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...
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...
Genome Informatics 14: 569--570 (2003) 569 Real-Time Mapping System of cDNAs and Genomes (2004)
Yusuke Saito, Manabu Gomi, Hideo Matsuda, Ken Kurokawa, Teruo Yasunaga
Introduction 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....
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...
An Application of a Pathway Alignment Method to the Analysis of Amino Acid Biosynthesis (2001)
Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto
Introduction Metabolic pathway is a network ofenzym( which are coded by genes. It has im ortantinformfi([[ ingenom analysis. In this study, we introduce am[:F d for thecom]7[9( e analysis ofmv(9 olic...
Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto
Syntax Notation One (ASN.1), SGML, and the eXtensible Markup Language (XML) 23) . Among these languages, ASN.1 has been used as an alternative to the flat file in GenBank. ASN.1 is a powerful...
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...
A Method for Querying Complete Genomes by Viewing Them as Structured Documents (1998)
Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto
Introduction Recently, database tools for manipulating structured documents have attracted much attention. The application of database technology to querying structured documents makes it possible to...
ORF Clustering Analysis of 17 Complete Genomes (1998)
Takeshi Ara, Hideo Matsuda, Hirotada Mori
Introduction With thanks to the rapid improvement of sequencing technique, many micro organisms have been revealed the entire structure of their genomes. At present, the complete genome sequences of...
ORF Clustering Analysis of 17 Complete Genomes (1998)
Takeshi Ara, Hideo Matsuda, Hirotada Mori
Introduction With thanks to the rapid improvement of sequencing technique, many micro organisms have been revealed the entire structure of their genomes. At present, the complete genome sequences of...
Automatic Detection of Gene Clusters by P-Quasi Complete Linkage Grouping (1998)
Wataru Fujibuchi, Hiroyuki Ogata, Hideo Matsuda, Minoru Kanehisa
Introduction It is known that bacteria genomes are highly organized to express functions cooperatively, for instance, by operons or by locating related genes adjacently on the genome for the...
A Sample LaTeX Format for the Ninth Workshop on Genome Informatics (1998)
Ayumi Shinohara, Hideo Matsuda, Satoru Miyano
This is the abstract of a sample paper for the 8th Workshop on Genome Informatics. The workshop is intended to provide a forum for researchers working in interdisciplinary areas between biological...
Overview of the JUMP-1, an MPP Prototype for General-Purpose Parallel Computations (1995)
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...
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...