Our group is interested in different aspects of Bioinformatics, Computational Biology and Systems Biology.
Our goal is to obtain new biological knowledge with an "in-silico" approach which complements the "in-vivo"
and "in-vitro" methodologies of Biology. This mainly involves mining the massive amounts of
information stored in biological databases.
Besides our lines of scientific research, we also collaborate with experimental groups providing them with bioinformatics
support for their specific needs, and participate in different teaching projects.
A brief summary of our main working lines follows. You can find more information in the links below and in
our list of publications.
Prediction of Protein Functional and Binding Sites
We have developed evolutionary-based method for predicting sites with some functional importance in protein sequences and structures.
Experimental determination of functional/active sites can not cope with the massive stream of new sequences comming from genome sequencing projects.
Hence, computational methods are highly demanded for this task. The methods we develop in this area are based on the fact that functional sites
are subject to certain evolutionary constraints whose landmarks can be detected on multiple sequence alignments.
Prediction of Protein Interactions
Functional Study of Biological Networks
The study of living systems from a network perspective is providing new biological knowledge which could have never been obtained from the study
of the individual components (genes, proteins, ...) no matter how detailed it was. As a prototype of complex systems, in biological
systems many times "the whole is more than the sum of the parts". The biological knowledge obtained with this "top-down" approach is still
modest compared with the whealt of information the "bottom-up" approach (exemplified by the Molecular Biology) has produced. Nevertheless, it
is clear that this new approach is required to complement the intrinsic limitations of the reductionist approach due
to the complexity of living systems. We are studying metabolic networks (central metabolism and biodegradation) and protein interaction
networks from this new "top-down" approach. Of special interest for us is the study of the complex phenomenon of "protein function" from
a systemic perspective, trying to understand how complex functions arise by combining the molecular functions of proteins when these interact in intricate networks.
Bioinformatics Support for Experimental Groups
Many research projects in Bioinformatics and Computational Biology have ended up in practical tools which can help in the daily work
of experimental Molecular Biologists, specially in protein and DNA sequence analysis. In spite that many of these tools can be easily used
by the community through web interfaces, others either are more difficult to use or their results are not straightforward to interpret
without some knowledge on Bioinformatics. Moreover, many bioinformatics "protocols" are difficult to implement in automatic tools and they
require manual intervention or expert knowledge to be carried out.
We provide experimental groups with bioinformatics expert knowledge,
specially in the areas of protein sequence analysis (remote homology detection, domain identification, functional evolution, ...).