Naotaka Yamamoto, Futoshi Shimizu, Mitsuo Yokokawa, Satoshi Sekiguchi, Hideo Kaburaki, Motoyoshi Kurokawa, ...
Biogrid project is one of national R&D projects on grid in IT-Program granted by Ministry of Education, Culture, Sports, Science and Technology since 2002. In this project, we consider a grid...
Gendoo: Functional profiling of gene and disease features using MeSH vocabulary (2009)
Nakazato, Takeru, Bono, Hidemasa, Matsuda, Hideo, Takagi, Toshihisa
Genome-wide data enables us to clarify the underlying molecular mechanisms of complex phenotypes. The Online Mendelian Inheritance in Man (OMIM) is a widely employed knowledge base of human genes and...
genes modules module network (2008)
Kohei Taki, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda, Cln Cln, Cln Cln
We propose a novel method for an exhaustive inference of gene regulatory networks from genome-wide expression data and biological knowledge. Our method performs the inferences based on module network...
H: Heterogeneous Database Federation using Grid Technology for Drug Discovery Process (2008)
Yukako Tohsato, Takahiro Kosaka, Susumu Date, Shinji Shimojo, Hideo Matsuda
Abstract. The rapid progress of biotechnology provides an increasing number of life science databases. These databases have been operated and managed individually on the Internet. Under such a...
Genome Informatics 15(2): 3--12 (2004) 3 Architecture of a Grid-Enabled Research Platform (2008)
The recent advance in information technologies has bought about the borderlessness in every field of both science and business. The borderlessness has increasingly made activities in...
Overview of the JUMP-1, an MPP Prototype for General-Purpose Parallel Computations (2008)
Kei Hiraki, Hideharu Amano, Morihiro Kuga, Toshinori Sueyoshi, Tomohiro Kudoh, Hironori Nakajo, ...
this paper, we discuss the importance of flexible distributed shared memory in a MPP system for general-purpose computations. The main features of JUMP-1 memory system are: 1. Flexible...
Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto
yy Complete DNA sequences (complete genomes) for an increasing number of organisms are becoming available eachyear for use in biological research. However, genome project groups incorporate their own...
Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto
Metabolic pathway is a network of enzymes which are coded by genes. It has important information in genome analysis. In this study, we introduce a method for the comparative analysis of metabolic...
A Method for Querying Complete Genomes by Viewing Them as Structured Documents (2007)
Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto
Recently, database tools for manipulating structured documents have attracted much attention. The application of database technology to querying structured documents makes it possible to retrieve...
Real-Time Mapping System of cDNAs and Genomes Using Grid Computing (2007)
Yusuke Saito, Manabu Gomi, Hideo Matsuda, Naohisa Goto, Ken Kurokawa, Teruo Yasunaga
DataGrid group of BioGrid project [1], in which we are joining, is aiming to establish a methodology which enables to choose target proteins easily through the process of drug discovery. For that...
A Method for Similarity Search of Genomic Positional Expression Using CAGE (2006)
Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, ...
With the advancement of genome research, it is becoming clear that genes are not distributed on the genome in random order. Clusters of genes distributed at localized genome positions have been...
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...
A Method for Clustering Gene Expression Data Based on Graph Structure (2004)
Shigeto Seno, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda
Recently, gene expression data under various conditions have largely been obtained by the utilization of the DNA microarrays and oligonucleotide arrays. There have been emerging demands to analyze...
S.: A Challenge towards NextGeneration Research Infrastructure for Advanced Life (2004)
Haruki Nakamura, Susumu Date, Hideo Matsuda, Shinji Shimojo
Recently, life scientists have expressed a strong need for computational power sufficient to complete their analyses within a realistic time as well as for a computational power capable of seamlessly...
Graph-based clustering for finding distant relationships in a large set of protein sequences (2004)
Kawaji, Hideya, Takenaka, Yoichi, Matsuda, Hideo
Motivation: Clustering of protein sequences is widely used for the functional characterization of proteins. However, it is still not easy to cluster distantly-related proteins, which have only...
FREP: a database of functional repeats in mouse cDNAs (2004)
Nagashima, Takeshi, Matsuda, Hideo, Silva, Diego G., Petrovsky, Nikolai, GSL Members,, ...
The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker‐identified non‐redundant variant repeat sequences derived from 16 527 mouse cDNAs with...
Mapping of Artificial Nucleosome Positioning Sequences to the Saccharomyces cerevisiae Genome (2003)
Vorathaya Tantoolvesm, Yoichi Takenaka, Satoshi Harashima, Hideo Matsuda
Introduction Structures that consist of DNA wrapped around the histone octamer are known as nucleosomes, which are recognized as a fundamental unit of chromatin structure [1]. Besides playing an...
Mouse Proteome Analysis (2003)
Kanapin, Alexander, Batalov, Serge, Davis, Melissa J., Gough, Julian, Grimmond, Sean, Kawaji, Hideya, ...
A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein...
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System (2003)
Kasukawa, Takeya, Furuno, Masaaki, Nikaido, Itoshi, Bono, Hidemasa, Hume, David A., Bult, Carol, ...
Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed...
Hideya Kawaji, Christian Schönbach, Yo Matsuo, Jun Kawai, Yasushi Okazaki, Yoshihide Hayashizaki, ...
service
Exploration of Novel Motifs Derived from Mouse cDNA Sequences (2002)
Kawaji, Hideya, Schönbach, Christian, Matsuo, Yo, Kawai, Jun, Okazaki, Yasushi, Hayashizaki, Yoshihide, ...
Exploration of Novel Motifs Derived from Mouse cDNA Sequences (2002)
Kawaji, Hideya, Schönbach, Christian, Matsuo, Yo, Kawai, Jun, Okazaki, Yasushi, Hayashizaki, Yoshihide, ...
Hideya Kawaji, Yosuke Yamaguchi, Hideo Matsuda, Akihiro Hashimoto
A graph-based clustering method is proposed to cluster protein sequences into families, which automatically improves clusters of the conventional single linkage clustering method. Our approach...
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) (2001)
Noguchi, Tamotsu, Matsuda, Hideo, Akiyama, Yutaka
PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). The previous version of PDB-REPRDB provided 48 representative sets, whose similarity criteria were...
A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy (2000)
Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto
In many of the chemical reactions in living cells, enzymes act as catalysts in the conversion of certain compounds (substrates) into other compounds (products). Comparative analyses of the metabolic...
Quick selection of representative protein chain sets based on customizable requirements (2000)
Noguchi, Tamotsu, Onizuka, Kentaro, Ando, Makoto, Matsuda, Hideo, Akiyama, Yutaka
Motivation: Protein structure classification has been recognized as one of the most important research issues in protein structure analysis. A substantial number of methods for the classification...
Fujibuchi, Wataru, Ogata, Hiroyuki, Matsuda, Hideo, Kanehisa, Minoru
We previously reported two graph algorithms for analysis of genomic information: a graph comparison algorithm to detect locally similar regions called correlated clusters and an algorithm to find a...
Itoh, Takeshi, Matsuda, Hideo, Mori, Hirotada
Novel members of the highly conserved protein family, Hsp70, have been found in the complete sequences of several genomes. To elucidate a phylogenetic relationship among Hsp70 proteins of Escherichia...
Modelling reactive behaviour in vetically layered agent architectures (1998)
Shigeto Seno, Reiji Teramoto, Hideo Matsuda
In order to find the function of genes from geneexpression profiles, the hierarchical clustering has been used generally. But this method has problems, for example a dendrogram tends to change by...
Olsen, Gary J., Matsuda, Hideo, Hagstrom, Ray, Overbeek, Ross
We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix workstations to...
An integrated database to support research on escherichia coli (1992)
Ra Baehr, George Dunham, Adam Ginsburg, Ray Hagstrom, David Joerg, Toni Kazic, ...
by the Office of Energy Research, U.S. Department of Energy, under Contract W-31-109-Eng-38. 1
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)
Noguchi, Tamotsu, Matsuda, Hideo, Akiyama, Yutaka
PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). The previous version of PDB-REPRDB provided 48 representative sets, whose similarity criteria were...
Fujibuchi, Wataru, Ogata, Hiroyuki, Matsuda, Hideo, Kanehisa, Minoru
We previously reported two graph algorithms for analysis of genomic information: a graph comparison algorithm to detect locally similar regions called correlated clusters and an algorithm to find a...
FREP: a database of functional repeats in mouse cDNAs
Nagashima, Takeshi, Matsuda, Hideo, Silva, Diego G., Petrovsky, Nikolai, Konagaya, Akihiko, Schönbach, Christian
The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16 527 mouse cDNAs with protein-coding potential....
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...
Kanapin, Alexander, Batalov, Serge, Davis, Melissa J., Gough, Julian, Grimmond, Sean, Kawaji, Hideya, ...
A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein...
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
Kasukawa, Takeya, Furuno, Masaaki, Nikaido, Itoshi, Bono, Hidemasa, Hume, David A., Bult, Carol, ...
Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed...
Exploration of Novel Motifs Derived from Mouse cDNA Sequences
Kawaji, Hideya, Schönbach, Christian, Matsuo, Yo, Kawai, Jun, Okazaki, Yasushi, Hayashizaki, Yoshihide, ...
We performed a systematic maximum density subgraph (MDS) detection of conserved sequence regions to discover new, biologically relevant motifs from a set of 21,050 conceptually translated mouse cDNA...
A Method for Similarity Search of Genomic Positional Expression Using CAGE
Seno, Shigeto, Takenaka, Yoichi, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, ...
With the advancement of genome research, it is becoming clear that genes are not distributed on the genome in random order. Clusters of genes distributed at localized genome positions have been...
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)
Noguchi, Tamotsu, Matsuda, Hideo, Akiyama, Yutaka
PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). The previous version of PDB-REPRDB provided 48 representative sets, whose similarity criteria were...
Fujibuchi, Wataru, Ogata, Hiroyuki, Matsuda, Hideo, Kanehisa, Minoru
We previously reported two graph algorithms for analysis of genomic information: a graph comparison algorithm to detect locally similar regions called correlated clusters and an algorithm to find a...
Exploration of Novel Motifs Derived from Mouse cDNA Sequences
Kawaji, Hideya, Schönbach, Christian, Matsuo, Yo, Kawai, Jun, Okazaki, Yasushi, Hayashizaki, Yoshihide, ...
We performed a systematic maximum density subgraph (MDS) detection of conserved sequence regions to discover new, biologically relevant motifs from a set of 21,050 conceptually translated mouse cDNA...
FREP: a database of functional repeats in mouse cDNAs
Nagashima, Takeshi, Matsuda, Hideo, Silva, Diego G., Petrovsky, Nikolai, Konagaya, Akihiko, Schönbach, Christian
The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16 527 mouse cDNAs with protein-coding potential....
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...
Kanapin, Alexander, Batalov, Serge, Davis, Melissa J., Gough, Julian, Grimmond, Sean, Kawaji, Hideya, ...
A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein...
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
Kasukawa, Takeya, Furuno, Masaaki, Nikaido, Itoshi, Bono, Hidemasa, Hume, David A., Bult, Carol, ...
Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed...
A Method for Similarity Search of Genomic Positional Expression Using CAGE
Seno, Shigeto, Takenaka, Yoichi, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, ...
With the advancement of genome research, it is becoming clear that genes are not distributed on the genome in random order. Clusters of genes distributed at localized genome positions have been...
Gendoo: Functional profiling of gene and disease features using MeSH vocabulary
Nakazato, Takeru, Bono, Hidemasa, Matsuda, Hideo, Takagi, Toshihisa
Genome-wide data enables us to clarify the underlying molecular mechanisms of complex phenotypes. The Online Mendelian Inheritance in Man (OMIM) is a widely employed knowledge base of human genes and...