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Modeling in Systems Biology, The Petri Net Approach 2016

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Ina Koch, Wolfgang Reisig, Falk Schreiber:
Modeling in Systems Biology, The Petri Net Approach. Computational Biology 16, Springer 2011, ISBN 978-1-84996-473-9

Foundations

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Ina Koch, Falk Schreiber:
Introduction. 3-18
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Tiina Liiving, Syed Murtuza Baker, Björn H. Junker:
Biochemical Fundamentals. 19-36
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Wolfgang Reisig:
Petri Nets. 37-56

Modeling Techniques

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Andrea Sackmann:
Discrete Modeling. 59-72
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Richard Banks, Victor Khomenko, L. Jason Steggles:
Modeling Genetic Regulatory Networks. 73-100
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Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano:
Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling. 101-120
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Ivan Mura:
Stochastic Modeling. 121-151
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Jörg Ackermann, Ina Koch:
Quantitative Analysis. 153-178
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Lukas Windhager, Florian Erhard, Ralf Zimmer:
Fuzzy Modeling. 179-205

Biochemical Applications

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Stefan Schuster, Björn H. Junker:
Topological Analysis of Metabolic and Regulatory Networks. 209-224
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Simon Hardy, Ravi Iyengar:
Analysis of Dynamical Models of Signaling Networks with Petri Nets and Dynamic Graphs. 225-251
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Claudine Chaouiya, Hanna Klaudel, Franck Pommereau:
A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets. 253-279
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Natsumi Mitou, Hiroshi Matsuno, Satoru Miyano, Shin-Ichi T. Inouye:
A Case Study of HFPN Simulation: Finding Essential Roles of Ror Gene in the Interaction of Feedback Loops in Mammalian Circadian Clock. 281-306
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Annegret Wagler:
Prediction of Network Structure. 307-336

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