The architecture of large biochemical systems

It appears as a daunting task to understand the organization of complex systems constituted by many interacting components. This situation is particularly relevant in Biology.  Cell physiology, for instance, is the result of a set of biochemical networks working in combination. These networks were only imagined a few years ago. However, we now have tools to map them, and thus we can start analyzing their organization. We focused on different networks over the years to ask various questions. When considering protein-protein interaction networks, we studied to what extent their structure is composed of a combination of semi-isolated modules. Minimal components also appear in regulatory networks where they represent fundamental information-processing units. But how these regulatory motifs emerge, we do not understand. We tried to explain if part of this signal is caused by neutral evolutionary processes. More recently, we are investigating genetic interaction networks. In contrast to other biochemical networks, this class is not immediately linked to a molecular interaction but rather to the somehow abstract concept of the phenotype, e.g., fitness. Interesting questions associated with genetic interactions are their context-dependence and their relation to discussions on the robustness and evolvability of complex systems.

Some readings.

Genetic buffering and potentiation in metabolism (2019). [HTML].

Rewiring of genetic networks in response to modification of genetic background. With D. Bajic, and C. Moreno-Fenoll (2014). [HTML].

The balance of weak and strong interactions in genetic networks. (2011). [HTML].

Local gene regulation details a recognition code within the LacI transcriptional factor family. With E. J. Alm, and F. M. Camas (2010). [HTML].

What determines the assembly of transcriptional network motifs in Escherichia coli? With F. M. Camas (2008). [HTML], [Sup],[Operon_names,Interactions,FFLs].

How biologically relevant are interaction-based modules in protein networks? With L. D. Hurst (2004) [HTML].

Motif selection in a model of evolving replicators: The role of surfaces and limited transport in network topology. With S. C. Manrubia (2003). [PDF].