Ugo Bastolla

Ugo Bastolla Bufalini
PhD. Physics
Google Scholar Research Gate ubastolla@cbm.csic.es
Short CV. I am a physicist who has always been interested in Biology, since I am convinced that only a multidisciplinary approach allows understanding the complexity of living beings and that biology will strongly benefit from a mathematical formalization resting on statistical mechanics on one side and on evolution on the other side. In this framework, proteins are particularly interesting as a bridge between the two disciplines.
After my diploma work with Prof. Luca Peliti on a model of neutral evolution I did my PhD thesis with Prof. Giorgio Parisi, studying random Boolean networks as a null model of genetic regulation. Subsequently, I worked at Forschungszentrum Jülich (Germany) with Prof. Peter Grassberger, developing methods for the computational study of model proteins, which addressed me to investigate protein folding stability and its relationship with protein evolution, which is now my main research line. I developed this line in the groups of Prof. Walter Knapp in Berlin, Prof. Michael Lässig in the Max-Planck-Institute for Colloids, in the Center for Astrobiology in Madrid, supervised by Prof. Alfonso Valencia, and finally in the Bioinformatics Unit of the CBMSO directed by Prof. Angel R. Ortiz, which I came to direct after he sadly and prematurely passed away.
In this field I developed simple mathematical models that allow estimating the folding stability of proteins with known structure both with respect to unfolding and with respect to incorrect folding (misfolding), which is rarely taken into account, and I applied them to study protein evolution, focusing on the mutual relationship between folding stability and evolutionary parameters (mutation bias, population size), detecting selection for biophysical properties, and developing stability-aware substitution models that improve phylogenetic inference. I also investigated the occurrence and evolution of disordered proteins in the Centrosome.
Another subject of my interest is protein dynamics. I developed an analytically solvable elastic network model in torsion angle space, which allows addressing protein function through the identification of conformation changes favored by natural selection and the computation of dynamical couplings between pairs of residues.
Recently, in collaboration with experimental groups, I studied chromatin structure, developing a method for classifying chromatin states, and studying their relationship with the processes of genome transcription and replication.
My other main field of interest is theoretical ecology, in particular the question of which ecosystem properties favor the maintenance of biodiversity in the face of environmental changes. I contributed to develop structural stability as the mathematical framework that allows addressing this question, and in this context I characterized under which circumstances mutualistic interactions enhance structural stability and biodiversity. This work directed my interest towards studying interactions in bacterial communities, where there are many instances of cooperative interactions, and I developed a method to identify possible interactions from metagenomic data.