Hiroaki Kitano

Summary

Country: Japan

Publications

  1. 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
  2. pmc Payao: a community platform for SBML pathway model curation
    Yukiko Matsuoka
    The Systems Biology Institute, Tokyo, Japan
    Bioinformatics 26:1381-3. 2010
  3. 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
  4. pmc A comprehensive molecular interaction map of the budding yeast cell cycle
    Kazunari Kaizu
    Department of Science and Technology, Keio University, Kanagawa, Japan
    Mol Syst Biol 6:415. 2010
  5. pmc Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease
    Isaac Crespo
    Luxembourg Center for Systems Biomedicine LCSB, University of Luxembourg, Campus Belval, 7, avenue des Hauts Fourneaux, Luxembourg L 4362, Luxembourg
    BMC Syst Biol 6:132. 2012
  6. pmc Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs
    Jason E Shoemaker
    ERATO Infection Induced Host Responses Project, Saitama, 332 0012, Japan
    BMC Syst Biol 6:117. 2012
  7. pmc Violations of robustness trade-offs
    Hiroaki Kitano
    The Systems Biology Institute, Minato, Tokyo, Japan
    Mol Syst Biol 6:384. 2010
  8. 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
  9. pmc Fragilities caused by dosage imbalance in regulation of the budding yeast cell cycle
    Kazunari Kaizu
    Department of Science and Technology, Keio University, Yokohama shi, Kanagawa, Japan
    PLoS Genet 6:e1000919. 2010
  10. pmc CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data
    Jason E Shoemaker
    JST ERATO KAWAOKA Infection induced Host Responses Project, Tokyo, Japan
    BMC Genomics 13:460. 2012

Collaborators

Detail Information

Publications32

  1. 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
    ....
  2. 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...
  3. 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...
  4. pmc A comprehensive molecular interaction map of the budding yeast cell cycle
    Kazunari Kaizu
    Department of Science and Technology, Keio University, Kanagawa, Japan
    Mol Syst Biol 6:415. 2010
    ..We envisage the open access, comprehensive cell-cycle map to open roads toward community-based deeper understanding of cell-cycle dynamics...
  5. pmc Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease
    Isaac Crespo
    Luxembourg Center for Systems Biomedicine LCSB, University of Luxembourg, Campus Belval, 7, avenue des Hauts Fourneaux, Luxembourg L 4362, Luxembourg
    BMC Syst Biol 6:132. 2012
    ..To elucidate the mechanisms leading from abnormal protein deposition to neuronal injury, we have performed a detailed network analysis of genes differentially expressed in several mouse prion models...
  6. pmc Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs
    Jason E Shoemaker
    ERATO Infection Induced Host Responses Project, Saitama, 332 0012, Japan
    BMC Syst Biol 6:117. 2012
    ....
  7. pmc Violations of robustness trade-offs
    Hiroaki Kitano
    The Systems Biology Institute, Minato, Tokyo, Japan
    Mol Syst Biol 6:384. 2010
    ..Several testable predictions and implications for cell culture experiments are presented...
  8. 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...
  9. pmc Fragilities caused by dosage imbalance in regulation of the budding yeast cell cycle
    Kazunari Kaizu
    Department of Science and Technology, Keio University, Yokohama shi, Kanagawa, Japan
    PLoS Genet 6:e1000919. 2010
    ..The masking function of CLB2 was stabilization of Pds1 by its phosphorylation. We finally modified Chen's model according to our findings. We thus propose that dosage imbalance causes fragility in biological systems...
  10. pmc CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data
    Jason E Shoemaker
    JST ERATO KAWAOKA Infection induced Host Responses Project, Tokyo, Japan
    BMC Genomics 13:460. 2012
    ..To put gene expression into its proper biological context, it is necessary to distinguish differential gene transcription from artificial gene expression induced by changes in the cellular demographics...
  11. doi request reprint Connecting the dots: role of standardization and technology sharing in biological simulation
    Samik Ghosh
    The Systems Biology Institute, Tokyo, Japan
    Drug Discov Today 15:1024-31. 2010
    ....
  12. 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...
  13. doi request reprint Software for systems biology: from tools to integrated platforms
    Samik Ghosh
    The Systems Biology Institute, Minato, Tokyo, Japan
    Nat Rev Genet 12:821-32. 2011
    ..We also discuss the challenges and prospects for modelling the effects of genetic changes on physiology and the concept of an integrated platform...
  14. 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...
  15. 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...
  16. 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)...
  17. 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)...
  18. 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...
  19. ncbi request reprint Modeling and Simulation Using CellDesigner
    Yukiko Matsuoka
    The Systems Biology Institute, 5 6 9 Shirokanedai, Minato ku, Tokyo, 108 0071, Japan
    Methods Mol Biol 1164:121-45. 2014
    ..In this chapter, we explain how to build a model and run the simulation using CellDesigner, adopting the standards such as SBML and SBGN. ..
  20. 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
  21. doi request reprint Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases
    Tiago J S Lopes
    JST ERATO KAWAOKA Infection induced Host Responses Project, Tokyo, Japan
    Bioinformatics 27:2414-21. 2011
    ....
  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 Cancer robustness: tumour tactics
    Hiroaki Kitano
    Sony Computer Science Laboratories Inc, 3 14 13 Higashi Gotanda, Shinagwa, Tokyo 141 0022
    Nature 426:125. 2003
  24. pmc Harnessing diversity towards the reconstructing of large scale gene regulatory networks
    Takeshi Hase
    The Systems Biology Institute, Shirokanedai, Minato, Tokyo, Japan Laboratory of Disease Systems Modeling, Center for Integrative Medical Sciences, RIKEN, Suehiro cho, Tsurumi ku, Yokohama City, Kanagawa, Japan
    PLoS Comput Biol 9:e1003361. 2013
    ..The consensus framework, TopkNet, together with the similarity measure proposed in this study provides a powerful strategy towards harnessing the wisdom of the crowds in reconstruction of unknown regulatory networks. ..
  25. 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
    ....
  26. 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...
  27. ncbi request reprint Integrating pathways of Parkinson's disease in a molecular interaction map
    Kazuhiro A Fujita
    The Systems Biology Institute, Minato ku, Tokyo, Japan
    Mol Neurobiol 49:88-102. 2014
    ..We also present bioinformatics tools for the analysis, enrichment and annotation of the map, allowing the research community to open new avenues in PD research. The PD map is accessible at http://minerva.uni.lu/pd_map . ..
  28. doi request reprint The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
    Harukazu Suzuki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    Nat Genet 41:553-62. 2009
    ....
  29. pmc A comprehensive map of the toll-like receptor signaling network
    Kanae Oda
    The Systems Biology Institute, Shibuya, Tokyo, Japan
    Mol Syst Biol 2:2006.0015. 2006
    ....
  30. pmc Robustness trade-offs and host-microbial symbiosis in the immune system
    Hiroaki Kitano
    The Systems Biology Institute, Jingumae, Shibuya, Tokyo, Japan
    Mol Syst Biol 2:2006.0022. 2006
    ....
  31. pmc Towards a theory of biological robustness
    Hiroaki Kitano
    Mol Syst Biol 3:137. 2007