Murakami, Katsuhiko, Imanishi, Tadashi, Gojobori, Takashi, Nakai, Kenta
Abstract Background It is essential in modern biology to understand how transcriptional regulatory regions are composed of cis -elements, yet we have limited knowledge of, for example, the...
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates (2007)
Hurng-Yi Wang, Huan-Chieh Chien, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Takashi Gojobori, ...
Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their...
Homma, Keiichi, Fukuchi, Satoshi, Nakamura, Yoji, Gojobori, Takashi, Nishikawa, Ken
The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur,...
Homma, Keiichi, Fukuchi, Satoshi, Nakamura, Yoji, Gojobori, Takashi, Nishikawa, Ken
This paper was withdrawn by the authors.
Genome Informatics 14: 452--453 (2003) Detection of Processed Pseudogenes Based on cDNA (2004)
Human Genome, Hiroaki Sakai, Kanako O. Koyanagi, Takeshi Itoh, Tadashi Imanishi, Takashi Gojobori
Introduction Processed pseudogenes are defined as those obtained by reverse transcription of messenger RNAs followed by reintegration into genomic DNA and subsequent degradation with disablements...
Genome Informatics 14: 454--455 (2003) Improvement in the Accuracy of Gene Prediction in (2004)
Fusano Todokoro, Takeshi Itoh, Chisato Yamasaki, Hiroaki Kawashima, Tadashi Imanishi, Takashi Gojobori
Introduction GeneMark is a gene prediction program which has been designed to predict prokaryotic genes [2]. In addition the program may be used to search for eukaryotic genes in cDNA sequences and...
Hideaki Sugawara, Kazuho Ikeo, Satoru Miyazaki, Takashi Gojobori, Kenji Satou, Akihiko Konagaya
Introduction Tsunami of biological data and multiple views of the data analysis require an expandable and flexible information environment. GRID computing is expected to be the solution. We prepared...
Genome Informatics 14: 466--467 (2003) Genome-Scale Detection of Tandemly-Duplicated Gene (2004)
Keisuke Onishi, Hao Zhang, Takuro Tamura, Takashi Gojobori, Shintaroh Ueda
Introduction Genomic sequences of several animals were almost completely sequenced, and it was shown that human genome has relatively small numbers of genes. This suggests that not mere gene number...
Genome Informatics 14: 671--672 (2003) 671 A Prototype of PubMed Central Japan (2004)
Hideaki Sugawara, Takashi Gojobori, Takeshi Konno, Yasumasa Shigemoto, Masahito Yamaguchi
Introduction "PubMed Central (PMC) is the U.S. National Library of Medicine's digital archive of life sciences journal literature. Access to PMC is free and unrestricted." [3]. It covers 78 journals...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
Abstract Background Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian...
The evolutionary position of nematodes (2002)
Blair, Jaime E, Ikeo, Kazuho, Gojobori, Takashi, Hedges, S Blair
Abstract Background The complete genomes of three animals have been sequenced by global research efforts: a nematode worm ( Caenorhabditis elegans ), an insect ( Drosophila melanogaster ), and a...
Guy Perrire, Manolo Gouy, Takashi Gojobori
The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is...
Estimating the Number of Mouse Genes and the Duplicated Regions within the Mouse Genome (2001)
Yasuhiko Wada, Tadashi Imanishi, Takashi Gojobori
Introduction To elucidate the evolution of mammalian genomes, it is crucial to estimate the number of genes in the genome and to measure the degree of redundancy in the genome in various species. The...
Codon usage tabulated from the international DNA sequence databases; its status 1999 (1999)
Yasukazu Nakamura, Takashi Gojobori
Frequencies for each of the 206 526 complete proteincoding genes (CDS's) have been compiled from taxonomical divisions of the GenBank DNA sequence database. The sum of the codon use of 7434 organisms...
Hayasaka, Daisuke, Suzuki, Yoshiyuki, Kariwa, Hiroaki, Ivanov, Leonid, Volkov, Vladimir, Demenev, Vladimir, ...
We have previously reported that tick-borne encephalitis (TBE) is endemic in a specific area of Hokkaido, Japan. In Oshima, the southern part of Hokkaido, TBE virus was isolated from sentinel dogs,...
Hayasaka, Daisuke, Suzuki, Yoshiyuki, Kariwa, Hiroaki, Ivanov, Leonid, Volkov, Vladimir, Demenev, Vladimir, ...
We have previously reported that tick-borne encephalitis (TBE) is endemic in a specific area of Hokkaido, Japan. In Oshima, the southern part of Hokkaido, TBE virus was isolated from sentinel dogs,...
Hayasaka, Daisuke, Suzuki, Yoshiyuki, Kariwa, Hiroaki, Ivanov, Leonid, Volkov, Vladimir, Demenev, Vladimir, ...
We have previously reported that tick-borne encephalitis (TBE) is endemic in a specific area of Hokkaido, Japan. In Oshima, the southern part of Hokkaido, TBE virus was isolated from sentinel dogs,...
The non-redundant Bacillus subtilis (NRSub) database: update 1998 (1997)
Database Update Perrière, Manolo Gouy, Takashi Gojobori
The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is...
DNA Data Bank of Japan at work on genome sequence data (1997)
Yoshio Tateno, Kaoru Fukami-kobayashi, Satoru Miyazaki, Hideaki Sugawara, Takashi Gojobori
We at the DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp ) have recently begun receiving, processing and releasing EST and genome sequence data submitted by various Japanese genome...
Codon usage tabulated from the international DNA sequence databases (1997)
Yasukazu Nakamura, Takashi Gojobori
CUTG (codon usage tabulated from GenBank) is a comprehensive database for codon usage. The codon usage for each full-length protein gene has been calculated using the nucleotide sequence obtained...
Yamaguchi, Yumi, Gojobori, Takashi
Clonal diversifications of HIV virus were monitored by periodic samplings on each of the six patients with regard to 183- to 335-bp segments of the env gene, which invariably included the...
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams
Tateno, Yoshio, Miyazaki, Satoru, Ota, Motonori, Sugawara, Hideaki, Gojobori, Takashi
We at DDBJ (http://www.ddbj.nig.ac.jp ) process and publicise the massive amounts of data submitted mainly by Japanese genome projects and sequencing teams. It is emphasised that the collaboration...
Codon usage tabulated from international DNA sequence databases: status for the year 2000
Nakamura, Yasukazu, Gojobori, Takashi, Ikemura, Toshimichi
The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by...
The evolutionary position of nematodes
Blair, Jaime E, Ikeo, Kazuho, Gojobori, Takashi, Hedges, S Blair
Yamaguchi-Kabata, Yumi, Gojobori, Takashi
To elucidate the evolutionary mechanisms of the human immunodeficiency virus type 1 gp120 envelope glycoprotein at the single-site level, the degree of amino acid variation and the numbers of...
In silico chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence
Niimura, Yoshihito, Gojobori, Takashi
Giemsa staining has been used for identifying individual human chromosomes. Giemsa-dark and -light bands generally are thought to correspond to GC-poor and GC-rich regions; however, several...
Akashi, Hiroshi, Gojobori, Takashi
Biosynthesis of an Escherichia coli cell, with organic compounds as sources of energy and carbon, requires approximately 20 to 60 billion high-energy phosphate bonds [Stouthamer, A. H. (1973) Antonie...
Tanaka, Yasuhito, Hanada, Kousuke, Mizokami, Masashi, Yeo, Anthony E. T., Shih, J. Wai-Kuo, Gojobori, Takashi, ...
The prevalence of hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) is considerably lower in the U.S. than in Japan. To elucidate this difference, we determined the time origin of the...
Mineta, Katsuhiko, Nakazawa, Masumi, Cebrià, Francesc, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
Among the bilateral animals, a centralized nervous system is found in both the deuterostome and protostome. To address the question of whether the CNS was derived from a common ancestor of...
Anzai, Tatsuya, Shiina, Takashi, Kimura, Natsuki, Yanagiya, Kazuyo, Kohara, Sakae, Shigenari, Atsuko, ...
Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (≈6 million years ago), the molecular basis of traits unique to humans vs. their...
Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes
Niimura, Yoshihito, Terabe, Mahito, Gojobori, Takashi, Miura, Kin-ichiro
Adenine nucleotides have been found to appear preferentially in the regions after the initiation codons or before the termination codons of bacterial genes. Our previous experiments showed that AAA...
Gaudieri, Silvana, Dawkins, Roger L., Habara, Kaori, Kulski, Jerzy K., Gojobori, Takashi
The human major histocompatibility complex (MHC) is characterized by polymorphic multicopy gene families, such as HLA and MIC (PERB11); duplications; insertions and deletions (indels); and uneven...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Wada, Yoshiko, Doi, Hirofumi, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Aota, Shin-ichi, Tsuchiya, Rye, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Wada, Ken-nosuke, Wada, Yoshiko, Ishibashi, Fumie, Gojobori, Takashi, Ikemura, Toshimichi
Codon usage tabulated from the GenBank Genetic Sequence Data
Aota, Shin-ichi, Gojobori, Takashi, Ishibashi, Fumie, Maruyama, Takeo, Ikemura, Toshimichi
Codon usage tabulated from the GenBank genetic sequence data
Maruyama, Takeo, Gojobori, Takashi, Aota, Shin-ichi, Ikemura, Toshimichi
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Nishio, Yousuke, Nakamura, Yoji, Kawarabayasi, Yutaka, Usuda, Yoshihiro, Kimura, Eiichiro, Sugimoto, Shinichi, ...
Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above...
Ogura, Atsushi, Ikeo, Kazuho, Gojobori, Takashi
Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been...
Iwama, Hisakazu, Gojobori, Takashi
Identifying evolutionarily conserved blocks in orthologous genomic sequences is an effective way to detect regulatory elements. In this study, with the aim of elucidating the architecture of the...
Novel algorithm for automated genotyping of microsatellites
Matsumoto, Toshiko, Yukawa, Wataru, Nozaki, Yasuyuki, Nakashige, Ryo, Shinya, Minori, Makino, Satoshi, ...
Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits....
Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, ...
The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein...
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information
Ohyanagi, Hajime, Tanaka, Tsuyoshi, Sakai, Hiroaki, Shigemoto, Yasumasa, Yamaguchi, Kaori, Habara, Takuya, ...
With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice...
DDBJ in preparation for overview of research activities behind data submissions
Okubo, Kousaku, Sugawara, Hideaki, Gojobori, Takashi, Tateno, Yoshio
In the past year, DDBJ () collected and released 1 956 826 entries or 1 741 313 111 bases. The released data include ∼90 000 ESTs and cDNAs of Macaca fascicularis, and 280 million bases of mouse...
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
Yamasaki, Chisato, Kawashima, Hiroaki, Todokoro, Fusano, Imamizu, Yasuhiro, Ogawa, Makoto, Tanino, Motohiko, ...
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity...
Codon Substitution in Evolution and the "Saturation" of Synonymous Changes
A mathematical model for codon substitution is presented, taking into account unequal mutation rates among different nucleotides and purifying selection. This model is constructed by using a 61 x 61...
Andrews, T Daniel, Gojobori, Takashi
The PilE protein is the major component of the Neisseria meningitidis pilus, which is encoded by the pilE/pilS locus that includes an expressed gene and eight homologous silent fragments. The silent...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
Shiina, Takashi, Ota, Masao, Shimizu, Sayoko, Katsuyama, Yoshihiko, Hashimoto, Nami, Takasu, Miwa, ...
A plausible explanation for many MHC-linked diseases is lacking. Sequencing of the MHC class I region (coding units or full contigs) in several human and nonhuman primate haplotypes allowed an...
A C + + computational environment for biomolecular sequence management
M. Chiusano, Takashi Gojobori, G. Toraldo
The wide production of biomolecular data of the last 30 years, mainly due to the rapid evolving of technologies as well as to the accomplishment of the Genome Projects, led to the necessity of...
Yamaguchi, Yumi, Gojobori, Takashi
Clonal diversifications of HIV virus were monitored by periodic samplings on each of the six patients with regard to 183- to 335-bp segments of the env gene, which invariably included the...
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams
Tateno, Yoshio, Miyazaki, Satoru, Ota, Motonori, Sugawara, Hideaki, Gojobori, Takashi
We at DDBJ (http://www.ddbj.nig.ac.jp ) process and publicise the massive amounts of data submitted mainly by Japanese genome projects and sequencing teams. It is emphasised that the collaboration...
Codon usage tabulated from international DNA sequence databases: status for the year 2000
Nakamura, Yasukazu, Gojobori, Takashi, Ikemura, Toshimichi
The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by...
The evolutionary position of nematodes
Blair, Jaime E, Ikeo, Kazuho, Gojobori, Takashi, Hedges, S Blair
Yamaguchi-Kabata, Yumi, Gojobori, Takashi
To elucidate the evolutionary mechanisms of the human immunodeficiency virus type 1 gp120 envelope glycoprotein at the single-site level, the degree of amino acid variation and the numbers of...
In silico chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence
Niimura, Yoshihito, Gojobori, Takashi
Giemsa staining has been used for identifying individual human chromosomes. Giemsa-dark and -light bands generally are thought to correspond to GC-poor and GC-rich regions; however, several...
Akashi, Hiroshi, Gojobori, Takashi
Biosynthesis of an Escherichia coli cell, with organic compounds as sources of energy and carbon, requires approximately 20 to 60 billion high-energy phosphate bonds [Stouthamer, A. H. (1973) Antonie...
Tanaka, Yasuhito, Hanada, Kousuke, Mizokami, Masashi, Yeo, Anthony E. T., Shih, J. Wai-Kuo, Gojobori, Takashi, ...
The prevalence of hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) is considerably lower in the U.S. than in Japan. To elucidate this difference, we determined the time origin of the...
Mineta, Katsuhiko, Nakazawa, Masumi, Cebrià, Francesc, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
Among the bilateral animals, a centralized nervous system is found in both the deuterostome and protostome. To address the question of whether the CNS was derived from a common ancestor of...
Anzai, Tatsuya, Shiina, Takashi, Kimura, Natsuki, Yanagiya, Kazuyo, Kohara, Sakae, Shigenari, Atsuko, ...
Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (≈6 million years ago), the molecular basis of traits unique to humans vs. their...
Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes
Niimura, Yoshihito, Terabe, Mahito, Gojobori, Takashi, Miura, Kin-ichiro
Adenine nucleotides have been found to appear preferentially in the regions after the initiation codons or before the termination codons of bacterial genes. Our previous experiments showed that AAA...
Gaudieri, Silvana, Dawkins, Roger L., Habara, Kaori, Kulski, Jerzy K., Gojobori, Takashi
The human major histocompatibility complex (MHC) is characterized by polymorphic multicopy gene families, such as HLA and MIC (PERB11); duplications; insertions and deletions (indels); and uneven...