Related Publication

2011

  • Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, and Miyano S. Systems biology model repository for macrophage pathway simulation. Bioinformatics. 27:1591--1593, 2011.

2010

  • Li C*, Nagasaki M*, Saito A and Miyano S, Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram, BMC Syst Biol., 4:39, 2010 Apr. (*Equal contributor) .
  • Nagasaki, M., Saito A., Jeong E, Li C., Kojima, K, Ikeda, E., Miyano, S. Cell Illustrator 4.0: A computational platform for systems biology. In silico biology, 10:0002. http://www.bioinfo.de/isb/2010/10/0002/main.html
  • Koh CH*, Nagasaki M*, Saito A, Wong L, Miyano S. DA 1.0: Parameter Estimation of Biological Pathways using Data Assimilation approach. Bioinformatics. 2010 May 26. (*Equal contributor) .
  • Do JH, Nagasaki M, Miyano S. The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosystems. 2010 Jun;100(3):178-84 .

2009

  • Li, C.*, Nagasaki, M.*#, Ueno, K., Miyano, S. Simulation-based model checking approach to cell fate pecification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Systems Biology. 3:42, 2009. doi:10.1186/1752-0509-3-42 (*: These authors equally contributed, #: Corresponding author) .
  • Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S. Foundations of Systems Biology - Using Cell Illustrator and Pathway Databases. Springer, 2009. Springer

2008

  • Jeong, E., Nagasaki, M., Miyano, S. Rule-based reasoning for system dynamics in cell systems. Genome Informatics. 20:25-36, 2008 .
  • Kojima, K., Nagasaki, M.*, Miyano, S. Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics. 24(12): 1426-1432, 2008 (*: Corresponding author) .
  • Nagasaki, M.*, Saito, A., Chen, L., Jeong, E., Miyano, S. Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Systems Biology. 2:53 (23Jun2008), 2008 (*: Corresponding author) .

2007

  • Jeong, E.*, Nagasaki, M.*, Miyano, S. Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway. Genome Informatics. 18, 225-236, 2007 (* These authors equally contributed) .
  • Jeong, E.*, Nagasaki, M.*, Saito, A., Miyano, S. Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways. In Silico Biology 7, 0055, 2007 (* These authors equally contributed) .
  • Kojima, K.*, Nagasaki, M.*, Jeong, E., Kato, M., Miyano, S. An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics 2007, 8:76 (6 March 2007) (* These authors equally contributed) .

2006

  • Doi, A., Nagasaki, M., Matsuno, H., Miyano, S. Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biology. 6(1-2): 1-13, 2006 .
  • Doi, A., Nagasaki, M., Ueno, K., Matsuno, H., Miyano, S. A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Informatics. 17(1): 112-123, 2006 .
  • Jeong, E., Miyano, S. A weighted profile based method for protein-RNA interacting residue prediction. Transactions on Computational Systems Biology. Lecture Notes in Computer Science. 3939: 123-139, 2006.
  • Nagasaki, M.*, Yamaguchi, R.*, Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Informatics. 17(1): 46-61, 2006 (* These authors equally contributed) .
  • Saito, A., Nagasaki, M., Doi, A., Ueno, K., Miyano, S. Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loops by hybrid functional Petri net with extension. Genome Informatics. 17(1): 100-111, 2006 .
  • Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano, S., Miyano, S. Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Informatics. 17(2): 226-228, 2006 .

2005

  • Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Petri net modeling of biological pathways. Proc. Algebraic Biology 2005 (Universal Academy Press). 19-31, 2005.
  • Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Computational modeling of biological processes with Petri net based architecture. In \u201cBioinformatics Technologies\u201d (Y.P. Chen, ed). Springer Press. 179-243, 2005.

2004

  • Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Integrating biopathway databases for large-scale modeling and simulation. Proc. Second Asia-Pacific Bioinformatics Conference (APBC2004) (Y.P. Chen, Ed.). Conferences in Research and Practice in Information Technology. 29: 43-52, 2004.
  • Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Informatics. 15(1):180-197, 2004 .

2003

  • Doi, A., Nagasaki, M., Matsuno, H., Miyano, S. Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Applied Bioinformatics. 2(3):185-188, 2003 .
  • Nagasaki, M. Doi, A., Matsuno, H., Miyano, S. Genomic Object Net: I. a platform for modeling and simulating biopathways. Applied Bioinformatics. 2(3):181-184, 2003 .