Yutaka Suzuki

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. pmc 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 request reprint 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
  3. ncbi request reprint [Transcriptome analyses and transcriptome databases]
    Yutaka Suzuki
    Tanpakushitsu Kakusan Koso 49:1859-65. 2004
  4. pmc 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
  5. pmc 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
  6. ncbi request reprint 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
  7. pmc 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
  8. ncbi request reprint 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
  9. pmc 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
  10. pmc 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

Collaborators

Detail Information

Publications119 found, 100 shown here

  1. pmc 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 request reprint 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...
  3. ncbi request reprint [Transcriptome analyses and transcriptome databases]
    Yutaka Suzuki
    Tanpakushitsu Kakusan Koso 49:1859-65. 2004
  4. pmc 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
    ....
  5. pmc 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
    ....
  6. ncbi request reprint 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...
  7. pmc 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...
  8. ncbi request reprint 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...
  9. pmc 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...
  10. pmc 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...
  11. pmc 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. pmc 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
    ....
  13. ncbi request reprint 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...
  14. ncbi request reprint 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...
  15. pmc 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. pmc 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...
  17. ncbi request reprint Laparoscopic Collis gastroplasty and Nissen fundoplication for reflux esophagitis with shortened esophagus in Japanese patients
    Kazuto Tsuboi
    Department of Surgery, Jikei University School of Medicine, Minato ku, Tokyo, Japan
    Surg Laparosc Endosc Percutan Tech 16:401-5. 2006
    ..There is an extremely small number of surgical cases of laparoscopic Collis gastroplasty and Nissen fundoplication (LCN procedure) in Japan, and it is a fact that the surgical results are not thoroughly examined...
  18. ncbi request reprint Gastric ulcer after laparoscopic fundoplication for gastroesophageal reflux disease: significance of the eradication of Helicobacter pylori
    Nobuo Omura
    Department of Surgery, Jikei University School of Medicine, Minato ku, Tokyo, Japan
    Surg Laparosc Endosc Percutan Tech 17:193-6. 2007
    ..The eradication of H. pylori may be an effective therapeutic means to prevent gastric ulcers recurrence after fundoplication...
  19. pmc 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...
  20. pmc 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...
  21. pmc 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/...
  22. pmc 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
    ....
  23. doi request reprint Characterization of a novel chromodomain-containing gene from the silkworm, Bombyx mori
    Keisuke Shoji
    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
    Gene 527:649-54. 2013
    ..siRNA-mediated knockdown of BmCdp1 in BmN4 cells and early embryos did not affect the expression of the gene located close to the BmCdp1-bound locus...
  24. doi request reprint 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...
  25. ncbi request reprint Therapeutic effects of laparoscopic fundoplication for nonerosive gastroesophageal reflux disease
    Nobuo Omura
    Department of Surgery, Jikei University School of Medicine, 3 25 8 Nishi shinbashi, Minato ku, Tokyo, 105 8461, Japan
    Surg Today 36:954-60. 2006
    ..Surgical treatments for nonerosive gastroesophageal reflux disease (NERD) have not been investigated sufficiently. We examined the results of laparoscopic fundoplication for patients with NERD...
  26. pmc 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...
  27. pmc 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...
  28. ncbi request reprint 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...
  29. pmc 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...
  30. doi request reprint 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...
  31. pmc 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...
  32. pmc 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...
  33. pmc 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/...
  34. pmc 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
    ....
  35. ncbi request reprint 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
    ....
  36. pmc 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...
  37. ncbi request reprint 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
    ....
  38. pmc 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...
  39. doi request reprint 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...
  40. pmc Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins
    Natsuko Izumi
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    RNA 19:896-901. 2013
    ..Our data highlight a role of Hsp90 in accurate loading of precursor piRNAs into PIWI proteins...
  41. pmc 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
    ....
  42. ncbi request reprint 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...
  43. pmc 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...
  44. pmc 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...
  45. pmc 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
    ....
  46. doi request reprint 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...
  47. pmc 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...
  48. ncbi request reprint 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
  49. pmc 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...
  50. doi request reprint 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...
  51. pmc 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...
  52. doi request reprint Integrated molecular analysis of clear-cell renal cell carcinoma
    Yusuke Sato
    Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    Nat Genet 45:860-7. 2013
    ..This integrated molecular analysis unmasked new correlations between DNA methylation, gene mutation and/or gene expression and copy number profiles, enabling the stratification of clinical risks for patients with ccRCC. ..
  53. doi request reprint Modified Glasgow prognostic score in patients with incurable stage IV colorectal cancer
    Tomokazu Kishiki
    Department of Surgery, Kyorin University, School of Medicine, 6 20 2 Shinkawa, Mitaka City, Tokyo, Japan
    Am J Surg 206:234-40. 2013
    ..The modified Glasgow prognostic score is an inflammation-based prognostic score. This study examined whether this score, measured before surgical procedures, could predict postoperative cancer-specific survival...
  54. ncbi request reprint Effect of Dai-kenchu-to on gastrointestinal motility based on differences in the site and timing of administration
    Naruo Kawasaki
    Department of Surgery, The Jikei University School of Medicine, 3 25 8 Nishi shinbashi, Minato ku, Tokyo, 105 8461, Japan
    Dig Dis Sci 52:2684-94. 2007
    ..These results indicate that the prokinetic effects of dai-kenchu-to differ with the site or timing of administration...
  55. doi request reprint 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...
  56. pmc MAML1 enhances the transcriptional activity of Runx2 and plays a role in bone development
    Takashi Watanabe
    Department of Systems Biomedicine, National Research Institute for Child Health and Development, Tokyo, Japan
    PLoS Genet 9:e1003132. 2013
    ..These observations suggest that chondrocyte maturation was impaired in MAML1(-/-) mice. MAML1 enhances the transcriptional activity of Runx2 and plays a role in bone development...
  57. ncbi request reprint CD147 and matrix metalloproteinase-2 protein expression as significant prognostic factors in esophageal squamous cell carcinoma
    Yoshio Ishibashi
    Department of Surgery, Jikei University School of Medicine, Tokyo, Japan
    Cancer 101:1994-2000. 2004
    ..The authors investigated whether the presence of matrix metalloproteinase-2 (MMP-2) and its inducer, CD147, in cancerous esophageal lesions and surrounding tissue might help to predict patient prognosis...
  58. ncbi request reprint Alendronate improves vitamin D-resistant osteopenia triggered by gastrectomy in patients with gastric cancer followed long term
    Yutaka Suzuki
    Department of Surgery, and Division of Clinical Research and Development, Jikei University School of Medicine, Tokyo, Japan
    J Gastrointest Surg 9:955-60. 2005
    ..01), and increased serum levels of intact parathyroid hormone (P<0.05), although body weight did not alter. These results suggest that bisphosphonate may improve osteopenia after gastrectomy/gastric bypass...
  59. ncbi request reprint Prognostic significance of vascular endothelial growth factor D in gastric carcinoma
    Atsuo Shida
    Department of Surgery, Jikei University School of Medicine, Nishi Shinbashi, 3 25 8, Minato ku, Tokyo, 105 8461, Japan
    World J Surg 29:1600-7. 2005
    ..Our data indicate the involvement of VEGF-D in tumor progression via lymphoangiogenic pathways. Practically, VEGF-D expression can be useful for predicting RFS and OS in patients with gastric carcinoma...
  60. pmc Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113 8657, Japan
    Open Biol 2:120043. 2012
    ..We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome...
  61. pmc 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...
  62. pmc 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...
  63. ncbi request reprint 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...
  64. doi request reprint 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...
  65. ncbi request reprint Therapeutic effects of a laparoscopic Heller myotomy and Dor fundoplication on the chest pain associated with achalasia
    Nobuo Omura
    Department of Surgery, Jikei University School of Medicine, 3 25 8 Nishishinbashi, Minato ku, Tokyo, 105 8461, Japan
    Surg Today 36:235-40. 2006
    ..The therapeutic effects of a laparoscopic Heller myotomy and Dor fundoplication (LHD) on the chest pain associated with achalasia were investigated...
  66. pmc 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...
  67. doi request reprint 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...
  68. pmc 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...
  69. pmc 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...
  70. pmc 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...
  71. ncbi request reprint [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...
  72. doi request reprint 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...
  73. pmc 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...
  74. doi request reprint 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...
  75. ncbi request reprint 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...
  76. ncbi request reprint 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...
  77. pmc 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...
  78. ncbi request reprint 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...
  79. ncbi request reprint 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...
  80. doi request reprint 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...
  81. pmc 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...
  82. doi request reprint 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...
  83. doi request reprint 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...
  84. ncbi request reprint 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...
  85. ncbi request reprint 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...
  86. ncbi request reprint 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...
  87. ncbi request reprint 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...
  88. ncbi request reprint 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...
  89. pmc 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...
  90. ncbi request reprint 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...
  91. ncbi request reprint 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...
  92. ncbi request reprint 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...
  93. ncbi request reprint 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...
  94. ncbi request reprint 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...
  95. pmc 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
    ....
  96. ncbi request reprint 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...
  97. pmc 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/...
  98. pmc 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...
  99. ncbi request reprint 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...
  100. pmc 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...
  101. ncbi request reprint 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
    ....