Yutaka Suzuki

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. ncbi Characterisation of full-length cDNA sequences provides insights into the Eimeria tenella transcriptome
    Nadzirah Amiruddin
    School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
    BMC Genomics 13:21. 2012
  2. ncbi [Transcriptome analyses and transcriptome databases]
    Yutaka Suzuki
    Tanpakushitsu Kakusan Koso 49:1859-65. 2004
  3. ncbi DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
    Yutaka Suzuki
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 32:D78-81. 2004
  4. ncbi Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions
    Yutaka Suzuki
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
    Genome Res 14:1711-8. 2004
  5. ncbi Large-scale collection and characterization of promoters of human and mouse genes
    Yutaka Suzuki
    Human Genome Center, The Institute of Medical Science, The University of Tokyo 4 6 1 Shirokanedai, Tokyo, 108 8639, Japan
    In Silico Biol 4:429-44. 2004
  6. ncbi Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries
    Y Suzuki
    Department of Virology, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Genomics 64:286-97. 2000
  7. ncbi Transcriptome analyses of human genes and applications for proteome analyses
    Yutaka Suzuki
    Laboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Curr Protein Pept Sci 7:147-63. 2006
  8. ncbi Identification and characterization of the potential promoter regions of 1031 kinds of human genes
    Y Suzuki
    Department of Virology, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    Genome Res 11:677-84. 2001
  9. ncbi Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
    Riu Yamashita
    Frontier Research Initiative, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Res 21:775-89. 2011
  10. ncbi Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
    Wei Qu
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277 0882, Japan
    Genome Res 22:1419-25. 2012

Collaborators

Detail Information

Publications105 found, 100 shown here

  1. ncbi Characterisation of full-length cDNA sequences provides insights into the Eimeria tenella transcriptome
    Nadzirah Amiruddin
    School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
    BMC Genomics 13:21. 2012
    ..Characterisation of the E. tenella transcriptome may provide a better understanding of the biology of the parasite and aid in the development of a more effective control for coccidiosis...
  2. ncbi [Transcriptome analyses and transcriptome databases]
    Yutaka Suzuki
    Tanpakushitsu Kakusan Koso 49:1859-65. 2004
  3. ncbi DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
    Yutaka Suzuki
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 32:D78-81. 2004
    ....
  4. ncbi Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions
    Yutaka Suzuki
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
    Genome Res 14:1711-8. 2004
    ....
  5. ncbi Large-scale collection and characterization of promoters of human and mouse genes
    Yutaka Suzuki
    Human Genome Center, The Institute of Medical Science, The University of Tokyo 4 6 1 Shirokanedai, Tokyo, 108 8639, Japan
    In Silico Biol 4:429-44. 2004
    ..All the data were deposited and made available through a database for comparative studies, DBTSS...
  6. ncbi Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries
    Y Suzuki
    Department of Virology, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Genomics 64:286-97. 2000
    ..These findings are contrary to the typical translation initiation model, which states that translation is initiated from the "first" ATG codon...
  7. ncbi Transcriptome analyses of human genes and applications for proteome analyses
    Yutaka Suzuki
    Laboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Curr Protein Pept Sci 7:147-63. 2006
    ..Rapidly accumulating genome data as well as versatile use of the transcriptome information will shortly lay a firm foundation for proteome-level understanding of human gene networks...
  8. ncbi Identification and characterization of the potential promoter regions of 1031 kinds of human genes
    Y Suzuki
    Department of Virology, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    Genome Res 11:677-84. 2001
    ..In the PPRs of the CGM2 gene, the DRA gene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs...
  9. ncbi Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
    Riu Yamashita
    Frontier Research Initiative, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Res 21:775-89. 2011
    ..The collected integrative information should provide a useful basis for future biological characterization of TSCs...
  10. ncbi Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
    Wei Qu
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277 0882, Japan
    Genome Res 22:1419-25. 2012
    ..This is the first report of findings showing that the CpG methylation state is significantly correlated with the characteristics of evolutionary change in neighboring DNA...
  11. ncbi Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation
    Kahori Hara
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
    BMC Genomics 13:119. 2012
    ..A recent study has identified a novel mutant silkworm line called KG, whose mutation in the W chromosome causes severe female masculinization. However, the molecular nature of KG line has not been well characterized yet...
  12. ncbi Diverse DNA methylation statuses at alternative promoters of human genes in various tissues
    Jieun Cheong
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan
    DNA Res 13:155-67. 2006
    ..DNA methylation appears to play a significant role in differential usage of alternative promoters and may be related to functional diversification between CpG-island-containing promoters and CpG-island-less promoters...
  13. ncbi Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs
    Jun Ichi Takeda
    Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio IT Research Building, Aomi 2 42, Koto ku, Tokyo, Japan
    Nucleic Acids Res 36:6386-95. 2008
    ..This suggests that non-conserved exons in the CDSs of transcripts cause functional constraint. These findings should enhance our understanding of the relationship between AS and species specificity of human genes...
  14. ncbi Intrinsic promoter activities of primary DNA sequences in the human genome
    Yuta Sakakibara
    Graduate School of Frontier Sciences, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    DNA Res 14:71-7. 2007
    ....
  15. ncbi DBTSS provides a tissue specific dynamic view of Transcription Start Sites
    Riu Yamashita
    Frontier Research Initiative, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
    Nucleic Acids Res 38:D98-104. 2010
    ..Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated. DBTSS can be accessed at http://dbtss.hgc.jp/...
  16. ncbi Characterization of STAT6 target genes in human B cells and lung epithelial cells
    Akinori Kanai
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwashi, Chiba 277 8562, Japan
    DNA Res 18:379-92. 2011
    ..The rough landscape of STAT6-responsive sites was found to be shaped by chromatin structure, but distinct cellular responses were mainly mediated by distinct sets of transcription factors...
  17. ncbi Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer
    Nuankanya Sathira
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa shi, Chiba 277 8568, Japan
    DNA Res 17:169-83. 2010
    ....
  18. ncbi DBTSS: database of transcription start sites, progress report 2008
    Hiroyuki Wakaguri
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 36:D97-101. 2008
    ..With the expanded dataset and the enhanced functionalities, DBTSS provides a unique platform that enables in-depth transcriptome analyses. DBTSS is accessible at http://dbtss.hgc.jp/...
  19. ncbi Predicting promoter activities of primary human DNA sequences
    Takuma Irie
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwashi, Chiba 277 8562, Japan
    Nucleic Acids Res 39:e75. 2011
    ..Furthermore, we found that nucleosomes occasionally formed open chromatin structures with RNA polymerase II recruitment where the program predicted significant promoter activities, although no transcripts were observed...
  20. ncbi Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes
    Katsuki Tsuritani
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minatoku, Tokyo 108 8639, Japan
    Genome Res 17:1005-14. 2007
    ..Taken together, our data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution...
  21. ncbi Epidural administration of morphine facilitates time of appearance of first gastric interdigestive migrating complex in dogs with paralytic ileus after open abdominal surgery
    Tomoko Nakayoshi
    Department of Surgery, Jikei University School of Medicine, Tokyo, Japan
    J Gastrointest Surg 11:648-54. 2007
    ..These results suggest that epidural administration of morphine may facilitate recovery from paralytic ileus after open abdominal surgery, perhaps through its effects on the central nervous system...
  22. ncbi Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs
    Hiroyuki Wakaguri
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
    BMC Genomics 10:312. 2009
    ..To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites...
  23. ncbi Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  24. ncbi The comprehensive epigenome map of piRNA clusters
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi, Tokyo, Japan
    Nucleic Acids Res 41:1581-90. 2013
    ..Collectively, we envision that the euchromatic, opened nature of unique piRNA clusters or piRNA cluster-associated TSSs allows piRNA clusters to capture new insertions efficiently...
  25. ncbi Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs
    Junichi Watanabe
    Department of Parasitology, Institute of Medical Science, Graduate School of Frontier Sciences, University of Tokyo, 4 6 1, Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Nucleic Acids Res 35:D431-8. 2007
    ..Our full-length cDNA databases and Comparasite are accessible from http://fullmal.ims.u-tokyo.ac.jp...
  26. ncbi Effects of half-solid nutrients on gastroesophageal reflux in beagle dogs with or without cardioplasty and intrathoracic cardiopexy
    Yuichiro Tanishima
    Department of Surgery, Jikei University School Medicine, Tokyo, Japan
    J Surg Res 161:272-7. 2010
    ..Nevertheless, aspiration of liquid nutrients due to vomiting and reflux esophagitis caused by gastroesophageal reflux (GER) is a significant problem associated with tube feeding by PEG...
  27. ncbi Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokane-dai Minato-ku, Tokyo 108-8639, Japan
    Gene 350:129-36. 2005
    ....
  28. ncbi Diversity of translation start sites may define increased complexity of the human short ORFeome
    Masaaki Oyama
    Medical Proteomics Laboratory, University of Tokyo, Japan
    Mol Cell Proteomics 6:1000-6. 2007
    ....
  29. ncbi DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
    Yutaka Suzuki
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 30:328-31. 2002
    ....
  30. ncbi Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009
    Hiroyuki Wakaguri
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo 4 6 1, Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D520-5. 2009
    ..Full-Malaria/Parasites and Full-Arthropods are accessible from http://fullmal.hgc.jp/...
  31. ncbi Expressed sequence tags from cynomolgus monkey (Macaca fascicularis) liver: a systematic identification of drug-metabolizing enzymes
    Yasuhiro Uno
    Division of Genetic Diagnosis, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, Japan
    FEBS Lett 582:351-8. 2008
    ..Our comparative genomics approach identified nine lineage-specific candidate ESTs, including three drug-metabolizing enzymes, which could be important for understanding the physiological differences between monkeys and humans...
  32. ncbi Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 36:3707-15. 2008
    ....
  33. ncbi The silkworm W chromosome is a source of female-enriched piRNAs
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
    RNA 17:2144-51. 2011
    ..Collectively, we revealed the nature of the silkworm W chromosome as a source of piRNAs...
  34. ncbi Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
    Shin Sasaki
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, 277 0882, Japan
    Science 323:401-4. 2009
    ..These data exemplify the potential for genetic activity (transcription) and chromatin structure to contribute to molding the DNA sequence on an evolutionary time scale...
  35. ncbi Molecular cloning, mRNA expression and chromosomal localization of mouse angiotensin-converting enzyme-related carboxypeptidase (mACE2)
    Takami Komatsu
    Laboratory of Genome Structure Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    DNA Seq 13:217-20. 2002
    ..Mouse ACE2 showed 83% identity with human ACE2. Northern blot analysis revealed that 2.8- and 2.0-kb transcripts were expressed mainly in the kidney and the lungs. The mouse ACE2 gene was mapped to chromosome X 70.5 cM...
  36. ncbi Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species
    Junichi Watanabe
    Department of Parasitology, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1, Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Nucleic Acids Res 32:D334-8. 2004
    ....
  37. ncbi Preoperative dilatation does not affect the surgical outcome of laparoscopic Heller myotomy and Dor fundoplication for esophageal achalasia
    Kazuto Tsuboi
    Department of Surgery, Jikei University School of Medicine, Tokyo, Japan
    Surg Laparosc Endosc Percutan Tech 19:98-100. 2009
    ..In patients who have had dilatation in the past, inflammation between the esophageal mucosal and muscular layers may make it difficult to perform myotomy...
  38. ncbi Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly
    Reginaldo M Kuroshu
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
    PLoS ONE 5:e10517. 2010
    ..However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded...
  39. ncbi Delayed traumatic diaphragmatic hernia after open splenectomy: report of a case
    Kazuto Tsuboi
    Department of Surgery, Jikei University School of Medicine, 3 25 8 Nishishinbashi, Minato ku, Tokyo 105 8461, Japan
    Surg Today 38:352-4. 2008
    ..We sutured the hernial orifice closed and performed Dor fundoplication. Although sporadic reports on this type of hernia following laparoscopic surgery have been reported, delayed diaphragmatic hernia following open splenectomy is rare...
  40. ncbi Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method
    Yutaka Suzuki
    Laboratory of Genome Structure Analysis, HGC, Institute of Medical Science, University of Tokyo, Japan
    Methods Mol Biol 221:73-91. 2003
  41. ncbi DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
    Nucleic Acids Res 34:D86-9. 2006
    ..Third, DBTSS provides detailed sequence comparisons of user-specified TSSs. Finally, we have added TSS information for zebrafish, malaria and schyzon (a red algae model organism). DBTSS is accessible at http://dbtss.hgc.jp...
  42. ncbi Zygotic amplification of secondary piRNAs during silkworm embryogenesis
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    RNA 17:1401-7. 2011
    ..These results provide on-site evidence for the ping-pong cycle...
  43. ncbi Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability
    Hidenori Tani
    Radioisotope Center, University of Tokyo, Tokyo, Japan
    RNA Biol 9:1370-9. 2012
    ..Many UPF1 targets in this study were newly identified. This study clearly demonstrates that direct determination of RNA stability is a powerful approach for identifying targets of RNA degradation factors...
  44. ncbi A role for transcription from a piRNA cluster in de novo piRNA production
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo, Japan
    RNA 18:265-73. 2012
    ..Bioinformatic analyses suggest that the fusion transcript is a source of GFP primary piRNAs. Our data implicate a role for transcription from a piRNA cluster in initiating de novo piRNA production against a new insertion...
  45. ncbi Primary gastric plasmacytoma refractory to Helicobacter pylori eradication therapy
    Naruo Kawasaki
    Department of Surgery, Jikei University School of Medicine, Tokyo, Japan
    Dig Endosc 21:37-9. 2009
    ..Primary gastric plasmacytoma was diagnosed. Total gastrectomy was carried out with splenectomy and regional lymph node dissection. The patient remains disease free as of 6 years postoperatively...
  46. ncbi Early postoperative enteral nutrition is useful for recovering gastrointestinal motility and maintaining the nutritional status
    Naruo Kawasaki
    Department of Surgery, Jikei University School of Medicine, 3 25 8 Nishi shinbashi, Minato ku, Tokyo, 105 8461, Japan
    Surg Today 39:225-30. 2009
    ..The purpose of this study was to compare the effects of enteral and parenteral nutrition soon after open abdominal surgery on gastrointestinal motility and nutritional status...
  47. ncbi High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer
    Shin Ichi Hashimoto
    Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    PLoS ONE 4:e4108. 2009
    ..The high-resolution 5'end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology...
  48. ncbi Effect of gelatinization on gastric emptying and absorption
    Naruo Kawasaki
    Department of Surgery, Jikei University School of Medicine, 3 25 8 Nishi shinbashi, Minato ku, Tokyo 105 8461, Japan
    Hepatogastroenterology 55:1843-5. 2008
    ..The aim of this study was to compare the gastric emptying and absorption obtained by 13C-breath test after ingestion of liquid or gelatinized liquid nutrients...
  49. ncbi Coordinated changes in DNA methylation in antigen-specific memory CD4 T cells
    Shin Ichi Hashimoto
    Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113 0033, Japan
    J Immunol 190:4076-91. 2013
    ..By comparing DMRs between naive and Ag-specific memory T cells, this study provides new insights into the functional status of memory T cells...
  50. ncbi DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
    Riu Yamashita
    Frontier Research Initiative, Institute of Medical Science, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 40:D150-4. 2012
    ..DBTSS can be accessed at http://dbtss.hgc.jp...
  51. ncbi Genome-wide maps of mononucleosomes and dinucleosomes containing hyperacetylated histones of Aspergillus fumigatus
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
    PLoS ONE 5:e9916. 2010
    ..However, most of the nucleosome positions are conserved in the gene promoters, even after treatment with TSA, because of the low density of nucleosomes in the gene promoters...
  52. ncbi Modified liver hanging maneuver with extraparenchymal isolation of the middle hepatic vein in left hepatectomy
    Masanori Sugiyama
    Department of Surgery, Kyorin University School of Medicine, Mitaka, Tokyo, Japan
    J Hepatobiliary Pancreat Surg 16:156-9. 2009
    ..We devised a modified maneuver with tape repositioning between the MHV and left hepatic vein (LHV) after extraparenchymal isolation of the MHV, in left hepatectomy with the caudate lobe and without the MHV...
  53. ncbi Computation of rank and select functions on hierarchical binary string and its application to genome mapping problems for short-read DNA sequences
    Kouichi Kimura
    Central Research Laboratory, Hitachi, Ltd, Tokyo, Japan
    J Comput Biol 16:1601-13. 2009
    ..An experimentally implemented program mapped several thousands of sequences per second on a single 3.0-GHz CPU, several times faster than ELAND, a widely used mapping program with the Illumina-Solexa 1G analyser...
  54. ncbi Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing
    J Fah Sathirapongsasuti
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562, Japan
    Nucleic Acids Res 39:1967-79. 2011
    ..The discovery of UCSs shed new light on the multifaceted, fine-tuned and tight post-transcriptional regulation of gene families as conserved through the majority of the mammalian lineage...
  55. ncbi Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes
    Kouichi Kimura
    Life Science Research Laboratory, Central Research Laboratory, Hitachi, Ltd, Kokubunji, Tokyo, 185-8601, Japan
    Genome Res 16:55-65. 2006
    ..Our findings suggest that use of alternate promoters and consequent alternative use of first exons should play a pivotal role in generating the complexity required for the highly elaborated molecular systems in humans...
  56. ncbi Achalasia complicated by multiple intramucosal carcinomas: report of a case
    Naruo Kawasaki
    Department of Surgery, Jikei University School of Medicine, 3 25 8 Nishi shinbashi, Minato ku, Tokyo 105 8461, Japan
    Surg Today 37:897-900. 2007
    ..The main cause of dysphagia was due to a marked flexion of the upper esophagus. Even though we identified a precancerous state, we believe that surgery was an appropriate option in this case...
  57. ncbi [Pancreatic ductal carcinoma concomitant with intraductal papillaly mucinous neoplasm]
    Yutaka Suzuki
    Dept of Surgery, Kyorin University, Tokyo, Japan
    Gan To Kagaku Ryoho 39:347-50. 2012
    ..It is important to thoroughly examine the entire pancreas for the potentialco -occurrence of DC in patients with IPMN...
  58. ncbi The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113 8657, Japan
    RNA 15:1258-64. 2009
    ..Taken together, BmN4 is a unique cell line in which both primary and secondary steps of piRNA biogenesis pathways are active. This cell line would provide useful tools for analysis of piRNA biogenesis and function...
  59. ncbi Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis
    Nicolas Sierro
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Gene 430:44-9. 2009
    ..intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently...
  60. ncbi DKK1, a negative regulator of Wnt signaling, is a target of the beta-catenin/TCF pathway
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Oncogene 23:8520-6. 2004
    ..Our finding suggests the existence of a novel feedback loop in Wnt signaling...
  61. ncbi Falciform ligament in pancreatoduodenectomy for protection of skeletonized and divided vessels
    Nobutsugu Abe
    Department of Surgery, Kyorin University School of Medicine, Mitaka, Tokyo, Japan
    J Hepatobiliary Pancreat Surg 16:184-8. 2009
    ..We reviewed 36 patients who underwent PD that included this option...
  62. ncbi Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs
    Naoki Osada
    Division of Genetic Resources, National Institute of Infectious Diseases, Tokyo, Japan
    Mol Biol Evol 22:1976-82. 2005
    ..The results imply that positive selection increased K5UTR and structural alteration rate of a certain fraction of genes as well as Ka. We found that both positive and negative selection can act on the 5'UTR sequences...
  63. ncbi Analysis of transcriptomes of human malaria parasite Plasmodium falciparum using full-length enriched library: identification of novel genes and diverse transcription start sites of messenger RNAs
    Junichi Watanabe
    Department of Parasitology, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Gene 291:105-13. 2002
    ..The transcriptional start sites of all the genes studied were far more diverse than those of human genes. These observations may reflect unique mechanism(s) of gene expression in this organism, which has an extremely AT-rich genome...
  64. ncbi Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs
    Masaaki Oyama
    Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
    Genome Res 14:2048-52. 2004
    ..This investigation provides the first direct evidence of translation of upstream ORFs in human cells, which could greatly change the current outline of the human proteome...
  65. ncbi Small open reading frames in 5' untranslated regions of mRnas
    Riu Yamashita
    Laboratory of Genome Database, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
    C R Biol 326:987-91. 2003
    ..They require attention for further analysis to identify their biological role...
  66. ncbi Effects of Alu elements on global nucleosome positioning in the human genome
    Yoshiaki Tanaka
    Department of Medical Genome Sciences, University of Tokyo, Minato ku, Japan
    BMC Genomics 11:309. 2010
    ..As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still unclear whether this feature can be observed in the whole genomes of all eukaryotes...
  67. ncbi Advanced ampullary carcinoma showing complete response to S-1: report of a case
    Nobutsugu Abe
    Department of Surgery, Kyorin University School of Medicine, 6 20 2 Shinkawa, Mitaka, Tokyo, 181 8611, Japan
    Surg Today 40:574-7. 2010
    ..Thus, S-1 monotherapy may be considered as a chemotherapeutic strategy for unresectable ampullary carcinoma, although large-scale studies will be required to confirm its true efficacy...
  68. ncbi Predictive factors for cholangiocarcinoma associated with hepatolithiasis determined on the basis of Japanese Multicenter study
    Yutaka Suzuki
    Department of Surgery, Kyorin University School of Medicine, Tokyo, Japan
    Hepatol Res 42:166-70. 2012
    ..Choledocoenterostomy is thus contraindicated in patients with hepatolithiasis. An aggressive resection strategy is recommended for an atrophic segment...
  69. ncbi Direct percutaneous endoscopic duodenostomy: a case report
    Yuichiro Tanishima
    Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
    Surg Laparosc Endosc Percutan Tech 19:e98-9. 2009
    ..In this patient, we successfully performed a direct percutaneous endoscopic duodenostomy without any complication...
  70. ncbi Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D
    Motomichi Matsuzaki
    Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nature 428:653-7. 2004
    ..These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells...
  71. ncbi A transcription factor response element for gene expression during circadian night
    Hiroki R Ueda
    Molecular Medicine Laboratories, Institute for Drug Discovery Research, Yamanouchi Pharmaceutical Company, Ltd, 21 Miyukigaoka, Tsukuba, Ibaraki 305 8585, Japan
    Nature 418:534-9. 2002
    ..This role was verified using an in vitro validation system, in which cultured fibroblasts transiently transfected with clock-controlled reporter vectors exhibited robust circadian bioluminescence...
  72. ncbi Identification of two novel primate-specific genes in DSCR
    Kunihiko Takamatsu
    Laboratory of Functional Genomics Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
    DNA Res 9:89-97. 2002
    ..These results strongly suggest that DSCR9 and DSCR10 have emerged as a new class of gene in the primate lineage during evolution...
  73. ncbi OASIS is a transcriptional activator of CREB/ATF family with a transmembrane domain
    Yoshihiro Omori
    Laboratory of Genome Structure Analysis Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Biochem Biophys Res Commun 293:470-7. 2002
    ..Western blot analysis of transfected cells identified OASIS polypeptides of 82 and 66 kDa. These results suggest that the transmembrane domain plays an important role in the regulation of transcriptional activation by OASIS...
  74. ncbi SAGE analysis of early oogenesis in the silkworm, Bombyx mori
    Shunsuke Funaguma
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    Insect Biochem Mol Biol 37:147-54. 2007
    ..1-fold enriched) and ATP synthase coupling factor 6 (9.1-fold enriched), suggesting that they are involved in regulation of cell cycle of cystocytes...
  75. ncbi Functional gene screening system identified TRPV4 as a regulator of chondrogenic differentiation
    Shuji Muramatsu
    Laboratory for Drug Discovery, Research Center, Asahi Kasei Pharma Corp, 2 1 Samejima, Fuji, Shizuoka 416 8501, Japan
    J Biol Chem 282:32158-67. 2007
    ..We showed that activation of TRPV4 increased the steady-state levels of SOX9 mRNA and protein and SOX6 mRNA. Taken together, our results suggest that TRPV4 regulates the SOX9 pathway and contributes to the process of chondrogenesis...
  76. ncbi [Human transcriptome]
    Motohiko Tanino
    Tanpakushitsu Kakusan Koso 50:2059-64. 2005
  77. ncbi Gene expression analysis of human hepatocellular carcinoma by using full-length cDNA library
    Chia-Chu Tsai
    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan, ROC
    J Biomed Sci 13:241-9. 2006
    ..8, 8.5, 3.2, and 10.5-fold, respectively. Our results provide crucial candidate genes to develop clinical diagnosis and gene therapy of HCC...
  78. ncbi Large-scale identification and characterization of human genes that activate NF-kappaB and MAPK signaling pathways
    Akio Matsuda
    Laboratory for Biology, Institute for Life Science Research, Health Care Company, ASAH1 KASEI Corporation, 2 1 Samejima, Fuji shi, Shizuoka 416 8501, Japan
    Oncogene 22:3307-18. 2003
    ..Interestingly, 27 genes were overlapping between the NF-kappaB and the MAPK pathways, which may indicate that these genes play cross-talking roles between these two pathways...
  79. ncbi The 5' terminal oligopyrimidine tract of human elongation factor 1A-1 gene functions as a transcriptional initiator and produces a variable number of Us at the transcriptional level
    Akiko Shibui-Nihei
    Department of Preventive Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
    Gene 311:137-45. 2003
    ..Many other housekeeping genes, including ribosomal protein genes, are also members of the 5' TOP gene family, and the 5' TOP sequence may be an important core-promoter element of these genes...
  80. ncbi Gene structure, dual-promoters and mRNA alternative splicing of the human and mouse regulator of G protein signaling GAIP/RGS19
    Guo Xi Xie
    Department of Anesthesia and Perioperative Medicine, University of California, 513 Parnassus Avenue, San Francisco, CA 94143 0464, USA
    J Mol Biol 325:721-32. 2003
    ..GAIP/RGS19 alternative splicing patterns are differentially expressed in various tissues. The mRNA alternative splicing to produce multiple isoforms may play a significant role in regulating the function and selectivity of GAIP/RGS19...
  81. ncbi The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)
    Daniela S Gerhard
    Genome Res 14:2121-7. 2004
    ..Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline...
  82. ncbi Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs
    Jun-ichi Takeda
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio-IT Research, Building Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan
    Nucleic Acids Res 34:3917-28. 2006
    ....
  83. ncbi H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational
    Jun Ichi Takeda
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio IT Research, Building Aomi 2 42, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 35:D104-9. 2007
    ..H-DBAS is accessible at http://jbirc.jbic.or.jp/h-dbas/...
  84. ncbi Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event
    Kazuko Shiroki
    Institute for Biomolecular Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
    Nucleic Acids Res 30:2851-61. 2002
    ..These results suggest that Smad5 IRES activity displays cell specificity and that some as yet unidentified nuclear event may be required for efficient Smad5 IRES-driven translation initiation...
  85. ncbi Database and analysis system for cDNA clones obtained from full-length enriched cDNA libraries
    Tetsuo Nishikawa
    Helix Research Institute, Chiba, Japan
    In Silico Biol 2:5-18. 2002
    ..And various results such as ORF features and database search results can be shown on the same screen by multiple displays. Full-length clones having interesting functions can thus be retrieved efficiently by using this system...
  86. ncbi Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain
    Naoki Osada
    Division of Genetic Resources, National Institute of Infectious Diseases, 1 23 1 Toyama cho, Shinjuku ku, 162 8640, Japan
    Genome Biol 3:RESEARCH0006. 2002
    ..In this study, we used cDNA libraries of three other parts of the brain (frontal lobe, temporal lobe and medulla oblongata) to isolate novel full-length cDNAs...
  87. ncbi Neuroblastoma oligo-capping cDNA project: toward the understanding of the genesis and biology of neuroblastoma
    Miki Ohira
    Division of Biochemistry, Chiba Cancer Center Research Institute, 666 2 Nitona, Chuoh ku, 260 8717 Chiba, Japan
    Cancer Lett 197:63-8. 2003
    ..We have identified approximately 500 differentially expressed genes between favorable and unfavorable subsets of NBL, among which more than 250 were the genes with unknown function...
  88. ncbi The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
    Stefan A Rensing
    Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D 79104 Freiburg, Germany
    Science 319:64-9. 2008
    ..The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics...
  89. ncbi 5'-end SAGE for the analysis of transcriptional start sites
    Shin-Ichi Hashimoto
    Nat Biotechnol 22:1146-9. 2004
    ..8%-96.1% of the 5' SAGE tags were assigned within -500 to +200 nt of mRNA start sites using the RefSeq, UniGene and DBTSS databases. This technique should facilitate 5'-end transcriptome analysis in a variety of cells and tissues...
  90. ncbi Promoter prediction analysis on the whole human genome
    Vladimir B Bajic
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore
    Nat Biotechnol 22:1467-73. 2004
    ..Some PPPs even perform worse than, or close to, pure random guessing...
  91. ncbi GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene
    Duen Yi Huang
    Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, No 1 Jen Ai Road 1st section, Taipei, Taiwan, Republic of China
    Nucleic Acids Res 32:3935-46. 2004
    ..Here we conclude that functional cooperation between GATA-1 and NF-Y contributes to erythroid-specific transcriptional activation of Gfi-1B promoter...
  92. ncbi Expression profiling and differential screening between hepatoblastomas and the corresponding normal livers: identification of high expression of the PLK1 oncogene as a poor-prognostic indicator of hepatoblastomas
    Shin-ichi Yamada
    Division of Biochemistry, Chiba Cancer Center Research Institute, Chiba 260-8717, Japan
    Oncogene 23:5901-11. 2004
    ..Thus, the differentially expressed genes we have identified may become a useful tool to develop new diagnostic as well as therapeutic strategies of hepatoblastoma...
  93. ncbi Thyrotrophin in the pars tuberalis triggers photoperiodic response
    Nobuhiro Nakao
    Division of Biomodelling, Graduate School of Bioagricultural Sciences, Nagoya University, Furo cho, Chikusa ku, Nagoya 464 8601, Japan
    Nature 452:317-22. 2008
    ..Increased TSH in the pars tuberalis therefore seems to trigger long-day photoinduced seasonal breeding...
  94. ncbi Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice
    Shoshi Kikuchi
    Department of Molecular Biology, National Institute of Agrobiological Sciences, 2 1 2 Kannon dai, Tsukuba, Ibaraki 305 8602, Japan
    Science 301:376-9. 2003
    ..Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins...
  95. ncbi Characterization of genomic organization of the adenosine A2A receptor gene by molecular and bioinformatics analyses
    Liqun Yu
    Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
    Brain Res 1000:156-73. 2004
    ..This raises the possibility of generating multiple tissue-specific A(2A)R mRNA species by alternative promoters with varying regulatory susceptibility...
  96. ncbi Fugu ESTs: new resources for transcription analysis and genome annotation
    Melody S Clark
    MRC Rosalind Franklin Centre for Genomics Research, formerly known as the MRC UK HGMP Resource Centre, Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
    Genome Res 13:2747-53. 2003
    ..This is particularly timely with the increasing availability of draft genome sequence from different organisms and the mounting emphasis on gene function and regulation...
  97. ncbi Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta
    Naoki Osada
    Department of Biomedical Resources, National Institute of Biomedical Innovation, Ibaraki, Japan
    BMC Genomics 9:90. 2008
    ..These sequences were annotated based on homology to human genes and stored in a database, QFbase http://genebank.nibio.go.jp/qfbase/...
  98. ncbi Expression profiling and characterization of 4200 genes cloned from primary neuroblastomas: identification of 305 genes differentially expressed between favorable and unfavorable subsets
    Miki Ohira
    Division of Biochemistry, Chiba Cancer Center Research Institute, 666 2 Nitona, Chiba 260 8717, Japan
    Oncogene 22:5525-36. 2003
    ....
  99. ncbi Complete sequencing and characterization of 21,243 full-length human cDNAs
    Toshio Ota
    Helix Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan
    Nat Genet 36:40-5. 2004
    ..About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs...
  100. ncbi dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods
    Tomoko Tahira
    Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
    Hum Mutat 26:69-77. 2005
    ..A fraction of the SNPs revealed a significantly different allele frequency between the groups, suggesting differential selection of the genes involved...
  101. ncbi The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
    Chisato Yamasaki
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
    Nucleic Acids Res 36:D793-9. 2008
    ....