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Biophysics and evolution of proteins We look at proteins under the complementary points of view of biophysics and evolution, developing biophysics aware models of molecular evolution and predicting protein stability against unfolding and against misfolding from protein structure and sequence through a simple contact free energy function that allows detecting signs of selection in protein evolution.
We study the functional dynamics of proteins and their structural response to mutations through our elastic network model in torsional angle space (Torsional Network Model).
Finally, we aim to characterize the coevolution of protein structure, function and sequence.

Computational Genomics We are interested in the interrelation between chromatin structure and the organization of genome transcription and genome replication. In this context, we have developed our own HMM-based method for classifying genomic regions into chromatin states.

Theoretical ecology We are interested in understanding which ecosystem properties favor the maintenance of biodiversity in the face of environmental changes.
We contributed to develop structural stability as the mathematical framework that allows addressing this question, and characterizing under which circumstances mutualistic interactions enhance structural stability and biodiversity.
This work directed our interest towards studying interactions in bacterial communities, where there are many instances of cooperative interactions, and we developed methods to identify possible interactions from metagenomic data.

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