PUBLICATIONS

npj_Systems Biology and Applications

2021

  •  Tsuji S, Hase T, Yachie-Kinoshita A, Nishino T, Ghosh S, Kikuchi M, Shimokawa K, Aburatani H, Kitano H, Tanaka H. Artificial intelligence-based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer's disease. Alzheimers Res Ther. 2021 May 3;13(1):92. doi: 10.1186/s13195-021-00826-3. PMID: 33941241; PMCID: PMC8091739.
  • Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387. PMID: 34664389.
  • Avila-Magaña V, Kamel B, DeSalvo M, Gómez-Campo K, Enríquez S, Kitano H, Rohlfs RV, Iglesias-Prieto R, Medina M. Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. Nat Commun. 2021 Sep 30;12(1):5731. doi: 10.1038/s41467-021-25950-4. PMID: 34593802.
  • Kitano, H. Nobel Turing Challenge: creating the engine for scientific discovery. npj Syst Biol Appl 7, 29 (2021). https://doi.org/10.1038/s41540-021-00189-3
  • Nishi, A., Kaifuchi, N., Shimobori, C, Ohbuchi, K., Iizuka, S., Sugiyama, A.,  Ogura, K., Yamamoto, M., Kuroki, H., Nabeshima, S., Yachie, A.,  Matsuoka, Y. & Kitano, H.,Effects of maoto (ma-huang-tang) on host lipid mediator and transcriptome signature in influenza virus infection, Sci Rep 11, 4232 (2021). https://doi.org/10.1038/s41598-021-82707-1
  • Nishi, A., Ohbuchi, K., Kaifuchi, N., Shimobori, C ., Kushida,  H., Yamamoto,  M., Kita, Y.,  Tokuoka, S.M., Yachie,  A., Matsuoka, Y., & Kitano,  H., LimeMap: a comprehensive map of lipid mediator metabolic pathways., npj Syst Biol Appl 7, 6 (2021). https://doi.org/10.1038/s41540-020-00163-5

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*Please also check publication list (symbio.jst.go.jp) for extensive list of the publications up to 2007.

2007


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2005


2004

  • 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..

2003


2002

  • 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...

2000

  • 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 (symbio.jst.go.jp) for extensive list of the publication upto 2007.


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