This thesis presents a class of graphical models for directly representing the joint cumulative distribution function (CDF) of many random variables, called cumulative distribution networks (CDNs). Unlike graphical models for probability density and mass functions, in a CDN, the marginal...

We investigate the Minimum Evolution Problem (MEP), an NP-hard network design problem arising from computational biology. The MEP consists in finding a weighted unrooted binary tree having n leaves, minimal length, and such that the sum of the edge weights belonging to the unique path between...

Gene Regulatory Networks (GRNs) have become a major focus of interest in recent years. Although much work has been done in elucidating the transcriptional regulatory network, the underlying mechanisms that have possibly influenced the evolution of these GRNs are still debatable. We have...

Explaining embryonic development of multicellular organisms requires insight into complex interactions between genetic regulation and physical, generic mechanisms at multiple scales. As more physicists move into developmental biology, we need to be aware of the “cultural” differences between...

The activity of the cell is often coordinated by the organisation of proteins into regulatory circuits that share a common function. Genome-wide expression profiles might contain important information on these circuits. Current approaches for the analysis of gene expression data include...

In this paper we present three dimensional cellular automata models for tumour growth, with a focus on the tumour’s natural shrinkage caused by the removal of the dead cells’ mortal remains. The significance of this phenomenon for the resulting volume of the in silico tumour is shown. Two...