Inference of biochemical reaction systems considering physico-chemical constraints

Inference of biochemical reaction systems considering physico-chemical constrain


Mathematical modeling has gained lots of attention in the biological research. Nowadays, models are created on all possible levels of detail, dedicated to describe a finite part of the processes taking place within living organisms. On cellular level, three major types of pathway models are to be distinguished: Gene-regulatory, signaling, and metabolic networks. The different types of processes taking place in each one of these classes of networks and not least the different time scales on which these processes take place hamper the creation of a unified view on all three network types within a single model.


This project is funded by the University of Tuebingen and limited to one year for now but with a possible extension using different grants. There can be found a large overlap in the scope of the project Virtual Liver, in which Dr. Andreas Dräger is also involved.


Since October 2011 Dr. Andreas Dräger and Stephanie Tscherneck are working on this new project in aiming to develop novel strategies for dynamic modeling and horizontal model integration.


[1] Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, and Andreas Dräger. The systems biology simulation core algorithm. BMC Systems Biology, 7:55, July 2013. [ DOI | details | link | pdf ]
[2] Sebastian Vlaic, Bianca Hoffmann, Peter Kupfer, Michael Weber, and Andreas Dräger. GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML. Bioinformatics, 29:2216--2217, June 2013. [ DOI | details | link | pdf ]