原著論文｜研究業績

最終更新日 : 2015年5月13日

原著論文

2014年｜2013年｜2012年｜2011年｜2010年｜2009年｜2008年｜2007年｜2006年｜

2014年

Honma, N., Horii, R., Iwase, T., Saji, S., Younes, M., Ito, Y., Akiyama, F.

Proportion of estrogen or progesterone receptor expressing cells in breast cancers and response to endocrine therapy.
Breast, 23, 754-762 (2014)

2013年

Makanae, K., Kintaka, R., Makino, T., Kitano, H., Moriya, H.: Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method.
Geneome Res, 23, 300-311 (2013)
Naito, T., Yatsuhashi, A., Kaji, N., Ando, T., Sato, K., Moriya, H., Kitano, H., Yasui, T., Tokeshi, M., Baba, Y.: Parallel Real-Time PCR on a Chip for Genetic Tug-of-War (gTOW) Method.
Anal Sci, 29, 367-371 (2013)
Schaefer, M.H., Lopes, T.J., Mah, N., Shoemaker, J.E., Matsuoka, Y., Fontaine, J.F., Louis-Jeune, C., Eisfeld, A.J., Neumann, G., Perez-Iratxeta, C., Kawaoka, Y., Kitano, H., Andrade-Navarro, M.A.: Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.
PLoS computational biology, 9, e1002860 (2013)

2012年

Crespo, I., Roomp, K., Jurkowski, W., Kitano, H., del Sol, A.: Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease.
BMC Syst Biol, 6, 132 (2012)
Ghosh, S., Matsuoka, Y., Asai, Y., Kitano, H., Bhardwaj, A., Scaria, V., Vashisht, R., Shah, A., Mondal, A.K., Vishnoi, P., Sonal, K., Jain, A., Priyadarshini, P., Bhattacharyya, K., Kumar, V., Passi, A., Sharma, P., Brahmachari, S.: Software platform for metabolic network reconstruction of mycobacterium tuberculosis.
In Systems Biology of Tuberculosis, McFadden, J., Beste, D.J.V., Kierzek, A.M., (New York, Springer), 21-35 (2012)
Kitano, H.: Cancer systems biology: A robustness-based approach.
In Handbook of systems biology : concepts and insights, Walhout, A.J.M., Vidal, M., Dekker, J., (Amsterdam, Academic Press), 469-479 (2012)
Shoemaker, J.E., Fukuyama, S., Eisfeld, A.J., Muramoto, Y., Watanabe, S., Watanabe, T., Matsuoka, Y., Kitano, H., Kawaoka, Y.: Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs.
BMC Syst Biol, 6, 117 (2012)
Shoemaker, J.E., Lopes, T.J., Ghosh, S., Matsuoka, Y., Kawaoka, Y., Kitano, H.: CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data.
BMC Genomics, 13, 460 (2012)
Tiger, C.F., Krause, F., Cedersund, G., Palmer, R., Klipp, E., Hohmann, S., Kitano, H., Krantz, M.: A framework for mapping, visualisation and automatic model creation of signal-transduction networks.
Mol Syst Biol, 8, 578 (2012)
van Iersel, M.P., Villeger, A.C., Czauderna, T., Boyd, S.E., Bergmann, F.T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y., Funahashi, A., Aladjem, M.I., Mi, H., Moodie, S.L., Kitano, H., Le Novere, N., Schreiber, F.: Software support for SBGN maps: SBGN-ML and LibSBGN.
Bioinformatics, 28, 2016-2021 (2012)

2011年

Kitano, H.: Cancer robustness and therapy strategies.
In Cancer systems biology, bioinformatics and medicine, Cesario, A., Marcus, F., (Springer), 429-446 (2011)
Kitano, H., Ghosh, S., Matsuoka, Y.: Social engineering for virtual 'big science' in systems biology.
Nat Chem Biol, 7, 323-326 (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 Biol Med, 6, 12 (2011)
Lopes, T.J., Schaefer, M., Shoemaker, J., Matsuoka, Y., Fontaine, J.F., Neumann, G., Andrade-Navarro, M.A., Kawaoka, Y., Kitano, H.: Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases.
Bioinformatics, 27, 2414-2421 (2011)
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.
J Biol Chem, 286, 818-829 (2011)

2010年

Caron, E., Ghosh, S., Matsuoka, Y., Ashton-Beaucage, D., Therrien, M., Lemieux, S., Perreault, C., Roux, P.P., Kitano, H.: A comprehensive map of the mTOR signaling network.
Mol Syst Biol, 6, 453 (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 (2010)
Berrar, D., Sato, N., Schuster, A.: Quo vadis, artificial intelligence?
Adv Artif Intell, 2010, 629869 (2010)
Gehlenborg, N., O'Donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D., Gavin, A.C.: Visualization of omics data for systems biology.
Nat Methods, 7, S56-68 (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 (2010)
Kaizu, K., Moriya, H., Kitano, H.: Fragilities caused by dosage imbalance in regulation of the budding yeast cell cycle.
PLoS Genet, 6, e1000919 (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 (2010)
Kitano, H.: Grand challenges in systems physiology.
Frontiers in Systems Physiology, 1, doi:10.3389/fphys.2010.00003,02010 (2010)
Kitano, H.: Violations of robustness trade-offs.
Mol Syst Biol, 6, 384 (2010)
Matsuoka, Y., Ghosh, S., Kikuchi, N., Kitano, H.: Payao: a community platform for SBML pathway model curation.
Bioinformatics, 26, 1381-1383 (2010)
Shiraishi, T., Matsuyama, S., Kitano, H.: Large-scale analysis of network bistability for human cancers.
PLoS Comput Biol, 6, e1000851 (2010)

2009年

Hase, T., Tanaka, H., Suzuki, Y., Nakagawa, S., Kitano, H.: Structure of protein interaction networks and their implications on drug design.
PLoS Comput Biol, 5, e1000550 (2009)
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.
Mol Syst Biol, 5, 281 (2009)
Le Novere, N., Hucka, M., Mi, H., 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., 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 (2009)
Matsuoka, Y., Ghosh, S., Kitano, H.: Consistent design schematics for biological systems: standardization of representation in biological engineering.
J R Soc Interface, 6, S393-404 (2009)
Polouliakh, N., Nock, R., Nielsen, F., Kitano, H.: G-protein coupled receptor signaling architecture of mammalian immune cells.
PLoS One, 4, e4189 (2009)
Suzuki, H., Forrest, A.R., van Nimwegen, E., Daub, C.O., Balwierz, P.J., Irvine, K.M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M.J., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M., Asahara, H., Bailey, T., Bajic, V.B., Bauer, D., Beckhouse, A.G., Bertin, N., Bjorkegren, J., Brombacher, F., Bulger, E., Chalk, A.M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engstrom, P.G., Essack, M., Faulkner, G.J., Fink, J.L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S.M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hornquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M.C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., MacPherson, C., Maeda, N., Maher, C.A., Maqungo, M., Mar, J., Matigian, N.A., Matsuda, H., Mattick, J.S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schonbach, C., Schwartz, A.S., Semple, C.A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M.J., Taft, R.J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M.S., Teasdale, R.D., Tegner, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C.A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D.A., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J., Hayashizaki, Y.: The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nat Genet, 41, 553-562 (2009)

2008年

Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N., Kitano, H.: CellDesigner 3.5: A versatile modeling tool for biochemical networks.
Proceedings of the IEEE Special Issue: Computational Systems Biology, 96, 1254-1265 (2008)

2007年

Funahashi, A., Jouraku, A., Matsuoka, Y., Kitano, H.: Integration of CellDesigner and SABIO-RK.
In Silico Biol, 7, S81-90 (2007)
Kitano, H.: Biological robustness in complex host-pathogen systems.
Prog Drug Res, 64, 239, 241-263 (2007)
Kitano, H.: A robustness-based approach to systems-oriented drug design.
Nat Rev Drug Discov, 6, 202-210 (2007)
Kitano, H.: The theory of biological robustness and its implication in cancer.
Ernst Schering Res Found Workshop, 69-88 (2007)
Kitano, H.: Towards a theory of biological robustness.
Mol Syst Biol, 3, 137 (2007)
Murray, D.B., Beckmann, M., Kitano, H.: Regulation of yeast oscillatory dynamics.
Proc Natl Acad Sci U S A, 104, 2241-2246 (2007)
Nordling, T.E., Hiroi, N., Funahashi, A., Kitano, H.: Deduction of intracellular sub-systems from a topological description of the network.
Mol Biosyst, 3, 523-529 (2007)

2006年

Hiroi, N., Funahashi, A., Kitano, H.: Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA.
Cancer Gene Ther, 13, 7-12 (2006)
Kitano, H.: Computational cellular dynamics: a network-physics integral.
Nat Rev Mol Cell Biol, 7, 163 (2006)
Kitano, H., Oda, K.: Robustness trade-offs and host-microbial symbiosis in the immune system.
Mol Syst Biol, 2, 2006 0022 (2006)
Kitano, H., Oda, K.: Self-extending symbiosis: A mechanisms for increasing robustness through evolution.
Biol Theory, 1, 61-66 (2006)
Moriya, H., Shimizu-Yoshida, Y., Kitano, H.: In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae.
PLoS Genet, 2, e111 (2006)
Oda, K., Kitano, H.: A comprehensive map of the toll-like receptor signaling network.
Mol Syst Biol, 2, 2006 0015 (2006)
Onami, S., Kitano, H.: Genome-wide prediction of genetic interactions in a metazoan.
Bioessays, 28, 1087-1090 (2006)

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