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The First ISB Book
Biological Petri Nets
 
Edgar Wingender
Preface
Published in the Special Issue: Petri Net Applications in Molecular Biology, ISB 10:0001, 2010

Ralf Hofestädt
Petri nets and the simulation of metabolic networks
Published in the Special Issue: Petri Nets for Metabolic Networks, ISB 03:0028, 2003

R. Hofestädt and S. Thelen
Quantitative modeling of biochemical networks
Published in ISB 01:0006, 1998

Ionela Zevedei-Oancea and Stefan Schuster
Topological analysis of metabolic networks based on Petri net theory
Published in the Special Issue: Petri Nets for Metabolic Networks, ISB 03:0029, 2003

Ming Chen and Ralf Hofestaedt
Quantitative Petri net model of gene regulated metabolic networks in the cell
Published in the Special Issue: Petri Nets for Metabolic Networks, ISB 03:0030, 2003

Klaus Voss, Monika Heiner and Ina Koch
Steady state analysis of metabolic pathways using Petri nets
Published in the Special Issue: Petri Nets for Metabolic Networks, ISB 03:0031, 2003

Hiroshi Matsuno, Yukiko Tanaka, Hitoshi Aoshima, Atsushi Doi, Mika Matsui and Satoru Miyano
Biopathways representation and simulation on hybrid functional Petri net
Published in the Special Issue: Petri Nets for Metabolic Networks, ISB 03:0032, 2003

Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki and Satoru Miyano
Constructing biological pathway models with hybrid functional Petri net
Published in ISB 04:0023, 2004

Ina Koch, Markus Schüler and Monika Heiner
STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks
Published in the Special Issue: Dagstuhl Seminar "Integrative Bioinformatics", ISB 05:0014, 2004

Takako Takai-Igarashi
Ontology based standardization of Petri net modeling for signaling pathways
Published in ISB 05:0047, 2005

Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno and Satoru Miyano
Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net
Published in ISB 06:0001, 2006

Anna Gambin, Sławomir Lasota and Michał Rutkowski
Analyzing stationary states of gene regulatory network using Petri nets
Published in ISB 06:0010, 2006

Satoru Miyano and Masao Nagasaki
Cell Illustrator 4.0: A Computational Platform for Systems Biology
Published in the Special Issue: Petri Net Applications in Molecular Biology, ISB 10:0002, 2010

Sebastian Janowski, Benjamin Kormeier, Thoralf Töpel, Klaus Hippe, Ralf Hofestädt, Nils Willassen, Rafael Friesen, Sebastian Rubert, Daniela Borck, Peik Haugen and Ming Chen
Modeling of cell-cell communication processes using Petri nets in the example of quorum sensing
Published in the Special Issue: Petri Net Applications in Molecular Biology, ISB 10:0003, 2010

Yoshimasa Miwa, Chen Li, Qi-Wei Ge, Hiroshi Matsuno and Satoru Miyano
On determining firing delay time of transitions for Petri net based signaling pathways by introducing stochastic decision rules
Published in the Special Issue: Petri Net Applications in Molecular Biology, ISB 10:0004, 2010

Jialiang Wu, Zhen Qi and Eberhard O. Voit
Impacts of delays and noise on dopamine signal transduction
Published in the Special Issue: Petri Net Applications in Molecular Biology, ISB 10:0005, 2010

Attila Csikász-Nagy and Ivan Mura
Role of mRNA gestation and senescence in noise reduction during the cell cycle
Published in the Special Issue: Petri Net Applications in Molecular Biology, ISB 10:0006, 2010

Ralf H. Bortfeldt, Stefan Schuster and Ina Koch
Exhaustive analysis of the modular structure of the spliceosomal assembly network &ndash a Petri net approach
Published in the Special Issue: Petri Net Applications in Molecular Biology, ISB 10:0007, 2010

Kerstin Kaufmann, Masao Nagasaki and Ruy Jáuregui
Modelling the molecular interactions in the flower developmental network of Arabidopsis thaliana
Published in the Special Issue: Petri Net Applications in Molecular Biology, ISB 10:0008, 2010










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