OReFiL: an online resource finder for life sciences (2007)
Yamamoto, Yasunori, Takagi, Toshihisa
Abstract Background Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis...
Satoko Yamamoto, Takao Asanuma, Toshihisa Takagi, Ken Ichiro Fukuda
In general, it is not easy to specify a single sequence identity for each molecule name that appears in a pathway in the scientific literature. A molecule name may stand for concepts of various...
Shinsuke Dohkan, Asako Koike, Toshihisa Takagi
Introduction Protein-protein interactions play a crucial role in cellular processes. Although these interactions should be determined by stringent experiments and succeeded assays, these steps are...
Genome Informatics 14: 500--501 (2003) Prediction of Protein Interaction Sites and (2004)
Introduction Proteins perform a biological function by interacting with other proteins, compounds, RNA, and DNA. Understanding the characteristics of interfacial sites is necessary to understand the...
Takayuki Takahata, Yasuhiro Kouchi, Kaoru Asano, Toshihisa Takagi
Introduction and Background Databases such as MEDLINE, OMIM, RefSeq and LocusLink serve as important information sources for biomedical studies. A search of several databases can yield vast...
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)...
INOH: A Textual Knowledge Based Pathway Database (2004)
Satoko Yamamoto, Tatsuya Kushida, Naotaka Ono, Toshihisa Takagi, Ken-ichiro Fukuda
molecule functions required for biological processes over multiple species can be annotated by the sig-family ontology. By grouping smaller sub-processes, e.g. enzyme reactions into a larger STP...
Evaluation System for Information Retrieval in Biomedical Field (2004)
Yasunori Yamamoto, Toshihisa Takagi
Introduction Information Retrieval (IR) technology has grown rapidly accompanied by the development of the advanced computational power. More information is being stored as electro-magnetic forms,...
An Algorithm to Identify Abbreviations from MEDLINE (2004)
Introduction With the rapid growth of machine-readable literature, such like MEDLINE database, new abbreviations are increasing. They make it di#cult for researchers to follow the enormous size of...
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...
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...
A Transcription Regulatory Region Analysis System (2001)
Katsuhiko Murakami, Yohinori Ohta, Koji Tanikawa, Hiroki Nakae, Shigeo Ihara, Toshihisa Takagi
Introduction Despite the enormous growthof genomic sequence data, computational analysisof regulatory sequences remains a relatively marginal domain. Pol II Promoter prediction programs were assessed...
SIGNAL-ONTOLOGY: Ontology for Cell Signaling (2001)
Takako Takai-igarashi, Toshihisa Takagi
Introduction In t e poBF;hN#FF sequencing era, t emo# significant issue isreco;]hN#FFF[ o t ecoBB2[ living oivingh2 incoYYF]] standingo t egeno2 info2hN#B# o its po]F2Y2hN y. T usrecoYFhN#B#YB and...
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...
A System for Finding Association Rules from Microarray Data and Public Databases (2001)
Takahiro Naitou, Kenji Satou, Emiko Furuichi, Satoru Kuhara, Toshihisa Takagi
Introduction As the research trend of genome analysis changes from sequencing to gene expression and genetic network identification, microarray has attracted a great deal of attention. However, the...
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
Tatsuhiko Tsunoda, Masao Fukagawa, Toshihisa Takagi
Introduction It is quite common that the same sequence of characters appears at different positions in nucleic acids. First of all, let's classify such cases: (1) Direct repeats: simple repetitive...
Tomoko Okazaki-ohta, Toshihisa Takagi
Introduction In connection with the development of the molecular biology in recentyears, the amount of information in genome area has been growing rapidly. Although many data about biomolecular...
Kenichiro Fukuda, Mikio Yoshida, Toshihisa Takagi
Introduction To understand the phenomena of life, we need to grasp all events that occur in the life of a living cell, and then describe and comprehend the cell as a system. To that end, all proteins...
Clustering and Detection of 5' Splice Sites of mRNA by (1998)
Katsuhiko Murakami, Toshihisa Takagi
Introduction Biological signals on DNA sequences such as TATA box, GC box, CAAT box, the Shine-Dalgarno sequence in the promoter regions, and splice sites (donor/acceptor sites) in eukaryotic mRNA...
Mikio Yoshida, Kenichiro Fukuda, Toshihisa Takagi
Introduction Integration of knowledge described in a huge number of biomedical papers is a very important subject in the genome informatics area [1, 2]. Therefore, we need an intelligent information...
Kenichiro Fukuda, Mikio Yoshida, Toshihisa Takagi
Introduction To understand the phenomena of life, we need to grasp all events that occur in the life of a living cell, and then describe and comprehend the cell as a system. To that end, all proteins...
Correlation between Exons and Dispersed Repetitive DNA Distribution on the Human Genome (1998)
Yoshiaki Hojo, Ikuo Uchiyama, Yataro Daigo, Toshihisa Takagi
Introduction The human nuclear genome contains a large number of highly repeated DNA sequences. The Alu sequences are primate specific and are the most abundant family of repeated DNA sequences in...
Clustering and Detection of 5' Splice Sites of mRNA by k Weight Matrix Model (1998)
Katsuhiko Murakami, Toshihisa Takagi
Introduction Biological signals on DNA sequences such as TATA box, GC box, CAAT box, the Shine-Dalgarno sequence in the promoter regions, and splice sites (donor/acceptor sites) in eukaryotic mRNA...
Mikio Yoshida, Kenichiro Fukuda, Toshihisa Takagi
Introduction Integration of knowledge described in a huge number of biomedical papers is a very important subject in the genome informatics area [1, 2]. Therefore, we need an intelligent information...
Tomoko Okazaki-ohta, Toshihisa Takagi
Introduction In connection with the development of the molecular biology in recent years, the amount of information in genome area has been growing rapidly. Although many data about biomolecular...
Tatsuhiko Tsunoda, Masao Fukagawa, Toshihisa Takagi
Introduction It is quite common that the same sequence of characters appears at different positions in nucleic acids. First of all, let's classify such cases: (1) Direct repeats: simple repetitive...
Gene Recognition Using Multiple Gene-Finding Programs (1997)
Katsuhiko Murakami, Toshihisa Takagi
This paper demonstrates how effective re-analysis of the results of multiple gene-finding programs is. Four simple algorithms to integrate the results of some programs are proposed and tested. Our...
Similar Structure Search in a Deductive Database (1997)
Kenji Satou, Emiko Furuichi, Toshihisa Takagi, Satoru Kuhara, Kazuo Ushijima
We developed a deductive database system PACADE (Protein Coordinate Analyzer with Deductive Engine) for analyzing three dimensional and secondary structures of protein. This system has an inference...
Searches for Topologically and Three Dimensionally (1997)
Kenji Satou, Emiko Furuichi, Satoru Kuhara, Toshihisa Takagi
We developed a deductive database system PACADE for analyzing three dimensional and secondary structures of protein. PACADE is equipped with a function to search for similar structures in proteins....
Katsuhiko Murakami, Toshihisa Takagi
We have developed a coding region prediction system. It is constructed from several measures that indicate exonness of a region in DNA sequence. The system includes a new statistical measure called...
Mining Association Rules from Signals found in Mammalian Promoter Sequences (1997)
Gen Shibayama, Kenji Satou, Toshihisa Takagi
To find associations among large amount of genome data, we implemented a data mining algorithm developed by Houtsma et al. As the result of a computer experiment about signals found in mammalian...
Evaluation of exon prediction tools using a long DNA sequence data (1997)
Katsuhiko Murakami, Shiho Tsukuni, Toshihisa Takagi, Masahira Hattori
We have evaluated the ability to locate coding regions of two exon prediction software, GRAIL and FEX, using a long (about 301k bases) genomic DNA sequence. We performed an experiment to check the...
Katsuhiko Murakami, Toshihisa Takagi
We have developed a coding region prediction system. It is constructed from several measures that indicate exonness of a region in DNA sequence. The system includes a new statistical measure called...
Evaluation of exon prediction tools using a long DNA sequence data (1995)
Katsuhiko Murakami, Shiho Tsukuni, Toshihisa Takagi, Masahira Hattori
We have evaluated the ability to locate coding regions of two exon prediction software, GRAIL and FEX, using a long (about 301k bases) genomic DNA sequence. We performed an experiment to check the...
Mining Association Rules from Signals found in Mammalian Promoter Sequences (1995)
Gen Shibayama, Kenji Satou, Toshihisa Takagi
To find associations among large amount of genome data, we implemented a data mining algorithm developed by Houtsma et al. As the result of a computer experiment about signals found in mammalian...
Mining Association Rules from Signals found in Mammalian Promoter Sequences (1995)
Gen Shibayama, Kenji Satou, Toshihisa Takagi
To find associations among large amount of genome data, we implemented a data mining algorithm developed by Houtsma et al. As the result of a computer experiment about signals found in mammalian...
Mining Association Rules from Signals found in Mammalian Promoter Sequences (1995)
Gen Shibayama, Kenji Satou, Toshihisa Takagi
To find associations among large amount of genome data, we implemented a data mining algorithm developed by Houtsma et al. As the result of a computer experiment about signals found in mammalian...
Evaluation of exon prediction tools using a long DNA sequence data (1995)
Katsuhiko Murakami, Shiho Tsukuni, Toshihisa Takagi, Masahira Hattori
We have evaluated the ability to locate coding regions of two exon prediction software, GRAIL and FEX, using a long (about 301k bases) genomic DNA sequence. We performed an experiment to check the...
Evaluation of exon prediction tools using a long DNA sequence data (1995)
Katsuhiko Murakami, Shiho Tsukuni, Toshihisa Takagi, Masahira Hattori
We have evaluated the ability to locate coding regions of two exon prediction software, GRAIL and FEX, using a long (about 301k bases) genomic DNA sequence. We performed an experiment to check the...
Extension of the Integrated Database "HyperGenome" for Genome Maps and Sequence Information (1995)
Satoru Kuhara, Toshihisa Takagi, Minoru Kanehisa
Introduction The Human Genome Project is rapidly accumulating various kinds of data on the genome. Databases were developed in order to organize data obtained during experiments (GenBank, EMBL, DDBJ,...
JSNP: a database of common gene variations in the Japanese population
Hirakawa, Mika, Tanaka, Toshihiro, Hashimoto, Yoichi, Kuroda, Masako, Takagi, Toshihisa, Nakamura, Yusuke
JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister’s Millennium Project. The aim of this undertaking is to identify...
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...
Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource
Koike, Asako, Kobayashi, Yoshiyuki, Takagi, Toshihisa
Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism...
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...
Paroxysmal Kinesigenic Choreoathetosis Locus Maps to Chromosome 16p11.2-q12.1
Tomita, Hiro-aki, Nagamitsu, Shinichiro, Wakui, Keiko, Fukushima, Yoshimitsu, Yamada, Koki, Sadamatsu, Miyuki, ...
Paroxysmal kinesigenic choreoathetosis (PKC), the most frequently described type of paroxysmal dyskinesia, is characterized by recurrent, brief attacks of involuntary movements induced by sudden...
ALICE: An Algorithm to Extract Abbreviations from MEDLINE
Objective: To help biomedical researchers recognize dynamically introduced abbreviations in biomedical literature, such as gene and protein names, we have constructed a support system called ALICE...
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
Noguchi, Hideki, Park, Jungho, Takagi, Toshihisa
Exhaustive gene identification is a fundamental goal in all metagenomics projects. However, most metagenomic sequences are unassembled anonymous fragments, and conventional gene-finding methods...
JSNP: a database of common gene variations in the Japanese population
Hirakawa, Mika, Tanaka, Toshihiro, Hashimoto, Yoichi, Kuroda, Masako, Takagi, Toshihisa, Nakamura, Yusuke
JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister’s Millennium Project. The aim of this undertaking is to identify...
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...
Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource
Koike, Asako, Kobayashi, Yoshiyuki, Takagi, Toshihisa
Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism...
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...
ALICE: An Algorithm to Extract Abbreviations from MEDLINE
Objective: To help biomedical researchers recognize dynamically introduced abbreviations in biomedical literature, such as gene and protein names, we have constructed a support system called ALICE...
Paroxysmal Kinesigenic Choreoathetosis Locus Maps to Chromosome 16p11.2-q12.1
Tomita, Hiro-aki, Nagamitsu, Shinichiro, Wakui, Keiko, Fukushima, Yoshimitsu, Yamada, Koki, Sadamatsu, Miyuki, ...
Paroxysmal kinesigenic choreoathetosis (PKC), the most frequently described type of paroxysmal dyskinesia, is characterized by recurrent, brief attacks of involuntary movements induced by sudden...
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
Noguchi, Hideki, Park, Jungho, Takagi, Toshihisa
Exhaustive gene identification is a fundamental goal in all metagenomics projects. However, most metagenomic sequences are unassembled anonymous fragments, and conventional gene-finding methods...
Yamamoto, Satoko, Asanuma, Takao, Takagi, Toshihisa, Fukuda, Ken Ichiro
In general, it is not easy to specify a single sequence identity for each molecule name that appears in a pathway in the scientific literature. A molecule name may stand for concepts of various...