Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

The aging process is driven at the cellular level by random molecular damage that slowly
accumulates with age. Although cells possess mechanisms to repair or remove damage …

The design of biocatalytic reaction systems is highly complex owing to the dependency of
the estimated kinetic parameters on the enzyme, the reaction conditions, and the modeling …

Background Dynamic modelling provides a systematic framework to understand function in
biological systems. Parameter estimation in nonlinear dynamic models remains a very …

Background The development of large-scale kinetic models is one of the current key issues
in computational systems biology and bioinformatics. Here we consider the problem of …

Computational models are most impactful when they explain and characterize biological
phenomena that are non-intuitive, unexpected, or difficult to study experimentally. Countless …

Biocatalysis is entering a promising era as a data-driven science. High-throughput
experimentation generates a rapidly increasing stream of biocatalytic data, which is the raw …

Recent philosophical work has explored the distinction between causal and non-causal
forms of explanation. In this literature, topological explanation is viewed as a clear example …

For many biological systems, a variety of simulation models exist. A new simulation model is
rarely developed from scratch, but rather revises and extends an existing one. A key …

Bacterial genome reduction is a common phenomenon in nature that has also inspired
several projects with biotechnologically relevant organisms. In many cases, however, no …