Yura, Kei, Sulaiman, Sintawee, Hatta, Yosuke, Shionyu, Masafumi, Go, Mitiko
Transcripts from mitochondrial and chloroplast DNA of land plants often undergo cytidine to uridine conversion-type RNA editing events. RESOPS is a newly built database that specializes in displaying...
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species (2008)
Akihiro Yamaguchi, Mitsuo Iwadate, Ei-ichiro Suzuki, Kei Yura, Shigetsugu Kawakita, Hideaki Umeyama, ...
Enlarged FAMSBASE is a relational database of comparative protein structure models for the whole genome of 41 species,presented in the GTOP database. The models are calculated by Full
Hisashi Ishida, Kei Yura, Takuma Kano, Atsushi Matsumoto
The Earth Simulator has the highest power ever achieved to perform molecular dynamics simulation of large-scale supramolecular systems. We are developing a molecular dynamics simulation system,...
Abstract Background In plant organelles, specific messenger RNAs (mRNAs) are subjected to conversion editing, a process that often converts the first or second nucleotide of a codon and hence the...
A Resource Discovery Service for Bioinformatics Applications in a Grid-Based Environment (2008)
Xiujun Gong, Jitender Jit, Singh Cheema, Kensuke Nakamura, Kei Yura
Bioinformatics is a collaborative discipline, in which bioinformatics scientists need to share their ideas and analysis method not only through manuscripts, but also through information repositories,...
BAAQ: A Grid-based Infrastructure for Integrating Bioinformatics Applications 1 (2008)
Xiujun Gong, Kei Yura, Nobuhiro Go
Amount of available biological data is increasing at explosive speed. These huge data are heterogeneous, autonomous and dynamic. At the same time, many tools to analyze these data are produced by...
BAAQ: A Platform for Integrating Bioinformatics Tools and Sharing Knowledge (2008)
Jitender Jit, Singh Cheema, Xiujun Gong, Kensuke Nakamura, Kei Yura
Researchers in biology need to combine a growing number of computational tools and biological databases to carry out their analyses. To carry out the analysis effectively, proper knowledge for...
Genome Informatics 14: 589--590 (2003) 589 Novel Types of Two-Domain Multi-Copper Oxidases: (2008)
Possible Missing Links, Kensuke Nakamura, Takeshi Kawabata, Kei Yura, Nobuhiro Go
Introduction Metal ions bound to proteins exhibit various fundamental functions such as catalysis, electron transfer, oxigen transfer and signal transmission. Despite its importance, only a little of...
coliSNP database server mapping nsSNPs on protein structures (2008)
Kono, Hidetoshi, Yuasa, Tomo, Nishiue, Shinya, Yura, Kei
We have developed coliSNP, a database server (http://yayoi.kansai.jaea.go.jp/colisnp) that maps non-synonymous single nucleotide polymorphisms (nsSNPs) on the three-dimensional (3D) structure of...
Yura, Kei, Miyata, Yuki, Arikawa, Tomotsugu, Higuchi, Masanobu, Sugita, Mamoru
RNA editing in land plant organelles is a process primarily involving the conversion of cytidine to uridine in pre-mRNAs. The process is required for gene expression in plant organelles, because this...
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...
Kim, Oanh T. P., Yura, Kei, Go, Nobuhiro
Protein–RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number...
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...
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...
Kim, Oanh T. P., Yura, Kei, Go, Nobuhiro
Protein–RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number...
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...
Highly Divergent Actins from Karyorelictean, Heterotrich, and Litostome Ciliates1 (2004)
KEI YURA, NOBUHIRO GO, TERUE HARUMOTO
We have cloned, sequenced, and characterized cDNA of actins from five ciliate species of three different classes of the phylum Ciliophora: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma...
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species (2003)
Yamaguchi, Akihiro, Iwadate, Mitsuo, Suzuki, Ei-ichiro, Yura, Kei, Kawakita, Shigetsugu, Umeyama, Hideaki, ...
Enlarged FAMSBASE is a relational database of comparative protein structure models for the whole genome of 41 species, presented in the GTOP database. The models are calculated by Full Automatic...
Yoshihara, Shizue, Geng, Xiao Xing, Okamoto, Shinobu, Yura, Kei, Murata, Takashi, Go, Mitiko, ...
The relevance of pilus-related genes to motility, pilus structure on the cell surface and competency of natural transformation was studied by gene disruption analysis in the unicellular motile...
Kaneko, Satoshi, Iwamatsu, Shinnosuke, Kuno, Atsushi, Fujimoto, Zui, Sato, Yoko, Yura, Kei, ...
To facilitate an understanding of structure–function relationships, chimeric xylanases were constructed by module shuffling between the catalytic domains of the FXYN from Streptomyces...
Putative Mechanism of Natural Transformation as Deduced from Genome Data (1999)
Yura, Kei, Toh, Hiroyuki, Go, Mitiko
Genetic transformation is widely utilized in molecular biology as a tool for gene cloning in Escherichia coli and for gene mapping in Bacillus subtilis. Several strains of eubacteria can naturally...
Repeat of a helix-turn-helix module in DNA-binding proteins (1993)
Yura, Kei, Tomoda, Shirou, Go, Mitiko
helix–turn–helix motif is one of the common motifs observed in DNA-binding proteins. The motif interacts with DNA double helix and recognizes specific base sequences. It is assumed that the...
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species
Yamaguchi, Akihiro, Iwadate, Mitsuo, Suzuki, Ei-ichiro, Yura, Kei, Kawakita, Shigetsugu, Umeyama, Hideaki, ...
Enlarged FAMSBASE is a relational database of comparative protein structure models for the whole genome of 41 species, presented in the GTOP database. The models are calculated by Full Automatic...
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...
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...
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species
Yamaguchi, Akihiro, Iwadate, Mitsuo, Suzuki, Ei-ichiro, Yura, Kei, Kawakita, Shigetsugu, Umeyama, Hideaki, ...
Enlarged FAMSBASE is a relational database of comparative protein structure models for the whole genome of 41 species, presented in the GTOP database. The models are calculated by Full Automatic...
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...
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...
Yura, Kei, Yamaguchi, Akihiro, Go, Mitiko
We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/),...
Kim, Oanh T. P., Yura, Kei, Go, Nobuhiro
Protein–RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number...
coliSNP database server mapping nsSNPs on protein structures
Kono, Hidetoshi, Yuasa, Tomo, Nishiue, Shinya, Yura, Kei
We have developed coliSNP, a database server (http://yayoi.kansai.jaea.go.jp/colisnp) that maps non-synonymous single nucleotide polymorphisms (nsSNPs) on the three-dimensional (3D) structure of...
Miyazawa, Yuji, Nishioka, Hirotaka, Yura, Kei, Yamato, Takahisa
DNA photolyase recognizes ultraviolet-damaged DNA and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer by a light-activated electron transfer reaction between the...
Yura, Kei, Miyata, Yuki, Arikawa, Tomotsugu, Higuchi, Masanobu, Sugita, Mamoru
RNA editing in land plant organelles is a process primarily involving the conversion of cytidine to uridine in pre-mRNAs. The process is required for gene expression in plant organelles, because this...
Matsumoto, Atsushi, Kamata, Tetsuji, Takagi, Junichi, Iwasaki, Kenji, Yura, Kei
Integrin, a membrane protein with a huge extracellular domain, participates in cell-cell and cell-extracellular-matrix interactions for metazoan. A group of integrins is known to perform a...
Yura, Kei, Sulaiman, Sintawee, Hatta, Yosuke, Shionyu, Masafumi, Go, Mitiko
Transcripts from mitochondrial and chloroplast DNA of land plants often undergo cytidine to uridine conversion-type RNA editing events. RESOPS is a newly built database that specializes in displaying...
Motivation: Structural features at protein–protein interfaces can be studied to understand protein–protein interactions. It was noticed that in a dataset of 45 multimeric proteins the interface...