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Development of Systems Cancer Research by Computation and Simulation

Planned Research

Project AreaIntegrative Systems Understanding of Cancer for Advanced Diagnosis, Therapy and Prevention
Project/Area Number 22134004
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionThe University of Tokyo

Principal Investigator

MIYANO SATORU  東京大学, 医科学研究所, 教授 (50128104)

Co-Investigator(Kenkyū-buntansha) IMOTO Seiya  東京大学, 医科学研究所, 准教授 (10345027)
YAMAGUCHI Rui  東京大学, 医科学研究所, 講師 (90380675)
SHIRAISHI Yuichi  東京大学, 医科学研究所, 助教 (70516880)
TAMADA Yoshinori  東京大学, 大学院情報理工学研究科, 助教 (80435495)
SHIMAMURA Teppei  名古屋大学, 医学系研究科, 特任准教授 (00623943)
NAGASAKI Masao  東京大学, 医科学研究所, 准教授 (90396862)
Co-Investigator(Renkei-kenkyūsha) HIGUCHI Tomoyuki  大学共同利用機関法人情報, システム研究機構統計数理研究所, 所長 (70202273)
KAYANO Mitsunori  帯広畜産大学, 畜産学部, 講師 (20590095)
GOTOH Noriko  東京大学, 医科学研究所, 特任准教授 (10251448)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥207,740,000 (Direct Cost: ¥159,800,000、Indirect Cost: ¥47,940,000)
Fiscal Year 2014: ¥38,740,000 (Direct Cost: ¥29,800,000、Indirect Cost: ¥8,940,000)
Fiscal Year 2013: ¥40,690,000 (Direct Cost: ¥31,300,000、Indirect Cost: ¥9,390,000)
Fiscal Year 2012: ¥42,640,000 (Direct Cost: ¥32,800,000、Indirect Cost: ¥9,840,000)
Fiscal Year 2011: ¥42,250,000 (Direct Cost: ¥32,500,000、Indirect Cost: ¥9,750,000)
Fiscal Year 2010: ¥43,420,000 (Direct Cost: ¥33,400,000、Indirect Cost: ¥10,020,000)
Keywordsがん / システム生物学 / ゲノム科学 / バイオインフォマティクス / 統計的モデリング / 遺伝統計学 / スーパーコンピュータ / 遺伝子ネットワーク / シークエンス解析
Outline of Final Research Achievements

We developed a new research area “systems cancer research” by fusing large-scale data analysis and mathematical modelling that made full use of mathematics and supercomputers. Methodologies for system cancer research were installed in each cancer study of the members. Methodologies and utilization of supercomputers innovated integrative studies among “wet” and “dry” laboratories. As a result, our comprehensive understanding of cancer systems advanced drastically. Our collaboration with Seishi Ogawa about myelodysplasia (MDS) showed for the first time in the world that the abnormality of the RNA splicing is the cause of MDS. This discovery that abnormal RNA splicing is a cause of cancer held a special place in the pages of cancer research history. Our collaboration with Takashi Takahashi discovered the prognostic hubs and subnetworks which switch survival/death of lung cancer patients.

Report

(6 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (123 results)

All 2015 2014 2013 2012 2011 2010 Other

All Journal Article (93 results) (of which Peer Reviewed: 93 results,  Open Access: 29 results) Presentation (25 results) (of which Invited: 14 results) Remarks (5 results)

  • [Journal Article] Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data. Bioinformatics2015

    • Author(s)
      Chiba K, Shiraishi Y, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S.
    • Journal Title

      Bioinformatics

      Volume: 31(1) Pages: 116-118

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity2015

    • Author(s)
      Fujimoto A, Furuta M, Shiraishi Y, Gotoh K, Kawakami Y, Arihiro K, Nakamura T, Ueno M, Ariizumi SI, Hai Nguyen H, Shigemizu D, Abe T, Boroevich KA, Nakano K, Sasaki A, Kitada R, Maejima K, Yamamoto Y, Tanaka H, Shibuya T, Shibata T, Ojima H, Shimada K, Hayami S, Shigekawa Y, Aikata H, Ohdan H, Marubashi S, et al.
    • Journal Title

      Nat Commun.

      Volume: 6 Pages: 6120-6120

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] PRPF8 defects cause missplicing in myeloid malignancies2015

    • Author(s)
      Kurtovic-Kozaric A, Przychodzen B, Singh J, Konarska MM, Clemente MJ, Otrock ZK, Nakashima M, Hsi ED, Yoshida K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Boultwood J, Makishima H, Maciejewski JP, Padgett RA
    • Journal Title

      Leukemia

      Volume: 29(1) Pages: 126-136

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks2015

    • Author(s)
      Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T
    • Journal Title

      MC Syst Biol

      Volume: 9(1) Pages: 14-14

    • NAID

      120005749949

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features2014

    • Author(s)
      Arima C, Kajino T, Tamada Y, Imoto S, Shimada Y, Nakatochi M, Suzuki M, Isomura H, Yatabe Y, Yamaguchi T, Yanagisawa K, Miyano S, Takahashi T
    • Journal Title

      Carcinogenesis

      Volume: 35(10) Pages: 2224-2231

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Tracing the development of acute myeloid leukemia in CBL syndrome2014

    • Author(s)
      Becker H, Yoshida K, Blagitko-Dorfs N, Claus R, Pantic M, Abdelkarim M, Niemoller C, Greil C, Hackanson B, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Dohner K, Schnittger S, Henneke P, Niemeyer CM, Flotho C, Pfeifer D, Ogawa S, Lubbert M
    • Journal Title

      Blood

      Volume: 123(12) Pages: 1883-1886

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Acquired initiating mutations in early hematopoietic cells of CLL patients2014

    • Author(s)
      Damm F, Mylonas E, Cosson A, Yoshida K, Della Valle V, Mouly E, Diop M, Scourzic L, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Kikushige Y, Davi F, Lambert J, Gautheret D, Merle-Beral H, Sutton L, Dessen P, Solary E, Akashi K, Vainchenker W, Mercher T, Droin N, Ogawa S, Nguyen-Khac F, Bernard OA
    • Journal Title

      Cancer Discov

      Volume: 4(9) Pages: 1088-1101

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A tutorial to identify nonlinear associations in gene expression time series data2014

    • Author(s)
      Fujita A, Miyano S
    • Journal Title

      Methods Mol Biol.

      Volume: 1164 Pages: 87-95

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Landscape of genetic lesions in 944 patients with myelodysplastic syndromes2014

    • Author(s)
      Haferlach T, Nagata Y, Grossmann V, Okuno Y, Bacher U, Nagae G, Schnittger S, Sanada M, Kon A, Alpermann T, Yoshida K, Roller A, Nadarajah N, Shiraishi Y, Shiozawa Y, Chiba K, Tanaka H, Koeffler HP, Klein HU, Dugas M, Aburatani H, Kohlmann A, Miyano S, Haferlach C, Kern W, Ogawa S
    • Journal Title

      Leukemia

      Volume: 28(2) Pages: 241-247

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data2014

    • Author(s)
      Hasegawa T, Mori T, Yamaguchi R, Imoto S, Miyano S, Akutsu T
    • Journal Title

      J Comput Biol

      Volume: 21(11) Pages: 785-798

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An efficient method of exploring simulation models by assimilating literature and biological observational data2014

    • Author(s)
      Hasegawa T, Nagasaki M, Yamaguchi R, Imoto S, Miyano S
    • Journal Title

      Biosystems

      Volume: 121 Pages: 54-66

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Recurrent genetic defects on chromosome 7q in myeloid neoplasms2014

    • Author(s)
      Hosono N, Makishima H, Jerez A, Yoshida K, Przychodzen B, McMahon S, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Sanada M, Gomez-Segui I, Verma AK, McDevitt MA, Sekeres MA, Ogawa S, Maciejewski JP
    • Journal Title

      Leukemia

      Volume: 28(6) Pages: 1348-1351

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive analysis of genetic alterations and their prognostic impacts in adult acute myeloid leukemia patients2014

    • Author(s)
      Kihara R, Nagata Y, Kiyoi H, Kato T, Yamamoto E, Suzuki K, Chen F, Asou N, Ohtake S, Miyawaki S, Miyazaki Y, Sakura T, Ozawa Y, Usui N, Kanamori H, Kiguchi T, Imai K, Uike N, et. al.
    • Journal Title

      Leukemia

      Volume: 28(8) Pages: 1586-1595

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] CSML2SBML: a novel tool for converting quantitative biological pathway models from CSML into SBML2014

    • Author(s)
      Li C, Nagasaki M, Ikeda E, Sekiya Y, Miyano S
    • Journal Title

      Biosystems

      Volume: 121 Pages: 22-28

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Clonal leukemic evolution in myelodysplastic syndromes with TET2 and IDH1/2 mutations2014

    • Author(s)
      Lin TL, Nagata Y, Kao HW, Sanada M, Okuno Y, Huang CF, Liang DC, Kuo MC, Lai CL, Lee EH, Shih YS, Tanaka H, Shiraishi Y, Chiba K, Lin TH, Wu JH, Miyano S, Ogawa S, Shih LY
    • Journal Title

      Haematologica

      Volume: 99(1) Pages: 28-36

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Haploinsufficiency of Sf3b1 leads to compromised stem cell function but not to myelodysplasia2014

    • Author(s)
      Matsunawa M, Yamamoto R, Sanada M, Sato-Otsubo A, Shiozawa Y, Yoshida K, Otsu M, Shiraishi Y, Miyano S, Isono K, Koseki H, Nakauchi H, Ogawa S
    • Journal Title

      Leukemia

      Volume: 28(9) Pages: 1844-1850

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Robust prediction of anti-cancer drug sensitivity and sensitivity-specific biomarker2014

    • Author(s)
      Park H, Shimamura T, Miyano S, Imoto S
    • Journal Title

      PLoS One

      Volume: 9(1)

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Somatic RHOA mutation in angioimmunoblastic T cell lymphoma2014

    • Author(s)
      Sakata-Yanagimoto M, Enami T, Yoshida K, Shiraishi Y, Ishii R, Miyake Y, Muto H, Tsuyama N, Sato-Otsubo A, Okuno Y, Sakata S, Kamada Y, Nakamoto-Matsubara R, et. al.
    • Journal Title

      Nat Genet.

      Volume: 46(2) Pages: 171-175

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Recurrent somatic mutations underlie corticotropin-independent Cushing's syndrome2014

    • Author(s)
      Sato Y, Maekawa S, Ishii R, Sanada M, Morikawa T, Shiraishi Y, Yoshida K, Nagata Y, Sato-Otsubo A, Yoshizato T, Suzuki H, Shiozawa Y, Kataoka K, Kon A, Aoki K, Chiba K, Tanaka H, Kume H, Miyano S, Fukayama M, Nureki O, Homma Y, Ogawa S
    • Journal Title

      Science

      Volume: 344(6186) Pages: 917-920

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Loss of CDCP1 expression promotes invasiveness and poor prognosis in esophageal squamous cell carcinoma2014

    • Author(s)
      Sawada G, Takahashi Y, Niida A, Shimamura T, Kurashige J, Matsumura T, Ueo H, Uchi R, Takano Y, Ueda M, Hirata H, Sakimura S, Shinden Y, Eguchi H, Sudo T, Sugimachi K, Miyano S, Doki Y, Mori M, Mimori K
    • Journal Title

      Ann Surg Oncol

      Volume: 21 Suppl 4 Pages: 640-647

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Biallelic DICER1 mutations in sporadic pleuropulmonary blastoma2014

    • Author(s)
      Seki M, Yoshida K, Shiraishi Y, Shimamura T, Sato Y, Nishimura R, Okuno Y, Chiba K, Tanaka H, Kato K, Kato M, Hanada R, Nomura Y, Park MJ, Ishida T, Oka A, Igarashi T, Miyano S, Hayashi Y, Ogawa S, Takita J
    • Journal Title

      Cancer Res.

      Volume: 74(10) Pages: 2742-2749

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A feature selection method using fixed-point algorithm for DNA microarray gene expression data2014

    • Author(s)
      Sharma A, Paliwal KK, Imoto S, Miyano S, Sharma V, Ananthanarayanan R
    • Journal Title

      International Journal of Knowledge Based and Intelligent Engineering Systems

      Volume: 18(1) Pages: 55-59

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A feature selection method using improved regularized linear discriminant analysis2014

    • Author(s)
      Sharma A, Paliwal KK, Imoto S, Miyano S
    • Journal Title

      Mach Vis Appl.

      Volume: 25(3) Pages: 775-786

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria2014

    • Author(s)
      Shen W, Clemente MJ, Hosono N, Yoshida K, Przychodzen B, Yoshizato T, Shiraishi Y, Miyano S, Ogawa S, Maciejewski JP, Makishima H
    • Journal Title

      J Clin Invest

      Volume: 124(10) Pages: 4529-4538

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers2014

    • Author(s)
      Shiraishi Y, Fujimoto A, Furuta M, Tanaka H, Chiba K, Boroevich KA, Abe T, Kawakami Y, Ueno M, Gotoh K, Ariizumi S, Shibuya T, Nakano K, Sasaki A, Maejima K, Kitada R, Hayami S, Shigekawa Y, Marubashi S, Yamada T, Kubo M, et. al.
    • Journal Title

      PLoS One

      Volume: 9(12)

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Allelic Imbalance at an 8q24 Oncogenic SNP is involved in activating MYC in human colorectal cancer2014

    • Author(s)
      Sugimachi K, Niida A, Yamamoto K, Shimamura T, Imoto S, Iinuma H, Shinden Y, Eguchi H, Sudo T, Watanabe M, Tanaka J, Kudo S, Hase K, Kusunoki M, Yamada K, Shimada Y, Sugihara K, Maehara Y, Miyano S, Mori M, Mimori K
    • Journal Title

      Ann Surg Oncol

      Volume: 21 Suppl 4 Pages: 515-521

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The AURKA/TPX2 axis drives colon tumorigenesis cooperatively with MYC2014

    • Author(s)
      Takahashi Y, Sheridan P, Niida A, Sawada G, Uchi R, Mizuno H, Kurashige J, Sugimachi K, Sasaki S, Shimada Y, Hase K, Kusunoki M, Kudo S, Watanabe M, Yamada K, Sugihara K, Yamamoto H, Suzuki A, Doki Y, Miyano S, Mori M, Mimori K
    • Journal Title

      Ann Oncol.

      Volume: 26(5) Pages: 935-942

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Unique mutation portraits and frequent COL2A1 gene alteration in chondrosarcoma2014

    • Author(s)
      Totoki Y, Yoshida A, Hosoda F, Nakamura H, Hama N, Ogura K, Yoshida A, Fujiwara T, Arai Y, Toguchida J, Tsuda H, Miyano S, Kawai A, Shibata T
    • Journal Title

      Genome Res

      Volume: 24(9) Pages: 1411-1420

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations2014

    • Author(s)
      Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S
    • Journal Title

      Bioinformatics

      Volume: 30(23) Pages: 3302-3309

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders2013

    • Author(s)
      Damm F, Chesnais V, Nagata Y, Yoshida K, Okuno Y, Itzykson R, Sanada M, Shiraishi Y, Gelsi-Boyer V, Miyano S, Mori H, Shih LY, Park S, Dreyfus F, Rose C, Cheze S, Vey N, Legentil M, Duffourd Y, de Botton S, Preudhomme C, Birnbaum D, Bernard OA, Ogawa S, Fontenay M, Kosmider O.
    • Journal Title

      Blood

      Volume: 122(18) Pages: 3169-3177

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Novel recurrent mutations in the RAS-like GTP-binding gene RIT1 in myeloid malignancies2013

    • Author(s)
      Gomez-Segui I, Makishima H, Jerez A, Yoshida K, Przychodzen B, Miyano S, Shiraishi Y, Husseinzadeh HD, Guinta K, Clemente M, Hosono N, McDevitt MA, Moliterno AR, Sekeres MA, Ogawa S, Maciejewski JP.
    • Journal Title

      Leukemia

      Volume: 27(9) Pages: 1943-1946

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Twist2 functions as a tumor suppressor in murine osteosarcoma cells2013

    • Author(s)
      Ishikawa T, Shimizu T, Ueki A, Yamaguchi SI, Onishi N, Sugihara E, Kuninaka S, Miyamoto T, Morioka H, Nakayama R, Kobayashi E, Toyama Y, Mabuchi Y, Matsuzaki Y, Yamaguchi R, Miyano S, Saya H.
    • Journal Title

      Cancer Sci.

      Volume: 104(7) Pages: 880-888

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multi-omics approach for estimating metabolic networks using low-order partial correlations2013

    • Author(s)
      Kayano M, Imoto S, Yamaguchi R, Miyano S.
    • Journal Title

      J Comput Biol.

      Volume: 20(8) Pages: 571-582

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms2013

    • Author(s)
      Kon A, Shih LY, Sanada M, Shiraishi Y, Okuno Y, Nagae G, Nishimoto A, Nowak D, Sato Y, Shimamura T, Tanaka H, Chiba K, Yamaguchi T, Otsu M, Obara N, Nakamaki T, Ishiyama K, Nolte F, Hofmann WK, Miyawaki S, Chiba S, Mori H, Nakauchi H, Koeffler HP, Aburatani H, Haferlach T, Shirahige K, Miyano S, Ogawa S.
    • Journal Title

      Nature Genet.

      Volume: 45(10) Pages: 1232-1237

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Somatic SETBP1 mutations in myeloid malignancies2013

    • Author(s)
      Makishima H, Yoshida K, Nguyen N, Okuno Y, Ng KP, Gudmundsson KO, Vishwakarma BA, Jerez A, Gomez-Segui I, Takahashi M, Shiraishi Y, Nagata Y, Guinta K, Mori H, Sekeres MA, Chiba K, Tanaka H, Muramatsu H, Sakaguchi H, Paquette RL, McDevitt MA, Kojima S, Saunthararajah Y, Miyano S, Shih LY, Du Y, Ogawa S, Maciejewski JP.
    • Journal Title

      Nature Genet.

      Volume: 45(8) Pages: 942-946

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multilayer cluster heat map visualizing biological tensor data2013

    • Author(s)
      Niida A, Tremmel G, Imoto S, Miyano S.
    • Journal Title

      Lecture Notes in Bioinformatics

      Volume: 8213 Pages: 116-125

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inhibition of histone demethylase JMJD1A improves anti-angiogenic therapy and reduces tumor associated macrophages2013

    • Author(s)
      Osawa T, Tsuchida R, Muramatsu M, Shimamura T, Wang F, Suehiro JI, Kanki Y, Wada Y, Yuasa Y, Aburatani H, Miyano S, Minami T, Kodama T, Shibuya M.
    • Journal Title

      Cancer Res.

      Volume: 73(10) Pages: 3019-3028

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Clonal selection in xenografted TAM recapitulates the evolutionary process of myeloid leukemia in Down syndrome2013

    • Author(s)
      Saida S, Watanabe K, Sato-Otsubo A, Terui K, Yoshida K, Okuno Y, Toki T, Wang RN, Shiraishi Y, Miyano S, Kato I, Morishima T, Fujino H, Umeda K, Hiramatsu H, Adachi S, Ito E, Ogawa S, Ito M, Nakahata T, Heike T.
    • Journal Title

      Blood

      Volume: 121(21) Pages: 4377-4387

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia2013

    • Author(s)
      Sakaguchi H, Okuno Y, Muramatsu H, Yoshida K, Shiraishi Y, Takahashi M, Kon A, Sanada M, Chiba K, Tanaka H, Makishima H, Wang X, Xu Y, Doisaki S, Hama A, Nakanishi K, Takahashi Y, Yoshida N, Maciejewski JP, Miyano S, Ogawa S, Kojima S.
    • Journal Title

      Nature Genet.

      Volume: 45(8) Pages: 937-941

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Integrated molecular analysis of clear-cell renal cell carcinoma2013

    • Author(s)
      Sato Y, Yoshizato T, Shiraishi Y, Maekawa S, Okuno Y, Kamura T, Shimamura T, Sato-Otsubo A, Nagae G, Suzuki H, Nagata Y, Yoshida K, Kon A, Suzuki Y, Chiba K, Tanaka H, Niida A, Fujimoto A, Tsunoda T, Morikawa T, Maeda D, Kume H, Sugano S, Fukayama M, Aburatani H, Sanada M, Miyano S, Homma Y, Ogawa S.
    • Journal Title

      Nature Genet.

      Volume: 45(8) Pages: 860-867

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition2013

    • Author(s)
      Sharma A, Paliwal KK, Dehzangi A, Lyons J, Imoto S, Miyano S.
    • Journal Title

      BMC Bioinformatics

      Volume: 14(1) Pages: 233-233

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Principal component analysis using QR decomposition2013

    • Author(s)
      Sharma A, Paliwal KK, Imoto S, Miyano S
    • Journal Title

      International J Machine Learning and Cybernetics

      Volume: 4(6) Pages: 679-683

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An empirical Bayesian framework for somatic mutation detection from cancer2013

    • Author(s)
      Shiraishi Y, Sato Y, Chiba K, Okuno Y, Nagata Y, Yoshida K, Shiba N, Hayashi Y, Kume H, Homma Y, Sanada M, Ogawa S, Miyano S
    • Journal Title

      Nucleic Acids Res.

      Volume: 41(7)

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The rs6983267 SNP is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer2013

    • Author(s)
      Takatsuno Y, Mimori K, Yamamoto K, Sato T, Niida A, Inoue H, Imoto S, Kawano S, Yamaguchi R, Toh H, Iinuma H, Ishimaru S, Ishii H, Suzuki S, Tokudome S, Watanabe M, Tanaka JI, Kudo SE, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Miyano S, Sugihara K, Mori M
    • Journal Title

      Ann Surg Oncol.

      Volume: 20(4) Pages: 1395-1402

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis2013

    • Author(s)
      Yokobori T, Iinuma H, Shimamura T, Imoto S, Sugimachi K, Ishii H, Iwatsuki M, Ota D, Ohkuma M, Iwaya T, Nishida N, Kogo R, Sudo T, Tanaka F, Shibata K, Toh H, Sato T, Barnard GF, Fukagawa T, Yamamoto S, Nakanishi H, Sasaki S, Miyano S, Watanabe T, Kuwano H, Mimori K, Pantel K, Mori M
    • Journal Title

      Cancer Res.

      Volume: 73(7) Pages: 2059-2069

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The landscape of somatic mutations in Down syndrome-related myeloid disorders2013

    • Author(s)
      Yoshida K, Toki T, Okuno Y, Kanezaki R, Shiraishi Y, Sato-Otsubo A, Kon A, Nagata Y, Sato Y, Wang R, Shiba N, Chiba K, Tanaka H, Hama A, Hasegawa D, Nakamura K, Kanegane H, Tsukamoto K, Adachi S, Kawakami K, Kato K, Nishimura R, Izraeli S, Hayashi Y, Miyano S, Kojima S, Ito E, Ogawa S
    • Journal Title

      Nature Genet.

      Volume: 45 Pages: 1293-1299

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells2013

    • Author(s)
      Yoshimaru T, Komatsu M, Matsuo T, Chen YA, Murakami Y, Mizuguchi K, Mizohata E, Inoue T, Akiyama M, Yamaguchi R, Imoto S, Miyano S, Miyoshi Y, Sasa M, Nakamura Y, Katagiri T
    • Journal Title

      Nature Commun.

      Volume: 4 Pages: 2443-2013

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis2013

    • Author(s)
      Affara M, Sanders D, Araki H, Tamada Y, Dunmore B, Humphreys S, Imoto S, Savoie C, Miyano S, Kuhara S, Print C, Charnock-Jones DS
    • Journal Title

      BMC Genomics

      Volume: 14(1) Issue: 1 Pages: 23-23

    • DOI

      10.1186/1471-2164-14-23

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Tumor-suppressive mir-497-195 cluster targets multiple cell-cycle regulators in hepatocellular carcinoma.2013

    • Author(s)
      Furuta M
    • Journal Title

      PLoS One

      Volume: 8 Issue: 3 Pages: e60155-e60155

    • DOI

      10.1371/journal.pone.0060155

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis.2013

    • Author(s)
      Komatsu M, Yoshimaru T, Matsuo T, Kiyotani K, Miyoshi Y, Tanahashi T, Rokutan K, Yamaguchi R, Saito A, Imoto S, Miyano S, Nakamura Y, Sasa M, Shimada M, Katagiri T.
    • Journal Title

      Int J Oncol.

      Volume: 42(2) Issue: 2 Pages: 478-506

    • DOI

      10.3892/ijo.2012.1744

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] XiP: a computational environment to create, extend and share workflows2013

    • Author(s)
      Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 29(1) Issue: 1 Pages: 137-139

    • DOI

      10.1093/bioinformatics/bts630

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] PRD : A protein-RNA interaction database2012

    • Author(s)
      Shigeo Fujimori, Katsuya Hino, Ayumu Saito, Satoru Miyano, Etsuko Miyamoto-Sato
    • Journal Title

      Bioinformation

      Volume: 8(15) Issue: 15 Pages: 729-730

    • DOI

      10.6026/97320630008729

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] IRView : a database and viewer for protein interacting regions2012

    • Author(s)
      Shigeo Fujimori, Naoya Hirai, Kazuyo Masuoka, Tomohiro Oshikubo, Tatsuhiro Yamashita, Takanori Washio, Ayumu Saito, Masao Nagasaki, Satoru Miyano, Etsuko Miyamoto-Sato
    • Journal Title

      Bioinformatics

      Volume: 28(14) Issue: 14 Pages: 1949-1950

    • DOI

      10.1093/bioinformatics/bts289

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators.2012

    • Author(s)
      Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, Nakagawa H
    • Journal Title

      Nature Genetic

      Volume: 44 Issue: 7 Pages: 760-764

    • DOI

      10.1038/ng.2291

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Functional clustering of time series gene expression data by Granger causality2012

    • Author(s)
      Fujita A, Severino P, Kojima K, Sato JR, Patriota AG, Miyano S
    • Journal Title

      BMC Systems Biology

      Volume: 6 Issue: 1 Pages: 137-137

    • DOI

      10.1186/1752-0509-6-137

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Gene network inference and visualization tools for biologists: application to new human transcriptome datasets2012

    • Author(s)
      Hurley D, Araki H, Tamada Y, (4名), Imoto S, Yasuda K, Tomiyasu Y, Tashiro K, Savoie C, Cho V, Smith S, Kuhara S, Miyano S, Charnock-Jones DS, Crampin EJ, Print CG
    • Journal Title

      Nucleic Acids Res

      Volume: 40(6) Issue: 6 Pages: 2377-2398

    • DOI

      10.1093/nar/gkr902

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Increased Risk for CRC in Diabetic Patients with the Nonrisk Allele of SNPs at 8q242012

    • Author(s)
      Ishimaru S, Iinuma H, et al
    • Journal Title

      Ann Surg Oncol

      Volume: 21(in press) Issue: 9 Pages: 21-21

    • DOI

      10.1245/s10434-012-2278-6

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identifying Gene pathways associated with cancer characteristics via sparse statistical methods2012

    • Author(s)
      Kawano S, Shimamura T, Niida A, Imoto S, Yamaguchi R, Nagasaki M, Yoshida R, Print C, Miyano S
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 9(4) Issue: 4 Pages: 966-972

    • DOI

      10.1109/tcbb.2012.48

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Statistical model-based testing to evaluate the recurrence of genomic aberrations2012

    • Author(s)
      Niida A, Imoto S, Shimamura T, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 28(12) Issue: 12 Pages: i115-i120

    • DOI

      10.1093/bioinformatics/bts203

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computational gene network analysis reveals TNF-induced angiogenesis2012

    • Author(s)
      Ogami K, Yamaguchi R, Imoto S, Tamada Y, Araki H, Print C, Miyano S
    • Journal Title

      BMC Systems Biology

      Volume: 6(Supple 2) Issue: S2

    • DOI

      10.1186/1752-0509-6-s2-s12

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A between-class overlapping filter-based method for transcriptome data analysis2012

    • Author(s)
      Sharma A, Imoto S, Miyano S
    • Journal Title

      J Bioinformatics and Computational Biology

      Volume: 10(5) Issue: 05 Pages: 1250010-1250010

    • DOI

      10.1142/s0219720012500102

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A top-r feature selection algorithm for microarray gene expression data2012

    • Author(s)
      Sharma A, Imoto S, Miyano S
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 9(3) Issue: 3 Pages: 754-764

    • DOI

      10.1109/tcbb.2011.151

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cell cycle gene networks are associated with melanoma prognosis2012

    • Author(s)
      Wang L, Hurley D, Watkins W, Araki H, Tamada Y, Muthukaruppan A, Ranjard L, Derkac E, Imoto S, Miyano S, Crampin E, Print C
    • Journal Title

      PLoS One

      Volume: 7(4) Issue: 4 Pages: e34247-e34247

    • DOI

      10.1371/journal.pone.0034247

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma2012

    • Author(s)
      後藤 典子
    • Journal Title

      PLoS ONE

      Volume: 7 Issue: 9 Pages: e43923-e43923

    • DOI

      10.1371/journal.pone.0043923

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs2012

    • Author(s)
      Yasuda T, Suzuki S, Nagasaki M, Miyano S
    • Journal Title

      BMC Bioinformatics

      Volume: 13(1) Issue: 1 Pages: 279-279

    • DOI

      10.1186/1471-2105-13-279

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing2012

    • Author(s)
      後藤 典子
    • Journal Title

      BMC Genomics

      Volume: Suppl. 1, Issue: S1

    • DOI

      10.1186/1471-2164-13-s1-s6

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of genes up-regulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinoma.2012

    • Author(s)
      後藤 典子
    • Journal Title

      Cancer Res

      Volume: 72 Issue: 1 Pages: 100-111

    • DOI

      10.1158/0008-5472.can-11-1403

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inferring contagion in regulatory networks2011

    • Author(s)
      Fujita A, Sato JR, Demas MAA, Yamaguchi R, Shimamura T, Ferreira CE, Sogayar, MC, Miyano S
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 8(2) Issue: 2 Pages: 570-576

    • DOI

      10.1109/tcbb.2010.40

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive pharmacogenomic pathway screening by data assimilation2011

    • Author(s)
      Hasegawa T, Yamaguchi R, Nagasaki M, Imoto S, Miyano S
    • Journal Title

      Lecture Notes in Bioinformatics

      Volume: 6674 Pages: 160-171

    • DOI

      10.1007/978-3-642-21260-4_18

    • ISBN
      9783642212598, 9783642212604
    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MIRACH : Efficient model checker for quantitative biological pathway models2011

    • Author(s)
      Koh CH, Nagasaki M, Saito A, Li C, Wong L, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(5) Issue: 5 Pages: 734-735

    • DOI

      10.1093/bioinformatics/btq727

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition2011

    • Author(s)
      Shimamura, T., Imoto, S., Shimada, Y., Hosono, Y., Niida, A., Nagasaki, M., Yamaguchi, R., Takahashi, T., Miyano, S
    • Journal Title

      PLoS ONE

      Volume: 6 Issue: 6 Pages: e20804-e20804

    • DOI

      10.1371/journal.pone.0020804

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A rank-based statistical test for measuring synergistic effects between two gene sets2011

    • Author(s)
      Shiraishi U, Okada-Hatakeyama M, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(17) Issue: 17 Pages: 2399-2405

    • DOI

      10.1093/bioinformatics/btr382

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ClipCrop : a tool for detecting structural variations with single-base resolution using soft-clipping information2011

    • Author(s)
      Suzuki S, Yasuda T, Shiraishi Y, Miyano S, Nagasaki M
    • Journal Title

      BMC Bioinformatics

      Volume: 12 Issue: S14

    • DOI

      10.1186/1471-2105-12-s14-s7

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Parallel algorithm for learning optimal Bayesian network structure2011

    • Author(s)
      Tamada Y, Imoto S, Miyano S
    • Journal Title

      J Machine Learning Research

      Volume: 12 Pages: 2437-2459

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers2011

    • Author(s)
      Tamada Y, Imoto S, Araki H, Nagasaki M, Print C, Charnock-Jones DS, Miyano S
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 8(3) Issue: 3 Pages: 683-697

    • DOI

      10.1109/tcbb.2010.68

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] SiGN : large-scale gene network estimation environment for high performance computing2011

    • Author(s)
      Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S
    • Journal Title

      Genome Informatics

      Volume: 25 Pages: 40-52

    • NAID

      130004567842

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] SiGN-SSM : open source parallel software for estimating gene networks with state space models2011

    • Author(s)
      Tamada Y, Yamaguchi R, Imoto S, Hirose O, Yoshida R, Nagasaki M, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(8) Issue: 8 Pages: 1172-1173

    • DOI

      10.1093/bioinformatics/btr078

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MRG-binding protein contributes to development of colorectal cancer2011

    • Author(s)
      Yamaguchi K, Sakai M, Kim J, Tsunesumi SI, Fujii T, Ikenoue T, Yamada Y, Akiyama Y, Muto Y, Yamaguchi R, Miyano S, Nakamura Y, Furukawa Y
    • Journal Title

      Cancer Science

      Volume: 102(8) Issue: 8 Pages: 1486-1492

    • DOI

      10.1111/j.1349-7006.2011.01971.x

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells2011

    • Author(s)
      Yamauchi M, Yoshino I, Yamaguchi R, Shimamura T, Nagasaki M, Imoto S, Niida A, Koizumi F, Kohno T, Yokota J, Miyano S, Gotoh N
    • Journal Title

      Am J Cancer Res

      Volume: 1(7) Pages: 828-833

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Frequent pathway mutations of splicing machinery in myelodysplasia2011

    • Author(s)
      Kenichi Yoshida
    • Journal Title

      Nature

      Volume: 478 Issue: 7367 Pages: 64-69

    • DOI

      10.1038/nature10496

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing2010

    • Author(s)
      Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, G., Boroevich, K.A., Nagasaki, M., Yamaguchi, R., Shibuya, T., Kubo, M., Miyano, S., Nakamura, Y., Tsunoda, T.
    • Journal Title

      Nature Genetics

      Volume: 42 Pages: 931-936

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets2010

    • Author(s)
      Fujita, A., Kojima, K., Patriota, A.G., Sato, J.R., Severino, P., Miyano, S.
    • Journal Title

      Bioinformatics

      Volume: 26(18) Pages: 2349-2351

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identifying hidden confounders in gene networks by Bayesian networks2010

    • Author(s)
      Higashigaki, T., Kojima, K., Yamaguchi, R., Inoue, M., Imoto, S., Miyano, S.
    • Journal Title

      Proc.10th IEEE Bioinformatics and Bioengineering

      Pages: 168-173

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Granger causality in systems biology : modeling gene networks in time series microarray data using vector autoregressive models2010

    • Author(s)
      Fujita, A., Severino, P., Sato, J.R., Miyano, S.
    • Journal Title

      Lecture Notes in Computer Science

      Volume: 6268 Pages: 13-24

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning2010

    • Author(s)
      Kawano, S., Shimamura, T., Niida, A., Imoto, S., Yamaguchi, R., Nagasaki, M., Yoshida, R., Print, C., Miyano, S.
    • Journal Title

      Proc.IEEE 10th International Symposium on Bioinformatics & Bioengineering

      Pages: 253-258

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Gene regulatory network clustering for graph layout based on microarray gene expression data2010

    • Author(s)
      Kojima, K., Imoto, S., Nagasaki, M., Miyano, S.
    • Journal Title

      Genome Informatics

      Volume: 24 Pages: 84-95

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information2010

    • Author(s)
      Kojima, K., Nagasaki, M., Miyano, S.
    • Journal Title

      BMC Bioinformatics

      Volume: 11:335(掲載確定)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cell Illustrator 4.0 : A computational platform for systems biology2010

    • Author(s)
      Nagasaki, M., Saito, A., Jeong, E., Li, C., Kojima, K., Ikeda, E., Miyano, S.
    • Journal Title

      In Silico Biology

      Volume: 10:0002(掲載確定)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues2010

    • Author(s)
      Niida, A., Imoto, S., Yamaguchi, R., Nagasaki, M., Miyano, S.
    • Journal Title

      PLoS ONE

      Volume: 5(6):e10910(掲載確定)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Model-free unsupervised gene set screening based on information enrichment in expression profiles2010

    • Author(s)
      Niida, A., Imoto, S., Yamaguchi, R., Nagasaki, M., Fujita, A., Shimamura, T., Miyano, S.
    • Journal Title

      Bioinformatics

      Volume: 26(24) Pages: 3090-3097

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inferring dynamic gene networks under varying conditions for transcriptomic network comparison2010

    • Author(s)
      Shimamura, T., Imoto, S., Yamaguchi, R., Nagasaki, M., Miyano, S.
    • Journal Title

      Bioinformatics

      Volume: 26(8) Pages: 1064-1072

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Collocation-based sparse estimation for constructing dynamic gene networks2010

    • Author(s)
      Shimamura, T., Imoto, S., Nagasaki, M., Yamauchi, M., Yamaguchi, R., Fujita, A., Tamada, Y, Gotoh, N., Miyano, S.
    • Journal Title

      Genome Informatics

      Volume: 24 Pages: 164-178

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling2010

    • Author(s)
      Tasaki, S., Nagasaki, M., Kozuka-Hata, H., Semba, K., Gotoh, N., Hattori, S., Inoue, J., Yamamoto, T., Miyano, S., Sugano, S., Oyama, M.
    • Journal Title

      PLoS ONE

      Volume: 5(11):e13926

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] スーパーコンピュータによる薬物標的、疾病応答遺伝子の探索2015

    • Author(s)
      宮野 悟
    • Organizer
      医薬ライセンシング協会第 239回月例会
    • Place of Presentation
      学士会館(東京都千代田区)
    • Year and Date
      2015-03-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Understanding Cancer Heterogeneity with Supercomputers2015

    • Author(s)
      Satoru Miyano
    • Organizer
      The Third BMIRC International Symposium
    • Place of Presentation
      池のおく園(福岡県田川市)
    • Year and Date
      2015-03-05
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Identification of Oncogenic Co-regulators using Infinite Relational Models2014

    • Author(s)
      Yoichi Chikahara, Atsushi Niida, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
    • Organizer
      The 15th International Conference on Systems Biology (ICSB) 2014
    • Place of Presentation
      メルボルン(オーストラリア)
    • Year and Date
      2014-09-14 – 2014-09-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Supercomputers for Cancer Research and Cancer Big Data2014

    • Author(s)
      Satoru Miyano
    • Organizer
      The 3rd SNU International Bioinformatics Workshop 2014
    • Place of Presentation
      ソウル(韓国)
    • Year and Date
      2014-06-23
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] バイオインフォマティクスとシステム生物学によるバイオマーカー探索2014

    • Author(s)
      宮野 悟
    • Organizer
      第21回HAB研究機構学術年会
    • Place of Presentation
      昭和大学(東京都品川区)
    • Year and Date
      2014-05-17
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Cancer Gene Network Analysis with Supercomputer2013

    • Author(s)
      Satoru Miyano
    • Organizer
      The 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2013)
    • Place of Presentation
      Crowne Plaza New Orleans-Airport, New Orleans, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] ancer Gene Network Analysis with Supercomputer2013

    • Author(s)
      Satoru Miyano
    • Organizer
      The 9th ISCB Student Council Symposium
    • Place of Presentation
      Roof Graden, ICC, Berlin, Germany
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Uncovering Gene Networks in Cancer by Computational Systems Biology2013

    • Author(s)
      Satoru Miyano
    • Organizer
      The 48th Meeting of The Polish Biochemistry Society
    • Place of Presentation
      Torun, Poland
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Accelerating Systems Cancer Research by Supercomputer2013

    • Author(s)
      Satoru Miyano
    • Organizer
      CSHL Asia Symposium “Frontiers in Bioinformatics and Computational Biology”
    • Place of Presentation
      Suzhou Dushu Lake Conference Center, Cold Spring Harbor Laboratory Asia Watson Auditorium, PR China
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Cancer Gene Network Analysis2013

    • Author(s)
      Satoru Miyano
    • Organizer
      The 24th International Conference on Genome Informatics (GIW 2013)
    • Place of Presentation
      Biopolis, Singapore
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Supercomputer for Personalized Genomic Medicine and Cancer Systems Biology2013

    • Author(s)
      Satoru Miyano
    • Organizer
      The University of Chicago Department of Medicine Section of Hematology/ Oncology Seminar
    • Place of Presentation
      米国 シカゴ
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Uncovering Diversity of Cancer as System by supercomputer2013

    • Author(s)
      Satoru Miyano
    • Organizer
      第6回高度医療都市を創出する未来技術国際シンポジウム
    • Place of Presentation
      岡山大学
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Supercomputing for Next-Generation Cancer Research2012

    • Author(s)
      Satoru Miyano
    • Organizer
      The Fourth Biosupercomputing Symposium
    • Place of Presentation
      東京国際フォーラム
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] スパコンで焙り出すがんのシステムとしての薬剤応答性と多様性2012

    • Author(s)
      宮野 悟
    • Organizer
      第71回日本癌学会学術総会 モーニングレクチャー
    • Place of Presentation
      札幌市教育文化会館
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Whole genome sequencing and supercomputer for personalized genomic medicine: The IMSUT plan2012

    • Author(s)
      Satoru Miyano
    • Organizer
      The 11th Surugadai International Symposium
    • Place of Presentation
      東京医科歯科大学
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Uncovering Molecular Networks in Cancer by Supercomputer Towards Personalized Medicine2011

    • Author(s)
      Miyano S
    • Organizer
      The 11th IEEE International Conference on BIOINFORMATICS & BIOENGINEERING
    • Place of Presentation
      Splendor Hotel Taichung, Taiwan(招待講演)
    • Year and Date
      2011-10-24
    • Related Report
      2011 Annual Research Report
  • [Presentation] Uncovering Systems in Cancer by Supercomputer2011

    • Author(s)
      Miyano S
    • Organizer
      JCA-AACR Joint Symposium at the 70th Annual Meeting of JCA
    • Place of Presentation
      Nagoya Congress Center(招待講演)
    • Year and Date
      2011-10-03
    • Related Report
      2011 Annual Research Report
  • [Presentation] スパコンで焙り出すがんのシステム2011

    • Author(s)
      宮野悟
    • Organizer
      生物物理学会シンポジウム
    • Place of Presentation
      兵庫県立大学(招待講演)
    • Year and Date
      2011-09-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] スパコンが焙り出すシステムとしてのがんの薬剤応答性、個性、多様性2011

    • Author(s)
      宮野悟
    • Organizer
      日本がん分子標的治療学会学術集会
    • Place of Presentation
      ホテル日航東京(招待講演)
    • Year and Date
      2011-06-24
    • Related Report
      2011 Annual Research Report
  • [Presentation] Breaking the Keys to Cancer Systems by Supercomputer2010

    • Author(s)
      Satoru Miyano
    • Organizer
      The 21st International Conference on Genome Informatics
    • Place of Presentation
      The First World Hotel, Hangzhou, China
    • Year and Date
      2010-12-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] Can Supercomputer Hack Cancer Systems?2010

    • Author(s)
      Satoru Miyano
    • Organizer
      Asian Regional Conference on Systems Biology
    • Place of Presentation
      The Royal Chulan Kuala Lumpur, Malaysia
    • Year and Date
      2010-11-30
    • Related Report
      2010 Annual Research Report
  • [Presentation] Breaking the Keys to Cancer Systems with Supercomputer2010

    • Author(s)
      Satoru Miyano
    • Organizer
      Seoul National University Cancer Research Institute Symposium
    • Place of Presentation
      Seoul National University Dental Hospital, Seoul, Korea
    • Year and Date
      2010-11-06
    • Related Report
      2010 Annual Research Report
  • [Presentation] Can Supercomputer Hack Cancer Systems?2010

    • Author(s)
      Satoru Miyano
    • Organizer
      CSH Asia Conference on Computational Biology
    • Place of Presentation
      Suzhou, China
    • Year and Date
      2010-09-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] がんをシステムとして読み解くために2010

    • Author(s)
      宮野悟
    • Organizer
      統計関連連合大会
    • Place of Presentation
      早稲田大学
    • Year and Date
      2010-09-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] Supercomputing for Systems Biology2010

    • Author(s)
      Satoru Miyano
    • Organizer
      Brazilian Symposium on Bioinformatics 2010
    • Place of Presentation
      Ferradura Resort, Buzios, Rio de Janeiro, Brazil
    • Year and Date
      2010-09-01
    • Related Report
      2010 Annual Research Report
  • [Remarks] システム的統合理解に基づくがんの先端的診断、治療、予防法の開発

    • URL

      http://cancersystem.hgc.jp/

    • Related Report
      2013 Annual Research Report
  • [Remarks] PART and PART-up

    • URL

      http://www.hgc.jp/~niiyan/PART/manual.html

    • Related Report
      2012 Annual Research Report
  • [Remarks] Genomon-fusion

    • URL

      http://genomon.hgc.jp/rna/

    • Related Report
      2012 Annual Research Report
  • [Remarks] Cancer integrative Pipeline

    • URL

      http://cancerip.hgc.jp/

    • Related Report
      2012 Annual Research Report
  • [Remarks] エキソームシークエンサーデータ解析パイプラインGENOMON

    • URL

      http://genomon.hgc.jp/exome/

    • Related Report
      2011 Annual Research Report

URL: 

Published: 2010-08-23   Modified: 2019-07-29  

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