Ugo Bastolla
Bioinformatics Unit
Centre for Molecular Biology "Severo Ochoa"
Universidad Autonoma de Madrid
Cantoblanco, 28049 Madrid (Spain)
Tel:: (34) 91-196-4634 (Lab)
ubastolla@cbm.uam.es
http://ub.cbm.uam.es

Vitae

Ugo Bastolla directs since 2008 the Bioinformatics Unit of the CBMSO. He graduated in Physics in 1992 in the Uniersity of Rome La Sapienza, with a diploma thesis on a model of neutral evolution directed by Luca Peliti, and got his PhD in physics in the same university in 1996 with a thesis on Random Boolean Networks (Kauffman networks) as a model of gene regulation and on other disordered dynamical systems, under the supervision of Giorgio Parisi. He then worked with Peter Grassberger on the statistical mechanics of polymers and model proteins at the Supercomputing center (HLRZ) of Juelich, Germany, he developed a new folding free energy function in collaboration with Walter Knapp and Michele Vendruscolo at the Free University of Berlin, Germany, and studied the forces that affect biodivertiy in model ecosystems in collaboration with Michael Lassig, Susanna Manrubia and Angelo Valleriani at the Max Planck Insitute of Golm, Germany. After a stay in the bioinformatics group of the Center for Astrobiology of Madrid directed by Alfonso Valencia, he joined in 2005 the Bioinformatics Unit of the CBMSO directed by Angel Ortiz.

Scientific Interests

The main interests in this group are centered on the design of biological systems ranging from proteins to cells.For this, the group combines software development for protein and cell design with experimental validation of the models.While doing basic science the group is always looking for the possible translation of the results into technology in the form of patents, software licenses and creation of spin-off companies.

  • Evolution, Classification and Networks of protein structures. Structural comparison of proteins with the algorithms Mammoth and Sabertooth. Structural divergence of proteins and its relationship with sequence and function divergence.
  • Prediction of the thermodynamic stability of proteins with respect to unfolding and misfolding, and its application to protein structure prediction (threading).
  • Models of protein evolution with constraints on folding stability. Relationships with evolutionary variables such as population size and mutation bias. Models of inverse folding and correlated mutations.
  • Analysis of the evolution and function of disordered proteins, in particular in the centrosome.
  • Conformation changes in proteins analyzed with our newly proposed Torsional Network Model.
  • Ecological models: how competition, mutualism and migrations influence the structural stability and biodiversity of ecosystems. Ecological interactions in bacterial communities determined in metagenomic studies.
  • Drug design through docking and virtual screening (this research line is currently directed by Antonio Morreale)
  • Bioinformatics facility for the CBMSO (this line is competence of David Abia)
  • Web design: Alfonso Núñez Salgado
    BIOINFORMATICS UNIT RESEARCH INTERESTS: The main research interests of the Bioinformatics Unit are in the fields of - - . - - - - - -