Suzaku Results on the Obscured Low-Luminosity Active Galactic Nucleus in NGC 4258 (2008)
Yamada, Shin'ya, Itoh, Takeshi, Makishima, Kazuo, Nakazawa, Kazuhiro
In 2006 June, the obscured low luminosity active galactic nucleus in the nearby Seyfert 1.9 galaxy NGC 4258 was observed with Suzaku for ~ 100 ks. Utilizing the XIS and the HXD, the nucleus emission...
TACT: Transcriptome Auto-Annotation Conducting Tool of H-InvDB (2008)
Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa, Motohiko Tanino, ...
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the
Genome Informatics 14: 454--455 (2003) Improvement in the Accuracy of Gene Prediction in (2008)
Human Cdna Sequences, Fusano Todokoro, Takeshi Itoh, Chisato Yamasaki, Hiroaki Kawashima
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...
Suzaku Results on Cygnus X-1 in the Low/Hard State (2008)
Makishima, Kazuo, Takahashi, Hiromitsu, Yamada, Shin'ya, Done, Chris, Kubota, Aya, Dotani, Tadayasu, ...
The black-hole binary Cygnus X-1 was observed for 17 ks with the Suzaku X-ray observatory in 2005 October, while it was in a low/hard state with a 0.7-300 keV luminosity of 4.6 x 10^37 erg/s. The XIS...
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...
Mihara, Motohiro, Itoh, Takeshi, Izawa, Takeshi
Microarray analysis of tiny amounts of RNA extracted from plant section samples prepared by laser microdissection (LM) can provide high-quality information on gene expression in specified plant cells...
Construction and analysis of Escherichia coli genome database (2007)
Takeshi Itoh, Minoru Yano, Keiko Takemoto, Yutaka Akiyama, Hirotada Mori
It is possible to elucidate whole genome structure by current technique. The genome projects of some species, C.elegans, Yeast, Escherichia coli, Bacillus subtilis, Arabidopsis, rice and human are...
TTOP: A System for Phylogenetic Tree Editing and Evolutionary Annotation of Genes (2007)
Srinesh Kundu, Masato Hagiwara, Kanako O. Koyanagi, Tadashi Imanishi, Takeshi Itoh
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 characteristics...
Discovery of a bright transient ultraluminous X-ray source Suzaku J1305-4931 in NGC 4945 (2007)
Isobe, Naoki, Kubota, Aya, Makishima, Kazuo, Gandhi, Poshak, Griffiths, Richard E., Dewangan, Gulab C., ...
This paper reports the discovery of a bright X-ray transient source, Suzaku J1305-4913, in the south-west arm of the nearby Seyfert II galaxy NGC 4945. It was detected at a 0.5 -- 10 keV flux of $2.2...
Suzaku wide-band X-ray Spectroscopy of the Seyfert 2 AGN in NGC 4945 (2007)
Itoh, Takeshi, Done, Chris, Makishima, Kazuo, Madejski, Grzegorz, Awaki, Hisamitsu, Isobe, Naoki, ...
Suzaku observed a nearby Seyfert 2 galaxy NGC4945, which hosts one of the brightest active galactic nuclei above 20 keV. Combining data from the X-ray CCD camera (XIS) and the Hard X-ray Detector...
Low/Hard State Spectra of GRO J1655-40 Observed with Suzaku (2007)
Takahashi, Hiromitsu, Fukazawa, Yasushi, Mizuno, Tsunefumi, Hirasawa, Ayumi, Kitamoto, Shunji, Sudoh, Keisuke, ...
The Galactic black-hole binary GRO J1655$-$40 was observed with Suzaku on 2005 September 22--23, for a net exposure of 35 ks with the X-ray Imaging Spectrometer (XIS) and 20 ks with the Hard X-ray...
Wide-band spectroscopy of the Compton thick Seyfert 2 galaxy Mrk 3 with Suzaku (2007)
Awaki, Hisamitsu, Anabuki, Naohisa, Fukazawa, Yasuchi, Gallo, Luigi, Ikeda, Shinya, Isobe, Naoki, ...
We obtained a wide-band spectrum of the Compton-thick Seyfert 2 galaxy Mrk 3 with Suzaku. The observed spectrum was clearly resolved into weak, soft power-law emission, a heavily absorbed power-law...
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...
Rate and Polarity of Gene Fusion and Fission in Oryza sativa and Arabidopsis thaliana (2007)
Nakamura, Yoji, Itoh, Takeshi, Martin, William
Eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryotes, and their quantitative contributions to genome evolution are still poorly understood. We have...
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...
Yaqoob, Tahir, Murphy, Kendrah D., Griffiths, Richard E., Haba, Yoshito, Inoue, Hajime, Itoh, Takeshi, ...
We present detailed time-averaged X-ray spectroscopy in the 0.5--10 keV band of the Seyfert~1.9 galaxy NGC 2992 with the Suzaku X-ray Imaging Spectrometers (XIS). We model the complex continuum in...
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB (2006)
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...
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...
Rate and Polarity of Gene Fusion and Fission in Oryza sativa and Arabidopsis thaliana (2006)
Nakamura, Yoji, Itoh, Takeshi, Martin, William
Eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryotes and their quantitative contributions to genome evolution are still poorly understood. We have...
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...
Detection of Processed Pseudogenes Based on cDNA Mapping to the Human Genome (2003)
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...
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...
Yamamoto, Yoshihiro, Aiba, Hiroji, Baba, Tomoya, Hayashi, Kouji, Inada, Toshifumi, Isono, Katumi, ...
Yamamoto, Yoshihiro, Aiba, Hiroji, Baba, Tomoya, Hayashi, Kouji, Inada, Toshifumi, Isono, Katumi, ...
The contiguous 874.423 base pair sequence corresponding to the 50.0–68.8 min region on the genetic map of the Escherichia coli K-12 (W3110) was constructed by the determination of DNA sequences in...
Aiba, Hiroji, Baba, Tomoya, Hayashi, Kouji, Inada, Toshifumi, Isono, Katumi, Itoh, Takeshi, ...
The 569,750 base pair sequence corresponding to the 28.0–40.1 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. This region includes the replication terminus region and...
Itoh, Takeshi, Aiba, Hiroji, Baba, Tomoya, Hayashi, Kouji, Inada, Toshifumi, Isono, Katumi, ...
The 465,813 base pair sequence corresponding to the 40.1–50.0 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. Analysis of the sequence revealed that this region...
Oshima, Taku, Aiba, Hiroji, Baba, Tomoya, Fujita, Katsutoshi, Hayashi, Kouji, Honjo, Atsuko, ...
The 718,122 base pair (bp) sequence of the Escherichia coli K-12 genome corresponding to the region from 12.7 to 28.0 minutes on the genetic map is described. This region contains at least 682...
Crystal Structure of RNase T1(Y45W) Complexed with 3' AMP and Gf1pA (1993)
Gohda, Keigo, Itoh, Takeshi, Hiramatsu, Yasuyuki, Tomita, Ken-ichi, Nishikawa, Satoshi, Uesugi, Sei-ichi, ...
We have previously reported the crystallization of a mutant RNase T1(Y46W) with a synthetic modified trinucleotide ApGflpA [Hakoshima, T. et al. (1990) J. Biochem 108, 695–698]. In the present...
Hakoshima, Toshio, Tanaka, Masahiro, Itoh, Takeshi, Tomita, Ken-khi, Amisaki, Takashi, Nishikawa, Satoshi, ...
Hydrophobic effects on binding of ribonuclease Tl to guanine bases of several ribonucleotides have been proved by mutating a hydrophobic residue at the recognition site and by measuring the effect on...
Itoh, Takeshi, Tomita, Ken-ichi, Hakoshima, Toshio, Hiroaki, Hidekazu, Uesugi, Sei-ichi, Nishikawa, Satoshi, ...
The crystal structure of a mutant ribonuclease T1(Y45W) complexed with a specific inhibitor, 2′GMP, has been determined by X-ray diffraction and refined at 1.9 A� resolution to a conventional...
Hakoshima, Toshio, Oka, Ken-ichi, Toda, Shyoji, Tanaka, Masahiro, Goda, Keigo, Higo, Takashi, ...
Ribonuclease T1 and the mutant enzymes were cocrystallized with several ribonucleotides, including non-hydrolyzable substrate analogs of di- and triribonucleotides, which have a novel guanylate in...
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts
Itoh, Takeshi, Martin, William, Nei, Masatoshi
Endosymbionts, which are widely observed in nature, have undergone reductive genome evolution because of their long-term intracellular lifestyle. Here we compared the complete genome sequences of two...
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...
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...
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts
Itoh, Takeshi, Martin, William, Nei, Masatoshi
Endosymbionts, which are widely observed in nature, have undergone reductive genome evolution because of their long-term intracellular lifestyle. Here we compared the complete genome sequences of two...
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...
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...
Glycoproteomic probes for fluorescent imaging of fucosylated glycans in vivo
Sawa, Masaaki, Hsu, Tsui-Ling, Itoh, Takeshi, Sugiyama, Masakazu, Hanson, Sarah R., Vogt, Peter K., ...
Glycomics is emerging as a new field for the biology of complex glycoproteins and glycoconjugates. The lack of versatile glycan-labeling methods has presented a major obstacle to visualizing at the...
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...
Mihara, Motohiro, Itoh, Takeshi, Izawa, Takeshi
Microarray analysis of tiny amounts of RNA extracted from plant section samples prepared by laser microdissection (LM) can provide high-quality information on gene expression in specified plant cells...
Tanaka, Tsuyoshi, Koyanagi, Kanako O., Itoh, Takeshi
Alternative usage of transcription start sites (TSSs) is one of the key mechanisms to generate gene variation in eukaryotes. Here, we show diversified molecular evolution of TSSs in remotely related...