Synthetic biology is interpreted as the engineering-driven building of increasingly complex
biological entities for novel applications. Encouraged by progress in the design of artificial …

The massive acquisition of data in molecular and cellular biology has led to the renaissance
of an old topic: simulations of biological systems. Simulations, increasingly paired with …

Since the first edition of Stochastic Modelling for Systems Biology, there have been many
interesting developments in the use of" likelihood-free" methods of Bayesian inference for …

Background Genome-scale metabolic reconstructions under the Constraint Based
Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the …

Understanding of the logic and dynamics of gene-regulatory and biochemical networks is a
major challenge of systems biology. To facilitate this research topic, we have developed a …

Biological function and cellular responses to environmental perturbations are regulated by a
complex interplay of DNA, RNA, proteins and metabolites inside cells. To understand these …

Most cellular processes depend on intracellular locations and random collisions of
individual protein molecules. To model these processes, we developed algorithms to …

Bi-stable chemical systems are the basic building blocks for intracellular memory and cell
fate decision circuits. These circuits are built from molecules, which are present at low copy …

MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular, it
is an implementation of the next subvolume method, which is an exact method to simulate …

Negative feedback loops have been invoked as a way to control and decrease
transcriptional noise. Here, we have built three circuits to test the effect of negative feedback …