  • Journal Title: Gene 350 Pages: 149-160
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studies c. (2005)
  • Author(s): Saka, K.
  • Journal Title: DNA Res. 12 Pages: 63-68
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The Human Anatomic Gene Expression Library(H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. (2005)
  • Author(s): Tanino, M.
  • Journal Title: Nucleic Acids Res. 33
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] DDBJ in collaboration with mass-sequencing teams on annotation. (2005)
  • Author(s): Tateno Y
  • Journal Title: Nucleic Acids Res. 33
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2fMash2-Igf2-II19 region. (2005)
  • Author(s): Yokomine T
  • Journal Title: Genome Research 15 Pages: 154-65
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] DDBJ in collaboration with mass-sequencing teams on annotation. (2005)
  • Author(s): Tateno Y., Saitou N., Okubo K., Sugawara H., Gojobori T.
  • Journal Title: Nucleic Acids Research 33
• [Journal Article] Evolution of hominoids and the search for a genetic basis for creating humanness. (2005)
  • Author(s): Saitou N.
  • Journal Title: Cytogenetic and Genome Research 108 Pages: 16-21
• [Journal Article] Nucleotide sequence comparison of a chromosome rearrangement on the human chromosome 12 and corresponding ape chromosomes. (2005)
  • Author(s): Shimada M., Kim C.-G, Kitano T., Ferell R.E., Kohara Y., Saitou N.
  • Journal Title: Cytogenetic and Genome Research 108 Pages: 83-90
• [Journal Article] Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabokic genes. (2005)
  • Author(s): Uchiyama T., Abe T., Ikemura T., Watanabe K.
  • Journal Title: Nature biotechnology 23 Pages: 88-93
• [Journal Article] Direct cloning of genes encoding novel xylanases from the human gut (2005)
  • Author(s): Hayashi H., Abe T., Skamoto M., Ohara H., Ikemura T., Sakka K., Benno Y.
  • Journal Title: Can.J.Microbiol. 51 Pages: 251-259
• [Journal Article] Novel Phylogenetic Studies of Genomic Sequence Fragments Derived from Uncultured Microbe Mixtures in Environmental and Clinical Samples. (2005)
  • Author(s): Abe T., Sugawara H., Kinouchi M., Kanaya S., Ikemura T.
  • Journal Title: DNA Reserch 12 Pages: 281-290
• [Journal Article] Identification of differentially expressed genes in psoriasis using expression profiling approaches. (2005)
  • Author(s): Itoh K, Kawasaki S, Kawamoto S, Seishima M, Chiba H, Michibata H, Wakimoto K, Imai Y, Minesaki Y, Otsuji M, Okubo K.
  • Journal Title: Exp Dermatol. 14(9) Pages: 667-674
• [Journal Article] The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. (2005)
  • Author(s): 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.
  • Journal Title: Nucleic Acids Res. 33
• [Journal Article] ポストゲノム時代に高まるバイオ自然言語処理への期待:バイオ自然言語処理最新事情 5.ゲノムデータの機械解釈 (2005)
  • Author(s): 大久保公策, 日紫喜光良
  • Journal Title: 情報処理 46(480) Pages: 137-142
  • NAID: 110002768351
• [Journal Article] Predicting absolute contact numbers of native protein structure from amino acid sequence c (2005)
  • Author(s): Kinjo, A.R., Horimoto, K., Nishikawa, K.
  • Journal Title: Proteins 58 Pages: 158-165
• [Journal Article] A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studies c (2005)
  • Author(s): Saka, K., Tadenuma, M., Nakade, S., Tanaka, N., Sugawara, H., Nishikawa, K., Ichiyoshi, N., Kitagawa, M., Mori, H., Ogasawara, N., Nishimura, A.
  • Journal Title: DNA Res. 12 Pages: 63-68
• [Journal Article] Recoverable one-dimensional encoding of three-dimensional protein structures c (2005)
  • Author(s): Kinjo, A.R., Nishikawa, K.
  • Journal Title: Bioinformatics 21(10) Pages: 2167-2170
• [Journal Article] Predicting secondary structures, contact numbers and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks c (2005)
  • Author(s): Kinjo, A.R., Nishikawa, K.
  • Journal Title: Biophysics 1 Pages: 67-74
• [Journal Article] Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. (2005)
  • Author(s): Tanaka, T., Tateno, Y., Gojobori, T.
  • Journal Title: Mol Biol Evol 22 Pages: 243-250
• [Journal Article] Development of a spot evaluation score for DNA microarrays. (2005)
  • Author(s): Matsumura, Y., Shimokawa, K., Hayashizaki, Y., Ikeo, K., Tateno, Y., Kawai, J.
  • Journal Title: Gene 350 Pages: 149-160
• [Journal Article] Genomic evolution of MHC class I region in primates. (2005)
  • Author(s): Fukami-Kobayashi, K., Shiina, T., Anzai, T., Sano, K., Yamazaki, M., Inoko, H., Tateno, Y.
  • Journal Title: Proc Natl Acad Sci USA 102 Pages: 9230-9234
• [Journal Article] Large-scale analysis of human alternative protein isoforms : pattern classification and correlation with subcellular localization signals. (2005)
  • Author(s): Nakao M, Barrero RA, Mukai Y, Motono C, Suwa M, Nakai K.
  • Journal Title: Nucleic Acids Res. 33 Pages: 2355-2363
• [Journal Article] Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational Database (H-InvDB). (2005)
  • Author(s): Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T
  • Journal Title: Gene 364 Pages: 99-107
• [Journal Article] The transcriptional landscape of the mammalian genome. (2005)
  • Author(s): The FANTOM Consortium : Carninci, P., Gojobori, T., Ikeo, K., other 157 authors, Hume, D.A., Riken Genome Exploration Research Group, Genome Science Group.(Genome Network Project Core Group) : Kai, C., other 31 authors, Hayashizaki, Y.
  • Journal Title: Science 309 Pages: 1559-1563
• [Journal Article] The map-based sequence of the rice genome. (2005)
  • Author(s): (International Rice Genome Sequencing Project : Annotation and Analysis) Iwama, H., Gojobori, T., Itoh, T., Niimura, Y., Fujii, Y., Habara T., Sakai, H., Sato, Y., Wilson, G., Kumar, K., McCouch, S., Juretic, N., Hoen, D., Wright, S., Bruskiewich, R., Bureau T., Miyao, A., Hirochika, H., Nishikawa, T., Kadowaki, K., Sugiura, M.
  • Journal Title: Nature 436 Pages: 793-800
• [Journal Article] The origin and evolution of porcine reproductive and respiratory syndrome viruses. (2005)
  • Author(s): Hanada, K., Suzuki, Y., Nakane, T., Hirose, O., Gojobori, T.
  • Journal Title: Mol.Biol.Evol. 22(4) Pages: 1024-1031
• [Journal Article] Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Asc12/Mash2-Igf2-H19-region. (2005)
  • Author(s): 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.
  • Journal Title: Genome Res. 15(1) Pages: 154-165
• [Journal Article] The Human Anatomic Gene Expression Library (H-Angel), the H-Invintegrative display of human gene expression across disparate technologies and platforms. (2005)
  • Author(s): Tanino, M., Debily, M.-A-., Tamura, T., Hishiki, T., Ogasawara, O., Murakawa, K., Kawamoto, S., Itoh K., Watanabe, S., Souza, S.J.d., Imbeaud, S., Graucens, E., Eveno, E., Hilton, P., Sudo, Y., Kelso, J., Ikeo, K., Imanishi, T., Gojobori, T., Auffray, C., Hide, W., Okubo, K.
  • Journal Title: Nucleic Acids Res. 33
• [Journal Article] Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-Igf2-H19 region. (2005)
  • Author(s): 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.
  • Journal Title: Genome Research 15(1) Pages: 154-165
• [Journal Article] Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins (2004)
  • Author(s): Kinjo, A.R.
  • Journal Title: Bioinformatics 20 Pages: 2504-2508
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J,as defined by BAC end sequence-SNP analysis (2004)
  • Author(s): Abe K.
  • Journal Title: Genome Research 14 Pages: 2239-2247
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] DNA sequence and comparative analysis of chimpanzee chromosome 22 (2004)
  • Author(s): Watanabe, H.
  • Journal Title: Nature 429 Pages: 382-388
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Biased biological functions of horizontally transferred genes on 324,653 open reading frames of 116 prokaryotic complete genomes (2004)
  • Author(s): Nakamura, Y.
  • Journal Title: Nature Genetics 36 Pages: 760-6
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Integrative annotation of 21,037 human genes validated by full-length cDNA clones (2004)
  • Author(s): Imanishi, T.
  • Journal Title: PLoS Biology 2 Pages: 1-21
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] DDBJ in the stream of various biological data (2004)
  • Author(s): Miyazaki, S.
  • Journal Title: Nucleic Acids Research 32
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. (2004)
  • Author(s): Kinjo, A. R.
  • Journal Title: Bioinformatics 20 Pages: 2504-2508
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC end sequence-SNP analysis. (2004)
  • Author(s): Abe K.
  • Journal Title: Genome Research 14 Pages: 2239-2247
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] DNA sequence and comparative analysis of chimpanzee chromosome 22. (2004)
  • Author(s): Watanabe H.
  • Journal Title: Nature 429 Pages: 382-388
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Biased biological functions of horizontally transferred genes on 324, 653 open reading frames of 116 prokaryotic complete genomes. (2004)
  • Author(s): Nakamura, Y
  • Journal Title: Nature Genetics 36 Pages: 760-6
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Integrative annotation of 21, 037 human genes validated by full-length cDNA clones. (2004)
  • Author(s): Imanishi, T.
  • Journal Title: PLoS Biology Pages: 21-21
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] DDBJ in the stream of various biological data. (2004)
  • Author(s): Miyazaki, S.
  • Journal Title: Nucleic Acids Res. 32
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] DBJ in the stream of various biological data. (2004)
  • Author(s): Miyazaki, S., Sugawara, H., Ikeo, K., Gojobori, T., Tateno.Y.
  • Journal Title: Nucleic Acids Research 32
• [Journal Article] Integrative annotation of 21,037 human genes validated by full-length cDNA clones. (2004)
  • Author(s): Imanishi, T., other 152 authors, Gojobori, T., Sugano S.
  • Journal Title: PLoS Biology 2 Pages: 1-21
  • NAID: 120004667172
• [Journal Article] Submission of microarray data to public repositories. (2004)
  • Author(s): Ball, C.A., Brazma, A., Causon, H., Chervitz, S., Edgar, R., Hingamp, P., Matese, J.C., Parkinson, H., Quackenbush, J., Ringwald, M., Sansone, S.-A., Sherlock, G., Spellman, P., Stoeckert, C., Tateno, Y., Taylor, R., White, J., Winegarden, N.
  • Journal Title: PLoS Biology 2 Pages: 1276-1277
• [Journal Article] Novel algorithm for automated genotyping of microsatelites. (2004)
  • Author(s): Matsumoto, T., Yukawa, W., Nozaki, Y., Nakashige, R., Shinya, M., Makino, S., Yagura, M., Ikuta, T., Imanishi, T., Inoko, H., Tamiya, G., Gojobori, T.
  • Journal Title: Nucleic Acids Research 32 Pages: 6069-6077
• [Journal Article] Evolution of gap junctions : the missing link? (2004)
  • Author(s): Alexopoulos, H., Bottger, A., Fischer, S., Levin, A., Wolf, A., Fujisawa, T., Hayakawa, S., Gojobori, T., Davies, J., David, C., Bacon, J.
  • Journal Title: Current Biology 14(20)
• [Journal Article] Japanese domesticated chickens have been drived from Shamo, traditional fighting cocks. (2004)
  • Author(s): Komiyama, T., Ikeo, K., Tateno, Y., Gojobori, T.
  • Journal Title: Molecular Phylogeny and Evolution 33 Pages: 16-21
• [Journal Article] Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human. (2004)
  • Author(s): Ogura, A., Ikeo, K., Gojobori, T.
  • Journal Title: Genome Research 14 Pages: 1555-1561
• [Journal Article] The evolutionary origin of long-crowing chicken : its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis. (2004)
  • Author(s): Komiyama, T., Ikeo, K., Gojobori, T.
  • Journal Title: GENE 333 Pages: 91-99
• [Journal Article] Evolutionary process of the amino acids biosynthesis in Corynebacterium at the whole qenome level. (2004)
  • Author(s): Nishio, Y., Nakamura, Y., Usuda, Y., Sugimoto, S., Matsui, K., Kawarabayashi, Y., Kikuchi, H., Gojobori, T., Ikeo, K.
  • Journal Title: Molecular Biology and Evolution 21 Pages: 1683-1691
• [Journal Article] Biased biological functions of horizontally transferred genes on 324,653 open reading frames of 116 prokaryotic complete genomes. (2004)
  • Author(s): Nakamura, Y., Itoh, T., Matsuda, H., Gojobori, T.
  • Journal Title: Nature Genetics 36 Pages: 760-766
• [Journal Article] A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. (2004)
  • Author(s): Hanada, K., Suzuki, Y., Gojobori, T.
  • Journal Title: Molecular Biology and Evolution 21 Pages: 1074-1080
• [Journal Article] DNA sequence and comparative analysis of chimpanzee chromosome 22. (2004)
  • Author(s): The International Chimpanzee Chromosome 22 Consortium
  • Journal Title: Nature 429 Pages: 382-388
• [Journal Article] Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC end sequence-SNP analysis. (2004)
  • Author(s): Abe K., Noguchi H., Tagawa K., Yuzuriha M., Toyoda A., Kojima T., Ezawa K., Saitou N., Hattori M., Sakaki Y., Moriwaki K., Shiroishi T.
  • Journal Title: Genome Research 14 Pages: 2239-2247
• [Journal Article] Splicing Profile-based Protein Categorization between Human and Mouse Genome by use of DDBJ Web Services. (2004)
  • Author(s): Vastermark, A., Shigemoto, Y., Abe, T., Sugawara, H.
  • Journal Title: Genome Informatics 15 Pages: 13-20
  • NAID: 130003997345
• [Journal Article] Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. (2004)
  • Author(s): Kinjo, A.R., Nishikawa, K.
  • Journal Title: Bioinformatics 20(16) Pages: 2504-2508
• [Journal Article] Estimation of the number of authentic orphan genes in bacterial genomes. (2004)
  • Author(s): Fukuchi, S., Nishikawa, K.
  • Journal Title: DNA Research 11 Pages: 219-231
• [Journal Article] Indexing anatomical concepts to OMIM Clinical Synopsis using the UMLS Metathesaurus. (2004)
  • Author(s): Hishiki, T., Ogasawara, O., Tsuruoka, Y., Okubo.K.
  • Journal Title: In Silico Biology 4 Pages: 31-54
• [Book] DDBJの利用法 (2005)
  • Author(s): 五條堀 孝
  • Total Pages: 181
  • Publisher: 共立出版
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 「DDBJの利用法」 (2005)
  • Author(s): Gojobori, T.
  • Total Pages: 181
  • Publisher: KYORITSU SHUPPAN
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] DNAから見た日本人 (2005)
  • Author(s): 斎藤成也
  • Total Pages: 215
  • Publisher: 筑摩書房
• [Book] 「バイオインフォマティックス」、「プロテオーム」、細胞生物学事典(石川統・黒岩常祥・永田和宏編集) (2005)
  • Author(s): 舘野義男
  • Total Pages: 464
  • Publisher: 朝倉書店
• [Book] DDBJの利用法 (2005)
  • Author(s): 五條堀 孝, 菅原 秀明(編著)
  • Total Pages: 181
  • Publisher: 共立出版
• [Book] 「ウイルスの多様性と系統」『バイオディバーシティ・シリーズ4 菌類・細菌・ウイルスの多様性と系統』 (2005)
  • Author(s): 花田 耕介, 五條堀 孝
  • Total Pages: 492
  • Publisher: 裳華房
• [Book] 「マイクロアレイ遺伝子発現デーベース」, 『ゲノミクス・プロテオミクスの新展開〜生物情報の解析と応用』 (2004)
  • Author(s): 池尾 一穂
  • Total Pages: 9
  • Publisher: (株)エヌ・ティー・エス
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 「ゲノムの再編成」第一章ヒトゲノムの全貌, 『Molecular Medicine』増刊号 (2004)
  • Author(s): 花田 耕介
  • Total Pages: 9
  • Publisher: 中山書店
  • Description: 「研究成果報告書概要(和文)」より
• [Book] Tsunami of data:Data resources and utilization.Microbial Genetic Resources and Biodiscovery (2004)
  • Author(s): Sugawara, H.
  • Total Pages: 17
  • Publisher: National Library of Australia
  • Description: 「研究成果報告書概要(和文)」より
• [Book] Quantification of Gene Expression in Mouse and Human Renal Proximal Tubules.「Laser Capture Microdissection Methods and Protocols」Methods in Molecular Biology 293 (2004)
  • Author(s): Kaimori, J.
  • Total Pages: 12
  • Publisher: Humana Press
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 「マイクロアレイ遺伝子発現データベース」、『ゲノミクス・プロテオミクスの新展開-生物情報の解析と応用』. (2004)
  • Author(s): Ikeo, K.
  • Total Pages: 9
  • Publisher: NTS Inc.
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] 「ゲノムの再編成」第一章ヒトゲノム全貌『Molecular Medicine』増刊号. (2004)
  • Author(s): Hanada, K.
  • Total Pages: 9
  • Publisher: Nakayama Shoten
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] Tsunami of data : Data resources and utilization. Microbial Genetic Resources and Biodiscovery. (2004)
  • Author(s): Sugawara, H.
  • Total Pages: 17
  • Publisher: National Library of Australia
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] Quantification of Gene Expression in Mouse and Human Renal Proximal Tubules, Laser capture Microdissection Methods and Protocols, Methods in Molecular Bilolgy (2004)
  • Author(s): Kaimori, J.
  • Total Pages: 12
  • Publisher: Humana Press
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] マイクロアレイ遺伝子発現デーベース、『ゲノミクス・プロテオミクスの新展開〜生物情報の解析と応用』 (2004)
  • Author(s): 池尾一穂, 舘野義男
  • Total Pages: 9
  • Publisher: (株)エヌ・ティー・エス
• [Book] 総合化生命科学としての現代進化学(巻頭言)、『科学』10月号 (2004)
  • Author(s): 五條堀 孝
  • Total Pages: 1
  • Publisher: 岩波書店
• [Book] 「ゲノムの再編成」第一章ヒトゲノムの全貌,『Molecular Medicine』増刊号 (2004)
  • Author(s): 花田 耕介, 五條堀 孝
  • Total Pages: 9
  • Publisher: 中山書店
• [Book] 『ゲノムと進化-ゲノムから立ち昇る生命-』ワードマップシリーズ (2004)
  • Author(s): 斎藤成也
  • Publisher: 新曜社
• [Book] Tsunami of data : Data resources and utilization.(Microbial Genetic Resources and Biodiscovery.) (2004)
  • Author(s): Sugawara, H.
  • Total Pages: 17
  • Publisher: National Library of Australia
• [Book] Quantification of Gene Expression in Mouse and Human Renal Proximal Tubules.「Laser Capture Microdissection Methods and Protocols」Methods in Molecular Biology 293 (2004)
  • Author(s): Kaimori, J., Takenaka, M., Okubo, K.
  • Total Pages: 12
  • Publisher: Humana Press
• [Remarks] 「研究成果報告書概要(和文)」より
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