Takashi Gojobori

Main publications
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), 14735-40; The Rice Annotation Project: Ito, T. and Gojobori, T., et al. (2007), Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana, Genome Res. 17(2), 175-83; 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. and Sugiura, M. (2005), The map-based sequence of the rice genome, Nature 436: 793-800; Nakamura, Y., Itoh, T., Matsuda, H. and Gojobori, T. (2004), Biased biological functions of horizontally transferred genes on 324,653 open reading frames of 116 prokaryotic complete genomes, Nature Genetics 36(7): 760-6; Iwama, H. and Gojobori, T. (2004), Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network, Proc. Natl. Acad. Sci. USA. 101, 17156-61; Imanishi, T., other 152 authors, Gojobori, T., and Sugano S. (2004), Integrative annotation of 21,037 human genes validated by full-length cDNA clones, PLoS Biol. 2, 1-21; Andrews, T.D. and Gojobori, T. (2004), Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen neisseria meningitidis, Genetics 166, 25-32; Anzai, T., Shiina, T., Kimura, N., Yanagiya, K., Kohara, S., Shigenari, A., Yamagata, T., Kulski, J.K., Naruse, T.K., Fujimori, Y., Fukuzumi, Y., Yamazaki, M., Tashiro, H., Iwamoto, C., Umehara, Y., Imanishi, T., Meyer, A., Ikeo, K., Gojobori, T., Bahram, S. and 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. USA. 100(13):7708-13; Nakazawa, M., Cebria, F., Mineta, K., Ikeo, K., Agata, K. and Gojobori, T. (2003), Search for the evolutionary origin of a brain. Planarian brain characterized by microarray, Mol. Biol. Evol.20(5): 784-91; Mineta, K., Nakazawa, M., Cebria, F., Ikeo, K., Agata, K. and Gojobori, T. (2003), Origin and evolutionary process of CNS elucidated by comparative genomics analysis of planarian ESTs, Proc. Natl. Acad. Sci. USA. 100(13): 7666-71; Niimura, Y. and Gojobori, T. (2002), In silico chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence, Proc. Natl. Acad. Sci. USA. 99(2): 797-802; Tanaka, Y., Hanada, K., Mizokami, M., Yeo, A.E.T., Shih, J.W.-K., Gojobori, T.. and Alter, H.J. (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. Natl. Acad. Sci. USA. 99, 15584-9; Sasaki, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura Y., Cheng Z., Nagamura Y., Kanamori, H., Hosokawa, S., Masukawa, M., Arikawa, Antonio, B.A. and Gojobori, T. (2002), The genome sequence and structure of rice chromosome 1., Nature 420: 312-6; Fantom Consortium (Okazaki, Y., Gojobori, T., et al.), Riken Genome Exploration Research Group Phase I & II Team, Mouse Genome Sequencing Consortium, Scientific management: Y. Hayashizaki (2002). Analysis of the Mouse Transcriptome based on Functional Annotation of 60,770 full-length cDNAs, Nature 420: 563-73; RIKEN Genome Exploration Research Group Phase II Team and FANTOM Consortium (Okazaki, Y., Gojobori, T., et al.), General organizer: Y. Hayashizaki (2001). Functional annotation of a full-length mouse cDNA collection, Nature 409(6821): 685-90; International Human Genome sequencing Consortium (DNA sequence databases: DNA Data Bank of Japan et al.) (2001). Initial sequencing and analysis of the human genome, Nature, 409(6822): 860-921; 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 Res. 10(10): 1579-86; 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):4335-50; Gaudieri, S., Kulski, J., Dawkins, R., and Gojobori, T. (1999), Different evolutionary histories in two subgenomic regions of the major histocompatibility complex,Genome Res. 9(6): 541-9; Bellgard, M. and Gojobori, T. (1999), Inferring the direction of evolutionary changes of genomic base composition, Trends in Genetics 15(7): 254-6; 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(3): 332-46; 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. USA. 94(4): 1264-9; Gojobori, T., Tateno, Y., and Ohta, T., ed. (1997), Special Issue: Networks and Evolution of Molecular Information, J. Mol. Evol., Vol. 44. S1-S180; Endo, T., Ikeo, K., and Gojobori, T. (1996), Large-scale search for genes on which positive selection may operate, Mol. Biol. Evol. 13(5): 685-90; Miura, T., Fukunaga, T., Igarashi, T., Yamashita, M., Ido, E., Funahashi, S.-I., Ishida, T., Washio, K., Ueda, S., Hashimoto, K.-I., Yoshida, M., Osame, M., Singhal, B.S., Zaninovic, V., Cartier, L., Sonoda, S., Tajima, K., Ina, Y., Gojobori, T., and Hayami, M. (1994), Phylogenetic subtypes of human T-lymphotropic virus type I and their relations to the anthropological background, Proc. Natl. Acad. Sci. USA. 91: 1124-7; Gojobori, T. and Ikeo, K. (1994), Molecular evolution of serine protease and its inhibitor with special reference to domain evolution, Philos. Trans. R. Soc. Lond. B Biol. Sci. 344(1310): 411-5; Gojobori, T., Moriyama, E.N., Ina, Y., Ikeo, K., Miura, T., Tsujimoto, H., Hayami, M., and Yokoyama, S. (1990), Evolutionary origin of human and simian immunodeficiency viruses, Proc. Natl. Acad. Sci. USA. 87(11): 4108-11; Orito, E., Mizokami, M., Ina, Y., Moriyama, E.N., Kameshima, N., Yamamoto, M., and Gojobori, T. (1989), Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences, Proc. Natl. Acad. Sci. USA. 86(18): 7059-62; Tsujimoto, H., Hasegawa, A., Maki, N., Fukasawa, M., Miura, T., Speidel, S., Cooper, R.W., Moriyama, E.N., Gojobori, T., and Hayami, M. (1989), Sequence of a novel simian immunodeficiency virus from a wild-caught African mandrill, Nature 341(6242): 539-41; Gojobori, T. and Yokoyama, S. (1985), Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues, Proc. Natl. Acad. Sci. USA. 82(12): 4198-201; Shimotohno, K., Takahashi, Y., Shimizu, N., Gojobori, T., Golde, D.W., Chen, I.S.Y., Miwa, M., and Sugimura, T. (1985), Complete nucleotide sequence of an infectious clone of human T-cell leukemia virus type II: An open reading frame for the protease gene, Proc. Natl. Acad. Sci. USA. 82(10): 3101-5; Gojobori, T. (1983), Codon substitution in evolution and the 'saturation' of synonymous changes, Genetics 105(4): 1011-27; Li, W.-H., Gojobori, T., and Nei, M. (1982), Reply on Goodman's comment 'Positive selection causes purifying selection', Nature 295: 630; Gojobori, T., Li, W.-H., and Graur, D. (1982). Patterns of nucleotide substitution in pseudo-genes and functional genes, J. Mol. Evol. 18(5): 360-9; Gojobori, T., Ishii, K., and Nei, M. (1982), Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide, J. Mol. Evol. 18(6): 414-23; Li, W.-H., Gojobori, T., and Nei, M. (1981), Pseudogenes as a paradigm of neutral evolution, Nature 292(5820): 237-9.