H Kitano

Summary

Affiliation: Sony Computer Science Laboratories
Country: Japan

Publications

  1. ncbi request reprint Systems biology: a brief overview
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
    Science 295:1662-4. 2002
  2. ncbi request reprint Computational systems biology
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, Shinagwa, Tokyo, Japan
    Nature 420:206-10. 2002
  3. pmc Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking
    Shugo Hamahashi
    Kitano Symbiotic Systems Project, ERATO, Japan Science and Technology Corporation, M31 6A, 6 31 15 Jingumae, Shibuya, Tokyo 150 0001, Japan
    BMC Bioinformatics 6:125. 2005
  4. ncbi request reprint The two-process model of cellular aging
    H Kitano
    Sony Computer Science Laboratory, Tokyo, Japan
    Exp Gerontol 33:393-419. 1998
  5. ncbi request reprint Metabolic syndrome and robustness tradeoffs
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc 3 14 13, Higashi Gotanda, Shinagawa, Tokyo 141 0022 Japan
    Diabetes 53:S6-S15. 2004
  6. ncbi request reprint Cancer as a robust system: implications for anticancer therapy
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
    Nat Rev Cancer 4:227-35. 2004
  7. ncbi request reprint [Exploring the architecture of genome-wide biological network]
    Hiroaki Kitano
    Tanpakushitsu Kakusan Koso 49:2855-63. 2004
  8. ncbi request reprint Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology
    Hiroaki Kitano
    The Systems Biology Institute, Suite 6A, M31 6 31 15 Jinguu mae, Shibuya, Tokyo 150 0001 Japan
    Curr Genet 41:1-10. 2002
  9. ncbi request reprint The perfect C. elegans project: an initial report
    H Kitano
    Sony Computer Science Laboratory, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141, Japan
    Artif Life 4:141-56. 1998
  10. ncbi request reprint Biological robustness
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
    Nat Rev Genet 5:826-37. 2004

Collaborators

Detail Information

Publications35

  1. ncbi request reprint Systems biology: a brief overview
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
    Science 295:1662-4. 2002
    ..However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential...
  2. ncbi request reprint Computational systems biology
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, Shinagwa, Tokyo, Japan
    Nature 420:206-10. 2002
    ..Computational systems biology addresses questions fundamental to our understanding of life, yet progress here will lead to practical innovations in medicine, drug discovery and engineering...
  3. pmc Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking
    Shugo Hamahashi
    Kitano Symbiotic Systems Project, ERATO, Japan Science and Technology Corporation, M31 6A, 6 31 15 Jingumae, Shibuya, Tokyo 150 0001, Japan
    BMC Bioinformatics 6:125. 2005
    ..However, the system needed laborious hand-tuning of its parameters every time a new image set was used. It could not detect nuclei in the process of cell division, and could detect nuclei only from the two- to eight-cell stages...
  4. ncbi request reprint The two-process model of cellular aging
    H Kitano
    Sony Computer Science Laboratory, Tokyo, Japan
    Exp Gerontol 33:393-419. 1998
    ..From these theoretical considerations, we discuss the validity of the two-process model and the possible involvement of the heterochromatin structure as a determinant of the replicative lifespan of cells...
  5. ncbi request reprint Metabolic syndrome and robustness tradeoffs
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc 3 14 13, Higashi Gotanda, Shinagawa, Tokyo 141 0022 Japan
    Diabetes 53:S6-S15. 2004
    ..A detailed molecular interaction map for adipocyte, hepatocyte, skeletal muscle cell, and pancreatic beta-cell cross-talk in the metabolic syndrome can be viewed at http://www.systems-biology.org/001/003.html...
  6. ncbi request reprint Cancer as a robust system: implications for anticancer therapy
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
    Nat Rev Cancer 4:227-35. 2004
  7. ncbi request reprint [Exploring the architecture of genome-wide biological network]
    Hiroaki Kitano
    Tanpakushitsu Kakusan Koso 49:2855-63. 2004
  8. ncbi request reprint Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology
    Hiroaki Kitano
    The Systems Biology Institute, Suite 6A, M31 6 31 15 Jinguu mae, Shibuya, Tokyo 150 0001 Japan
    Curr Genet 41:1-10. 2002
    ..However, the meaning of "system-level understanding" is still ambiguous. This paper reviews the current status of the field and outlines future research directions and issues that need to be addressed...
  9. ncbi request reprint The perfect C. elegans project: an initial report
    H Kitano
    Sony Computer Science Laboratory, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141, Japan
    Artif Life 4:141-56. 1998
    ..elegans Project, which aims to produce ultimately a complete synthetic model of C. elegans' cellular structure and function. This article describes the goal, the approach, and the initial results of the project...
  10. ncbi request reprint Biological robustness
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
    Nat Rev Genet 5:826-37. 2004
    ..Insights into inherent properties of robust systems will provide us with a better understanding of complex diseases and a guiding principle for therapy design...
  11. ncbi request reprint Heterochromatin islands and their dynamic reorganization: a hypothesis for three distinctive features of cellular aging
    S Imai
    Department of Microbiology, Keio University School of Medicine, Tokyo, Japan
    Exp Gerontol 33:555-70. 1998
    ..The importance of a dynamic equilibrium in heterochromatin islands is also discussed for cellular and organismic aging...
  12. pmc Large-scale analysis of network bistability for human cancers
    Tetsuya Shiraishi
    Sony Computer Science Laboratories, Shinagawa ku, Tokyo, Japan
    PLoS Comput Biol 6:e1000851. 2010
    ..This paper shows how a large-scale analysis of network bistability for various human cancers can identify genes that can potentially serve as drug targets or diagnosis biomarkers...
  13. pmc Consistent design schematics for biological systems: standardization of representation in biological engineering
    Yukiko Matsuoka
    The Systems Biology Institute, Tokyo, Japan
    J R Soc Interface 6:S393-404. 2009
    ..We envision that such a synergistic approach would lead to the development of global, standardized schemata in biology, empowering deeper understanding of molecular mechanisms as well as engineering of novel biological systems...
  14. ncbi request reprint DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants
    Koji Kyoda
    Kitano Symbiotic Systems Project, ERATO, Japan Science and Technology Corporation, Shibuya, Tokyo 150 0001, Japan
    Bioinformatics 20:2662-75. 2004
    ..Signed directed graph (SDG) is the most common representation of gene networks in genetics and cell biology. However, no practical procedure that deduces SDGs consistent with such profiles has been developed...
  15. ncbi request reprint Cancer robustness: tumour tactics
    Hiroaki Kitano
    Sony Computer Science Laboratories Inc, 3 14 13 Higashi Gotanda, Shinagwa, Tokyo 141 0022
    Nature 426:125. 2003
  16. pmc In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae
    Hisao Moriya
    ERATO SORST Kitano Symbiotic Systems Project, Japan Science and Technology Agency, Shibuya ku, Tokyo, Japan
    PLoS Genet 2:e111. 2006
    ..The data were used to evaluate the current computational model, and refinements to the model were suggested...
  17. ncbi request reprint A robustness-based approach to systems-oriented drug design
    Hiroaki Kitano
    Sony Computer Science Laboratories Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
    Nat Rev Drug Discov 6:202-10. 2007
    ....
  18. ncbi request reprint Using process diagrams for the graphical representation of biological networks
    Hiroaki Kitano
    The Systems Biology Institute, Suite 6A, M31 6 31 15 Jingumae, Shibuya, Tokyo, 150 0001 Japan
    Nat Biotechnol 23:961-6. 2005
    ..It is supported by CellDesigner, a diagrammatic network editing software (http://www.celldesigner.org/), and has been used to represent a variety of networks of various sizes (from only a few components to several hundred components)...
  19. pmc Structure of protein interaction networks and their implications on drug design
    Takeshi Hase
    Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo ku, Tokyo, Japan
    PLoS Comput Biol 5:e1000550. 2009
    ..Such network properties provide the rationale for combinatorial drugs that target less prominent nodes to increase synergetic efficacy and create fewer side effects...
  20. pmc Payao: a community platform for SBML pathway model curation
    Yukiko Matsuoka
    The Systems Biology Institute, Tokyo, Japan
    Bioinformatics 26:1381-3. 2010
    ..Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported...
  21. pmc G-protein coupled receptor signaling architecture of mammalian immune cells
    Natalia Polouliakh
    Sony Computer Science Laboratories Inc, Tokyo, Japan
    PLoS ONE 4:e4189. 2009
    ..Groups of potential transcription factors for each specific group of genes were found to be partly conserved across B-cell and macrophage. A series of findings support the hypothesis...
  22. pmc PathText: a text mining integrator for biological pathway visualizations
    Brian Kemper
    Department of Computer Science, University of Tokyo, Tokyo, Japan
    Bioinformatics 26:i374-81. 2010
    ....
  23. ncbi request reprint Biological robustness in complex host-pathogen systems
    Hiroaki Kitano
    The Systems Biology Institute, Suite 6A, M31 6 31 15 Jingumae, Shibuya, Tokyo 150 0001, Japan
    Prog Drug Res 64:239, 241-63. 2007
    ....
  24. pmc A comprehensive pathway map of epidermal growth factor receptor signaling
    Kanae Oda
    The Systems Biology Institute, Tokyo, Japan
    Mol Syst Biol 1:2005.0010. 2005
    ..The map is created using CellDesigner software that enables us to graphically represent interactions using a well-defined and consistent graphical notation, and to store it in Systems Biology Markup Language (SBML)...
  25. ncbi request reprint Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration
    Herbert M Sauro
    Keck Graduate Institute, Claremont, California 91711, USA
    OMICS 7:355-72. 2003
    ....
  26. ncbi request reprint [Introductions to systems biology]
    Hiroaki Kitano
    Tanpakushitsu Kakusan Koso 48:789-93. 2003
  27. ncbi request reprint The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks
    Yoshiyuki Sakaki
    Syst Biol (Stevenage) 152:53-4. 2005
  28. pmc The PANTHER database of protein families, subfamilies, functions and pathways
    Huaiyu Mi
    Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA
    Nucleic Acids Res 33:D284-8. 2005
    ..Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com...
  29. ncbi request reprint Standards for modeling
    Hiroaki Kitano
    Nat Biotechnol 20:337. 2002
  30. ncbi request reprint Modeling the impact of store-operated Ca2+ entry on intracellular Ca2+ oscillations
    Jacob M Kowalewski
    Cell Physics, Royal Institute of Technology, Roslagstullsbacken 21, 106 91 Stockholm, Sweden
    Math Biosci 204:232-49. 2006
    ..These findings increase knowledge concerning store-operated Ca2+ entry and its impact on intracellular Ca2+ oscillations...
  31. pmc Towards a theory of biological robustness
    Hiroaki Kitano
    Mol Syst Biol 3:137. 2007
  32. ncbi request reprint Integration of CellDesigner and SABIO-RK
    Akira Funahashi
    JST ERATO SORST Kitano Symbiotic Systems Project, Japan
    In Silico Biol 7:S81-90. 2007
    ..By using the Web service API provided by the SABIO-RK team, we have succeeded to directly connect to the database, send search queries by ID or name of its component, and then import the query results into CellDesigner...
  33. ncbi request reprint Deduction of intracellular sub-systems from a topological description of the network
    Torbjörn E M Nordling
    Automatic Control School of Electrical Engineering, Royal Institute of Technology KTH, Sweden
    Mol Biosyst 3:523-9. 2007
    ..e. graphs that only contain edges representing interactions active in the specific mode. In general, when an interaction between two molecules is established, one should always state the mode of the system in which it is active...
  34. ncbi request reprint Genome-wide prediction of genetic interactions in a metazoan
    Shuichi Onami
    Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Bioessays 28:1087-90. 2006
    ..cerevisiae, C. elegans and Drosophila melanogaster. This achievement is an important step toward system-level understanding of biological systems and human diseases...
  35. ncbi request reprint [Developmental systems biology]
    Shuichi Onami
    Tanpakushitsu Kakusan Koso 50:798-803. 2005