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Analysis of Structure and Dynamics of Biological Information Networks

Research Project

Project/Area Number 17017019
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyoto University

Principal Investigator

AKUTSU Tatsuya  Kyoto University, 化学研究所, 教授 (90261859)

Co-Investigator(Kenkyū-buntansha) GOTO Susumu  京都大学, 化学研究所, 准教授 (40263149)
MOCHIZUKI Atsushi  理化学研究所, 望月理論生物学研究室, 主任研究員 (10304726)
TOKITA Keiichirou  大阪大学, サーバーメディアセンター, 准教授 (00263195)
Project Period (FY) 2005 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥82,200,000 (Direct Cost: ¥82,200,000)
Fiscal Year 2009: ¥16,300,000 (Direct Cost: ¥16,300,000)
Fiscal Year 2008: ¥18,500,000 (Direct Cost: ¥18,500,000)
Fiscal Year 2007: ¥15,200,000 (Direct Cost: ¥15,200,000)
Fiscal Year 2006: ¥15,200,000 (Direct Cost: ¥15,200,000)
Fiscal Year 2005: ¥17,000,000 (Direct Cost: ¥17,000,000)
Keywords遺伝子ネットワーク / 代謝ネットワーク / タンパク質相互作用 / スケールフリーネットワーク / タンパク質ドメイン / 遺伝子発現 / 大規模進化動力学モデル / 生物情報ネットワーク / スケールフリー / 進化動力学モデル / 緑膿菌 / ブーリアンネットワーク / 形態形成 / 神経細胞 / 遺伝子発現データ / オペロン / ネットワーク定常状態 / 概日リズム / バイオインフォマティクス / システム生物学 / べき乗則 / 遺伝子間相互作用
Research Abstract

We studied genetic, metabolic, and protein-protein interaction networks mainly from a viewpoint of mathematical models. To analyze evolution of proteins and their interactions, we developed a domain-based mathematical model and performed domain combination-based database analysis. To analyze dynamics of networks, we developed a general theory on relations between network structure and its dynamics, and a statistical mechanical theory on large-scale evolutionary dynamical systems. We also developed several computational tools for analyzing network and related data.

Report

(6 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • Research Products

    (107 results)

All 2010 2009 2008 2007 2006 2005 Other

All Journal Article (55 results) (of which Peer Reviewed: 32 results) Presentation (44 results) Book (3 results) Remarks (5 results)

  • [Journal Article] Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs2009

    • Author(s)
      Nacher, J.C., Hayashida, M., Akutsu, T.
    • Journal Title

      Bio Systems 95

      Pages: 155-159

    • Related Report
      2009 Final Research Report
  • [Journal Article] Systems biology approaches and tools for investigating cardiovascular disease2009

    • Author(s)
      Wheelock, C.E., Wheelock, A.M., Kawashima, S., Diez, D., Kanehisa, M., van Erk, M., Kleemann, R., Haeggstrom, J.Z., Goto, S.
    • Journal Title

      Molecular Biosystems 5

      Pages: 588-602

    • Related Report
      2009 Final Research Report
  • [Journal Article] Steepness of thermal gradient is essential to obtain a unified view of thermotaxis in C.elegans2009

    • Author(s)
      Nakazato, K., Mochizuki, A.
    • Journal Title

      Journal of Theoretical Biology 260

      Pages: 56-65

    • Related Report
      2009 Final Research Report
  • [Journal Article] Algorithms for singleton attractor detection in planar and nonplanar AND/OR Boolean networks2009

    • Author(s)
      T.Tamura, T.Akutsu
    • Journal Title

      Mathematics in Computer Science

      Volume: 2 Pages: 401-420

    • NAID

      120001921981

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation of ATM2009

    • Author(s)
      K.Mouri, J.C.Nacher, T.Akutsu
    • Journal Title

      PLoS ONE

      Volume: 4

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Distribution and enumeration of attractors in probabilistic Boolean networks2009

    • Author(s)
      M.Hayashida, T.Tamura, T.Akutsu, W-K.Ching, Y.Cong
    • Journal Title

      IET Systems Biology

      Volume: 3 Pages: 465-474

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A mathematical model for generating bipartite graphs and its application to protein networks2009

    • Author(s)
      J.C.Nacher, T.Ochiai, M.Hayashida, T.Akutsu
    • Journal Title

      Journal of Physics A : Mathematical and Theoretical

      Volume: 42

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Finding minimum reaction cuts of metabolic networks under a Boolean model using integer programming and feedback vertex sets2009

    • Author(s)
      T.Tamura, K.Takemoto, T.Akutsu
    • Journal Title

      International Journal of Knowledge Discovery in Bioinformatics

      Volume: 1 Pages: 14-31

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Systems biology approaches and tools for investigating cardiovascular disease2009

    • Author(s)
      C.E.Wheelock, A.M.Wheelock, S.Kawashima, D.Diez, M.Kanehisa, M.van Erk, R.Kleemann, J.Z.Haeggstrom, S.Goto
    • Journal Title

      Molecular Biosystems

      Volume: 5 Pages: 588-602

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Steepness of thermal gradient is essential to obtain a unified view of thermotaxis in C.elegans2009

    • Author(s)
      K.Nakazato, A.Mochizuki
    • Journal Title

      Journal of Theoretical Biology

      Volume: 260 Pages: 56-65

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Optimal control policy for probabilistic Boolean networks with hard constraints2009

    • Author(s)
      W-K. Ching, S-Q. Zhang, Y. Jiao, T. Akutsu, N-K. Tsing and A.S. Wong
    • Journal Title

      IET Systems Biology 3

      Pages: 90-99

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Detecting a singleton attractor in a Boolean network utilizing SAT algorithms2009

    • Author(s)
      T. Tamura and T. Akutsu
    • Journal Title

      IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences E92-A

      Pages: 493-501

    • NAID

      10026855697

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs2009

    • Author(s)
      J. C. Nacher, M. Hayashida and T. Akutsu
    • Journal Title

      BioSystems 95

      Pages: 155-159

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of regulatory networks and diversity of gene expression patterns2008

    • Author(s)
      Mochizuki, A.
    • Journal Title

      Journal of Theoretical Biology 250

      Pages: 307-321

    • Related Report
      2009 Final Research Report
  • [Journal Article] Rank abundance relations in evolutionary dynamics of random replicators2008

    • Author(s)
      Yoshino, Y., Galla, T., Tokita, K.
    • Journal Title

      Physical Review E 78

      Pages: 31924-31924

    • Related Report
      2009 Final Research Report
  • [Journal Article] Algorithms and complexity analyses for control of singleton attractors in Boolean networks2008

    • Author(s)
      M. Hayashida, T. Tamura, T. Akutsu. S-Q. Zhang and W-K. Ching
    • Journal Title

      EURASIP Journal on Bioinformatics and Systems Biology 2008

    • NAID

      120004754352

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analyses and algorithms for predecessor and control problems for Boolean networks of bounded indegree2008

    • Author(s)
      T. Akutsu, M. Hayashida, S-Q. Zhang, W-K. Ching and M. K. Ng
    • Journal Title

      IPST Transactions on Bioinformatics 1

      Pages: 23-34

    • NAID

      130000120676

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Origin of structural difference in metabolic networks with respect to temperature2008

    • Author(s)
      K. Takemoto and T. Akutsu
    • Journal Title

      BMC Syslems Biology 2

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Integer programming-based approach to allocation of reporter genes for cell array analysis2008

    • Author(s)
      M. Hayashida, F. Sun, S. Aburatani, K. Horimoto and T. Akutsu
    • Journal Title

      International Journal of Bioinformatics Research and Applications 4

      Pages: 385-399

    • NAID

      110006402728

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 遺伝子制御ネットワークの離散モデルと制御2008

    • Author(s)
      阿久津達也
    • Journal Title

      計測と制御 47

      Pages: 664-669

    • Related Report
      2008 Annual Research Report
  • [Journal Article] varDB : a pathogen-specific database of protein families involved in antigenic variation2008

    • Author(s)
      C.N. Hayes, D. Diez, N. Joannin, W. Honda, M. Kanehisa, W. Wahlgren. C.E Wheelock and S. Goto
    • Journal Title

      Bioinformatics 24

      Pages: 2564-2565

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] KEGG Atlas mapping for global analysis of metabolic pathways2008

    • Author(s)
      S. Okuda, T. Yamada, M. Hamajima, M. Itoh, T. Katayama, P. Bork, S. Goto and M. Kanehisa
    • Journal Title

      Nucleic Acids Research 36

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of regulatory networks and diversity of gene expression patterns2008

    • Author(s)
      A. Mochizuki
    • Journal Title

      Journal of Theoretical Biology 250

      Pages: 307-321

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rank abundance relations in evolutionary dynamics of random replicators2008

    • Author(s)
      Y. Yoshino, T. Gal la and K. Tokita
    • Journal Title

      Physical Review E 78

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Control of Boolean networks: hardness results and algorithms for tree structured networks2007

    • Author(s)
      Akutsu, T., Hayashida, M., Ching, W-K., Ng, M.K.
    • Journal Title

      Journal of Theoretical Biology 24

      Pages: 670-679

    • Related Report
      2009 Final Research Report
  • [Journal Article] Prediction of missing enzyme genes in bacterial metabolic network : A reconstruction of lysine degradation pathway of Pseudomonas aeruginosa2007

    • Author(s)
      Yamanishi, Y., Mihara, H., Osaki, M., Muramatsu, H., Esaki, N., Sato, T., Hizukuri, Y., Goto, S., Kanehisa, M.
    • Journal Title

      FEBS Journal 274

      Pages: 2262-2273

    • Related Report
      2009 Final Research Report
  • [Journal Article] Transient and steady state of mass-conserved reaction-diffusion systems2007

    • Author(s)
      Ishihara, S., Otsuji, M., Mochizuki, A.
    • Journal Title

      Physical Review E 75

      Pages: 15203-15203

    • Related Report
      2009 Final Research Report
  • [Journal Article] Statistical mechanics and stability of a random eco-system2007

    • Author(s)
      Yoshino, Y., Galla, T., Tokita, K.
    • Journal Title

      Journal of Statistical Mechanics P09003

    • Related Report
      2009 Final Research Report
  • [Journal Article] Correlation between structure and temperature in prokaryotic metabolic networks2007

    • Author(s)
      Takemoto, K., Nacher, J. C., and Akutsu, T.
    • Journal Title

      BMC Bioinformatics 8(論文番号)

      Pages: 303-303

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recent progress on the analysis of power-law features in complex cellular networks2007

    • Author(s)
      Nacher, J. C., and Akutsu, T.
    • Journal Title

      Cell Biochemistry and Biophysics 49

      Pages: 37-47

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Emergence of the self-similar property in gene expression dynamics2007

    • Author(s)
      Ochiai, T., Nacher, J. C., and Akutsu, T.
    • Journal Title

      Physica A 382

      Pages: 739-752

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Algorithms for finding small attractors in Boolean networks2007

    • Author(s)
      Zhang, M-Q., Hayashida, M., Akutsu, T., Ching, W-K., and Ng, M. K.
    • Journal Title

      EURASIP Journal on Bioinformatics and Systems Biology 2007(論文番号)

      Pages: 20180-20180

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks2007

    • Author(s)
      Ching, W-K., Zhang, S-Q., Ng, M. K., and Akutsu, T.
    • Journal Title

      Bioinformatics 23

      Pages: 1511-1518

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli2007

    • Author(s)
      Okuda, S., Kawashima, S., Kobayashi, K., Ogasawara, N., Kanehisa, M., and Goto S.
    • Journal Title

      BMC Genomics 8(論文番号)

      Pages: 48-48

    • NAID

      120004770315

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Regulation of metabolic networks by small molecule metabolites2007

    • Author(s)
      Gutteridge, A., Kanehisa, M., and Goto S.
    • Journal Title

      BMC Bioinformatics 8(論文番号)

      Pages: 88-88

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of missing enzyme genes in bacterial metabolic network: A reconstruction of lysine degradation pathway of Pseudomonas aeruginosa2007

    • Author(s)
      Yamanishi, Y., Mihara, H., Osaki, M., Muramatsu, H., Esaki, N., Sato, T., Hizukuri, Y., Goto, S., and Kanehisa, M.
    • Journal Title

      FEBS Journal 274

      Pages: 2262-2273

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The commonality of protein interaction networks determined in neurode generative disorders (NDDs)2007

    • Author(s)
      Limviphuvadh, V., Tanaka, S., Goto, S., Ueda, K., and Kanehisa, M.
    • Journal Title

      Bioinformatics 23

      Pages: 2129-2138

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolutionary history and functional implication of protein domains and their combinations in eukaryotes2007

    • Author(s)
      Itoh, M., Nacher, J. C., Kuma, K., Goto, S., and Kanehisa, M.
    • Journal Title

      Genome Biology 8(論文番号)

      Pages: 121-121

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transient and steady state of mass-conserved reaction-diffusion systems2007

    • Author(s)
      Ishihara, S., Otsuji, M., and Mochizuki, A.
    • Journal Title

      Physical Review E 75

      Pages: 15203-15203

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A mass conserved reaction-diffusion system captures properties of cell polarity2007

    • Author(s)
      Otsuji, M., Ishihara, S., Co, C., Kaibuchi, K., Mochizuki, A., and Kuroda, S.
    • Journal Title

      PLoS Computational Biology 3

      Pages: 1040-1054

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Self-organizing mechanism for development of space-filling neuronal dendrites2007

    • Author(s)
      Sugimura, K., Shimono, K., Uemura. T., and Mochizuki, A.
    • Journal Title

      PLoS Computational Biology 3

      Pages: 2143-2154

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Statistical mechanics and stability of a model ecosystem2007

    • Author(s)
      Yoshino Y., Galla T. and Tokita, K.
    • Journal Title

      Journal of Statistical Mechanics

      Pages: 9003-9003

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein domain networks : scale-free mixing of positive and negative exponents2006

    • Author(s)
      Nacher, J.C., Hayashida, M., Akutsu, T.
    • Journal Title

      Physica A 367

      Pages: 538-552

    • Related Report
      2009 Final Research Report 2006 Annual Research Report
  • [Journal Article] Extraction of phylogenetic network modules from the metabolic network2006

    • Author(s)
      Yamada, T., Kanehisa, M., Goto, S.
    • Journal Title

      BMC Bioinformatics 7

      Pages: 130-130

    • NAID

      120004770316

    • Related Report
      2009 Final Research Report
  • [Journal Article] Statistical mechanics of relative species abundance2006

    • Author(s)
      Tokita, K.
    • Journal Title

      Ecological Informatics 1

      Pages: 315-324

    • Related Report
      2009 Final Research Report 2006 Annual Research Report
  • [Journal Article] Identification of metabolic units induced by environmental signals2006

    • Author(s)
      Nacher, J.C., Schwartz, J.M., Kanehisa, M., Akutsu, T.
    • Journal Title

      Bioinformatics 22

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes2006

    • Author(s)
      Tanaka, M., Yamada, T., Itoh, M., Okuda, S., Goto, S., Kanehisa, M.
    • Journal Title

      Genome Informatics 17

      Pages: 230-239

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Predicting regulation of the phosphorylation cycle of KaiC clock protein using mathematical analysis2006

    • Author(s)
      Takigawa-Imamura, H., Mochizuki, A.
    • Journal Title

      Journal of Biological Rhythms 21

      Pages: 405-416

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The origin of the diversity of leaf venation pattern2006

    • Author(s)
      Fujita, H., Mochizuki, A.
    • Journal Title

      Developmental Dynamics 235

      Pages: 2710-2721

    • Related Report
      2006 Annual Research Report
  • [Journal Article] ODB : a database of operons accumulating known operons across multiple genomes2006

    • Author(s)
      Okuda S., Katayama, T., Kawashima S., Goto, S., Kanehisa M.
    • Journal Title

      Nucleic Acids Research 34

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Flexible construction of hierarchical scale-free networks with general exponent2005

    • Author(s)
      Nacher, J.C., Ueda, N., Kanehisa, M., Akutsu, T.
    • Journal Title

      Physical Review E, 71

      Pages: 36132-36132

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A stochastic approach to multi-gene expression dynamics2005

    • Author(s)
      Ochiai, T.Nacher, J.C., Akutsu, T.
    • Journal Title

      Physics Letters A 839

      Pages: 1-9

    • Related Report
      2005 Annual Research Report
  • [Journal Article] On the relation between fluctuations and scaling-law in gene expression series from yeast to human2005

    • Author(s)
      Nacher, J.C., Ochiai, T., Akutsu, T.
    • Journal Title

      Modern Physics Letters B 19

      Pages: 1169-1177

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Conservation of gene co-regulation between two prokaryotes. Bacillus subtilis and Escherichia coli2005

    • Author(s)
      Okuda, S., Kawashima, S., Goto, S., Kanehisa, M.
    • Journal Title

      Genome Informatics 16

      Pages: 116-124

    • Related Report
      2005 Annual Research Report
  • [Journal Article] An analytical study of the number of steady states in gene regulatory networks2005

    • Author(s)
      Mochizuki, A.
    • Journal Title

      Journal of Theoretical Biology 236

      Pages: 291-310

    • Related Report
      2005 Annual Research Report
  • [Presentation] Structure of regulatory networks and dynamics of bio-molecules2010

    • Author(s)
      Mochizuki, A., Saito, D.
    • Organizer
      Spatio-Temporal Patterns-from Mathematics to Biomedical Applications-
    • Place of Presentation
      Archamps, France
    • Year and Date
      2010-03-17
    • Related Report
      2009 Final Research Report
  • [Presentation] Structure of regulatory networks and dynamics of bio-molecules2010

    • Author(s)
      A.Mochizuki, D.Saito
    • Organizer
      Spatio-Temporal Patterns -from Mathematics to Biomedical Applications-
    • Place of Presentation
      Archamps, France
    • Year and Date
      2010-03-17
    • Related Report
      2009 Annual Research Report
  • [Presentation] Integer programming-based methods for attractor detection and control of Boolean networks2009

    • Author(s)
      T.Akutsu, M.Hayashida, T.Tamura
    • Organizer
      The combined 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference
    • Place of Presentation
      Shanghai, China
    • Year and Date
      2009-12-17
    • Related Report
      2009 Annual Research Report
  • [Presentation] Random matrices and their application to mathematical biology2009

    • Author(s)
      K.Tokita
    • Organizer
      The International conference "Casimir Force, Casimir Operator and theRiemann Hypothesis"
    • Place of Presentation
      Fukuoka, Japan
    • Year and Date
      2009-11-10
    • Related Report
      2009 Annual Research Report
  • [Presentation] Completing networks using observed data2009

    • Author(s)
      Akustu, T., Tamura, T., Horimoto, K.
    • Organizer
      20th International Conference on Algorithmic Learning Theory
    • Place of Presentation
      Porto, Portugal
    • Year and Date
      2009-10-04
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] Comparing biological networks via graph compression2009

    • Author(s)
      M.Hayashida, T.Akutsu
    • Organizer
      3rd International Symposium on Optimization and Systems Biology
    • Place of Presentation
      Zhangjiajie, China
    • Year and Date
      2009-09-20
    • Related Report
      2009 Annual Research Report
  • [Presentation] Large-scale biological networks2009

    • Author(s)
      Tokita, K.
    • Organizer
      International Conference on Computational and Experimental Engineering and Sciences
    • Place of Presentation
      Phuket, Thailand
    • Year and Date
      2009-04-09
    • Related Report
      2009 Final Research Report
  • [Presentation] Large-scale biological networks2009

    • Author(s)
      K.Tokita
    • Organizer
      International Conference on Computational and Experimental Engineering and Sciences : ICCES'09
    • Place of Presentation
      Phuket, Thailand
    • Year and Date
      2009-04-09
    • Related Report
      2009 Annual Research Report
  • [Presentation] 生体分子ネットワークの構造とダイナミクス2009

    • Author(s)
      望月敦史
    • Organizer
      第2回東工大生命情報学セミナー
    • Place of Presentation
      東京工業大学
    • Year and Date
      2009-03-25
    • Related Report
      2008 Annual Research Report
  • [Presentation] Measuring structural robustness of metabolic networks under a Boolean model using integer programming and feedback vertex2009

    • Author(s)
      T. Tamura, K. Takemoto and T. Akutsu
    • Organizer
      The 2nd International Workshop on Intelligent Informatics in Biology and Medicine
    • Place of Presentation
      福岡工業大学
    • Year and Date
      2009-03-19
    • Related Report
      2008 Annual Research Report
  • [Presentation] 生体分子ネットワークの構造とダイナミクス2009

    • Author(s)
      望月敦史
    • Organizer
      日本バイオインフォマティクス学会第22回システムバイオロジー研究会
    • Place of Presentation
      癌研究所
    • Year and Date
      2009-03-11
    • Related Report
      2008 Annual Research Report
  • [Presentation] A bipartite graph based model of protein domain networks2009

    • Author(s)
      J. Nacher, T. Ochiai, M. Havashida and T. Akutsu
    • Organizer
      The First International Conference on Complex Sciences : Theory and Applications
    • Place of Presentation
      Shanghai, China
    • Year and Date
      2009-02-24
    • Related Report
      2008 Annual Research Report
  • [Presentation] Dynamical understanding for, the structure of complex regulatory networks2009

    • Author(s)
      A. Mochizuki
    • Organizer
      京都大学グローバルCOEプログラムGCOE生命数理セミナー
    • Place of Presentation
      京都大学
    • Year and Date
      2009-02-20
    • Related Report
      2008 Annual Research Report
  • [Presentation] 生体分子ネットワークの構造とダイナミクス2009

    • Author(s)
      望月敦史
    • Organizer
      広島大学大学院理学研究科数理分子生命理学専攻セミナー
    • Place of Presentation
      広島大学
    • Year and Date
      2009-02-03
    • Related Report
      2008 Annual Research Report
  • [Presentation] 酸化ストレス化におけるアポトーシス制御機構の数理的解明2008

    • Author(s)
      毛利一成,J. C. Nacher,阿久津達也
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2008-12-03
    • Related Report
      2008 Annual Research Report
  • [Presentation] On distribution and enumeration of attractors in probabilistic Boolean networks2008

    • Author(s)
      M. Hayashida, T. Tamura, T. Akutsu and W-K Ching
    • Organizer
      The 2nd International Symposium on Optimization and Systems Biology
    • Place of Presentation
      Lijiang, China
    • Year and Date
      2008-11-01
    • Related Report
      2008 Annual Research Report
  • [Presentation] Phase transition in replicator-mutator dynamics of biological and social systems2008

    • Author(s)
      K. Tokita, T. Galla, M. Sugiura and L. DallAsta
    • Organizer
      Mathematical Understanding of Complex Systems arising in Biology and Medicine
    • Place of Presentation
      明治大学
    • Year and Date
      2008-10-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] On distribution and enumeration of attractors in probabilistic Boolean networks2008

    • Author(s)
      Akutsu, M Hayashida, T. Tamura and W-K Ching
    • Organizer
      ReaDiLab : Mathematical Understanding of Complex Systems arising in Biology and Medicine
    • Place of Presentation
      明治大学
    • Year and Date
      2008-10-27
    • Related Report
      2008 Annual Research Report
  • [Presentation]2008

    • Author(s)
      Tokita, K.
    • Organizer
      The 4^<th> China-Italy Colloquium on Applied Mathematics
    • Place of Presentation
      Chongqing, China
    • Year and Date
      2008-10-12
    • Related Report
      2009 Final Research Report
  • [Presentation] Statistical mechanics of a random community model2008

    • Author(s)
      K. Tokitaa
    • Organizer
      The 4th China-Italy Colloquium on Applied Mathematics
    • Place of Presentation
      Chongqing, China
    • Year and Date
      2008-10-12
    • Related Report
      2008 Annual Research Report
  • [Presentation] Field theory for field ecology2008

    • Author(s)
      K. Tokita
    • Organizer
      Annual Meeting of Korean Society for Mathematical Biology
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2008-10-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] Detection and enumeration of steady states in biological information networks2008

    • Author(s)
      T. Akutsu
    • Organizer
      Kyoto RIMS Workshop on Acceleration and Visualization of Computation for Enumeration Problems
    • Place of Presentation
      京都大学数理解析研究所
    • Year and Date
      2008-09-30
    • Related Report
      2008 Annual Research Report
  • [Presentation] 線虫の温度走性の数理モデリング2008

    • Author(s)
      中里研一, 望月敦史
    • Organizer
      第18回日本数理生物学会大会
    • Place of Presentation
      同志社大学
    • Year and Date
      2008-09-18
    • Related Report
      2008 Annual Research Report
  • [Presentation] Dynamical analysis of structure of gene regulatory networks2008

    • Author(s)
      A. Mochizuki
    • Organizer
      第18回日本数理生物学会大会
    • Place of Presentation
      同志社大学
    • Year and Date
      2008-09-17
    • Related Report
      2008 Annual Research Report
  • [Presentation] Effects of mutation in ecological and cultural systems2008

    • Author(s)
      M. Sugiura and K. Tokita
    • Organizer
      The Second China-Japan Colloquium of Mathematical Biology
    • Place of Presentation
      岡山大学
    • Year and Date
      2008-08-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] Dynamic theory of species abundance distributions2008

    • Author(s)
      K. Tokita
    • Organizer
      The Second China-Japan Colloquium of Mathematical Biology
    • Place of Presentation
      岡山大学
    • Year and Date
      2008-08-04
    • Related Report
      2008 Annual Research Report
  • [Presentation] Algorithms for inference, analysis and control of Boolean networks2008

    • Author(s)
      Akutsu, T., Hayashida, M., Tamura, T.
    • Organizer
      The 3rd International Conference on Algebraic Biology
    • Place of Presentation
      Hagenberg, Austria
    • Year and Date
      2008-07-31
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes2008

    • Author(s)
      T. Tamura and T. Akutsu
    • Organizer
      The 3rd International Conference on Algebraic Biology
    • Place of Presentation
      Hagenberg, Austria
    • Year and Date
      2008-07-31
    • Related Report
      2008 Annual Research Report
  • [Presentation] Random community model with resource competition2008

    • Author(s)
      K. Tokita
    • Organizer
      The 9th Taiwan International Symposium on Statistical Physics
    • Place of Presentation
      Taipei, Taiwan
    • Year and Date
      2008-07-11
    • Related Report
      2008 Annual Research Report
  • [Presentation] Structural Analysis of Biological Information Networks2008

    • Author(s)
      Tatsuya Akutsu
    • Organizer
      RERF Symposium on Bioinformatics
    • Place of Presentation
      放射線影響研究所(広島)
    • Year and Date
      2008-03-24
    • Related Report
      2007 Annual Research Report
  • [Presentation] ESTからの植物ゲノムアノテーションとパスウェイ解析2008

    • Author(s)
      五斗進
    • Organizer
      日本植物生理学会第49回年会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2008-03-20
    • Related Report
      2007 Annual Research Report
  • [Presentation] 遺伝子ネットワークの離散モデルとその制御2008

    • Author(s)
      阿久津 達也
    • Organizer
      第2回SICE生物制御システム調査研究会
    • Place of Presentation
      京都工芸繊維大学
    • Year and Date
      2008-01-31
    • Related Report
      2007 Annual Research Report
  • [Presentation] Statistical Mechanics of Species Abundance Distributions2007

    • Author(s)
      Kei Tokita
    • Organizer
      2007 Annual Meeting of Korean Society for Mathematical Biology
    • Place of Presentation
      Korea Institute of Science and Technology Information
    • Year and Date
      2007-11-02
    • Related Report
      2007 Annual Research Report
  • [Presentation] Network perspective in bioinformatics2007

    • Author(s)
      Goto, S.
    • Organizer
      Nishinomiya-Yukawa International & Interdisciplinary Symposium
    • Place of Presentation
      Kyoto, Japan
    • Year and Date
      2007-10-18
    • Related Report
      2009 Final Research Report
  • [Presentation] Network perspective in bioinformatics2007

    • Author(s)
      Susumu Goto
    • Organizer
      Nishinomiya-Yukawa International & Interdisciplinary Symposium
    • Place of Presentation
      コープイン京都
    • Year and Date
      2007-10-18
    • Related Report
      2007 Annual Research Report
  • [Presentation] Structure of regulatory network and diversity of cell types2007

    • Author(s)
      Atsushi Mochizuki
    • Organizer
      Deciphering the regulatory genome: development, evolution and disease
    • Place of Presentation
      Sede Antonio Machado, Baeza, Spain
    • Year and Date
      2007-10-09
    • Related Report
      2007 Annual Research Report
  • [Presentation] Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites2007

    • Author(s)
      Atsushi Mochizuki
    • Organizer
      Workshop on Mathematical Modelling and Analysis of Biological Pattern Formations and the Related Topics
    • Place of Presentation
      Nagoya University, Nagoya, Japan
    • Year and Date
      2007-09-26
    • Related Report
      2007 Annual Research Report
  • [Presentation] 生育温度による代謝ネットワーク構造の差異2007

    • Author(s)
      竹本和広, ホセ・C・ナチェル, 阿久津達也
    • Organizer
      情報処理学会 バイオ情報学研究会
    • Place of Presentation
      はこだて未来大学
    • Year and Date
      2007-09-13
    • Related Report
      2007 Annual Research Report
  • [Presentation] 代謝ネットワークのトポロジー解析2007

    • Author(s)
      五斗進
    • Organizer
      九州大学産業技術数理研究センターワークショップ
    • Place of Presentation
      福岡
    • Year and Date
      2007-09-05
    • Related Report
      2009 Final Research Report
  • [Presentation] 代謝ネットワークのトポロジー解析2007

    • Author(s)
      五斗進
    • Organizer
      九州大学産業技術数理研究センターワークショップ
    • Place of Presentation
      九州大学
    • Year and Date
      2007-09-05
    • Related Report
      2007 Annual Research Report
  • [Presentation] Diversity Dynamics in a Complex Ecological Community2007

    • Author(s)
      Kei Tokita
    • Organizer
      2007 Taiwan International Workshop on Biological Physics and Complex Systems
    • Place of Presentation
      台湾中央研究院物理学研究所
    • Year and Date
      2007-08-07
    • Related Report
      2007 Annual Research Report
  • [Presentation] Structure of regulatory networks and diversity of gene expression patterns2007

    • Author(s)
      Mochizuki, A.
    • Organizer
      SMB/JSMB 2007 Joint Annual Meeting of The Society for Mathematical Biology and The Japanese Society for Mathematical Biology
    • Place of Presentation
      San Jose, USA
    • Year and Date
      2007-08-01
    • Related Report
      2009 Final Research Report
  • [Presentation] Structure of regulatory networks and diversity of gene expression patterns2007

    • Author(s)
      Atsushi Mochizuki
    • Organizer
      SMB/JSMB 2007 Joint Annual Meeting of The Society for Mathematical Biology and The Japanese Society for Mathematical Biology
    • Place of Presentation
      Fairmont Hotel, San Jose, California
    • Year and Date
      2007-08-01
    • Related Report
      2007 Annual Research Report
  • [Presentation] A model ecosystem of resource competition and random interaction2007

    • Author(s)
      Yoshimi Yoshino, Tobias Galla and Kei Tokita
    • Organizer
      Joint Annual Meetings of The Society for Mathematica Biology and The Japanese Society for Mathematical Biology
    • Place of Presentation
      Fairmont Hotel, San Jose, California, USA
    • Year and Date
      2007-08-01
    • Related Report
      2007 Annual Research Report
  • [Book] バイオインフォマティクスの数理とアルゴリズム2007

    • Author(s)
      阿久津達也
    • Total Pages
      223
    • Publisher
      共立出版
    • Related Report
      2009 Final Research Report
  • [Book] バイオインフォマティクス-配列データ解析と構造予測-2007

    • Author(s)
      丸山修、阿久津達也
    • Total Pages
      190
    • Publisher
      朝倉書店
    • Related Report
      2009 Final Research Report
  • [Book] バイオインフォマティクスの数理とアルゴリズム2007

    • Author(s)
      阿久津 達也
    • Total Pages
      223
    • Publisher
      共立出版
    • Related Report
      2006 Annual Research Report
  • [Remarks] ホームページ等

    • Related Report
      2009 Final Research Report
  • [Remarks] GENIES

    • URL

      http://www.genome.jp/tools/genies/

    • Related Report
      2009 Final Research Report
  • [Remarks] KEGG Atlas

    • URL

      http://www.kegg.jp/kegg/atlas/

    • Related Report
      2009 Final Research Report
  • [Remarks] KegArray

    • URL

      http://www.genome.jp/download/

    • Related Report
      2009 Final Research Report
  • [Remarks] E-zyme

    • URL

      http://www.genome.jp/tools/e-zyme/

    • Related Report
      2009 Final Research Report

URL: 

Published: 2005-04-01   Modified: 2018-03-28  

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