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...
β-Globin Gene Cluster Haplotype Frequencies in Khalkhs and Buryats of Mongolia (2007)
Shimizu, Koji., Tokimasa, Kozue., Takeuchi, Yukiko., Gereksaikhan, Tudevdagva., Omoto, Keiichi., ...
Human Biology - Volume 78, Number 6, December 2006
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
Kawahara, Yoshihiro, Imanishi, Tadashi
Abstract Background Changes in protein evolutionary rates among lineages have been frequently observed during periods of notable phenotypic evolution. It is also known that, following gene...
β-Globin Gene Cluster Haplotype Frequencies in Khalkhs and Buryats of Mongolia (2006)
Koji Shimizu, Kozue Tokimasa, Yukiko Takeuchi, Tudevdagva Gereksaikhan, Yuichi Tanabe, Keiichi Omoto, ...
β-globin gene cluster haplotype frequencies of 169 Khalkhs and 145 Buryats were estimated, and their characteristics were compared with those of Evenkis, Oroqens, Koreans, Japanese, and three...
Characteristic [Beta]-Globin Gene Cluster Haplotypes of Evenkis and Oroqens in North China (2005)
Shimizu, Koji., Marubayashi, Azusa., Tokimasa, Kozue., Harihara, Shinji., Imanishi, Tadashi., ...
Human Biology - Volume 76, Number 5, October 2004
Genome Informatics 14: 452--453 (2003) Detection of Processed Pseudogenes Based on cDNA (2004)
Human Genome, Hiroaki Sakai, Kanako O. Koyanagi, Takeshi Itoh, Tadashi Imanishi, Takashi Gojobori
Introduction Processed pseudogenes are defined as those obtained by reverse transcription of messenger RNAs followed by reintegration into genomic DNA and subsequent degradation with disablements...
Genome Informatics 14: 454--455 (2003) Improvement in the Accuracy of Gene Prediction in (2004)
Fusano Todokoro, Takeshi Itoh, Chisato Yamasaki, Hiroaki Kawashima, Tadashi Imanishi, Takashi Gojobori
Introduction GeneMark is a gene prediction program which has been designed to predict prokaryotic genes [2]. In addition the program may be used to search for eukaryotic genes in cDNA sequences and...
Genome Informatics 14: 583--584 (2003) 583 TTOP : A System for Phylogenetic Tree Editing and (2004)
Srinesh Kundu, Masato Hagiwara, Kanako O. Koyanagi, Tadashi Imanishi, Takeshi Itoh
Introduction We have developed a tool called TTOP (stand for "Tree Topology Operation Tool"). TTOP has applications both in phylogenetic tree editing and in the annotation of the evolutionary...
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...
Integrative annotation of 21,037 human genes validated by full-length cDNA clones (2004)
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O., ...
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the...
Estimating the Number of Mouse Genes and the Duplicated Regions within the Mouse Genome (2001)
Yasuhiko Wada, Tadashi Imanishi, Takashi Gojobori
Introduction To elucidate the evolution of mammalian genomes, it is crucial to estimate the number of genes in the genome and to measure the degree of redundancy in the genome in various species. The...
Anzai, Tatsuya, Shiina, Takashi, Kimura, Natsuki, Yanagiya, Kazuyo, Kohara, Sakae, Shigenari, Atsuko, ...
Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (≈6 million years ago), the molecular basis of traits unique to humans vs. their...
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...
Novel algorithm for automated genotyping of microsatellites
Matsumoto, Toshiko, Yukawa, Wataru, Nozaki, Yasuyuki, Nakashige, Ryo, Shinya, Minori, Makino, Satoshi, ...
Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits....
Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, ...
The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein...
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information
Ohyanagi, Hajime, Tanaka, Tsuyoshi, Sakai, Hiroaki, Shigemoto, Yasumasa, Yamaguchi, Kaori, Habara, Takuya, ...
With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice...
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
Yamasaki, Chisato, Kawashima, Hiroaki, Todokoro, Fusano, Imamizu, Yasuhiro, Ogawa, Makoto, Tanino, Motohiko, ...
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity...
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...
Anzai, Tatsuya, Shiina, Takashi, Kimura, Natsuki, Yanagiya, Kazuyo, Kohara, Sakae, Shigenari, Atsuko, ...
Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (≈6 million years ago), the molecular basis of traits unique to humans vs. their...
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...
Novel algorithm for automated genotyping of microsatellites
Matsumoto, Toshiko, Yukawa, Wataru, Nozaki, Yasuyuki, Nakashige, Ryo, Shinya, Minori, Makino, Satoshi, ...
Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits....
Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, ...
The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein...
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information
Ohyanagi, Hajime, Tanaka, Tsuyoshi, Sakai, Hiroaki, Shigemoto, Yasumasa, Yamaguchi, Kaori, Habara, Takuya, ...
With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice...
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
Yamasaki, Chisato, Kawashima, Hiroaki, Todokoro, Fusano, Imamizu, Yasuhiro, Ogawa, Makoto, Tanino, Motohiko, ...
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity...
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, Kuroda, Tsuyoshi, Sugano, Sumio, Gojobori, Takashi, ...
The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a specialized database of alternatively spliced human transcripts. In this database, each of the alternative splicing (AS)...
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
Matsuya, Akihiro, Sakate, Ryuichi, Kawahara, Yoshihiro, Koyanagi, Kanako O., Sato, Yoshiharu, Fujii, Yasuyuki, ...
Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology...