Keynote Speakers

Antonio J. Pérez Pulido holds a degree in Biology from the University of Jaén and a PhD in Bioinformatics from the University of Málaga. He completed his postdoctoral studies at the National Institute of Bioinformatics, and since 2007 he has been a professor at Pablo de Olavide University and a researcher at the Andalusian Center for Developmental Biology, where he leads a computational biology group. Since his thesis, he has specialized in the development of computational tools for the functional annotation of proteins, and since 2017 he has specialized in the analysis of bacterial pangenomes, with a special interest in CRISPR-Cas systems and other phage defense systems.

Title of the presentation: AI applied to pangenomics to explore the constant war between viruses and bacteria

Abstract: Bacteriophages (bacterial viruses or phages) exist in a ratio of 1 to 10 with respect to bacteria, and it is estimated that they eliminate up to half of these bacteria daily in different natural environments. Bacteria, in turn, defend themselves using different biological weapons, of which there are currently more than a hundred known types.
Our group constructs and analyses bacterial pangenomes using thousands of public genomes of clinically relevant bacteria. These pangenomes are translated into binary matrices of gene presence-absence, with tens of thousands for each, to which information about phages, their receptors (proteins they use to enter the bacterium) and the defence and anti-defence systems of both are added. Finally, we apply machine learning techniques such as random forest with XGBoost and CN2 rule induction as tree-based algorithms, along with other standard data mining methods, to identify marker genes related to the characteristics of interest.
In this way, we have been able to establish relationships between bacterial adaptive immunity defence systems, CRISPR-Cas, and phages of different species, as well as find specific defence systems of groups of bacteria of great clinical concern. These results are useful for better understanding the genomic plasticity of this bacterium and could be used in phage therapy, the alternative to antibiotics that is becoming increasingly important.