Yutaka Suzuki

Collection of Macaca fasciculariscDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus (2009)

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....

Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs (2009)

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)...

Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009 (2009)

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...

Large-scale analysis of Macaca fascicularistranscripts and inference of genetic divergence between M. fascicularisand M. mulatta (2008)

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...

Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics (2008)

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,...

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs (2008)

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...

A Co2-Capturing Hybrid Power Generation System With High Efficient Use Of Solar Thermal Energy (2007)

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...

458 Genome Informatics 14: 458–459 (2003) Characterization of One-Pass and Full-Length Sequences of Oligo-Capping cDNA Clones by Genome Mapping (2007)

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...

Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis (2007)

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...

Distinct class of putative "non-conserved" promoters in humans: Comparative studies of alternative promoters of human and mouse genes (2007)

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...

H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational (2007)

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)...

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs (2007)

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...

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...

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs (2006)

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...

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs (2006)

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...

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs (2006)

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...

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes (2006)

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...

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs (2006)

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...

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs (2006)

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...

Substitution Rate and Structural Divergence of 5'UTR Evolution: Comparative Analysis Between Human and Cynomolgus Monkey cDNAs (2005)

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...

Signal Sequence and Keyword Trap in silico for Selection of Full-Length Human cDNAs Encoding Secretion or Membrane Proteins from Oligo-Capped cDNA Libraries (2005)

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...

Substitution Rate and Structural Divergence of 5'UTR Evolution: Comparative Analysis Between Human and Cynomolgus Monkey cDNAs (2005)

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...

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes (2005)

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...

Substitution Rate and Structural Divergence of 5'UTR Evolution: Comparative Analysis Between Human and Cynomolgus Monkey cDNAs (2005)

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...

Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species (2004)

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....

Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs (2004)

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...

Long-term prognosis of parathyroid function for chronic dialysis patients after minimally invasive radioguided parathyroidectomy (MIRP) (2003)

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...

Sentinel Lymph Node Detection with Tc-99m Tin Colloids in Patients with Esophagogastric Cancer (2003)

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...

Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event (2002)

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...

Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain (2001)

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...

Comparison of Sequences of cDNA Clones Obtained from Oligo-capping cDNA Libraries with Those from UniGene (2001)

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...

FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum (2001)

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...

CREB-H: a novel mammalian transcription factor belonging to the CREB/ATF family and functioning via the box-B element with a liver-specific expression (2001)

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...

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...

cDNA Cloning, Tissue Expression, and Chromosomal Assignment of a Mouse Gene, Encoding a 127 kDa UV-damaged DNA Binding Protein Which is Defective in XPE Cells (1999)

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...

Extracellular Matrix 22-kDa Protein Interacts with Decorin Core Protein and Is Expressed in Cutaneous Fibrosis (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...

FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum

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...

CREB-H: a novel mammalian transcription factor belonging to the CREB/ATF family and functioning via the box-B element with a liver-specific expression

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...

Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain

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....

Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species

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...

Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions

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...

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes

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...

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

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

Yutaka Suzuki

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...

FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum

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...

CREB-H: a novel mammalian transcription factor belonging to the CREB/ATF family and functioning via the box-B element with a liver-specific expression

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...

Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain

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....

Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species

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...

Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions

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...

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes

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...

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

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...

H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational

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)...

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs

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...

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

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,...

Integration versus non-integration: specific investments and ex-post resource distribution

Yutaka Suzuki

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...

Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics

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

Yutaka Suzuki

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...

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs

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...

Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009

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...

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...