Analysis of Structure and Dynamics of Biological Information Networks

2009 Fiscal Year Final Research Report

• Project/Area Number: 17017019
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyoto 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
• 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

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.

Research Products

• [Journal Article] Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs (2009)
  • Author(s): Nacher, J.C., Hayashida, M., Akutsu, T.
  • Journal Title: Bio Systems 95 Pages: 155-159
• [Journal Article] Systems biology approaches and tools for investigating cardiovascular disease (2009)
  • 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
• [Journal Article] Steepness of thermal gradient is essential to obtain a unified view of thermotaxis in C.elegans (2009)
  • Author(s): Nakazato, K., Mochizuki, A.
  • Journal Title: Journal of Theoretical Biology 260 Pages: 56-65
• [Journal Article] Structure of regulatory networks and diversity of gene expression patterns (2008)
  • Author(s): Mochizuki, A.
  • Journal Title: Journal of Theoretical Biology 250 Pages: 307-321
• [Journal Article] Rank abundance relations in evolutionary dynamics of random replicators (2008)
  • Author(s): Yoshino, Y., Galla, T., Tokita, K.
  • Journal Title: Physical Review E 78 Pages: 031924
• [Journal Article] Control of Boolean networks: hardness results and algorithms for tree structured networks (2007)
  • Author(s): Akutsu, T., Hayashida, M., Ching, W-K., Ng, M.K.
  • Journal Title: Journal of Theoretical Biology 24 Pages: 670-679
• [Journal Article] Prediction of missing enzyme genes in bacterial metabolic network : A reconstruction of lysine degradation pathway of Pseudomonas aeruginosa (2007)
  • 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
• [Journal Article] Transient and steady state of mass-conserved reaction-diffusion systems (2007)
  • Author(s): Ishihara, S., Otsuji, M., Mochizuki, A.
  • Journal Title: Physical Review E 75 Pages: 015203
• [Journal Article] Statistical mechanics and stability of a random eco-system (2007)
  • Author(s): Yoshino, Y., Galla, T., Tokita, K.
  • Journal Title: Journal of Statistical Mechanics P09003
• [Journal Article] Protein domain networks : scale-free mixing of positive and negative exponents (2006)
  • Author(s): Nacher, J.C., Hayashida, M., Akutsu, T.
  • Journal Title: Physica A 367 Pages: 538-552
• [Journal Article] Extraction of phylogenetic network modules from the metabolic network (2006)
  • Author(s): Yamada, T., Kanehisa, M., Goto, S.
  • Journal Title: BMC Bioinformatics 7 Pages: 130
• [Journal Article] Statistical mechanics of relative species abundance (2006)
  • Author(s): Tokita, K.
  • Journal Title: Ecological Informatics 1 Pages: 315-324
• [Presentation] Structure of regulatory networks and dynamics of bio-molecules (2010)
  • 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
• [Presentation] Completing networks using observed data (2009)
  • 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
• [Presentation] Large-scale biological networks (2009)
  • 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
• [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
• [Presentation] Algorithms for inference, analysis and control of Boolean networks (2008)
  • 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
• [Presentation] Network perspective in bioinformatics (2007)
  • Author(s): Goto, S.
  • Organizer: Nishinomiya-Yukawa International & Interdisciplinary Symposium
  • Place of Presentation: Kyoto, Japan
  • Year and Date: 2007-10-18
• [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
• [Presentation] Structure of regulatory networks and diversity of gene expression patterns (2007)
  • 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
• [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
• [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
• [Remarks] ホームページ等
• [Remarks] GENIES
  • URL: http://www.genome.jp/tools/genies/
• [Remarks] KEGG Atlas
  • URL: http://www.kegg.jp/kegg/atlas/
• [Remarks] KegArray
  • URL: http://www.genome.jp/download/
• [Remarks] E-zyme
  • URL: http://www.genome.jp/tools/e-zyme/