Osada, Naoki, Hirata, Makoto, Tanuma, Reiko, Suzuki, Yutaka, Sugano, Sumio, Terao, Keiji, ...
Abstract Background Consolidating transcriptome data of non-human primates is essential to annotate primate genome sequences, and will facilitate research using non-human primates in the genomic era....
Wakaguri, Hiroyuki, Suzuki, Yutaka, Sasaki, Masahide, Sugano, Sumio, Watanabe, Junichi
Abstract Background Apicomplexan parasites are causative agents of various diseases including malaria and have been targets of extensive genomic sequencing. We generated 5'-EST collections for six...
Positive Correlation between Alternative Splicing Events and Exon Structure Conservations (2009)
Hiroki Sakai, Yutaka Suzuki, Hiroo Murakami, Sachiyo Aburatani, Katsuhisa Horimoto, ...
One of the striking features in metazoan genomes is that the alternative pre-mRNA splicing is observed in many genes [1]. It was assumed that for a long time that alternative splicing was an...
Massive transcriptional start site analysis of human genes in hypoxia cells (2009)
Tsuchihara, Katsuya, Suzuki, Yutaka, Wakaguri, Hiroyuki, Irie, Takuma, Tanimoto, Kousuke, Hashimoto, Shin-ichi, ...
Combining our full-length cDNA method and the massively parallel sequencing technology, we developed a simple method to collect precise positional information of transcriptional start sites (TSSs)...
Wakaguri, Hiroyuki, Suzuki, Yutaka, Katayama, Toshiaki, Kawashima, Shuichi, Kibukawa, Eri, Hiranuka, Kazushi, ...
Full-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources. In this...
The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes (2009)
Kawaoka, Shinpei, Hayashi, Nobumitsu, Suzuki, Yutaka, Abe, Hiroaki, Sugano, Sumio, Tomari, Yukihide, ...
Genetic studies and large-scale sequencing experiments have revealed that the PIWI subfamily proteins and PIWI-interacting RNAs (piRNAs) play an important role in germ line development and transposon...
Resource Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation (2008)
Melody S. Clark, Dan Peterson, Ra W. Clifton, A J. Thompson, Masahide Sasaki, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Osada, Naoki, Hashimoto, Katsuyuki, Kameoka, Yosuke, Hirata, Makoto, Tanuma, Reiko, Uno, Yasuhiro, ...
Abstract Background Cynomolgus macaques ( Macaca fascicularis ) are widely used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as rhesus...
Yamashita, Riu, Suzuki, Yutaka, Takeuchi, Nono, Wakaguri, Hiroyuki, Ueda, Takuya, Sugano, Sumio, ...
Although the knowledge accumulated on the transcriptional regulations of eukaryotes is significant, the knowledge on their translational regulations remains limited. Thus, we performed a...
DBTSS: database of transcription start sites, progress report 2008 (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,...
Takeda, Jun-ichi, Suzuki, Yutaka, Sakate, Ryuichi, Sato, Yoshiharu, Seki, Masahide, Irie, Takuma, ...
Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice. The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants...
-Capturing Hybrid Power Generation System (2007)
With High Efficient, Pyong Sik Pak, Yutaka Suzuki, Takanobu Kosugi
A CO 2 -capturing hybrid-type power generation system with highly ecient use of solar thermal energy was proposed and its characteristics were investigated. In the system, relatively low temperature...
Pyong Sik Pak, Yutaka Suzuki, Takanobu KOSUGI
A CO 2 -capturing hybrid-type power generation system with highly ecient use of solar thermal energy was proposed and its characteristics were investigated. In the system, relatively low temperature...
Tetsuo Nishikawa, Jun-ichi Yamamoto, Ai Wakamatsu, Shizuko Ishii, Masashi Nemoto, ...
Whole human genome sequence determination was completed this year. To obtain accurate gene structures and promoter information, full-length cDNA sequence information as well as the genome sequences...
Yamamoto, Yoshiharu Y., Ichida, Hiroyuki, Abe, Tomoko, Suzuki, Yutaka, Sugano, Sumio, Obokata, Junichi
Mammalian promoters are categorized into TATA and CpG-related groups, and they have complementary roles associated with differentiated transcriptional characteristics. While the TATA box is also...
Inter-observer Variations in FDG-PET Interpretation for Cancer Screening (2007)
Suzuki, Akiko, Nakamoto, Yuji, Terauchi, Takashi, Kawamoto, Masami, Okumura, Yoshihiro, Suzuki, Yutaka, ...
Background Diagnostic guidelines for the use of 2-(fluorine 18) fluoro-2 deoxy-D-glucose (FDG)-positron emission tomography (PET) in cancer screening have yet to be established. We assessed...
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...
Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome (2007)
Sakakibara, Yuta, Irie, Takuma, Suzuki, Yutaka, Yamashita, Riu, Wakaguri, Hiroyuki, Kanai, Akinori, ...
In order to understand an overview of promoter activities intrinsic to primary DNA sequences in the human genome within a particular cell type, we carried out systematic quantitative luciferase...
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)...
Watanabe, Junichi, Wakaguri, Hiroyuki, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates...
DBTSS: database of human transcription start sites, progress report 2006 (2006)
Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano
DBTSS was first constructed in 2002 based on precise,experimentallydetermined50 endclones.Several major updates and additions have been made since the last report. First, the number of human clones...
Comparasite: a database for comparative study (2006)
Junichi Watanabe, Hiroyuki Wakaguri, Masahide Sasaki, Yutaka Suzuki, Sumio Sugano
of transcriptomes of parasites defined by full-length cDNAs
Diverse DNA Methylation Statuses at Alternative Promoters of Human Genes in Various Tissues (2006)
Cheong, Jieun, Yamada, Yoichi, Yamashita, Riu, Irie, Takuma, Kanai, Akinori, Wakaguri, Hiroyuki, ...
We characterized the DNA methylation status at 144 tissue-biased and 37 non-tissue-biased alternative promoters of 61 human genes in five normal tissues. Analysis of the collected data revealed that...
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii (2006)
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
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...
Watanabe, Junichi, Wakaguri, Hiroyuki, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates...
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...
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii (2006)
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006 (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...
Diverse DNA Methylation Statuses at Alternative Promoters of Human Genes in Various Tissues (2006)
Cheong, Jieun, Yamada, Yoichi, Yamashita, Riu, Irie, Takuma, Kanai, Akinori, Wakaguri, Hiroyuki, ...
We characterized the DNA methylation status at 144 tissue-biased and 37 non-tissue-biased alternative promoters of 61 human genes in five normal tissues. Analysis of the collected data revealed that...
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...
Watanabe, Junichi, Wakaguri, Hiroyuki, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates...
Osada, Naoki, Hirata, Makoto, Tanuma, Reiko, Kusuda, Jun, Hida, Munetomo, Suzuki, Yutaka, ...
The substitution rate and structural divergence in the 5' untranslated region (UTR) was investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in...
Otsuki, Tetsuji, Ota, Toshio, Nishikawa, Tetsuo, Hayashi, Koji, Suzuki, Yutaka, Yamamoto, Jun-ichi, ...
We have developed an in silico method of selection of human full-length cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Fullness rates were increased to about 80% by...
Osada, Naoki, Hirata, Makoto, Tanuma, Reiko, Kusuda, Jun, Hida, Munetomo, Suzuki, Yutaka, ...
The substitution rate and structural divergence in the 5′-untranslated region (UTR) were investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in...
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...
Osada, Naoki, Hirata, Makoto, Tanuma, Reiko, Kusuda, Jun, Hida, Munetomo, Suzuki, Yutaka, ...
The substitution rate and structural divergence in the 5' untranslated region (UTR) was investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in...
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...
GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene (2004)
Huang, Duen-Yi, Kuo, Yuan-Yeh, Lai, Jiann-Shiun, Suzuki, Yutaka, Sugano, Sumio, Chang, Zee-Fen
Expression of Gfi (growth factor-independence)-1B, a Gfi-1-related transcriptional repressor, is restricted to erythroid lineage cells and is essential for erythropoiesis. We have determined the...
Watanabe, Junichi, Suzuki, Yutaka, Sasaki, Masahide, Sugano, Sumio
Full‐malaria (http://fullmal.ims.u‐tokyo.ac.jp), a database for full‐length cDNAs from the human malaria parasite, Plasmodium falciparum has been updated in at least three points. (i)...
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004 (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....
Oyama, Masaaki, Itagaki, Chiharu, Hata, Hiroko, Suzuki, Yutaka, Izumi, Tomonori, Natsume, Tohru, ...
To find novel short coding sequences from accumulated full-length cDNA sequences, proteomic analysis of small proteins expressed in human leukemia K562 cells was performed using high-resolution...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation (2003)
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation (2003)
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Kakuta, Takatoshi, Suzuki, Yutaka, Tadaki, Futoshi, Tanaka, Reika, Tanaka, Shinichi, Sakai, Hideto, ...
Background. Minimally invasive radioguided parathyroidectomy (MIRP) for primary hyperparathyroidism for one gland, located by scanning with technetium 99m‐labelled sestamibi...
Yasuda, Seiei, Shimada, Hideo, Chino, Osamu, Tanaka, Hikaru, Kenmochi, Takahiro, Takechi, Masahiko, ...
Background: The aim of this study was to determine by radioisotope use whether the sentinel lymph node concept is applicable to esophagogastric cancers. In addition, we examined radioactivities of...
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs (2002)
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...
Identification of Two Novel Primate-Specific Genes in DSCR (2002)
Takamatsu, Kunihiko, Maekawa, Kohei, Togashi, Takushi, Choi, Dong-Kug, Suzuki, Yutaka, Taylor, Todd D., ...
We recently helped to complete the sequence of human chromosome 21 at a very high level of accuracy. Using this sequence we identified two novel genes, designated DSCR9 and DSCR10, in the so-called...
Shiroki, Kazuko, Ohsawa, Chieko, Sugi, Natuki, Wakiyama, Motoaki, Miura, Kin-ichiro, Watanabe, Manabu, ...
Smad5 is thought to relay signals of the bone morphogenetic protein pathway. The 5′ untranslated region (5′UTR) of human Smad5 mRNA is long, has the potential to form secondary structures and...
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Hirai, Momoki, ...
Abstract Background The complete assignment of the protein-coding regions of the human genome is a major challenge for genome biology today. We have already isolated many hitherto unknown full-length...
Nishikawa, Tetsuo, Ota, Toshio, Kawai, Yuri, Ishii, Shizuko, Saito, Kaoru, Yamamoto, Jun-ichi, ...
We compared in detail the characteristics of the sequences of the cDNA clones obtainedb y the oligo-capping method(oligo-capping clones) with that of the sequences in the UniGene database. To compare...
HUNT: launch of a full-length cDNA database from the Helix Research Institute (2001)
Yudate, Henrik T., Suwa, Makiko, Irie, Ryotaro, Matsui, Hiroshi, Nishikawa, Tetsuo, Nakamura, Yoshitaka, ...
The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project...
Watanabe, Junichi, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum (http://133.11.149.55/). Because of its medical importance, this...
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
Omori, Yoshihiro, Imai, Jun-ichi, Watanabe, Manabu, Komatsu, Takami, Suzuki, Yutaka, Kataoka, Kohsuke, ...
The expression of liver-specific genes is regulated by unequivocally allocated transcription factors via proper responsible elements within their promoters. We identified a novel transcription...
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
A Novel Gene, DSCR5, from the Distal Down Syndrome Critical Region on Chromosome 21q22.2 (2000)
Togashi, Takushi, Choi, Dong-Kug, Taylor, Todd D., Suzuki, Yutaka, Sugano, Sumio, Hattori, Masahira, ...
Based on a detailed sequence of the distal Down syndrome critical region (DSCR), we predicted and molecularly cloned a novel gene, designated DSCR5. We determined the sequences of expressed sequence...
CART Classification of Human 5' UTR Sequences (2000)
Davuluri, Ramana V., Suzuki, Yutaka, Sugano, Sumio, Zhang, Michael Q.
CART Classification of Human 5' UTR Sequences (2000)
Davuluri, Ramana V., Suzuki, Yutaka, Sugano, Sumio, Zhang, Michael Q.
Seki, Naohiko, Hayashi, Akiko, Hattori, Atsushi, Kozuma, Sumie, Sasaki, Masahide, Suzuki, Yutaka, ...
A subset of xeroderma pigmentosum (XP) group E cells lack a factor of the UV-damaged DNA binding activity. Both 127 kDa and 48 kDa proteins have been reported to be responsible for the binding...
The twisted SU(2) group and its representations /--by Yutaka Suzuki. (1996)
Thesis (M.A.)--Arizona State University, 1996.
Okamoto, Osamu, Suzuki, Yutaka, Kimura, Sadao, Shinkai, Hiroshi
A protein with an Mr of 22,000 was purified from bovine dermis. The amino acid sequence of the protein was identical to 22-kDa protein [Neame, P.J. et al. (1989) J. BioL Chem. 264, 5474–5479] and...
C-Terminal Peptidyl-L-Proline Hydrolase Activity of Aspergillus Acid Carboxypeptidase (1977)
ICHISHIMA, Eiji, TAKEUCHI, Michio, YASUDA, Ryuji, SUZUKI, Yutaka, KOBAYASHI, Setsuko
Aspergillus saitoi acid carboxypeptidase hydrolyzed C-terminal peptidyl-L-proline bonds and released the C-terminal proline from Z-Gly-Pro-Leu-GIy-Pro and Z-Gly-Pro at pH 3.3. Proline liberated by...
Watanabe, Junichi, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum (http://133.11.149.55/). Because of its medical importance, this organism is...
HUNT: launch of a full-length cDNA database from the Helix Research Institute
Yudate, Henrik T., Suwa, Makiko, Irie, Ryotaro, Matsui, Hiroshi, Nishikawa, Tetsuo, Nakamura, Yoshitaka, ...
The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project...
Omori, Yoshihiro, Imai, Jun-ichi, Watanabe, Manabu, Komatsu, Takami, Suzuki, Yutaka, Kataoka, Kohsuke, ...
The expression of liver-specific genes is regulated by unequivocally allocated transcription factors via proper responsible elements within their promoters. We identified a novel transcription...
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...
Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event
Shiroki, Kazuko, Ohsawa, Chieko, Sugi, Natuki, Wakiyama, Motoaki, Miura, Kin-ichiro, Watanabe, Manabu, ...
Smad5 is thought to relay signals of the bone morphogenetic protein pathway. The 5′ untranslated region (5′UTR) of human Smad5 mRNA is long, has the potential to form secondary structures and...
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Hirai, Momoki, ...
Twenty-nine novel human genes were predicted with putative coding regions sharing an open reading frame with the cynomolgus monkey, and the expression of 21 pairs of genes was confirmed by reverse...
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....
Watanabe, Junichi, Suzuki, Yutaka, Sasaki, Masahide, Sugano, Sumio
Full-malaria (http://fullmal.ims.u-tokyo.ac.jp), a database for full-length cDNAs from the human malaria parasite, Plasmodium falciparum has been updated in at least three points. (i) We added 8934...
CART Classification of Human 5′ UTR Sequences
Davuluri, Ramana V., Suzuki, Yutaka, Sugano, Sumio, Zhang, Michael Q.
A nonredundant database of 2312 full-length human 5′-untranslated regions (UTRs) was carefully prepared using state-of-the-art experimental and computational technologies. A comprehensive...
Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from...
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...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene
Huang, Duen-Yi, Kuo, Yuan-Yeh, Lai, Jiann-Shiun, Suzuki, Yutaka, Sugano, Sumio, Chang, Zee-Fen
Expression of Gfi (growth factor-independence)-1B, a Gfi-1-related transcriptional repressor, is restricted to erythroid lineage cells and is essential for erythropoiesis. We have determined the...
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...
Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs
Oyama, Masaaki, Itagaki, Chiharu, Hata, Hiroko, Suzuki, Yutaka, Izumi, Tomonori, Natsume, Tohru, ...
To find novel short coding sequences from accumulated full-length cDNA sequences, proteomic analysis of small proteins expressed in human leukemia K562 cells was performed using high-resolution...
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
Suzuki, Yutaka, Taira, Hirotoshi, Tsunoda, Tatsuhiko, Mizushima-Sugano, Junko, Sese, Jun, Hata, Hiroko, ...
Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The ‘oligo-capping’ method...
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...
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...
Equilibrium incentives and accumulation of relational skills in a dynamic model of hold up
We construct a dynamic model of Holdup by applying a framework in capital accumulation games, and derive the Markov perfect equilibrium of the game. Firmsf specific investments for the current period...
Watanabe, Junichi, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum (http://133.11.149.55/). Because of its medical importance, this organism is...
HUNT: launch of a full-length cDNA database from the Helix Research Institute
Yudate, Henrik T., Suwa, Makiko, Irie, Ryotaro, Matsui, Hiroshi, Nishikawa, Tetsuo, Nakamura, Yoshitaka, ...
The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project...
Omori, Yoshihiro, Imai, Jun-ichi, Watanabe, Manabu, Komatsu, Takami, Suzuki, Yutaka, Kataoka, Kohsuke, ...
The expression of liver-specific genes is regulated by unequivocally allocated transcription factors via proper responsible elements within their promoters. We identified a novel transcription...
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...
Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event
Shiroki, Kazuko, Ohsawa, Chieko, Sugi, Natuki, Wakiyama, Motoaki, Miura, Kin-ichiro, Watanabe, Manabu, ...
Smad5 is thought to relay signals of the bone morphogenetic protein pathway. The 5′ untranslated region (5′UTR) of human Smad5 mRNA is long, has the potential to form secondary structures and...
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Hirai, Momoki, ...
Twenty-nine novel human genes were predicted with putative coding regions sharing an open reading frame with the cynomolgus monkey, and the expression of 21 pairs of genes was confirmed by reverse...
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....
Watanabe, Junichi, Suzuki, Yutaka, Sasaki, Masahide, Sugano, Sumio
Full-malaria (http://fullmal.ims.u-tokyo.ac.jp), a database for full-length cDNAs from the human malaria parasite, Plasmodium falciparum has been updated in at least three points. (i) We added 8934...
CART Classification of Human 5′ UTR Sequences
Davuluri, Ramana V., Suzuki, Yutaka, Sugano, Sumio, Zhang, Michael Q.
A nonredundant database of 2312 full-length human 5′-untranslated regions (UTRs) was carefully prepared using state-of-the-art experimental and computational technologies. A comprehensive...
Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from...
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...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene
Huang, Duen-Yi, Kuo, Yuan-Yeh, Lai, Jiann-Shiun, Suzuki, Yutaka, Sugano, Sumio, Chang, Zee-Fen
Expression of Gfi (growth factor-independence)-1B, a Gfi-1-related transcriptional repressor, is restricted to erythroid lineage cells and is essential for erythropoiesis. We have determined the...
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...
Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs
Oyama, Masaaki, Itagaki, Chiharu, Hata, Hiroko, Suzuki, Yutaka, Izumi, Tomonori, Natsume, Tohru, ...
To find novel short coding sequences from accumulated full-length cDNA sequences, proteomic analysis of small proteins expressed in human leukemia K562 cells was performed using high-resolution...
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
Suzuki, Yutaka, Taira, Hirotoshi, Tsunoda, Tatsuhiko, Mizushima-Sugano, Junko, Sese, Jun, Hata, Hiroko, ...
Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The ‘oligo-capping’ method...
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...
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)...
Watanabe, Junichi, Wakaguri, Hiroyuki, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates...
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis
Yamamoto, Yoshiharu Y., Ichida, Hiroyuki, Abe, Tomoko, Suzuki, Yutaka, Sugano, Sumio, Obokata, Junichi
Mammalian promoters are categorized into TATA and CpG-related groups, and they have complementary roles associated with differentiated transcriptional characteristics. While the TATA box is also...
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,...
Osada, Naoki, Hashimoto, Katsuyuki, Kameoka, Yosuke, Hirata, Makoto, Tanuma, Reiko, Uno, Yasuhiro, ...
Integration versus non-integration: specific investments and ex-post resource distribution
I adopt a non-cooperative game theoretic approach to an incomplete contracting transaction model, à la Grossman & Hart (1986) , Hart & Moore (1990) and Bolton & Whinston (1993) , consisting of one...
Yamashita, Riu, Suzuki, Yutaka, Takeuchi, Nono, Wakaguri, Hiroyuki, Ueda, Takuya, Sugano, Sumio, ...
Although the knowledge accumulated on the transcriptional regulations of eukaryotes is significant, the knowledge on their translational regulations remains limited. Thus, we performed a...
Mechanism design with collusive supervision: a three-tier agency model with a continuum of types
We apply the "Monotone Comparative Statics" method ala Topkis (1978), Edlin and Shannon (1998), and Milgrom and Segal (2002)'s generalized envelope theorem to the three-tier agency model with hidden...
Takeda, Jun-ichi, Suzuki, Yutaka, Sakate, Ryuichi, Sato, Yoshiharu, Seki, Masahide, Irie, Takuma, ...
Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice. The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants...
High-Resolution Analysis of the 5′-End Transcriptome Using a Next Generation DNA Sequencer
Hashimoto, Shin-ichi, Qu, Wei, Ahsan, Budrul, Ogoshi, Katsumi, Sasaki, Atsushi, Nakatani, Yoichiro, ...
Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be...
Massive transcriptional start site analysis of human genes in hypoxia cells
Tsuchihara, Katsuya, Suzuki, Yutaka, Wakaguri, Hiroyuki, Irie, Takuma, Tanimoto, Kousuke, Hashimoto, Shin-ichi, ...
Combining our full-length cDNA method and the massively parallel sequencing technology, we developed a simple method to collect precise positional information of transcriptional start sites (TSSs)...
Transcriptome analysis and identification of regulators for long-term plasticity in Aplysia kurodai
Lee, Yong-Seok, Choi, Sun-Lim, Kim, Tae-Hyung, Lee, Jin-A, Kim, Hyong Kyu, Kim, Hyoung, ...
The marine mollusk Aplysia is a useful model organism for studying the cellular bases of behavior and plasticity. However, molecular studies of Aplysia have been limited by the lack of genomic...
Wakaguri, Hiroyuki, Suzuki, Yutaka, Katayama, Toshiaki, Kawashima, Shuichi, Kibukawa, Eri, Hiranuka, Kazushi, ...
Full-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources. In this...
Self-Contained Induction of Neurons from Human Embryonic Stem Cells
Okuno, Tsuyoshi, Nakayama, Takashi, Konishi, Nae, Michibata, Hideo, Wakimoto, Koji, Suzuki, Yutaka, ...
Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome
Sakakibara, Yuta, Irie, Takuma, Suzuki, Yutaka, Yamashita, Riu, Wakaguri, Hiroyuki, Kanai, Akinori, ...
In order to understand an overview of promoter activities intrinsic to primary DNA sequences in the human genome within a particular cell type, we carried out systematic quantitative luciferase...