A rapid and simple Transcriptional sequencing method for GC-rich DNA regions (2006)
Izawa, Masaki, Kitamura, Nobuo, Odake, Nanae, Maki, Fuminori, Kanehira, Kaoru, Nemoto, Hideyuki, ...
In genome sequencing project, we encounter the DNA regions that often contain stable secondary structure with high GC content. These regions are difficult to not only amplify by PCR for template...
A rapid and simple Transcriptional sequencing method for GC-rich DNA regions (2006)
Izawa, Masaki, Kitamura, Nobuo, Odake, Nanae, Maki, Fuminori, Kanehira, Kaoru, Nemoto, Hideyuki, ...
In genome sequencing project, we encounter the DNA regions that often
A rapid and simple Transcriptional sequencing method for GC-rich DNA regions (2006)
Izawa, Masaki, Kitamura, Nobuo, Odake, Nanae, Maki, Fuminori, Kanehira, Kaoru, Nemoto, Hideyuki, ...
In genome sequencing project, we encounter the DNA regions that often
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
Abstract Background Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian...
Construction and Analysis of a Human-Chimpanzee Comparative Clone Map (2002)
Fujiyama,Asao, Watanabe,Hidemi, Toyoda,Atsushi, Taylor,Todd D., Itoh,Takehiko, Tsai,Shih-Feng, ...
The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes...
Construction and Analysis of a Human-Chimpanzee Comparative Clone Map (2002)
Fujiyama, Asao, Watanabe, Hidemi, Toyoda, Atsushi, Taylor, Todd D., Itoh, Takehiko, Tsai, Shih-Feng, ...
The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes...
Todd Taylor, Masahira Hattori, Kiyoteru Noguchi, Tomomi Shobu, Kazuo Ishii, Atsushi Toyoda, ...
Introduction Down syndrome (MIM 190685) is the most common genetic form of mental retardation. It is caused by trisomy of all or a portion of chromosome 21. The 2.5-Mb region [3, 4] between DNA...
Todd Taylor, Masahira Hattori, Kiyoteru Noguchi, Tomomi Shobu, Kazuo Ishii, Atsushi Toyoda, ...
Introduction Down syndrome (MIM 190685) is the most common genetic form of mental retardation. It is caused by trisomy of all or a portion of chromosome 21. The 2.5-Mb region [3, 4] between DNA...
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...
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...
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...
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, Takashi, Chiba, Tomoko, Ozawa, Ritsuko, Yoshida, Mikio, Hattori, Masahira, Sakaki, Yoshiyuki
Protein–protein interactions play crucial roles in the execution of various biological functions. Accordingly, their comprehensive description would contribute considerably to the functional...
Ōmura, Satoshi, Ikeda, Haruo, Ishikawa, Jun, Hanamoto, Akiharu, Takahashi, Chigusa, Shinose, Mayumi, ...
Streptomyces avermitilis is a soil bacterium that carries out not only a complex morphological differentiation but also the production of secondary metabolites, one of which, avermectin, is...
Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA
Shirai, Mutsunori, Hirakawa, Hideki, Kimoto, Mitsuaki, Tabuchi, Mitsuaki, Kishi, Fumio, Ouchi, Kazunobu, ...
Chlamydia pneumoniae is a widespread pathogen of humans causing pneumonia and bronchitis. There are many reports of an association between C.pneumoniae infection and atherosclerosis. We determined...
Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater
Shimizu, Tohru, Ohtani, Kaori, Hirakawa, Hideki, Ohshima, Kenshiro, Yamashita, Atsushi, Shiba, Tadayoshi, ...
Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium that causes life-threatening gas gangrene and mild enterotoxaemia in humans, although it colonizes as normal intestinal...
The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans
Sasaki, Yuko, Ishikawa, Jun, Yamashita, Atsushi, Oshima, Kenshiro, Kenri, Tsuyoshi, Furuya, Keiko, ...
The complete genomic sequence of an intracellular bacterial pathogen, Mycoplasma penetrans HF-2 strain, was determined. The HF-2 genome consists of a 1 358 633 bp single circular chromosome...
Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region
Toyoda, Atsushi, Noguchi, Hideki, Taylor, Todd D., Ito, Takehiko, Pletcher, Mathew T., Sakaki, Yoshiyuki, ...
Comprehensive knowledge of the gene content of human chromosome 21 (HSA21) is essential for understanding the etiology of Down syndrome (DS). Here we report the largest comparison of finished mouse...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
Nakagawa, Ichiro, Kurokawa, Ken, Yamashita, Atsushi, Nakata, Masanobu, Tomiyasu, Yusuke, Okahashi, Nobuo, ...
Group Astreptococcus (GAS) is a gram-positive bacterial pathogen that causes various suppurative infections and nonsuppurative sequelae. Since the late 1980s, streptococcal toxic-shock like syndrome...
Ueda, Kenji, Yamashita, Atsushi, Ishikawa, Jun, Shimada, Masafumi, Watsuji, Tomo-o, Morimura, Kohji, ...
Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to...
Kuwahara, Tomomi, Yamashita, Atsushi, Hirakawa, Hideki, Nakayama, Haruyuki, Toh, Hidehiro, Okada, Natsumi, ...
Bacteroides are predominant human colonic commensals, but the principal pathogenic species, Bacteroides fragilis (BF), lives closely associated with the mucosal surface, whereas a second major...
The complete genomic sequence of Nocardia farcinica IFM 10152
Ishikawa, Jun, Yamashita, Atsushi, Mikami, Yuzuru, Hoshino, Yasutaka, Kurita, Haruyo, Hotta, Kunimoto, ...
We determined the genomic sequence of Nocardia farcinica IFM 10152, a clinical isolate, and revealed the molecular basis of its versatility. The genome consists of a single circular chromosome of...
Abe, Kuniya, Noguchi, Hideki, Tagawa, Keiko, Yuzuriha, Misako, Toyoda, Atsushi, Kojima, Toshio, ...
MSM/Ms is an inbred strain derived from the Japanese wild mouse, Mus musculus molossinus. It is believed that subspecies molossinus has contributed substantially to the genome constitution of common...
Yokomine, Takaaki, Shirohzu, Hisao, Purbowasito, Wahyu, Toyoda, Atsushi, Iwama, Hisakazu, Ikeo, Kazuho, ...
Previous studies revealed that Igf2 and Mpr/Igf2r are imprinted in eutherian mammals and marsupials but not in monotremes or birds. Igf2 lies in a large imprinted cluster in eutherians, and its...
Kuroda, Makoto, Yamashita, Atsushi, Hirakawa, Hideki, Kumano, Miyuki, Morikawa, Kazuya, Higashide, Masato, ...
Staphylococcus saprophyticus is a uropathogenic Staphylococcus frequently isolated from young female outpatients presenting with uncomplicated urinary tract infections. We sequenced the whole genome...
Sakaguchi, Yoshihiko, Hayashi, Tetsuya, Kurokawa, Ken, Nakayama, Keisuke, Oshima, Kenshiro, Fujinaga, Yukako, ...
Botulinum neurotoxins (BoNTXs) produced by Clostridium botulinum are among the most poisonous substances known. Of the seven types of BoNTXs, genes for type C1 and D toxins (BoNTX/C1 and D) are...
Toh, Hidehiro, Weiss, Brian L., Perkin, Sarah A.H., Yamashita, Atsushi, Oshima, Kenshiro, Hattori, Masahira, ...
Sodalis glossinidius is a maternally transmitted endosymbiont of tsetse flies (Glossina spp.), an insect of medical and veterinary significance. Analysis of the complete sequence of Sodalis'...
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, Takashi, Chiba, Tomoko, Ozawa, Ritsuko, Yoshida, Mikio, Hattori, Masahira, Sakaki, Yoshiyuki
Protein–protein interactions play crucial roles in the execution of various biological functions. Accordingly, their comprehensive description would contribute considerably to the functional...
Ōmura, Satoshi, Ikeda, Haruo, Ishikawa, Jun, Hanamoto, Akiharu, Takahashi, Chigusa, Shinose, Mayumi, ...
Streptomyces avermitilis is a soil bacterium that carries out not only a complex morphological differentiation but also the production of secondary metabolites, one of which, avermectin, is...
Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA
Shirai, Mutsunori, Hirakawa, Hideki, Kimoto, Mitsuaki, Tabuchi, Mitsuaki, Kishi, Fumio, Ouchi, Kazunobu, ...
Chlamydia pneumoniae is a widespread pathogen of humans causing pneumonia and bronchitis. There are many reports of an association between C.pneumoniae infection and atherosclerosis. We determined...
Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater
Shimizu, Tohru, Ohtani, Kaori, Hirakawa, Hideki, Ohshima, Kenshiro, Yamashita, Atsushi, Shiba, Tadayoshi, ...
Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium that causes life-threatening gas gangrene and mild enterotoxaemia in humans, although it colonizes as normal intestinal...
The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans
Sasaki, Yuko, Ishikawa, Jun, Yamashita, Atsushi, Oshima, Kenshiro, Kenri, Tsuyoshi, Furuya, Keiko, ...
The complete genomic sequence of an intracellular bacterial pathogen, Mycoplasma penetrans HF-2 strain, was determined. The HF-2 genome consists of a 1 358 633 bp single circular chromosome...
Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region
Toyoda, Atsushi, Noguchi, Hideki, Taylor, Todd D., Ito, Takehiko, Pletcher, Mathew T., Sakaki, Yoshiyuki, ...
Comprehensive knowledge of the gene content of human chromosome 21 (HSA21) is essential for understanding the etiology of Down syndrome (DS). Here we report the largest comparison of finished mouse...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
Nakagawa, Ichiro, Kurokawa, Ken, Yamashita, Atsushi, Nakata, Masanobu, Tomiyasu, Yusuke, Okahashi, Nobuo, ...
Group Astreptococcus (GAS) is a gram-positive bacterial pathogen that causes various suppurative infections and nonsuppurative sequelae. Since the late 1980s, streptococcal toxic-shock like syndrome...
Ueda, Kenji, Yamashita, Atsushi, Ishikawa, Jun, Shimada, Masafumi, Watsuji, Tomo-o, Morimura, Kohji, ...
Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to...
Kuwahara, Tomomi, Yamashita, Atsushi, Hirakawa, Hideki, Nakayama, Haruyuki, Toh, Hidehiro, Okada, Natsumi, ...
Bacteroides are predominant human colonic commensals, but the principal pathogenic species, Bacteroides fragilis (BF), lives closely associated with the mucosal surface, whereas a second major...
The complete genomic sequence of Nocardia farcinica IFM 10152
Ishikawa, Jun, Yamashita, Atsushi, Mikami, Yuzuru, Hoshino, Yasutaka, Kurita, Haruyo, Hotta, Kunimoto, ...
We determined the genomic sequence of Nocardia farcinica IFM 10152, a clinical isolate, and revealed the molecular basis of its versatility. The genome consists of a single circular chromosome of...
Abe, Kuniya, Noguchi, Hideki, Tagawa, Keiko, Yuzuriha, Misako, Toyoda, Atsushi, Kojima, Toshio, ...
MSM/Ms is an inbred strain derived from the Japanese wild mouse, Mus musculus molossinus. It is believed that subspecies molossinus has contributed substantially to the genome constitution of common...
Yokomine, Takaaki, Shirohzu, Hisao, Purbowasito, Wahyu, Toyoda, Atsushi, Iwama, Hisakazu, Ikeo, Kazuho, ...
Previous studies revealed that Igf2 and Mpr/Igf2r are imprinted in eutherian mammals and marsupials but not in monotremes or birds. Igf2 lies in a large imprinted cluster in eutherians, and its...
Kuroda, Makoto, Yamashita, Atsushi, Hirakawa, Hideki, Kumano, Miyuki, Morikawa, Kazuya, Higashide, Masato, ...
Staphylococcus saprophyticus is a uropathogenic Staphylococcus frequently isolated from young female outpatients presenting with uncomplicated urinary tract infections. We sequenced the whole genome...
Sakaguchi, Yoshihiko, Hayashi, Tetsuya, Kurokawa, Ken, Nakayama, Keisuke, Oshima, Kenshiro, Fujinaga, Yukako, ...
Botulinum neurotoxins (BoNTXs) produced by Clostridium botulinum are among the most poisonous substances known. Of the seven types of BoNTXs, genes for type C1 and D toxins (BoNTX/C1 and D) are...
Toh, Hidehiro, Weiss, Brian L., Perkin, Sarah A.H., Yamashita, Atsushi, Oshima, Kenshiro, Hattori, Masahira, ...
Sodalis glossinidius is a maternally transmitted endosymbiont of tsetse flies (Glossina spp.), an insect of medical and veterinary significance. Analysis of the complete sequence of Sodalis'...
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome
Miura, Fumihito, Kawaguchi, Noriko, Sese, Jun, Toyoda, Atsushi, Hattori, Masahira, Morishita, Shinichi, ...
We performed a large-scale cDNA analysis to explore the transcriptome of the budding yeast Saccharomyces cerevisiae. We sequenced two cDNA libraries, one from the cells exponentially growing in a...