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Nagasaki Masao  長崎 正朗

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NAGASAKI Masao  長崎 正朗

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Researcher Number 90396862
Other IDs
Affiliation (Current) 2022: 京都大学, スーパーグローバルコース医学生命系ユニット, 特定教授
Affiliation (based on the past Project Information) *help 2018 – 2022: 京都大学, スーパーグローバルコース医学生命系ユニット, 特定教授
2018 – 2019: 東北大学, 東北メディカル・メガバンク機構, 非常勤講師
2016 – 2018: 東北大学, 東北メディカル・メガバンク機構, 教授
2015: 東北大学, 東北メディカルメガバンク機構, 教授
2014: 東京大学, 医科学研究所, 准教授 … More
2014: 東北大学, 東北メディカル・メガバンク構, 教授
2012: 東北大学, 東北メディカル・メガバンク機構, 教授
2010 – 2012: 東京大学, 医科学研究所, 准教授
2011: 東京大学, 医科学研究所, 助教
2007 – 2009: The University of Tokyo, 医科学研究所, 助教
2005 – 2006: 東京大学, 医科学研究所, 助手 Less
Review Section/Research Field
Principal Investigator
Bioinformatics/Life informatics / Complex Systems Disease Theory / Basic Section 62010:Life, health and medical informatics-related / Basic Section 48040:Medical biochemistry-related
Except Principal Investigator
Biological Sciences / Bioinformatics/Life informatics / Basic Section 56060:Ophthalmology-related / ゲノム情報科学 / General internal medicine (including Psychosomatic medicine) / Complex systems / Medical sociology / Sports science / Basic Section 56040:Obstetrics and gynecology-related
Keywords
Principal Investigator
ペトリネット / 視覚的デバッグ / トランスクリプトーム / 妊娠期間 / マイクロアレイ / パラメータ推定 / モデル選択 / オントロジー / モデル検査 / OWL … More / HFPNe / 細胞分化 / ASTD / 次世代シーケンサ / 次世代シークエンサ / RNA-Seq / lincRNA / ベイズ法 / スーパーコンピュータ / 高性能シークエンサ / 数理統計モデル / ライフログ / オミクス / メタボローム / 出産 / 統合解析 / ロジスティック回帰 / 多層オミクス / リスク予測 / 多変量解析 / RNAシークエンシング / eQTL / 遺伝要因探索 / 全ゲノムシークエンシング / マタニティログ / RNS-Seq / 全ゲノム / データベース / 妊婦 / 構造多型 / クロマチン構造 / 大規模ゲノム情報解析 / 長鎖型シークエンサ … More
Except Principal Investigator
シミュレーション / 遺伝子ネットワーク / ペトリネット / システム生物学 / マイクロアレイ / タンパク質相互作用 / CSML / ベイジアンネットワーク / バイオインフォマティクス / SNP / がん / 生命パスウェイ / ニューラルネットワーク / 破綻部位推定 / モデリング / パスウェイモデリング / タンパク質ネットワーク / システムバイオロジー / マイクロアレイ解析 / Petriネット / 遺伝子発現マイクロアレイデータ / 創薬ターゲット遺伝子 / Fenofibrate / Gefitinib / 漢方薬 / 自己分泌パスウェイ / 生体内パスウェイ解析 / 多型 / パスウェイ / グラフ探索 / ASTD / パスウェイシミュレーション / Consumer Health Informatics / 十全大補湯 / インターフェロンα / toll like receptor / MyD88 / ノックアウトマ / ノックアウトマウス / toll like receptor 4 / ゲノム科学 / 統計的モデリング / 遺伝統計学 / スーパーコンピュータ / シークエンス解析 / 薬剤応答パスウェイ / 動的モデル / パ スウェイ解析 / 状態空間モデル / パスウェイ解析 / ベトリネット / 薬剤応答パスウェィ / Bayesiamネットワーク / 糖尿病 / 血糖値 / シミュレーションモデル / 食品摂取頻度 / トマト / 歯ブラシ / 口腔内メタゲノム / 筋力低下 / サルコペニア / 口腔内細菌叢 / 糞便細菌叢 / 歯磨き時間 / 喫煙 / 骨格筋 / 損傷 / 回復 / MRI / ミクロビオーム / 唾液 / 便 / 男性不妊 / ゲノム解析 / リファレンスパネル / 精子 / Y染色体 / 精液 / DNAパネル / 中心性漿液性脈絡網膜症 / パキコロイド / 機械学習 / 人工知能 / ゲノムワイド関連解析 / ゲノムワイド生存解析 / 加齢黄斑変性 / 近視 / 高度近視 Less
  • Research Projects

    (18 results)
  • Research Products

    (121 results)
  • Co-Researchers

    (66 People)
  •  日本人集団ゲノムワイドクロマチン相互作用情報と構造多型との関連解析と疾患要因探索Principal Investigator

    • Principal Investigator
      長崎 正朗
    • Project Period (FY)
      2021 – 2023
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Review Section
      Basic Section 48040:Medical biochemistry-related
    • Research Institution
      Kyoto University
  •  Comprehensive elucidation of the pathophysiology of myopia by big data analysis

    • Principal Investigator
      辻川 明孝
    • Project Period (FY)
      2021 – 2023
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Review Section
      Basic Section 56060:Ophthalmology-related
    • Research Institution
      Kyoto University
  •  Pathogenesis of age-related macular degeneration and pachychoroid neovasculopathy

    • Principal Investigator
      三宅 正裕
    • Project Period (FY)
      2020 – 2022
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Review Section
      Basic Section 56060:Ophthalmology-related
    • Research Institution
      Kyoto University
  •  Time-series muti-layered omics analysis during gestation period towards precision medicinePrincipal Investigator

    • Principal Investigator
      Nagasaki Masao
    • Project Period (FY)
      2018 – 2020
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Complex Systems Disease Theory
    • Research Institution
      Kyoto University
      Tohoku University
  •  Preparation and Application of Y chromosome Panel using BirThree Cohort Men

    • Principal Investigator
      Suzuki Kichiya
    • Project Period (FY)
      2018 – 2020
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Review Section
      Basic Section 56040:Obstetrics and gynecology-related
    • Research Institution
      Tohoku University
  •  Construction of eQTL database during pregnant periodPrincipal Investigator

    • Principal Investigator
      nagasaki masao
    • Project Period (FY)
      2018 – 2020
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Review Section
      Basic Section 62010:Life, health and medical informatics-related
    • Research Institution
      Kyoto University
  •  Association of microbiome profile with skeletal muscle function

    • Principal Investigator
      Nagatomi Ryoichi
    • Project Period (FY)
      2015 – 2018
    • Research Category
      Grant-in-Aid for Scientific Research (A)
    • Research Field
      Sports science
    • Research Institution
      Tohoku University
  •  A computer simulation model for glycemic control for the improvement of medication regimen compliance in patients with diabetes mellitus

    • Principal Investigator
      KUDO Mitsuhiro
    • Project Period (FY)
      2012 – 2014
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Medical sociology
    • Research Institution
      Nippon Medical School
  •  RNA-Seq data analysis for ncRNA function prediction to thousands public RNA-Seq data on super computerPrincipal Investigator

    • Principal Investigator
      NAGASAKI Masao
    • Project Period (FY)
      2011 – 2012
    • Research Category
      Grant-in-Aid for Challenging Exploratory Research
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      Tohoku University
      The University of Tokyo
  •  Development of Systems Cancer Research by Computation and Simulation

    • Principal Investigator
      MIYANO SATORU
    • Project Period (FY)
      2010 – 2014
    • Research Category
      Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    • Review Section
      Complex systems
    • Research Institution
      The University of Tokyo
  •  Drug-response pathway analysis methods based on network analysis

    • Principal Investigator
      MIYANO Satoru
    • Project Period (FY)
      2010 – 2012
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      The University of Tokyo
  •  Relations between characteristic features of biological dynamic pathway models and gene polymorphisms or gene functions

    • Principal Investigator
      HISHIKI Teruyoshi
    • Project Period (FY)
      2009 – 2011
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      ゲノム情報科学
    • Research Institution
      Toho University
  •  Investigation of Kampo medicine mechanism against the infection via type 1 interferon producing cells

    • Principal Investigator
      WATANABE Kenji
    • Project Period (FY)
      2009 – 2011
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      General internal medicine (including Psychosomatic medicine)
    • Research Institution
      Keio University
  •  Visual model checking approach of high level Petri-net and its application to dynamic biological pathway modelPrincipal Investigator

    • Principal Investigator
      NAGASAKI Masao
    • Project Period (FY)
      2008 – 2009
    • Research Category
      Grant-in-Aid for Young Scientists (B)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      The University of Tokyo
  •  In Silico Search for Drug Target Pathways by Gene Networks

    • Principal Investigator
      MIYANO Satoru
    • Project Period (FY)
      2006 – 2008
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      The University of Tokyo
  •  高機能ペトリネットによる動的生命パスウェイモデルの視覚的デバッグ手法の開発と適用Principal Investigator

    • Principal Investigator
      長崎 正朗
    • Project Period (FY)
      2006 – 2007
    • Research Category
      Grant-in-Aid for Young Scientists (B)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      The University of Tokyo
  •  がん発生・抑止機構の計算機モデル化によるシステム的理解と新分子標的推定手法の開発

    • Principal Investigator
      MATSUNO Hiroshi
    • Project Period (FY)
      2005
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      Yamaguchi University
  •  Estimation and simulation of gene networks for developing in silico biological networks

    • Principal Investigator
      MIYANO Satoru
    • Project Period (FY)
      2005 – 2009
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo

All 2020 2019 2018 2017 2016 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005

All Journal Article Presentation Book

  • [Book] Foundations of Systems Biology2009

    • Author(s)
      Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S.
    • Total Pages
      156
    • Publisher
      Springer
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Book] Foundations of Systems Biology : Using Cell Illustrator and Pathway Databases2009

    • Author(s)
      Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S.
    • Total Pages
      156
    • Publisher
      Springer
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Maternity Log study: a longitudinal lifelog monitoring and multiomics analysis for the early prediction of complicated pregnancy.2019

    • Author(s)
      Sugawara J, Ochi D, Yamashita R, Yamauchi T, Saigusa D, Wagata M, Obara T, Ishikuro M, Tsunemoto Y, 18名略, Hiyama S, Nagasaki M
    • Journal Title

      BMJOpen

      Volume: 9(2)

    • DOI

      10.1136/bmjopen-2018-025939

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-18KT0015, KAKENHI-PROJECT-17K07298, KAKENHI-PROJECT-18K11420, KAKENHI-PROJECT-18K11545, KAKENHI-PROJECT-16H05243, KAKENHI-PROJECT-15K00295, KAKENHI-PROJECT-15K09464, KAKENHI-PROJECT-16K00385, KAKENHI-PROJECT-18H03326
  • [Journal Article] Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing.2018

    • Author(s)
      Mimori T, Fumiki K, Sakae S、Naoki N, 、Akira O, Minegishi N, Kinoshita K, Nagasaki M, Yamamoto M
    • Journal Title

      Pharmacogenomics J.

      Volume: 63 Pages: 136-146

    • DOI

      10.1038/s41397-017-0010-4

    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-15K09464, KAKENHI-PROJECT-17K17589, KAKENHI-PROJECT-17K07193, KAKENHI-PROJECT-16K10488, KAKENHI-PROJECT-18H02940
  • [Journal Article] Comparison of boiling and robotics automation method in DNA extraction for metagenomic sequencing of humanoral microbes2016

    • Author(s)
      Yamagishi, J, Sato, Y, Shinozaki N, Ye, B, Tsuboi A, Nagasaki M, & Yamashita R
    • Journal Title

      PLoS One

      Volume: accepted

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15H01827
  • [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

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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) Pages: 137-139

    • DOI

      10.1093/bioinformatics/bts630

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22300099, KAKENHI-PROJECT-23650150, KAKENHI-PLANNED-22134004
  • [Journal Article] Wnt3a stimulates maturation of impaired neutrophils developed from severe congenital neutropenia patient-derived pluripotent stem cells.2013

    • Author(s)
      Hiramoto T
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 110 Pages: 3023-3028

    • DOI

      10.1073/pnas.1217039110

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22591161, KAKENHI-PROJECT-23310137, KAKENHI-PROJECT-23650150, KAKENHI-PROJECT-23790126, KAKENHI-PROJECT-24390257, KAKENHI-PROJECT-24390272, KAKENHI-PROJECT-24659489, KAKENHI-PROJECT-25293231, KAKENHI-PLANNED-23106004
  • [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) Pages: 279-279

    • DOI

      10.1186/1471-2105-13-279

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [Journal Article] Epidermal growth factor receptor tyrosine kinase defines criticalprognostic genes of stage I lung adenocarcinoma2012

    • Author(s)
      後藤 典子
    • Journal Title

      PLoS One

      Volume: 7

    • DOI

      10.1371/journal.pone.0043923

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22130009, KAKENHI-PROJECT-22300099, KAKENHI-PROJECT-23390062, KAKENHI-PLANNED-22134004
  • [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) Pages: 966-972

    • DOI

      10.1109/tcbb.2012.48

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [Journal Article] Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators2012

    • 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

      Nat Genet

      Volume: 44 Pages: 760-764

    • DOI

      10.1038/ng.2291

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22310123, KAKENHI-PROJECT-24659368, KAKENHI-PLANNED-22116010, KAKENHI-PLANNED-22134004, KAKENHI-PLANNED-22134008
  • [Journal Article] IRView: a database and viewer for protein interacting regions.2012

    • 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) Pages: 1949-1950

    • DOI

      10.1093/bioinformatics/bts289

    • Peer Reviewed
    • Data Source
      KAKENHI-PUBLICLY-23134510, KAKENHI-PROJECT-23651190, KAKENHI-PLANNED-22134004
  • [Journal Article] CSO validator: improving manual curation workflow for biological pathways2011

    • Author(s)
      Jeong E, Nagasaki M, Ikeda E, Saito A, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(17) Pages: 2471-2472

    • DOI

      10.1093/bioinformatics/btr395

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22300099
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004, KAKENHI-PROJECT-22300099
  • [Journal Article] Ontology-based instance data validation for high-quality curated biological pathways2011

    • Author(s)
      Jeong E, Nagasaki M, Ueno K, Miyano S
    • Journal Title

      BMC Bioinformatics

      Volume: 12(Suppl 1)

    • DOI

      10.1186/1471-2105-12-s1-s8

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22300099
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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

    • DOI

      10.1186/1471-2105-12-s14-s7

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004, KAKENHI-PROJECT-23650150
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [Journal Article] Frequent pathway mutations of splicing machinery in myelodysplasia., Nature2011

    • Author(s)
      Kenichi Yoshida
    • Journal Title

      Nature

      Volume: 478 Pages: 332-339

    • DOI

      10.1038/nature10496

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22130002, KAKENHI-PLANNED-22134004, KAKENHI-PROJECT-22390191, KAKENHI-PROJECT-22659058, KAKENHI-PROJECT-22790895, KAKENHI-PLANNED-23106004, KAKENHI-PUBLICLY-23118503, KAKENHI-PROJECT-23390269, KAKENHI-PROJECT-23659482, KAKENHI-PROJECT-23659533, KAKENHI-PROJECT-23791068, KAKENHI-PROJECT-23791075
  • [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

    • DOI

      10.1371/journal.pone.0020804

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21249037, KAKENHI-PLANNED-22134004, KAKENHI-PLANNED-22134005
  • [Journal Article] MIRACH : Efficient Model Checker for Quantitative Biological Pathway Models2011

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

      Bioinformatics

      Volume: Vol.27 Pages: 734-735

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21310132
  • [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) Pages: 734-735

    • DOI

      10.1093/bioinformatics/btq727

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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) Pages: 1172-1173

    • DOI

      10.1093/bioinformatics/btr078

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004, KAKENHI-PROJECT-22300099, KAKENHI-PROJECT-22700308, KAKENHI-PROJECT-23700346
  • [Journal Article] Systems biology model repository for macrophage pathway simulation2011

    • Author(s)
      Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, Miyano S
    • Journal Title

      Bioinformatics.

      Volume: 27 (11) Pages: 1591-1593

    • DOI

      10.1093/bioinformatics/btr173

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22300099
  • [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) Pages: 683-697

    • DOI

      10.1109/tcbb.2010.68

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [Journal Article] Systems biology model repository for macrophage pathway simulation2011

    • Author(s)
      Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, Miyano S
    • Journal Title

      Bioinformatics

      Volume: Vol.27 Pages: 1591-1593

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21310132
  • [Journal Article] CSO validator : improving manual curation workflow for biological pathways2011

    • Author(s)
      Jeong E, Nagasaki M, Ikeda E, Saito A, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(17) Pages: 2471-2472

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22300099
  • [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)

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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)

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [Journal Article] Online model checking approach based parameter estimation to a neuronal fate decision simulation model in C. elegans with hybrid functional Petri net with extension2010

    • Author(s)
      Li C, Nagasaki M, Hock Koh C, Miyano S
    • Journal Title

      Mol. Biosyst.

      Volume: Vol.7 Pages: 1576-1592

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21310132
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram2010

    • Author(s)
      Li, C., Nagasaki, M., Saito, A., Miyano, S.
    • Journal Title

      BMC Systems Biology

      Volume: 439 Pages: 1-1

    • Data Source
      KAKENHI-PROJECT-22300099
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram2010

    • Author(s)
      Li C*, Nagasaki M*, Saito A, Miyano S.
    • Journal Title

      BMC Systems Biology 4

      Pages: 39-39

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram2010

    • Author(s)
      Li C*, Nagasaki M*, Saito A, Miyano S(*Equal contributor)
    • Journal Title

      BMC Systems Biology 4

      Pages: 39-39

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21310132
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram2010

    • Author(s)
      Li C, Nagasaki M, Saito A and Miyano S
    • Journal Title

      BMC Systems Biology

      Volume: Vol.4 Pages: 39-45

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21310132
  • [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)

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22134004
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram2010

    • Author(s)
      Li C, Nagasaki M, Saito A, Miyano S.
    • Journal Title

      BMC Systems Biology

      Volume: 4 Pages: 39-39

    • DOI

      10.1186/1752-0509-4-39

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22300099
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petrinet model with active state transition diagram2010

    • Author(s)
      Li C, Nagasaki M, Saito A, Miyano S.(Equal contributor)
    • Journal Title

      BMC Systems Biology 4:39(online journal)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Online model checking approach based parameter estimation to a neuronal fate decision simulation model in C.elegans with hybrid functional Petri net with extension2010

    • Author(s)
      Li C, Nagasaki M, Hock Koh C, Miyano S
    • Journal Title

      Mol.Biosyst

      Volume: 7 Pages: 1576-1592

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21310132
  • [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

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22300099
  • [Journal Article] Simulation-based model checking approach to cell fate pecification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension2009

    • Author(s)
      Li, C., Nagasaki, M., Ueno, K., Miyano, S.(Equal contributor)
    • Journal Title

      BMC Systems Biology 3:42(Online journal)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Cell Illustrator 4.0 : A computational platform for systems biology. 10:00022009

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

      In Silico Biology 10:0002(online journal)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] A state space representation of VAR models with sparse learning for dynamic gene networks2009

    • Author(s)
      Kojima, K., Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Ueno, K., Higuchi, T., Gotoh, N., Miyano, S.
    • Journal Title

      Genome Informatics 22

      Pages: 56-68

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine2009

    • Author(s)
      Watanabe-Fukuda, Y., Yamamoto, M., Miura, N., Fukutake, M., Ishige, A., Yamaguchi, R., Nagasaki, M., Saito, A., Imoto, S., Miyano, S., Takeda, J., Watanabe, K.
    • Journal Title

      J.Gastroenterology 44(5)

      Pages: 380-389

    • NAID

      10025174631

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18300097
  • [Journal Article] Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine2009

    • Author(s)
      Watanabe, Y., Yamamoto, M., Miura, N., Fukutake, M., Ishige, A., Yamaguchi, R., Nagasaki, M., Saito, A., Imoto, S., Miyano, S., Takeda, J., Watanabe, K.
    • Journal Title

      J. Gastroenterology (印刷中)

    • NAID

      10025174631

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18300097
  • [Journal Article] Better decomposition heuristics for the maximum-weight connected graph problem using betweenness centrality2009

    • Author(s)
      Yamamoto, T., Miyano, S., Nagasaki, M., Bannai, H.
    • Journal Title

      Lecture Notes in Artificial Intelligence 5808

      Pages: 465-472

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid function Petri net with2009

    • Author(s)
      Chen Li^*, Nagasaki M^*, Ueno K, Miyano S (equal contributor)
    • Journal Title

      BMC Systems Biology 3:42(online journal)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Unraveling dynamic activities of autocrine pathways that control drug-esponse transcriptome networks2009

    • Author(s)
      Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y. Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D. S., Tashiro, K., Kuhara, S., Miyano, S.
    • Journal Title

      Pacific Symposium on Biocomputing 14

      Pages: 251-263

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18300097
  • [Journal Article] A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells2009

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

      Genome Informatics 22

      Pages: 121-131

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] BFL : a node and edge betweenness based fast layout algorithm for large scale networks2009

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

      BMC Bioinformatics 10

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] BFL: a node and edge betweenness based fast layout algorithm for large scale networks2009

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

      BMC Bioinformatics 10

      Pages: 19-19

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Simulation-based model checking approach to cell fate pecification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension2009

    • Author(s)
      Li, C. *, Nagasaki, M. *, Ueno, K., Miyano, S.
    • Journal Title

      BMC Systems Biology 3

      Pages: 42-42

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension2009

    • Author(s)
      Li, C., Nagasaki, M., Ueno, K., Miyano, S.
    • Journal Title

      BMC Systems Biology 3

      Pages: 42-42

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Recursive regularization for inferring gene networks from time-course gene expression profiles2009

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

      BMC Systems Biology 3

      Pages: 41-41

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks2009

    • Author(s)
      Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D.S., Tashiro, K., Kuhara, S., Miyano, S.
    • Journal Title

      Pacific Symposium on Biocomputing 14

      Pages: 251-263

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18300097
  • [Journal Article] A computational platform for systems biology2009

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

      Cell Illustrator 4. 0 10

      Pages: 2-2

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Systematic reconstruction of TRANSPATH data into Cell System Markup Language2008

    • Author(s)
      Nagasaki M, Saito A, Li C, Jeong
    • Journal Title

      BMC Systems Biology 2

      Pages: 53-53

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Systematic reconstruction of TRANSPATH data into Cell System Markup Language2008

    • Author(s)
      Nagasaki, M., Saito, A., Chen, L. , Jeong, E. , Miyano, S.
    • Journal Title

      BMS Systems Biology 2

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Rule-based reasoning for system dynamics in cell systems2008

    • Author(s)
      Jeong E, Nagasaki M, Miyano S.
    • Journal Title

      Genome Informatics 20

      Pages: 25-36

    • NAID

      130003997509

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Systematic reconstruction of TRANSPATH data into Cell System Markup Language2008

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

      BMC Systems Biology 2

      Pages: 53-53

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Systematic reconstruction of TRANSPATH data into Cell System Markup Language2008

    • Author(s)
      Nagasaki, M., Saito, A., Chen, L., Jeong, E., Miyano, S.
    • Journal Title

      BMC Systems Biology 2

      Pages: 53-53

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Fast grid layout algorithm for biological networks with sweep calculation2008

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

      Bioinformatics 24(12)

      Pages: 1433-1441

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Predicting differences in gene regulatory systems by state space models2008

    • Author(s)
      Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Hatanaka, Y., Ueno, K., Higuchi, T., Gotoh, N., Miyano, S.
    • Journal Title

      Genome Informatics 21

      Pages: 101-113

    • NAID

      130003997534

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18300097
  • [Journal Article] Rule-based reasoning for system dynamics in cell systems2008

    • Author(s)
      Jeong E, Nagasaki M, Miyano S
    • Journal Title

      Genome Informatics 20

      Pages: 25-36

    • NAID

      130003997509

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20700265
  • [Journal Article] Fast grid layout algorithm for biological networks with sweep calculation2008

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

      Bioinformatics 24(12)

      Pages: 1433-1441

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Rule-based reasoning for system dynamics in cell systems2008

    • Author(s)
      Jeong, E. Nagasaki, M., MiYano, S.
    • Journal Title

      Genome Informatics 20

      Pages: 25-36

    • NAID

      130003997509

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] ExonMiner: Web service for analysis of GeneChip exon array data2008

    • Author(s)
      Numata, K., Yoshida, R., Nagasaki, M., Saito, S., Imoto, S., Miyano, S.
    • Journal Title

      BMC Bioinformatics 9

      Pages: 494-494

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Rule-based reasoning for system dynamics in cell systems2008

    • Author(s)
      Jeong, E., Nagasaki, M., Miyano, S.
    • Journal Title

      Genome Informatics 20

      Pages: 25-36

    • NAID

      130003997509

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Conversion from BioPAX to CSO for System Dynamics and Visualization of Biological Pathway2007

    • Author(s)
      Jeong E, Nagasaki M, Miyano S.
    • Journal Title

      Genome Informatics 18

      Pages: 225-236

    • NAID

      130003812146

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18700285
  • [Journal Article] Computational discovery of aberrant splice variations with genome-wide exon expression profiles2007

    • Author(s)
      Yoshida, R., Numata, K., Imoto, S., Nagasaki, M., Doi, A., Ueno, K., Miyano, S.
    • Journal Title

      Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering 7

      Pages: 715-722

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice2007

    • Author(s)
      Yamaguchi, R., M. Yamamo to, S. Imoto, M. Nagasaki, R. Yoshida, K. Tsuiji, A. Ishige, H. Asou, K. Watanabe, and S. Miyano
    • Journal Title

      Genomic Informatics 18

      Pages: 119-129

    • NAID

      130003812136

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18700285
  • [Journal Article] Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway2007

    • Author(s)
      Jeong, E., Nagasaki, M., Miyano, S.
    • Journal Title

      Genome Informatics 18

      Pages: 225-236

    • NAID

      130003812146

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways2007

    • Author(s)
      Jeong E* Nagasaki M*, Saito A, Miyano S.
    • Journal Title

      In Silico Biology 7

      Pages: 623-638

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18700285
  • [Journal Article] Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice2007

    • Author(s)
      Yamaguchi, R., Yamamoto, M., Imoto, S., Nagasaki, M., Yoshida, R., Tsujii, K., Ishiga, A., Asou, H., Watanabe, K., Miyano, S.
    • Journal Title

      Genome Informatics 18

      Pages: 119-129

    • NAID

      130003812136

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18300097
  • [Journal Article] AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction2007

    • Author(s)
      Saito, A., Nagasaki, M., Oyama, M., Kozuka-Hata, H., Semba, K., Sugano, S., Yamamoto, T., Miyano, S.
    • Journal Title

      BMC Bioinformatics 8

      Pages: 15-15

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] An efficient grid layout algorithm for biological networks utilizing various biological attributes2007

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

      BMC Bioinformatics 8

      Pages: 76-76

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice2007

    • Author(s)
      Yamaguchi, R., Yamamoto, M., Imoto, S., Nagasaki, M. Ybshida, R., Tsujii, K., Ishiga, A., Asou, H., Watanabe, K., Miano, S.
    • Journal Title

      Genome Informatics 18

      Pages: 119-129

    • NAID

      130003812136

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18300097
  • [Journal Article] Computational genome-wide discovery of aberrant splice variations with exon expression profiles2007

    • Author(s)
      R. Yoshida, K.Numata, S. Imoto, M. Nagasaki, A. Doi, K. Ueno, S. Miyano
    • Journal Title

      Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering

      Pages: 715-722

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18700285
  • [Journal Article] Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways2007

    • Author(s)
      Jeong, E., Nagasaki, M., Saito, A., Miyano, S.
    • Journal Title

      In Silico Biology 7

      Pages: 55-55

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] An efficient grid layout algorithm for biological networks utilizing various biological attributes2007

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

      BMC Bioinformatics 8

      Pages: 76-76

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data2006

    • Author(s)
      Tasaki S, Nagasaki M, Oyama M, Hata H, Ueno K, Yoshida R, Higuchi T, Sugano S, Miyano S
    • Journal Title

      Genome Informatics 17・2

      Pages: 226-238

    • NAID

      130003997452

    • Data Source
      KAKENHI-PROJECT-18700285
  • [Journal Article] Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net2006

    • Author(s)
      Doi, A., Nagasaki, M., Matsuno, H., Miyano, S.
    • Journal Title

      In Silico Biology 6

      Pages: 1-1

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data2006

    • Author(s)
      Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano, S., Miyano, S.
    • Journal Title

      Genome Informatics 17(2)

      Pages: 226-228

    • NAID

      130003997452

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Simulation based validation of the p53 transcriptional activity with hybrid unctional Petri net2006

    • Author(s)
      Doi, A., Nagasaki, M., Matsuno, H., Miyano, S.
    • Journal Title

      In Silico Biology 6(In press)(印刷中)

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data2006

    • Author(s)
      Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T.
    • Journal Title

      Genome Informatics 17・1

      Pages: 46-61

    • NAID

      130003812105

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loops by hybrid functional Petri net with extension2006

    • Author(s)
      Saito, A., Nagasaki, M., Doi, A., Ueno, K., Miyano, S.
    • Journal Title

      Genome Informatics 17(1)

      Pages: 100-111

    • NAID

      130003812110

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Genomic data assimilation for estimating. hybrid functional Petri net from time-course gene expression data2006

    • Author(s)
      Nagasaki M, Yamaguchi R, Yoshida R, Imoto S, Doi A, Tamada Y, Matsuno H, Miyano S, Higuchi T
    • Journal Title

      Genome Informatics 17・1

      Pages: 46-61

    • NAID

      130003812105

    • Data Source
      KAKENHI-PROJECT-18700285
  • [Journal Article] Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loops by hybrid functional Petri net with extension2006

    • Author(s)
      Saito, A., Nagasaki, M., Doi, A., Ueno, K., Miyano, S.
    • Journal Title

      Genome Informatics 17・1

      Pages: 100-111

    • NAID

      130003812110

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net.2006

    • Author(s)
      Doi A, Nagasaki M, Matsuno H, Miyano S
    • Journal Title

      In Silico Biology 6(1-2)

      Pages: 1-1

    • Data Source
      KAKENHI-PROJECT-18700285
  • [Journal Article] Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data2006

    • Author(s)
      Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T.
    • Journal Title

      Genome Informatics 17(1)

      Pages: 46-61

    • NAID

      130003812105

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity2006

    • Author(s)
      Doi A, Nagasaki M, Ueno K, Matsuno H, Miyano S
    • Journal Title

      Genome Informatics 17・1

      Pages: 112-123

    • NAID

      130003812111

    • Data Source
      KAKENHI-PROJECT-18700285
  • [Journal Article] A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity2006

    • Author(s)
      Doi, A., Nagasaki, M., Ueno, K., Matsuno, H., Miyano, S.
    • Journal Title

      Genome Informatics 17・1

      Pages: 112-123

    • NAID

      120003184319

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data2006

    • Author(s)
      Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano, S., Miyano, S.
    • Journal Title

      Genome Informatics 17・2

      Pages: 226-228

    • NAID

      130003997452

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Automatic drawings of biological networks using cross cost and subcomponent data.2005

    • Author(s)
      Kato, M., Nagasaki, M., Doi, A., Miyano, S.
    • Journal Title

      Genome Informatics 16・2

      Pages: 22-31

    • NAID

      130003997409

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Automatic drawing of biological networks using cross cost and subcomponent data2005

    • Author(s)
      Kato, M., Nagasaki, M., Doi, A., Miyano, S.
    • Journal Title

      Genome Informatics 16(2)

      Pages: 22-31

    • NAID

      130003997409

    • Data Source
      KAKENHI-PROJECT-17017008
  • [Journal Article] Petri net modeling of biological pathways2005

    • Author(s)
      M.Nagasaki
    • Journal Title

      Proc.Algebraic Biology 2005 (Universal Academy Press)

      Pages: 19-31

    • Data Source
      KAKENHI-PROJECT-17014067
  • [Presentation] Genome-Wide mapping of 4,483 protein QTLs Of the 743 Japanese population2020

    • Author(s)
      Masao Nagasaki
    • Organizer
      The American Society of Human Genetics (ASHG) 2020 Virtual Meeting(国際学会)
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-18KT0015
  • [Presentation] 日本人集 のタンパク質発現量と関連するゲノム遺伝子座との統合解析2020

    • Author(s)
      長﨑 正朗
    • Organizer
      日本人類遺伝学会第65回大会
    • Invited
    • Data Source
      KAKENHI-PROJECT-18KT0015
  • [Presentation] Genome-Wide mapping of 4,483 protein QTLs Of the 743 Japanese population2020

    • Author(s)
      Masao Nagasaki
    • Organizer
      The American Society of Human Genetics (ASHG) 2020 Virtual Meeting
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-18H03326
  • [Presentation] 日本人集団のタンパク質発現量と関連するゲノム遺伝子座との統合解析2020

    • Author(s)
      長﨑 正朗
    • Organizer
      日本人類遺伝学会第65回大会
    • Data Source
      KAKENHI-PROJECT-18H03326
  • [Presentation] Genome cohort projects in Japan and biomedical analyses toward the discoveries of disease-causing variants2019

    • Author(s)
      Masao Nagasaki
    • Organizer
      Genome Expo 2019
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-18H03326
  • [Presentation] Development and application of biomedical methods to facilitate the detection of disease-causing variants based on whole genome data from Japanese2019

    • Author(s)
      Masao Nagasaki
    • Organizer
      The 3rd JCS Council Forum on Basic CardioVascular Research (BCVR 2019)
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-18H03326
  • [Presentation] Physical Activity and Periodontal Bacteria in Saliva among Japanese Adults2017

    • Author(s)
      Huang, C, Yamashita, R, Sato, Y, Momma, H, Kawashima, J, Ye, B, Sugiyama, S, Nanno, M, Tsuboi, A, Nagasaki, M, Nagatomi, R
    • Organizer
      nnual Meeting of the American-College-of-Sports-Medicine
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-15H01827
  • [Presentation] スーパーコンピュータを用いた超快適高速次世代シークエンスデータ解析環境の構築と解析2012

    • Author(s)
      長﨑正朗
    • Organizer
      研究科シンポジウム
    • Place of Presentation
      仙台・川内キャンパス
    • Invited
    • Data Source
      KAKENHI-PROJECT-23650150
  • [Presentation] Data Managenoment and Bioinformatics of High Throughput Sequencing Data on the Massive Parallel Supercomputer Environment2012

    • Author(s)
      長﨑正朗
    • Organizer
      CSI-GCOE Joint workshop on Genome Science
    • Place of Presentation
      シンガポール(Cancer Science Institute of Singapore)
    • Invited
    • Data Source
      KAKENHI-PROJECT-23650150
  • [Presentation] 血糖制御に関わる分子機構シミュレーションモデルの構築2012

    • Author(s)
      工藤光洋、斉藤あゆむ、長﨑正朗、山本哲志、彭為霞、川原清子、藤井雄文、手塚潔、宮野悟、内藤善哉
    • Organizer
      第101回 日本病理学会総会
    • Place of Presentation
      京王プラザホテル
    • Data Source
      KAKENHI-PROJECT-24590639
  • [Presentation] Data Management and Bioinformatics of High Throughput Sequencing Data on the Massive Parallel Supercomputer Environment and Future2012

    • Author(s)
      長﨑正朗
    • Organizer
      Bilateral Workshop between Tohoku University and National Tsing Hua University
    • Place of Presentation
      仙台・秋保
    • Invited
    • Data Source
      KAKENHI-PROJECT-23650150
  • [Presentation] ゲノム超ビックデータ時代における次世代シークエンスデータ解析環境の構築と解析2012

    • Author(s)
      長﨑正朗
    • Organizer
      化学工学会第44回秋季大会秋季大会シンポジウム
    • Place of Presentation
      仙台・川内キャンパス
    • Invited
    • Data Source
      KAKENHI-PROJECT-23650150
  • [Presentation] 高性能シークエンサ大規模データのスーパコンピュータ上での効率的な管理と解析環境の構築2011

    • Author(s)
      長崎正朗
    • Organizer
      第12回IPABシンポジウム~超並列スパコンとバイオ計算、(招待講演)
    • Place of Presentation
      東京(秋葉原)
    • Data Source
      KAKENHI-PROJECT-23650150
  • [Presentation] Parameter Estimation of Biological Pathways Using Data Assimilation and Model Checking2011

    • Author(s)
      Chen Li, Keisuke Kuroyanagi, Masao Nagasaki, Satoru Miyano
    • Organizer
      International Workshop on Biological Processes & Petri Nets (BioPPN 2011)
    • Place of Presentation
      Newcastle upon Tyne, UK
    • Year and Date
      2011-06-20
    • Data Source
      KAKENHI-PROJECT-21310132
  • [Presentation] Parameter Estimation of Biological Pathways Using Data Assimilation and Model Checking2011

    • Author(s)
      Chen Li, Keisuke Kuroyanagi, Masao Nagasaki and Satoru Miyano
    • Organizer
      International Workshop on Biological Processes & Petri Nets(BioPPN 2011)
    • Place of Presentation
      Newcastle upon Tyne, UK
    • Year and Date
      2011-06-20
    • Data Source
      KAKENHI-PROJECT-21310132
  • [Presentation] Data Management and Bioinformatics of Next Generation Sequencing Data on the Massive Parallel Supercomputer2011

    • Author(s)
      Masao Nagasaki
    • Organizer
      Next Generation Sequencing Asia Congress 2011(招待講演)
    • Place of Presentation
      Singapore(Concorde Hotel)
    • Data Source
      KAKENHI-PROJECT-23650150
  • [Presentation] Cell Illustrator 3.5 and Cell System Ontology 3.02007

    • Author(s)
      Nagasaki, M.
    • Organizer
      The 2007 Annual Conference of Japanese Society for Bioinformatics
    • Place of Presentation
      日本科学未来館
    • Year and Date
      2007-12-17
    • Data Source
      KAKENHI-PROJECT-17017008
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