Jun 19, 2017 — Jun 18, 2020

Boolean Automata Networks are formal prototypes of networks. Using them as such, this project studies general, scalable network features (eg synchronism, reversibility, non-monotony) and addresses questions about (1) the intrinsic effect of these features, (2) their vicariousness, i.e. the different ways to formally implement the effects that they are known, recognised and sometimes disregarded for, (3) their expressivity and the consistency of their possible meanings with respect to the ...


SE16 Numerical solution of dynamic metabolic resource allocation problems for bioenergy production

Jun 01, 2017 — Dec 31, 2018

In the field of sustainable energies, microbial cell factories such as yeasts and cyanobacteria are receiving increasing interest due to their potential to produce biofuels. A major question is how the metabolism of these microorganisms is coordinated in a dynamic environment such that the correct macromolecules are synthesized at the right time in order to enable growth and survival. Recent mathematical modeling approaches have made it possible to study this problem using an optimal dynamic ...

Gefördert vom BMBF_2


Dec 01, 2015 — Nov 30, 2018

Microbial strains used in biotechnological industry need to produce their biotechnological products at high yield and at the same time they are desired to be robust to the intrinsic nutrient dynamics of large-scale bioreactors, most noticeably to transient limitations of carbon sources and oxygen. The engineering principles for robustness of metabolism to nutrient dynamics are however not yet well understood. The ROBUSTYEAST project aims to reveal these principles for microbial strain ...


GRK 1772: Computational Systems Biology

Feb 01, 2011 — Jan 31, 2020

Biology has turned into a quantitative, information-driven science. Like physics in the first half of the twentieth century, biology now generates very challenging questions and masses of data that drive the development of theory and technology. There are numerous applications of biological research results in medicine and healthcare, biotechnology, and environmental sciences. Thus, there is an urgent need for highly educated researchers who are familiar with molecular and cellular biology and ...

Projects — finished


A-CH5 Model classification under uncertainties for cellular signaling networks

Jun 01, 2014 — May 31, 2017

Mathematical modeling in biological and medical applications is almost always faced with the problem of incomplete and often noisy data. Rather than adding unsupported assumptions to obtain a unique model, a different approach generates a pool of models in agreement with all available observations. Analysis and classification of such models allow linking the constraints imposed by the data to essential model characteristics and showcase different implementations of key mechanisms. The results ...


Übergangsmetalle und phototrophes Wachstum: Ein neuer Ansatz der contraintbasierten Modellierung großer Stoffwechselnetzte

Apr 01, 2012 — Mar 31, 2015

Die Stoffwechselvorgänge von Blaualgen standen im Vordergrund des Vorhabens. Mathematische Modelle erlauben die Analyse und Vorhersage dieser Stoffwechselvorgänge mit weitreichenden Anwendungen in der Biotechnologie. Blaualgen sind beispielsweise für die Herstellung von Biokraftstoffen interessant. Die Forschungen in diesem Bereich haben bereits zu mehreren Ausgründungen in Berlin geführt. Projektkoordinator: Dr. Ralf Steuer Publication: Rügen M, Bockmayr A, Steuer R: Elucidating ...


A18 Mathematical Systems Biology

Jun 01, 2010 — May 31, 2014

Systems biology is a lively interdisciplinary research field that has received considerable attention in recent years. While traditional molecular biology studies the various components of a biological system (genes, RNAs, proteins,...) in isolation, systems biology aims to understand how these components interact in order to perform higher-level functions. Mathematical modeling then plays a major role not only in capturing and analyzing complex networks governing biological processes, but also ...


TiGeRNet - Timed Genetic Regulatory Networks

Jan 01, 2009 — Dec 31, 2010

Project partners Prof. Dr. Gilles Bernot, Ecole Polytechnique de l'Université de Nice Sophia Antipolis Prof. Dr. Jean-Paul Comet, Ecole Polytechnique de l'Université de Nice Sophia Antipolis Prof. Dr. Olivier Roux, Institut de Recherche en Communication et Cybernetique de Nantes


A8 Constraint-based Modeling in Systems Biology

Apr 01, 2005 — May 31, 2010

Systems biology is a new area of biology that studies how the various components of a biological system (genes, RNA, proteins) interact in order to perform complex biological functions. Given that biological information is typically incomplete, the idea of constraint-based modeling is to describe a biological system by a set of constraints, which characterize its possible behaviors, but in general do not allow to make a precise prediction. The classical starting point of constraint-based ...


Fast and Accurate Multiple Structural RNA Alignment by Mathematical Optimization

Mar 01, 2007 — Sep 30, 2009

During the last years, the number of genes known for producing non-coding functional RNA had increased significantly, and it was assumed that many more of these ncRNA genes were still undiscovered. Yet, many functional classes of RNA showed little sequence conservation, but rather a conserved secondary structure. A promising avenue to detecting new functional RNAs was thus to look for common structural features shared by a set of related sequences. With this project we intended to advance our ...