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Eduardo Eyras

Research Focus

Our group has wide experience in the development of novel strategies for gene prediction and in the use of comparative genomics for studying splicing. We have developed a computational method to predict transcript variants from expressed sequence information, which has been used for the annotation of the human, mouse, rat and chicken genomes.

Our current research line focuses in the study of the regulation of splicing using comparative genomics. We work on novel methods in order to gain knowledge in the mechanism of splicing and its evolution. One of our aims is to understand how the regulatory content of an exon and its flanking introns can determine the splicing phenotype. We have recently shown that the regulatory content is very dependent on the age of an exon.

We are also working on the study of the evolution of the RNAs and protein factors involved in splicing, and the correlation with changes in the splicing signals. In particular, we have found a relation between the properties of the SR proteins and the branch site signals. These analysis shows the plasticity of the factors involved in splicing and indicates a possible origin of regulated splicing.

Publications

  1. Schwartz, S.H., Silva, J., Burstein, D., Pupko, T., Eyras, E., Ast, G. (2008). Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Research 18(1), 88-103.
  2. Plass, M. and Eyras, E. Differentiated evolutionary rates in alternative exons and the implications for splicing regulation. (2006). BMC Evolutionary Biology 6(1), 50.
  3. Castelo, R., Reymond, A., Wyss, C., Camara, F., Parra, G., Antonarakis, S.E., Guigo, R., Eyras, E. (2005). Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes. Nucleic Acids Research 33(6), 1935-9.
  4. Eyras, E., Reymond, A., Castelo, R., Bye, J., Camara, F., Flicek, P., Huckle, E.J., Parra, G., Shteynberg, D.D., Wyss, C., Rogers, J., Antonarakis, S.E., Birney, E., Guigo, R., Brent, M.R. (2005). Gene finding in the chicken genome. BMC Bioinformatics 30;6(1), 131.
  5. Eyras, E. (2004). Using ESTs for genome annotation - predicting the Transcriptome. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons.
  6. Eyras, E., Caccamo, M., Curwen, V., Clamp, M. (2004). Using ESTs for genome annotation - predicting the Transcriptome. Genome Research 14(5), 976-87.

Key lab techniques: Comparative genomics methods for gene prediction, search of RNA sequences, analysis of alternative splicing events and study of regulatory sequences.

Lab contact: eduardo.eyras@upf.edu

Lab website: http://regulatorygenomics.imim.es/People/eeyras.html