DDBJ Activities: Contribution to the Research in Information Biology (2009)
Jun Mashima, Takehide Kosuge, Toshihisa Okido, Yuichi Kodama, Kazuho Ikeo, Hideaki Sugawara, ...
DDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International...
Genome Network Project: An Integrated Genomic Platform (2009)
Jose C. Clemente, So Nakagawa, Kazuho Ikeo, Takashi Gojobori
With the objective of elucidating the structure of gene interactions in the human genome, the Genome Network Project has generated a vast quantity of experimental data, mainly focusing on...
Optimized ancestral state reconstruction using Sankoff parsimony (2009)
Clemente, José C, Ikeo, Kazuho, Valiente, Gabriel, Gojobori, Takashi
Abstract Background Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of...
DDBJ dealing with mass data produced by the second generation sequencer (2009)
Sugawara, Hideaki, Ikeo, Kazuho, Fukuchi, Satoshi, Gojobori, Takashi, Tateno, Yoshio
DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008. The releases in this period...
Agrobiological Resources (2008)
Ha. Jime Kitakami, Tadasu Shin-i, Kazuho Ikeo, Yoshihiro Ugawa, Naruya Saitou, Takashi Gojobori, ...
305, Japan Recently, we newly developed a relrrtionrrl schema for eflectively building, integruting. and searching the DNA database on the relational datuhnse mcrnngement system, SYBASE, at DDBJ. The...
Hwang, Jung Shan, Takaku, Yasuharu, Chapman, Jarrod, Ikeo, Kazuho, David, Charles N., Gojobori, Takashi
The cnidocil at the apical end of Hydra nematocytes is a mechanosensory cilium, which acts as a “trigger” for discharge of the nematocyst capsule. The cnidocil protrudes from the center of the...
Matsuya, Akihiro, Sakate, Ryuichi, Kawahara, Yoshihiro, Koyanagi, Kanako O., Sato, Yoshiharu, Fujii, Yasuyuki, ...
Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology...
Structure and Developmental Expression of the Ascidian (2007)
Gene Insights Into, Shigeru Sato, Reiko Toyoda, You Katsuyama, Hidetoshi Saiga, Takaharu Numakunai, ...
The tyrosinase family in vertebrates consists of three related melanogenic enzymes: tyrosinase, tyrosinase-related protein-1 (TRP-1), and TRP-2. These proteins control melanin production in pigment...
Hideaki Sugawara, Yoji Nakamura, Kazuho Ikeo, Satoru Miyazaki, Takashi Gojobori, Kenji Satou, ...
clustering
Liu, Qing-Xin, Nakashima-Kamimura, Naomi, Ikeo, Kazuho, Hirose, Susumu, Gojobori, Takashi
To elucidate the transcriptional regulation in eukaryotic genome network, it is important to understand coevolution of transcription factors, transcriptional coactivators, and TATA-box–binding...
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...
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...
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...
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...
Yokomine, Takaaki, Shirohzu, Hisao, Purbowasito, Wahyu, Toyoda, Atsushi, Iwama, Hisakazu, Ikeo, Kazuho, ...
Previous studies revealed that Igf2 and Mpr/Igf2r are imprinted in eutherian mammals and marsupials but not in monotremes or birds. Igf2 lies in a large imprinted cluster in eutherians, and its...
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...
The Human Anatomic Gene Expression Library (2004)
Motohiko Tanino, Marie-anne Debily, Takuro Tamura, Teruyoshi Hishiki, Osamu Ogasawara, Katsuji Murakawa, ...
(H-ANGEL), the H-Inv integrative display of human gene expression across disparate
Nishio, Yousuke, Nakamura, Yoji, Usuda, Yoshihiro, Sugimoto, Shinichi, Matsui, Kazuhiko, Kawarabayasi, Yutaka, ...
Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and...
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...
Evolutionary Process of Amino Acid Biosynthesis in Corynebacterium at the Whole Genome Level (2004)
Nishio, Yousuke, Nakamura, Yoji, Usuda, Yoshihiro, Sugimoto, Shinichi, Matsui, Kazuhiko, Kawarabayasi, Yutaka, ...
Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and...
Yokomine, Takaaki, Shirohzu, Hisao, Purbowasito, Wahyu, Toyoda, Atsushi, Iwama, Hisakazu, Ikeo, Kazuho, ...
Previous studies revealed that Igf2 and Mpr/Igf2r are imprinted in eutherian mammals and marsupials but not in monotremes or birds. Igf2 lies in a large imprinted cluster in eutherians, and its...
Nishio, Yousuke, Nakamura, Yoji, Usuda, Yoshihiro, Sugimoto, Shinichi, Matsui, Kazuhiko, Kawarabayasi, Yutaka, ...
Corynebacterium glutamicum, which is the closest relative of Corynebacterium efficiens, is widely used for the large scale production of many kinds of amino acids, particularly glutamic acid and...
Search for the Evolutionary Origin of a Brain; Planarian Brain Characterized by Microarray (2003)
Nakazawa, Masumi, Cebrià, Francesc, Mineta, Katsuhiko, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
The origin of the brain remains a challenging problem in evolutionary studies. To understand when and how the structural brain emerged, we analyzed the central nervous system (CNS) of a lower...
Search for the Evolutionary Origin of a Brain: Planarian Brain Characterized by Microarray (2003)
Nakazawa, Masumi, Cebrià, Francesc, Mineta, Katsuhiko, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
The origin of the brain remains a challenging problem in evolutionary studies. To understand when and how the structural brain emerged, we analyzed the central nervous system (CNS) of a lower...
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...
Search for the Evolutionary Origin of a Brain; Planarian Brain Characterized by Microarray (2003)
Nakazawa, Masumi, Cebrià, Francesc, Mineta, Katsuhiko, Ikeo, Kazuho, Agata, Kiyokazu, Gojobori, Takashi
The origin of the brain remains a challenging problem in evolutionary studies. To understand when and how the structural brain emerged, we analyzed the central nervous system (CNS) of a lower...
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...
The evolutionary position of nematodes
Blair, Jaime E, Ikeo, Kazuho, Gojobori, Takashi, Hedges, S Blair
Callaerts, Patrick, Lee, Patricia N., Hartmann, Britta, Farfan, Claudia, Choy, Darrett W. Y., Ikeo, Kazuho, ...
Molluscs display a rich diversity of body plans ranging from the wormlike appearance of aplacophorans to the complex body plan of the cephalopods with highly developed sensory organs, a complex...
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...
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...
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...
Yokomine, Takaaki, Shirohzu, Hisao, Purbowasito, Wahyu, Toyoda, Atsushi, Iwama, Hisakazu, Ikeo, Kazuho, ...
Previous studies revealed that Igf2 and Mpr/Igf2r are imprinted in eutherian mammals and marsupials but not in monotremes or birds. Igf2 lies in a large imprinted cluster in eutherians, and its...
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...
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...
The evolutionary position of nematodes
Blair, Jaime E, Ikeo, Kazuho, Gojobori, Takashi, Hedges, S Blair
Callaerts, Patrick, Lee, Patricia N., Hartmann, Britta, Farfan, Claudia, Choy, Darrett W. Y., Ikeo, Kazuho, ...
Molluscs display a rich diversity of body plans ranging from the wormlike appearance of aplacophorans to the complex body plan of the cephalopods with highly developed sensory organs, a complex...
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...
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...
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...
Yokomine, Takaaki, Shirohzu, Hisao, Purbowasito, Wahyu, Toyoda, Atsushi, Iwama, Hisakazu, Ikeo, Kazuho, ...
Previous studies revealed that Igf2 and Mpr/Igf2r are imprinted in eutherian mammals and marsupials but not in monotremes or birds. Igf2 lies in a large imprinted cluster in eutherians, and its...
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...
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...
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...
Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice
Osato, Naoki, Suzuki, Yoshiyuki, Ikeo, Kazuho, Gojobori, Takashi
For a significant fraction of mRNAs, their expression is regulated by other RNAs, including cis natural antisense transcripts (cis-NATs) that are complementary mRNAs transcribed from opposite strands...
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
Matsuya, Akihiro, Sakate, Ryuichi, Kawahara, Yoshihiro, Koyanagi, Kanako O., Sato, Yoshiharu, Fujii, Yasuyuki, ...
Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology...
Hwang, Jung Shan, Ohyanagi, Hajime, Hayakawa, Shiho, Osato, Naoki, Nishimiya-Fujisawa, Chiemi, Ikeo, Kazuho, ...
Cell lineages of cnidarians including Hydra represent the fundamental cell types of metazoans and provides us a unique opportunity to study the evolutionary diversification of cell type in the animal...
Optimized ancestral state reconstruction using Sankoff parsimony
Clemente, José C, Ikeo, Kazuho, Valiente, Gabriel, Gojobori, Takashi
DDBJ dealing with mass data produced by the second generation sequencer
Sugawara, Hideaki, Ikeo, Kazuho, Fukuchi, Satoshi, Gojobori, Takashi, Tateno, Yoshio
DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008. The releases in this period...