Research lines

1. Evolution of lineage-specific genes

Lineage-specific genes are those exclusively found in one species or group of related species. Their study can shed light into the mechanisms of formation of new genes. Recent research in the group has shown that many lineage-specific genes are likely to have originated de novo from genomic non-coding regions. We are currently using RNA-Seq and Ribo-Seq data to further understand the mechanisms of formation of new genes.

2. Expression of neoantigens in cancer cells

We are investigating gene expression in cancer cells with the objective of identifying putative neoantigens that may trigger an immune response against the tumor. For this we are examining RNA-Seq data from cancer cells and comparing it to similar data for normal tissues. Novel translated ORFs can be predicted on the basis of the hexamer composition using the CIPHER program. We are also developing computational pipelines to predict the binding affinity of the neoantigens to HLA receptors.

3. Gene duplication and adaptive evolution

We are interested in the evolution of gene duplicates and have peformed several studies to investigate their expression and sequence diversification following duplication. We have also developed methods to identify shifts in the evolutionary rate of genes in the mammalian phylogeny and to measure adaptive evolution in individual genes or clusters of functionally-related genes. We have shown that selecting isoforms of similar length with our software PALO reduces the fraction of misaligned positions and false positives in tests of adaptive selection.