The lac operon in Escherichia coli has been studied extensively and is one of the earliest
gene systems found to undergo both positive and negative control. The lac operon is known to …

Cellular differentiation is one of the hallmarks of complex multicellularity, allowing individual
organisms to capitalize on among-cell functional diversity. The evolution of multicellularity is …

Neurons in the brain represent external stimuli via neural codes. These codes often arise from
stereotyped stimulus-response maps, associating to each neuron a convex receptive field. …

Boolean networks have been successfully used in modelling gene regulatory networks.
However, for large networks, analysis by simulation becomes unfeasible. In this paper we …

Motivation: An increasing number of discrete mathematical models are being published in
Systems Biology, ranging from Boolean network models to logical models and Petri nets. They …

Background A key problem in the analysis of mathematical models of molecular networks is
the determination of their steady states. The present paper addresses this problem for …

Background Many problems in biomedicine and other areas of the life sciences can be
characterized as control problems, with the goal of finding strategies to change a disease or …

Modeling stochasticity in gene regulatory networks is an important and complex problem in
molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as …

Background Many biological systems are modeled qualitatively with discrete models, such
as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to …

For many biological networks, the topology of the network constrains its dynamics. In particular,
feedback loops play a crucial role. The results in this paper quantify the constraints that (…