Hiroaki Kitano

President & CEO, Sony Computer Science Laboratories, Inc

President, The Systems Biology Institute

Selected Publications:

Martijn P. van Iersel, Alice C. Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly Sorokin, Ugur Dogrusoz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le Novère and Falk Schreiber. Software support for SBGN maps: SBGN-ML and LibSBGN. doi: 10.1093/bioinformatics/bts270. Bioinformatics. May 2012.

Carl-Fredrik Tiger, Falko Krause2, Gunnar Cedersund, Robert Palme, Edda Klipp, Stefan Hohmann, Hiroaki Kitano,and Marcus Krantz.  A Framework for mapping, visualization and automatic model creation of signal transduction networks. Molecular Systems Biology 8: 578. March 16, 2012.

Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin and Hiroaki Kitano. (2011) Software for systems biology: from tools to integrated platforms. Nature Reviews Genetics. Published online Nov. 3, 2011. 12(12), 821-832, Dec. 2011.

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 28 July 2011.

Hiroaki Kitano, Samik Ghosh & Yukiko Matsuoka. Social engineering for virtual 'big science' in systems biology. Nature Chemical Biology. 7, 323–326 (2011) doi:10.1038/nchembio.574. Published online 17 May 2011

Caron E., Ghosh S., Matsuoka Y., Ashton-Beaucage D., Therrien M., Lemieux S., Perreault C., Roux PP. & Kitano H. A comprehensive map of the mTOR signaling network. Mol Syst Biol 6, Article no. 453, doi:msb2010108 [pii] 10.1038/msb.2010.108 (November 2010).

Ghosh S., Matsuoka Y. & Kitano H. Connecting the dots: role of standardization and technology sharing in biological simulation. Drug Discov Today 15, 1024-1031, doi:S1359-6446(10)00336-3 [pii] 10.1016/j.drudis.2010.10.001 (Oct 2010).

北野宏明、松岡由紀子、ゴーシュ・サミック. システムバイオロジーにおける情報基盤. 計測と制御 49(8), 507-512, 2010-08-10.Kitano H., Matsuoka Y. & Ghosh S. Computational infrastructure for systems biology.  Instrument and Control Engineers 49, 507-512 (Aug 2010)

Shiraishi T., Matsuyama S. & Kitano H. Large-scale analysis of network bistability for human cancers. PLoS Comput Biol 6, e1000851, doi:10.1371/journal.pcbi.1000851 (July 2010).

Kemper B., Matsuzaki T., Matsuoka Y., Tsuruoka Y., Kitano H., Ananiadou S. & Tsujii J. PathText: a text mining integrator for biological pathway visualizations. Bioinformatics 26, i374-381, doi:btq221 [pii] 10.1093/bioinformatics/btq221 (July 2010).

Kaizu K., Ghosh S., Matsuoka Y., Moriya H., Shimizu-Yoshida Y. & Kitano H. A comprehensive molecular interaction map of the budding yeast cell cycle. Mol Syst Biol 6, 415, doi:msb201073 [pii] 10.1038/msb.2010.73 (July 2010).

Kitano H. Grand challenges in systems physiology. Frontiers in Physiology 1 (May 2010).

Kitano H. Violations of robustness trade-offs. Mol Syst Biol 6, Article no. 384, doi:msb201040 [pii] 10.1038/msb.2010.40 (May 2010).

Kazunari Kaizu, H. M., Hiroaki Kitano. Fragilities Caused by Dosage Imbalance in Regulation of the Budding Yeast Cell Cycle. PLoS Genetics6, e1000919 (April 2010).

Matsuoka Y., Ghosh S., Kikuchi N. & Kitano H. Payao: a community platform for SBML pathway model curation. Bioinformatics 26, 1381-1383, doi:btq143 [pii] 10.1093/bioinformatics/btq143 (March 2010).

Gehlenborg, N., O'Donoghue, S. I., Baliga, N. S., Goesmann, A., Hibbs, M. A., Kitano, H., Kohlbacher, O., Neuweger, H., Schnider, R., Tenebaum, D., Gavin, A. C. Visualization of omics data for systems biology. Nature Methods Supplement 7, S56-S68 (March 2010).

Hase, T., Tanaka, H., Suzuki, Y., Nakagawa, S. & Kitano, H. Structure of Protein Interaction Networks and Their Implications on Drug Design. Plos Computational Biology 5, -, doi:ARTN e1000550DOI 10.1371/journal.pcbi.1000550 (Oct 2009).

Le Novere, N., Hucka, M., Mi, H. Y., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villeger, A., Boyd, S. E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G. M., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K. & Kitano, H. The Systems Biology Graphical Notation. Nat Biotechnol 27, 735-741, doi:Doi 10.1038/Nbt.1558 (Sept 2009).

Matsuoka, Y., Ghosh, S. & Kitano, H. Consistent design schematics for biological systems: standardization of representation in biological engineering. Journal of the Royal Society Interface6, -, doi:DOI 10.1098/rsif.2009.0046.focus (June 2009). 76

Krantz, M., Ahmadpour, D., Ottosson, L. G., Warringer, J., Waltermann, C., Nordlander, B., Klipp, E., Blomberg, A., Hohmann, S. & Kitano, H. Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway. Molecular Systems Biology5, doi:Artn 281Doi 10.1038/Msb.2009.36 (June 2009).