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  • Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H., Software for systems biology: from tools to integrated platforms. Nature Reviews Genetics (2011) doi: 10.1038/nrg3096
  • Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD, BioPAX Support in CellDesigner. Bioinformatics (2011)
  • Kitano H, Ghosh S, Matsuoka Y, Social engineering for virtual big science in systems biology, Nat Chem Biol. (2011) 7, 323-6. doi:10.1038/nchembio.574
  • Oyama M, Nagashima T, Suzuki T, Kozuka-Hata H, Yumoto N, Shiraishi Y, Ikeda K, Kuroki Y, Gotoh N, Ishida T, Inoue S, Kitano H, Okada-Hatakeyama M., Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer, Biol. Chem. (2011) 286: 818-829. PMID: 21044952
  • Tiago J.S. Lopes; Martin Schaefer; Jason Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Gabriele Neumann; Miguel A. Andrade-Navarro; Yoshihiro Kawaoka and Hiroaki Kitano. Tissue Specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics. doi: 10.1093/bioinformatics/btr414, published online July 28, 2011, 27(17), 2414-21, Sep.1, 2011.
  • Kyoda, K.; Baba, K.; Kitano, H.; Onami, S. A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks. Source Code for Biology and Medicine. 6(12), June 24, 2011.




*Please also check publication list ( for extensive list of the publication up tp 2007.





  • NEW Kitano, H., Oda, K., Kimura, T., Matsuoka, Y., Csete, M., Doyle, J., Muramatsu, M.. Metabolic Syndrome and Robustness Tradeoffs, Diabetes 53, S6-S15, 2004 PFD file
  • Kitano, H.. Biological Robustness. Nature Review Genetics. 5, 826-837, 2004 PDF file
  • Oda, K.; Kimura, T, Matsuoka, Y.; Funahashi, A.; Muramatsu, M.; Kitano, H. Molecular Interaction Map of Macrophage. AfCS Report. 2004. PDF file
  • M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project. IEE Systems Biology. 1:41-53, 2004
  • Kitano, H. Cancer as a robust system: implications for anticancer therapy. Nature Reviews Cancer 4:227-235, 2004. Abstract..



  • Kitano, H. Systems Biology: A Brief Overview. Science. 295, 1662-1664, 2002. Abstract...
  • Kitano, H. Computational Systems Biology. Nature. 420, 206-210, 2002. Abstract...
  • Kitano, H. Standards for modeling. Nat. Biotech. 20, 337, 2002. Abstract...
  • Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H. The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology. Proc. Pac Symp Biocomput. 2002, 450-61, 2002. Abstract...
  • Kitano, H. Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology.
    Curr Genet. 41, 1-10, 2002. Abstract...
  • Morohashi, M., Winn, A. E., Borisuk, M. T., Bolouri, H., Doyle, J., and Kitano, H. Robustness as a measure of plausibility in models of biochemical networks. J. Theor. Biol. 216, 19-30, 2002. Abstract...


  • Kyoda, K. M., Morohashi, M., Onami, S., and Kitano, H. A gene network inference method from continuous-value gene expression data of wild-type and mutants. Genome Informatics. 11, 196-204, 2000. Abstract...

*Please also check publication list ( for extensive list of the publication up tp 2007.

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