 主な論文 |
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主要論文リスト(1981-2007)
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 Research 17, 175-183.
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 309(5740), 1559-1563.
(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. and Sugiura, M. (2005)
The map-based sequence of the rice genome.
Nature436, 793-800.
Tateno, Y., Saitou, N., Okubo, K., Sugawara, H. and Gojobori, T. (2005).
DDBJ in collaboration with mass-sequencing teams on annotation.
Nucleic Acids Res.33, D25-D28.
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): 760-766
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. (*correspondence author)
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): 7666-671
Nishio, Y., Nakamura, Y., Kawarabayashi, Y., Usuda, Y.,
Kimura, E., Sugimoto, S., Matsui, K., Yamagishi, A., Kikuchi, H.,
Ikeo, K. and Gojobori, T. (2003). Comparative complete genome
sequence analysis of the amino acid replacements responsible
for the thermostability of Corynebacterium efficiens.
Genome Res. 13(7): 1572-79
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, 15584-89.
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, 312-316
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, 620-24.
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: 563-573
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 USA.
99(6):3695-3700
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): 685-690.
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): 1579-1586
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
Suzuki, Y. and Gojobori, T. (1999)
A method for detecting positive selection at single amino acid sites.
Mol Bol Evol. (16): 1315-1328.
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): 541-549.
Bellgard, M. and Gojobori, T. (1999)
Inferring the direction of evolutionary changes of
genomic base composition.Trends in Genetics 15(7): 254-256.
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): 332-346.
Watanabe, H., Mori, H., Itoh, T., and Gojobori, T. (1997)
Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol. 44(Suppl 1): S57-S64.
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): 1264-1269.
Gojobori, T., Tateno, Y., and Ohta, T., ed. (1997)
Special Issue: Networks and Evolution of Molecular Information.
J Mol Evol., ed.^eds. Vol. 44. S1-S180.
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. Proc Natl Acad Sci. USA. 93(13): 6792-6795.
Endo, T., Ikeo, K., and Gojobori, T. (1996)
Large-scale search for genes on which positive selection may operate.
Mol Biol Evol. 13(5): 685-690.
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: 1124-1127.
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): 411-415.
Ishibashi, K., Sasaki, S., Fushimi, K., Uchida, S., Kuwahara, M.
Saito, H., Furukawa, T., Nakajima, K., Yamaguchi, Y., Gojobori, T.,
and Marumo, F. (1994) Molecular cloning and expression of a member
of the aquaporin family with permeability to glycerol and urea in addition
to water expressed at the basolateral membrane of kidney collecting duct cells.
Proc Natl Acad Sci USA. 91(14): 6269-6273
Ina, Y. and Gojobori, T. (1994)
Statistical analysis of nucleotide sequences of the hemagglutinin
gene of human influenza A viruses. Proc Natl Acad Sci USA. 91(18): 8388-8392.
Gojobori, T., Imanishi, T., Ina, Y., Saitou, N., Tateno, Y.
Sato, K., Takata, H., Kimura, A., Nishimura, Y., Akaza, T.
Miyoshi, H., Mura, T., Tokunaga, K., Tanaka, H., Konoeda, Y.
Wakisaka, A., Juji, T., Sasazuki, T., Tsuji, K., and Inoko, H. (1992)
Construction of the MHC database. in HLA 1991, Proceedings of the
Eleventh International Histocompatibility Workshop and Conference.
Oxford University Press, Oxford.
Gojobori, T., Moriyama, E.N., and Kimura, M. (1990)
Statistical methods for estimating sequence divergence.
Methods Enzymol. 183: 531-550.
Gojobori, T., Moriyama, E., and Kimura, M. (1990)
Molecular clock of viral evolution, and the neutral theory.
Proc Natl Acad Sci USA. 87(24): 10015-10018.
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): 4108-4111.
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): 7059-7062.
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): 539-541.
Nei, M. and Gojobori, T. (1986)
Simple methods for estimating the numbers of synonymous
and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3(5): 418-426.
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): 4198-4201.
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): 3101-3105.
Gojobori, T. (1983) Codon substitution in evolution and
the "saturation" of synonymous changes. Genetics 105(4): 1011-1027.
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 pseudogenes and functional genes.
J Mol Evol. 18(5): 360-369.
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): 414-423.
Li, W.-H., Gojobori, T., and Nei, M. (1981)
Pseudogenes as a paradigm of neutral evolution.
Nature 292(5820): 237-239.
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