Topology of molecular networks

Topology of molecular interaction networks

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that...

Robustness Envelopes of Networks

We study the robustness of networks under node removal, considering random node failure, as well as targeted node attacks based on network centrality measures. Whilst both of these have been studied in the literature, existing approaches tend to study random failure in terms of average-case behavior, giving no idea of how badly network...

Do greedy assortativity optimization algorithms produce good results?

Assortativity of complementary graphs

Correlating the topology of a metabolic network with its growth capacity

Metabolic network destruction: Relating topology to robustness

Biological networks exhibit intriguing topological properties such as small-worldness. In this paper, we investigate whether the topology of a metabolic network is related to its robustness. We do so by perturbing a metabolic system in silico, one reaction at a time and studying the correlations between growth, as predicted by flux balance...

Integrating genome assemblies with MAIA

De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for...