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Federico Abascal

Computational Evolutionary Biology Lab
Universidad de Vigo

Biología Evolutiva y Biodiversidad
Museo Nacional de Ciencias Naturales

editorial helice: La vida que llevamos dentro. Genes, células, historia y más.

Interests

The interaction between random changes occurring at genes and different selective forces, leaves a characteristic footprint in sequences. These footprints can tell us lots of things about protein function/structure or about the hystory of species, for instance.
It is like: trying to understand biology by using present sequences as mirrors of the past history.

[...more] [...what is genetic engineering for?]

Publications

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
Federico Abascal, Rafael Zardoya, Maximilian J Telford
Nucleic Acids Res. 2010; doi:10.1093/nar/gkq291
(TranslatorX web-server)
CentrosomeDB: a human centrosomal proteins database.
Ruben Nogales-Cadenas, Federico Abascal, Javier Díez-Pérez, José María Carazo, Alberto Pascual-Montano
Nucleic Acids Res.. 2009; 37:D175-D180
(centrosome:db)
Genetic code prediction for metazoan mitochondria with GenDecoder.
Federico Abascal, Rafael Zardoya, David Posada.
In "Bioinformatics for DNA Sequence Analysis" . Posada D (ed.). Methods in Molecular Biology Series. Humana Press. 2009; 537:233-242.
Web-server aimed to prioritize in the search of biomarkers and/or drug targets (druggability).
It can also be used to compile information about a list of genes.
ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data.
Federico Abascal, Carmona-Saez P, Carazo JM, Pascual-Montano A.
Bioinformatics. 2008; 24:1208-1209
(project web-site)
MtArt: A new model of amino acid replacement for Arthropoda.
Federico Abascal, David Posada, Rafael Zardoya.
Molecular Biology and Evolution. 2007; 24:1-5
(MtArt matrix.txt)
GenDecoder: genetic code prediction for metazoan mitochondria.
Federico Abascal, Rafael Zardoya, David Posada.
Nucleic Acids Research. 2006; 34:W389-W393.
(GenDecoder web-server)
Parallel evolution of the genetic code in arthropods mitochondria.
Federico Abascal, David Posada, Robin D. Knight, Rafael Zardoya.
PLoS Biology. 2006; 4:e127.
ProtTest: Selection of best-fit models of protein evolution.
Federico Abascal, Rafael Zardoya, David Posada.
Bioinformatics. 2005; 21:2104:2105
(project web-site)
Genome Analysis. Methods for the prediction and annotation of proteins function.
PhD Thesis, 2003 (in spanish).
Chapter "Bioinformática" in book Gen-Ética.
Federico Abascal and Alfonso Valencia
Ed. Ariel. 2003; 139-160.
Automatic annotation of protein function based on family identification.
Federico Abascal and Alfonso Valencia.
Proteins. 2003; 50:683-692.
(suplementary material)
Reductive genome evolution in Buchnera aphidicola.
Van Ham RC, Kamerbeek J, Palacios C, Rausell C, Abascal F, Bastolla U, Fernandez JM, Jimenez L, Postigo M, Silva J, Tamames J, Viguera E, Latorre A, Valencia A, Moran F, Moya A.
Proc Natl Acad Sci U S A. 2003; 100:581-586
(project web-site)
Clustering of proximal sequence space for the identification of protein families.
Federico Abascal and Alfonso Valencia
Bioinformatics 2002; 18:908-921.
(supplementary material)

Teaching

Classes on Sequence Analysis for several courses (Master in Bioinformatics of the UCM, summer courses of the UCM, PhD program of the UAM) (in spanish).

More recent material can be found at:

Masters in Biophysics (UAM) [larger, seq analysis + phylogenetics]
Bioinformatics PhD course (UAM) [shorter, seq analysis]