Nature exhibits modular design in biological systems. Gene module level analysis is based
on this module concept, aiming to understand biological network design and systems …

This work deals with the particular nature of network-based approach in biology. We will
comment about the shift from the consideration of the molecular layer as the definitive place …

High-throughput experiments are shedding light on the topology of large regulatory
networks and at the same time their functional states, namely the states of activation of the …

Motivation: The modularity of biochemical networks in general, and signaling networks in
particular, has been extensively studied over the past few years. It has been proposed to be …

Much of enzyme kinetics builds on simplifications enabled by the quasi‐steady‐state
approximation and is highly useful when the concentration of the enzyme is much lower than …

Recent technological advancements have made time-resolved, quantitative, multi-omics
data available for many model systems, which could be integrated for systems …

Analysis of gene expression data sets reveals that the variation in expression is
concentrated to significantly fewer 'characteristic modes' or 'eigengenes' than the number of …

In this thesis, inference of biological networks from in vivo data generated by perturbation
experiments is considered, ie deduction of causal interactions that exist among the observed …

Research using structural data puts pressure on validating structures in available
databases. For this reason, the validation tools are constantly developing and improving. In …

This thesis provides new insight into cellular signal transduction by integrating biological
knowledge into mathematical models, which are subsequently analysed using systems …