Network analysis of inflammation
Atherosclerosis is a complex disease with many factors involved. It is also the main cause of cardiovascular disease and stroke, the first cause of death on industrilized societies. Asthma is a common chronic inflammatory disease of the airways characterized by variable and recurring symtoms, airway obstruction and bronchospasm.
In this project I am interesting on the reconstruction of regulatory networks driving disease onset and progression. To this aim I apply a number of systems biology and bioinformatics approaches, and integrate patient's derivide expression data with existing knowledge about protein-protein interactions.
varDB: a database of antigenic variant gene sequences
Pathogens from very different taxonomic origins like viruses, bacteria and fungi, use antigenic variation as a way to generate epitope diversity. The mechanisms involved are various but shared in some cases. The varDB project aims to be a central repository for antigenic variant gene families that may provided a way for cross-species studies. Therefore, a method to automacally retrieved sequences from the original repositories, and classifiy them into gene families is being developed.
These sequences will be used to identify sets of shared regulatory motifs that may be hidden in the sequences of many pathogens, irrespective thir phylogenetic origin.
Evolution of the Ras switch in eukaryotes
The Ras switch is a regulatory module fundamental in many biological processes like cell proliferation and differentiation. Ras proteins are small guanine nucleotide binding proteins that alternate between a GDP-bound, inactive state and a GTP-bound active state. Two protein families regulate the activity of Ras proteins: Guanine nucleotiotide exchange factors (GEF) and GTPase activator proteins (GAP).
We analyzed the repertorie of Ras proteins and its regulators among several eukaryote organisms, including yeast, worm, insect, fish, birds and mammals. The results we describe are important to understand how complex regulatory networks, like the Ras switch, evolve from a set of limited paralogues sequences.
Thyroid hormone action in the brain
The effects of thyroid hormone (TH) in the brain are well studied in the postnatal period. However, the role of TH in the fetal and adult brain is less understood. TH exert most of their functions through the binding to nuclear receptors that act as transcription factors modulating the expression of target genes.
At Juan Bernal's laboratory we studied the roles of TH in both the developing and adult brain. A transcriptomic approach was used to identify genes sensitive to TH under different experimental paradigms. Validation of the candidate genes is done using RT-PCR. We found evidence of a role of TH in homeostasis of the adult and fetal brain.
Codelink: an R package for analysis of GE healthcare gene expression bioarrays
This Bioconductor package provides basic functionality to help in the analysis of Codelink™ arrays. Codelink™ is a microarray platform for assessing gene expression using short (30mer) oligonucleotide probes.
The codelink package has functions for reading, analyzing and assessing quality of microarray data. Further information can be found in the package vignette.
[Package home page]
I have supervised/helped in the development of other R packages, most of them submitted to Bioconductor:
GeneRegionScan: A package designed to help in the analysis of specific genes obtained from Affymetrix experiments, but using prove-level information. This kind of approach enables the study of alternative splicing events, and the association between genotypic differences (SNPs) and changes in expression levels.
[Package home page]
Agi4x44PreProcess: A package designed to help in the analysis of Agilent 4x44 microarray platform.
[Package home page]