Complex Networks in Systems Biology

Network biology covers a wide range of scales from molecular interactions in the cell to intercellular communication and the connections between organisms and species. With the unprecedented wealth of experimental and empirical data available, one of the many challenges is to produce coherent models to mimic observed biological responses.

Very recently, some promising steps haven been taken in this direction but still much has to be done before in silico models are able to describe accurately the real behavior of biological systems.

At the level of cells, turning the structural regularities observed in the patterns of interaction between the different molecular species -metabolites, proteins, and genes- into organizing principles underlying observed phenotypes is a crucial task that can be significantly addressed in the context of network science, which provides the framework for large-scale mathematical and computational analyses. Specifically, genome-scale reconstructions of metabolic networks of model organisms can be represented and studied as complex networks to elucidate different aspects of the relation between their structure and function. We have produced, for instance, cartographic maps of metabolism that enable a network-based definition of biochemical affinity and we have analyzed metabolic network responses to different forms of structural stress that unveil how evolutionary pressure affects the ability of efficient metabolic regulation at the expenses of robustness. We are also undertaking different multiplex and multilevel approaches modeling the interplay between linked molecular networks. One of our goals is to produce multilevel whole-cell models including all the relevant molecular interactions between metabolites, genes and proteins in the cell to be able to reproduce systemic cellular responses.