PUBLICATIONS (ENGLISH)

>>JAPANESE

2006

  1. A. Saito, M. Nagasaki, A. Doi, K. Ueno, S. Miyano, Cell Fate Simulation Model of Gustatory Neurons with MicroRNAs Double-Negative Feedback Loop by Hybrid Function Petri Net with Extension, Genome Informatics, Submitted.
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  2. H. Matsuno, S. T. Inouye, Y. Okitsu, Y. Fujii, S. Miyano, A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals, Journal of bioinformatics and computational biology, 4(1): 139-153 (2006).
    3.  (MubMed)

2005

  1. M. Nagasaki, A. Doi, H. Matsuno, S. Miyano, Peti Net Based Description and Modeling of Biologinal Pathways, Algebraic Biology 2005 - Computer Algebra in Biology, H. Anai and K. Horimoto, eds., Universal Academy Press, Inc., Tokyo, 19-31 (2005).
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  2. M. Nagasaki, A. Doi, H. Matsuno, S. Miyano, Software for Pathway Modeling and Simulation – From Bench to Computer, Asia Pacific Biotech News, World Scientific Publishing Co., Singapore (2005).
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  3. A. Doi, M. Nagasaki, H. Matsuno, S. Miyano, Simulation Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net, In Slico Biology, 6.0001 (2005).
    4.   (html)
  4. Kato M, Nagasaki M, Doi A, Miyano S, (2005) Automatic Drawing of Biological Networks Using Cross Cost and Subcomponent Data, Genome Informatics 16(2): 22-31 (2005).
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2004

  1. M. Nagasaki, A. Doi, H. Matsuno, S. Miyano, A versatile Petri net based architecture for modeling and simulation of complex biological processes, Genome Informatics 15(1): 180-197 (2004).
    2.  (pdf)
  2. M. Nagasaki, A. Doi, H. Matsuno, S. Miyano, Genomic Object Net: a platform for modeling and simulating biopathways, Applied Bioinformatics, 2:181-184 (2004).
    3.  (pdf)
  3. A. Doi, M. Nagasaki, S. Fujita, H. Matsuno, S. Miyano, Genomic Object Net: II. Modeling biopathways by hybrid functional Petri net with extension, Applied Bioinformatics 2:185–188 (2004).
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  4. M. Nagasaki, A Platform for Biopathway Modeling/Simulation and Recreating biopathway databases towards simulation, Ph.D Thesis, The University of Tokyo (2004).
    5. (pdf)
  5. M. Nagasaki, A. Doi, H. Matsuno, S. Miyano, Integrating biopathway databases for large-scale modeling and simulation. The Second Asia-Pacific Bioinformatics Conferences, Volume 29 of Conferences in Research and Practice in Information Technology, Australian Computer Society, 43-52 (2004).
    6.  (pdf)
  6. A. Doi, S. Fujita, H. Matsuno, M. Nagasaki, S. Miyano, Constructing biological pathway models with hybrid functional Petri nets. In Silico Biology 4(0013) (2004).
    7. (html)

2003

  1. H. Matsuno, R. Murakami, R. Yamane, N. Yamasaki, S. Fujita, H. Yoshimori, S. Miyano. Boundary formation by notch signaling in Drosophila multicellular systems: experimental observations and a gene network modeling by Genomic Object Net. Pacific Symposium on Biocomputing, 152-163 (2003).
  2. M. Nagasaki, A. Doi, H. Matsuno, S. Miyano. Recreating biopathway databases towards simulation. Proc. International workshop on Computational Methods in Systems Biology, in press (2003).

2002

  1. Atsushi Doi, Hiroshi Matsuno, Mika Matsui, Yuichi Hirata, Satoru Miyano. Simulation of biological systems by hybrid Petri net with an enhancement, Proc. The International Conference on Fundamentals of Electronics, Communications and Computer Science 2002, S5, 13-18 (2002).
  2. M. Matsui, A. Doi, H. Matsuno, Y. Hirata, S. Miyano. Converting biopathway models of E-Cell to Genomic Object Net. Pacific Symposium on Biocomputing, poster abstract, 117 (2002)
  3. H. Matsuno, Y. Hirata, A. Doi, S. Miyano. Genomic Object Net: On-going report on biopathway modeling and simulation. Currents in Computational Molecular Biology, 132-133 (2002).

2001

  1. H. Matsuno, A. Doi, Y. Hirata, S. Miyano. XML Documentation of Biopathways and Their Simulations in Genomic Object Net. Genome Informatics 12, 54-62 (2001).
  2. Hiroshi Matsuno, Atsushi Doi, Rainer Drath, Satoru Miyano, Genomic Object Net: Hybrid Petri net for describing biological systems. Currents in Computational Molecular Biology, 233-234 (2001).

2000

  1. H. Matsuno, A. Doi, M. Nagasaki, S. Miyano. Hybrid Petri net representation of gene regulatory network. Proc. Pacific Symposium on Biocomputing 5, 341-352 (2000).
  2. H. Matsuno, A. Doi, A. Tanaka, H. Aoshima, Y. Hirata, S. Miyano. Genomic Object Net: basic architecture for representing and simulating biopathways
    http://GenomicObject.Net/tutorial/BasicArchitecture.pdf
  3. A. Doi, H. Matsuno, S. Miyano. Induction mechanism description of lambda phage by hybrid Petri net. Currents in Computational Molecular Biology, 26-27 (2000).
  4. H. Matsuno, A. Doi, R. Drath, S. Miyano. Genomic Object Net: Object oriented representation of biological systems. Genome Informatics 11, .229-230 (2000).

1999

  1. Atsusi Doi, Rainer Drath, Masao Nagasaki, and Satoru Miyano, Protein dynamics observation of lambda phage by hybrid Petri net. Genome Informatics 10, 217-218 (1999).

© 2002-2006, Human Genome Center, Miyano Laboratory, All Rights Reserved.