Literature useful in course Bio-Modeling and Petri Nets

Books and papers listed below will provide background material for the subjects discussed in the course. Most papers are available through the universiy library. Books and papers can also be obtained (borrowed) from the lecturers.

---Overview

BMPN Material

Petri Nets

Interactive Tutorials on Petri Nets: [URL]

Tutorial Petri Nets in Systems Biology: [URL]

J.L.Peterson.
Petri Nets
Computing Surveys, 232-252, 1977
DOI:10.1145/356698.356702 [URL]

J. Desel, W. Reisig.
The concepts of Petri Nets.
Softw. Syst. Model 14, 669-683 2015 [URL]

Coloured Petri Nets
K. Jensen, L. Kristensen [URL]

Tool

Snoopy - a unifying Petri net tool: [URL]

The Manual for Colored Petri Nets in Snoopy: [URL]

Historical

Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
Goss, Peccoud 1998

Hybrid Petri net representation of gene regulatory network
Matsuno, Doi, Nagasaki, Miyano 2000

Petri Net Representations in Metabolic Pathway
Reddy, Mavrovouniotis, Liebman 1993

Qualitative analysis of biochemical reaction systems
Reddy, Liebman, Mavrovouniotis 1996

Reading material

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
Koch, Junker, Heiner 2005

Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development
Bonzanni, Krepska,Feenstra, Fokkink, Kielmann, Heringa, 2009
+ Erratum

Model validation of biological pathways using Petri nets — demonstrated for apoptosis
Heiner, Koch, Will 2004

Modelling and Analysis of the Feeding Regimen Induced Entrainment of Hepatocyte Circadian Oscillators Using Petri Nets
Tareen, Ahmad 2015

A discrete Petri net model for cephalostatin-induced apoptosis in leukemic cells
Rodriguez, Rudy, Rosario, Vollmar, Mendoza 2011



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