Yuichi Shiraishi

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. pmc An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data
    Yuichi Shiraishi
    Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 41:e89. 2013
  2. doi request reprint A rank-based statistical test for measuring synergistic effects between two gene sets
    Yuichi Shiraishi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
    Bioinformatics 27:2399-405. 2011
  3. doi request reprint Recurrent somatic mutations underlie corticotropin-independent Cushing's syndrome
    Yusuke Sato
    Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    Science 344:917-20. 2014
  4. pmc Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma
    Masafumi Seki
    Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113 8655, Japan
    Nat Commun 6:7557. 2015
  5. doi request reprint Biallelic DICER1 mutations in sporadic pleuropulmonary blastoma
    Masafumi Seki
    Authors Affiliations Department of Pediatrics Cancer Genomics Project, Graduate School of Medicine Laboratory of DNA Information Analysis and Sequence Data Analysis, Human Genome Center, Institute of Medical Science Department of Cell Therapy and Transplantation Medicine, The University of Tokyo, Tokyo Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto Division of Pediatric Hematology and Oncology, Ibaraki Children s Hospital, Mito, Ibaraki Department of Hematology Oncology, Saitama Children s Medical Center, Saitama, Saitama Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka Gunma Children s Medical Center, Shibukawa, Gunma Department of Hematology and Oncology, Hyogo Prefectural Kobe Children s Hospital, Kobe, Hyogo and National Center for Child Health and Development, Tokyo, Japan
    Cancer Res 74:2742-9. 2014
  6. doi request reprint Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data
    Kenichi Chiba
    Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108 8639 and Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606 8501, Japan
    Bioinformatics 31:116-8. 2015
  7. doi request reprint Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity
    Akihiro Fujimoto
    1 Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108 8639, Japan 2 Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama 230 0045, Japan
    Nat Commun 6:6120. 2015
  8. 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
  9. doi request reprint Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms
    Ayana Kon
    Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Nat Genet 45:1232-7. 2013
  10. pmc HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations
    Naoto Usuyama
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113 8655 and Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606 8501, Japan
    Bioinformatics 30:3302-9. 2014

Collaborators

Detail Information

Publications15

  1. pmc An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data
    Yuichi Shiraishi
    Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 41:e89. 2013
    ....
  2. doi request reprint A rank-based statistical test for measuring synergistic effects between two gene sets
    Yuichi Shiraishi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
    Bioinformatics 27:2399-405. 2011
    ..Although several approaches have been proposed for inferring cooperativity among multiple factors, most approaches are haunted by the issues of normalization and threshold values...
  3. doi request reprint Recurrent somatic mutations underlie corticotropin-independent Cushing's syndrome
    Yusuke Sato
    Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    Science 344:917-20. 2014
    ..These results highlight the major role of cAMP-independent activation of cAMP/PKA signaling by somatic mutations in corticotropin-independent Cushing's syndrome, providing insights into the diagnosis and therapeutics of this syndrome. ..
  4. pmc Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma
    Masafumi Seki
    Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113 8655, Japan
    Nat Commun 6:7557. 2015
    ..Despite the better prognosis of embryonal RMS, patients in the E2 are likely to have a poor prognosis. Our results highlight the close relationships of the methylation status and gene mutations with the biological behaviour in RMS. ..
  5. doi request reprint Biallelic DICER1 mutations in sporadic pleuropulmonary blastoma
    Masafumi Seki
    Authors Affiliations Department of Pediatrics Cancer Genomics Project, Graduate School of Medicine Laboratory of DNA Information Analysis and Sequence Data Analysis, Human Genome Center, Institute of Medical Science Department of Cell Therapy and Transplantation Medicine, The University of Tokyo, Tokyo Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto Division of Pediatric Hematology and Oncology, Ibaraki Children s Hospital, Mito, Ibaraki Department of Hematology Oncology, Saitama Children s Medical Center, Saitama, Saitama Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka Gunma Children s Medical Center, Shibukawa, Gunma Department of Hematology and Oncology, Hyogo Prefectural Kobe Children s Hospital, Kobe, Hyogo and National Center for Child Health and Development, Tokyo, Japan
    Cancer Res 74:2742-9. 2014
    ..Our results highlight the role of RNase IIIb domain mutations in DICER1 along with TP53 inactivation in PPB pathogenesis...
  6. doi request reprint Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data
    Kenichi Chiba
    Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108 8639 and Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606 8501, Japan
    Bioinformatics 31:116-8. 2015
    ..Availability and implementaion: Genomon ITDetector is freely available at https://github.com/ken0-1n/Genomon-ITDetector...
  7. doi request reprint Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity
    Akihiro Fujimoto
    1 Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108 8639, Japan 2 Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama 230 0045, Japan
    Nat Commun 6:6120. 2015
    ..This study reveals the strong impact of chronic hepatitis on the mutational landscape in liver cancer and the genetic diversity among LCBs. ..
  8. 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. ..
  9. doi request reprint Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms
    Ayana Kon
    Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Nat Genet 45:1232-7. 2013
    ..These findings suggest a role for compromised cohesin functions in myeloid leukemogenesis. ..
  10. pmc HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations
    Naoto Usuyama
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113 8655 and Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606 8501, Japan
    Bioinformatics 30:3302-9. 2014
    ..Although haplotype phasing information derived by using heterozygous germ line variants near candidate mutations would improve accuracy, no somatic mutation caller that uses such information is currently available...
  11. doi request reprint Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia
    Tetsuichi Yoshizato
    From the Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto T Y, K Y, A S O, Y Sato, H S, K K, Y Shiozawa, Y N, A K, M S, S O, Department of Cellular Transplantation Biology, Division of Cancer Medicine, Graduate School of Medical Sciences, Kanazawa University, Kanazawa K H, T K, S N, Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo Y Shiraishi, K C, H T, S M, and the Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya Y O all in Japan the Hematology Branch B D, K H, D T, D L, Lisbon
    N Engl J Med 373:35-47. 2015
    ..Patients have a response to immunosuppressive therapy, but myelodysplastic syndromes and acute myeloid leukemia develop in about 15% of the patients, usually many months to years after the diagnosis of aplastic anemia...
  12. pmc ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information
    Shin Suzuki
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo, 108 8639, Japan
    BMC Bioinformatics 12:S7. 2011
    ..Next-generation sequencing allows us to obtain a multitude of sequence data, some of which can be used to infer the position of SVs...
  13. doi request reprint Frequent pathway mutations of splicing machinery in myelodysplasia
    Kenichi Yoshida
    Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 8655, Japan
    Nature 478:64-9. 2011
    ..Our results provide the first evidence indicating that genetic alterations of the major splicing components could be involved in human pathogenesis, also implicating a novel therapeutic possibility for myelodysplasia...
  14. pmc A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures
    Yuichi Shiraishi
    Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    PLoS Genet 11:e1005657. 2015
    ..Our methods are implemented in an R package pmsignature (https://github.com/friend1ws/pmsignature) and a web application available at https://friend1ws.shinyapps.io/pmsignature_shiny/. ..
  15. pmc Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers
    Yuichi Shiraishi
    Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108 8639, Japan
    PLoS ONE 9:e114263. 2014
    ....