Chiba, Hirokazu, Yamashita, Riu, Kinoshita, Kengo, Nakai, Kenta
Abstract Background Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein...
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...
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species (2005)
Yuko Makita, Kenta Nakai, Satoru Miyano
In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a...
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species (2005)
Michiel De Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano
In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a...
Finding Optimal Pairs of Patterns (2004)
Hideo Bannai, Heikki Hyyro, Masayuki Takeda, Kenta Nakai, Satoru Miyano
We consider the problem of finding the optimal pair of string patterns for discriminating between two sets of strings, i.e. finding the pair of patterns that is best with respect to some appropriate...
Finding Optimal Pairs of Cooperative and (2004)
Shunsuke Inenaga, Hideo Bannai, Heikki Hyyro, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, ...
We consider the problem of discovering the optimal pair of substring patterns with bounded distance #, from a given set S of strings.
Genome Informatics 14: 406--407 (2003) Extraction of Biological Motifs by Gibbs Sampler from (2004)
Natalia Poluliakh, Kenta Nakai
Introduction Microarray analysis provides us with new information about genes regulatory network, and many novel candidates of co-regulated genes are being identified. It is assumed that co-regulated...
Genome Informatics 14: 402--403 (2003) Phylogenetic Analysis of Eubacterial Transcriptional (2004)
Yuko Makita, Naotake Ogasawara, Kenta Nakai
this report, we expand such an analysis into a systematic survey of the conservation of known cis-elements, as well as their binding factors, through available eubacterial genome sequences. This...
Genome Informatics 14: 404--405 (2003) Genome Wide Analysis Reveals Strong Correlation (2004)
Riu Yamashita, Toshihisa Takagi, Sumio Sugano, Kenta Nakai
Introduction Vertebrate genomes contain GC-rich or poor compartments, called isochores, It has been reported that heavy isochores (GC-rich) contain housekeeping genes while light ischores (GC-rich)...
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...
Genome informatics for data-driven biology (2002)
Nakai, Kenta, Vert, Jean-Philippe
A report on the 12th International Conference on Genome Informatics, Tokyo, Japan, 17-19 December 2001.
Terai, Goro, Takagi, Toshihisa, Nakai, Kenta
Abstract Background Identification of co-regulated genes is essential for elucidating transcriptional regulatory networks and the function of uncharacterized genes. Although co-regulated genes should...
Sequence Analysis of Less Hydrophobic Transmembrane Segments in Polytopic Membrane Proteins (2001)
Hiromitsu Araki, Toshihisa Takagi, Kenta Nakai, Human Geang
Introduction To undeG)/Nq the function of me brane prote];G the knowleN/ oftheF structure et etruct the knowleqfi ofthe position oftransme brane sene ts (TMSs) and oftheF me brane topology (i.eG orie...
Characterization of Subcellular Localization Signals Using (2001)
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano, Human Gean
Introduction Proteon are first synthefiOPP inthe cytosol and the carrie to spe1q[fi locations ofthe ce# The information whichde(].1zq# whe( the prote.1 are carrie is beq#P e to be e(. de inthe amino...
Goro Terai, Takeshi Mizuno, Kenta Nakai, Toshihisa Takagi, Intec Web, Genome Informatics Corp, ...
this paper, we describe the method and discussions on evaluation results follows
Views: Fundamental Building Blocks in the Process of Knowledge Discovery (2001)
Hideo Bannai, Osamu Maruyama, Yoshinori Tamada, Kenta Nakai, Satoru Miyano
We present a novel approach to describe the knowledge discovery process, focusing on a generalized form of attribute called view. It is observed that the process of knowledge discovery can, in fact,...
We have compared four classifiers on the problem of predicting the cellular localization sites of proteins in yeast and E.coli. A set of sequence derived features, such as regions of high...
Introduction Although the number of bacteria with their entire genomic sequence known is increasing, it is essential to study well-known genomes for understanding the 'blueprint` of bacteria more...
Modeling Transcriptional Units of (1998)
Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Takahiro Ishii, Kenta Nakai
Introduction In recentyears, the number of bacteria whose entire genomic sequence is determined is growing rapidly. However, the information which can be derived from computer analyses of them is...
Modeling Transcriptional Units of (1998)
Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Takahiro Ishii, Kenta Nakai
Introduction In recent years, the number of bacteria whose entire genomic sequence is determined is growing rapidly. However, the information which can be derived from computer analyses of them is...
Introduction Although the number of bacteria with their entire genomic sequence known is increasing, it is essential to study well-known genomes for understanding the 'blueprint` of bacteria more...
We have defined a simple model of classification which combines human provided expert knowledge with probabilistic reasoning. We have developed software to implement this model and have applied it to...
We have proposed that the prediction of protein subcellular localization sites can provide a good clue for the characterization of open reading frames of unknown function [1, 2]. Our program, PSORT,...
We have proposed that the prediction of protein subcellular localization sites can provide a good clue for the characterization of open reading frames of unknown function [1, 2]. Our program, PSORT,...
We have proposed that the prediction of protein subcellular localization sites can provide a good clue for the characterization of open reading frames of unknown function [1, 2]. Our program, PSORT,...
How reliable and useful are predictions of transmembrane segments(TMSs) of membrane proteins from the amino acid sequences? It remains still under debate. Kyte and Doolittle proposed a simple scheme...
DBTBS: a database of Bacillus subtilis promoters and transcription factors
Ishii, Takahiro, Yoshida, Ken-ichi, Terai, Goro, Fujita, Yasutaro, Nakai, Kenta
With the completion of the determination of its entire genome sequence, one of the next major targets of Bacillus subtilis genomics is to clarify the whole gene regulatory network. To this end, the...
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
Suzuki, Yutaka, Yamashita, Riu, Nakai, Kenta, Sugano, Sumio
Although the information of cDNAs is indispensable for analyzing gene function, most of the cDNA sequences stored in current databases are imperfect in the sense that they lack the precise...
Hagiwara, Kyoji, Tomita, Masahiro, Nakai, Kenta, Kobayashi, Jun, Miyajima, Shigetoshi, Yoshimura, Tetsuro
Cloning and sequencing of segment 9 of Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) strains H and I were performed. The segment consisted of 1,186 bp harboring 5′ and 3′ noncoding regions...
Genome informatics for data-driven biology
Nakai, Kenta, Vert, Jean-Philippe
A report on the 12th International Conference on Genome Informatics, Tokyo, Japan, 17-19 December 2001.
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria
Gardy, Jennifer L., Spencer, Cory, Wang, Ke, Ester, Martin, Tusnády, Gábor E., Simon, István, ...
Automated prediction of bacterial protein subcellular localization is an important tool for genome annotation and drug discovery. PSORT has been one of the most widely used computational methods for...
Makita, Yuko, Nakao, Mitsuteru, Ogasawara, Naotake, Nakai, Kenta
DBTBS (http://dbtbs.hgc.jp) was originally released in 1999 as a reference database of published transcriptional regulation events in Bacillus subtilis, one of the best studied bacteria. It is...
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
Suzuki, Yutaka, Yamashita, Riu, Sugano, Sumio, Nakai, Kenta
DBTSS (http://dbtss.hgc.jp) was originally constructed based on a collection of experimentally determined TSSs of human genes. Since its first release in 2002, it has been updated several times....
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...
Suzuki, Yutaka, Yamashita, Riu, Shirota, Matsuyuki, Sakakibara, Yuta, Chiba, Joe, Mizushima-Sugano, Junko, ...
Comparative sequence analysis was carried out for the regions adjacent to experimentally validated transcriptional start sites (TSSs), using 3324 pairs of human and mouse genes. We aligned the...
Kato, Kikuya, Yamashita, Riu, Matoba, Ryo, Monden, Morito, Noguchi, Shinzaburo, Takagi, Toshihisa, ...
Gene expression profiling of cancer tissues is expected to contribute to our understanding of cancer biology as well as developments of new methods of diagnosis and therapy. Our collaborative efforts...
Nakao, Mitsuteru, Barrero, Roberto A., Mukai, Yuri, Motono, Chie, Suwa, Makiko, Nakai, Kenta
We investigated human alternative protein isoforms of >2600 genes based on full-length cDNA clones and SwissProt. We classified the isoforms and examined their co-occurrence for each gene. Further,...
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species
Makita, Yuko, Nakai, Kenta, Miyano, Satoru
In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a...
DBTGR: a database of tunicate promoters and their regulatory elements
Sierro, Nicolas, Kusakabe, Takehiro, Park, Keun-Joon, Yamashita, Riu, Kinoshita, Kengo, Nakai, Kenta
The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and...
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
Yamashita, Riu, Suzuki, Yutaka, Wakaguri, Hiroyuki, Tsuritani, Katsuki, Nakai, Kenta, Sugano, Sumio
DBTSS was first constructed in 2002 based on precise, experimentally determined 5′ end clones. Several major updates and additions have been made since the last report. First, the number of human...
Kimura, Kouichi, Wakamatsu, Ai, Suzuki, Yutaka, Ota, Toshio, Nishikawa, Tetsuo, Yamashita, Riu, ...
By analyzing 1,780,295 5′-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites...
DBTBS: a database of Bacillus subtilis promoters and transcription factors
Ishii, Takahiro, Yoshida, Ken-ichi, Terai, Goro, Fujita, Yasutaro, Nakai, Kenta
With the completion of the determination of its entire genome sequence, one of the next major targets of Bacillus subtilis genomics is to clarify the whole gene regulatory network. To this end, the...
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
Suzuki, Yutaka, Yamashita, Riu, Nakai, Kenta, Sugano, Sumio
Although the information of cDNAs is indispensable for analyzing gene function, most of the cDNA sequences stored in current databases are imperfect in the sense that they lack the precise...
Hagiwara, Kyoji, Tomita, Masahiro, Nakai, Kenta, Kobayashi, Jun, Miyajima, Shigetoshi, Yoshimura, Tetsuro
Cloning and sequencing of segment 9 of Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) strains H and I were performed. The segment consisted of 1,186 bp harboring 5′ and 3′ noncoding regions...
Genome informatics for data-driven biology
Nakai, Kenta, Vert, Jean-Philippe
A report on the 12th International Conference on Genome Informatics, Tokyo, Japan, 17-19 December 2001.
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria
Gardy, Jennifer L., Spencer, Cory, Wang, Ke, Ester, Martin, Tusnády, Gábor E., Simon, István, ...
Automated prediction of bacterial protein subcellular localization is an important tool for genome annotation and drug discovery. PSORT has been one of the most widely used computational methods for...
Makita, Yuko, Nakao, Mitsuteru, Ogasawara, Naotake, Nakai, Kenta
DBTBS (http://dbtbs.hgc.jp) was originally released in 1999 as a reference database of published transcriptional regulation events in Bacillus subtilis, one of the best studied bacteria. It is...
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
Suzuki, Yutaka, Yamashita, Riu, Sugano, Sumio, Nakai, Kenta
DBTSS (http://dbtss.hgc.jp) was originally constructed based on a collection of experimentally determined TSSs of human genes. Since its first release in 2002, it has been updated several times....
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...
Suzuki, Yutaka, Yamashita, Riu, Shirota, Matsuyuki, Sakakibara, Yuta, Chiba, Joe, Mizushima-Sugano, Junko, ...
Comparative sequence analysis was carried out for the regions adjacent to experimentally validated transcriptional start sites (TSSs), using 3324 pairs of human and mouse genes. We aligned the...
Kato, Kikuya, Yamashita, Riu, Matoba, Ryo, Monden, Morito, Noguchi, Shinzaburo, Takagi, Toshihisa, ...
Gene expression profiling of cancer tissues is expected to contribute to our understanding of cancer biology as well as developments of new methods of diagnosis and therapy. Our collaborative efforts...
Nakao, Mitsuteru, Barrero, Roberto A., Mukai, Yuri, Motono, Chie, Suwa, Makiko, Nakai, Kenta
We investigated human alternative protein isoforms of >2600 genes based on full-length cDNA clones and SwissProt. We classified the isoforms and examined their co-occurrence for each gene. Further,...
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species
Makita, Yuko, Nakai, Kenta, Miyano, Satoru
In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a...
DBTGR: a database of tunicate promoters and their regulatory elements
Sierro, Nicolas, Kusakabe, Takehiro, Park, Keun-Joon, Yamashita, Riu, Kinoshita, Kengo, Nakai, Kenta
The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and...
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
Yamashita, Riu, Suzuki, Yutaka, Wakaguri, Hiroyuki, Tsuritani, Katsuki, Nakai, Kenta, Sugano, Sumio
DBTSS was first constructed in 2002 based on precise, experimentally determined 5′ end clones. Several major updates and additions have been made since the last report. First, the number of human...
Kimura, Kouichi, Wakamatsu, Ai, Suzuki, Yutaka, Ota, Toshio, Nishikawa, Tetsuo, Yamashita, Riu, ...
By analyzing 1,780,295 5′-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites...
Obayashi, Takeshi, Kinoshita, Kengo, Nakai, Kenta, Shibaoka, Masayuki, Hayashi, Shinpei, Saeki, Motoshi, ...
Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory...
Okumura, Toshiyuki, Makiguchi, Hiroki, Makita, Yuko, Yamashita, Riu, Nakai, Kenta
We present the second version of Melina, a web-based tool for promoter analysis. Melina II shows potential DNA motifs in promoter regions with a combination of several available programs, Consensus,...
WoLF PSORT: protein localization predictor
Horton, Paul, Park, Keun-Joon, Obayashi, Takeshi, Fujita, Naoya, Harada, Hajime, Adams-Collier, C.J., ...
WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction. WoLF PSORT converts protein amino acid sequences into numerical localization features; based on sorting...
Tsuritani, Katsuki, Irie, Takuma, Yamashita, Riu, Sakakibara, Yuta, Wakaguri, Hiroyuki, Kanai, Akinori, ...
Although recent studies have revealed that the majority of human genes are subject to regulation of alternative promoters, the biological relevance of this phenomenon remains unclear. We have also...
DBTSS: database of transcription start sites, progress report 2008
Wakaguri, Hiroyuki, Yamashita, Riu, Suzuki, Yutaka, Sugano, Sumio, Nakai, Kenta
DBTSS is a database of transcriptional start sites, based on our unique collection of precise, experimentally determined 5′-end sequences of full-length cDNAs. Since its first release in 2002,...
Sierro, Nicolas, Makita, Yuko, De Hoon, Michiel, Nakai, Kenta
DBTBS, first released in 1999, is a reference database on transcriptional regulation in Bacillus subtilis, summarizing the experimentally characterized transcription factors, their recognition...