@ARTICLE{BMC Systems Biology:x:xxx,
author = {Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, and Satoru Miyano},
title = {Systematic reconstruction of TRANSPATH data into Cell System Markup Language},
journal = {BMC Systems Biology
year = {2008,
volume = {}
pages = {}
}
@ARTICLE{Bioinformatics:x:xxx,
author = {Kaname Kojima, Masao Nagasaki, and Satoru Miyano},
title = {Fast grid layout algorithm for biological networks with sweep
calculation},
journal = {Bioinformatics
year = {2008,
volume = {}
pages = {}
}
@ARTICLE{InSilicoBiol:7:0055,
author = {Euna Jeong and Masao Nagasaki and Satoru Miyano},
title = {Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways},
journal = {In Silico Biol},
year = {2007},
volume = {7},
pages = {0055}
}
@ARTICLE{GenomeInform:18:225,
author = {Euna Jeong and Masao Nagasaki and Satoru Miyano},
title = {Conversion from BioPAX to CSO for System Dynamics and Visualization of Biological Pathway},
journal = {Genome Inform},
year = {2007},
volume = {18},
pages = {225-236}
}
@ARTICLE{PacSympBiocomput::152,
author = {Hiroshi Matsuno and  Ryutaro Murakami and  Rie Yamane and  Naoyuki Yamasaki and  Sachie Fujita and  Haruka Yoshimori and  Satoru Miyano},
title = {Boundary formation by notch signaling in {D}rosophila multicellular systems:
      experimental observations and gene network modeling by {G}enomic {O}bject {N}et},
journal = {Pac Symp Biocomput},
year = {2003},
volume = {NIL},
number = {NIL},
pages = {152-63}
}
@ARTICLE{InSilicoBiol:3:389,
author = {Hiroshi Matsuno and  Yukiko Tanaka and  Hitoshi Aoshima and  Atsushi Doi and  Mika Matsui and  Satoru Miyano},
title = {Biopathways representation and simulation on hybrid functional {P}etri net},
journal = {In Silico Biol},
year = {2003},
volume = {3},
number = {3},
pages = {389-404}
}
@ARTICLE{ApplBioinformatics:2:181,
author = {Masao Nagasaki and  Atsushi Doi and  Hiroshi Matsuno and  Satoru Miyano},
title = {Genomic {O}bject {N}et: {I}. {A} platform for modelling and simulating
      biopathways},
journal = {Appl Bioinformatics},
year = {2003},
volume = {2},
number = {3},
pages = {181-4}
}
@ARTICLE{ApplBioinformatics:2:185,
author = {Atsushi Doi and  Masao Nagasaki and  Sachie Fujita and  Hiroshi Matsuno and  Satoru Miyano},
title = {Genomic {O}bject {N}et: {I}{I}. {M}odelling biopathways by hybrid functional {P}etri
      net with extension},
journal = {Appl Bioinformatics},
year = {2003},
volume = {2},
number = {3},
pages = {185-8}
}
@ARTICLE{GenomeInform:15:180,
author = {Masao Nagasaki and  Atsushi Doi and  Hiroshi Matsuno and  Satoru Miyano},
title = {A versatile petri net based architecture for modeling and simulation of
      complex biological processes},
journal = {Genome Inform},
year = {2004},
volume = {15},
number = {1},
pages = {180-97}
}
@ARTICLE{InSilicoBiol:4:271,
author = {Atsushi Doi and  Sachie Fujita and  Hiroshi Matsuno and  Masao Nagasaki and  Satoru Miyano},
title = {Constructing biological pathway models with hybrid functional {P}etri nets},
journal = {In Silico Biol},
year = {2004},
volume = {4},
number = {3},
pages = {271-91}
}
@PHDTHESIS{Nagasaki2004,
author = {Masao Nagasaki},
school = {The University of Tokyo},
title = {A Platform for Biopathway Modeling/Simulation and Recreating biopathway databases towards simulation},
year = {2004}
}
@ARTICLE{GenomeInform:16:192,
author = {Hironori Kitakaze and  Hiroshi Matsuno and  Nobuhiko Ikeda and  Satoru Miyano},
title = {Prediction of debacle points for robustness of biological pathways by
      using recurrent neural networks},
journal = {Genome Inform},
year = {2005},
volume = {16},
number = {1},
pages = {192-202}
}
@ARTICLE{GenomeInform:16:22,
author = {Mitsuru Kato and Masao Nagasaki and Atsushi Doi and  Satoru Miyano},
title = {Automatic Drawing of Biological Networks Using Cross Cost and Subcomponent Data},
journal = {Genome Inform},
year = {2005},
volume = {16},
number = {2},
pages = {22-31}
}
@ARTICLE{JBioinformComputBiol:4:139,
author = {Hiroshi Matsuno and  Shin-Ichi T Inouye and  Yasuki Okitsu and  Yasushi Fujii and  Satoru Miyano},
title = {A new regulatory interaction suggested by simulations for circadian
      genetic control mechanism in mammals},
journal = {J Bioinform Comput Biol},
year = {2006},
volume = {4},
number = {1},
pages = {139-53}
}
@ARTICLE{InSilicoBiol:6:0001,
author = {Atsushi Doi and Masao Nagasaki and Hiroshi Matsuno and Satoru Miyano},
title = {Simulation-based validation of the p53 transcriptional activity with
      hybrid functional {P}etri net},
journal = {In Silico Biol},
year = {2006},
volume = {6},
number = {1-2},
pages = {0001}
}

@ARTICLE{GenomeInform:17:112,
author = {Atsushi Doi and Masao Nagasaki and Kazuko Ueno and  Hiroshi Matsuno and  Satoru Miyano},
title = {A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity},
journal = {Genome Inform},
year = {2006},
volume = {17},
number = {1},
pages = {112-123}
}
@ARTICLE{GenomeInform:17:100,
author = {Ayumu Saito and Masao Nagasaki and Atsushi Doi and Kazuko Ueno and  Satoru Miyano},
title = {Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loop by hybrid function Petri net with extension},
journal = {Genome Inform},
year = {2006},
volume = {17},
number = {1},
pages = {100-111}
}
@ARTICLE{GenomeInform:17:46,
author = {Masao Nagasaki and Rui Yamaguchi and Ryo Yoshida and Seiya Imoto and Atsushi Doi and Yoshinori Tamada and Hiroshi Matsuno and Satoru Miyano and Tomoyuki Higuchi},
title = {Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data},
journal = {Genome Inform},
year = {2006},
volume = {17},
number = {1},
pages = {46-61}
}
@ARTICLE{IEICE:89-A:3166,
author = {Hiroshi Matsuno and Chen Li and Satoru Miyano},
title = {Petri Net based description for systematic understanding of biological pathways},
journal = {IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences},
year = {2006},
volume = {89-A},
number = {11},
pages = {3166-3174}
}
@ARTICLE{GenomeInform:17:226,
author = {Shinya Tasaki and Masao Nagasaki and Masaaki Oyama and Hirokko Hata and Kazuko Ueno and Ryo Yoshida and Tomoyuki Higuchi and Sumio Sugano and Satoru Miyano},
title = {Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data},
journal = {Genome Inform},
year = {2006},
volume = {17},
number = {2},
pages = {226-238}
}
@PHDTHESIS{Doi2006,
author = {Atsushi Doi},
school = {The University of Tokyo},
title = {Modeling and simulation of biological pathways with Hybrid Functional Petri Net},
year = {2006}
}
@ARTICLE{BMCBioinformatics:8:76,
author = {Kaname Kojima and Masao Nagasaki and  Euna Jeong and Mitsuru Kato and Satoru Miyano},
title = {An efficient grid layout algorithm for biological networks utilizing various biological attributes},
journal = {BMC Bioinformatics},
year = {2007},
volume = {8},
pages = {76}
}
@INPROCEEDINGS{APBC2004:29:43,
author = {Masao Nagasaki and Atsushi Doi and Hiroshi Matsuno and Satoru Miyano},
booktitle = {Conferences in Research and Practice in Information Technology},
title = {Integrating biopathway databases for large-scale modeling and simulation},
year = {2004},
volume = {29},
pages = {43-52}
}
@INPROCEEDING{BIOINFO2005:348,
author = {Chen Li and Shunichi Suzuki and Qi-Wei Ge and Mitsuru Nakata and Hiroshi Matsuno and Satoru Miyano},
booktitle = {BIOINFO2005},
title = {On modeling and analyzing signaling pathways with inhibitory interactions based on Petri net},
year = {2005},
pages = {348-53}
}
@INPROCEEDING{AlgebraicBiol2005:19,
author = {Masao Nagasaki and Atsushi Doi and Hiroshi Matsuno and Satoru Miyano},
booktitle = {Algebraic Biology 2005 - Computer Algebra in Biology},
title = {Petri Net Based Description and Modeling of Biologinal Pathways},
year = {2005},
pages = {19-31}
}