Research

My main interest is in identifying the biological processes underlying the evolution of genes and proteins. My evolutionary interests spanned theoretical population genetics models of the evolution of social traits and sex-ratio (graduate studies), principles of protein structure (residue-type association, protein sequence structural connectivity, amino acid π-cloud/cationic interactions) and protein-DNA interaction (molecular modeling of Trp-repressor/DNA-operator interaction from NMR data). I have developed methods for multiple protein alignment and for gene finding, and studied evolutionary relations and functional properties of specific protein families (e.g., RecA, GroEL, homeobox genes). I am particularly interested in the study of the role of selection and mutation biases in characterizing composition and evolution of gene sequences, in modeling protein evolution and in studying the relation between sequence content and evolvability. These interests reflect in the following current research projects:

· Models of protein evolution. We are investigating new approaches to the determination of phylogenetic relations of homologous protein/gene sequences. We developed a new model of functionally-constrained protein evolution and we are using this model as a conceptual framework for reconstruction of phylogenetic trees.

· Gene differentiation and evolvability. We are interested in studying evolvability as an adaptive process in relation to sequence content with particular reference to the genetic and phenotypic plasticity of the opportunistic human pathogen Pseudomonas aeruginosa.

· Gene finding and characterization. We are developing new methodologies based on global compositional properties of coding sequences to identify with increased reliability short and/or anomalous genes in prokaryote genomes, for meaningful comparative analyses. Concomitantly we are developing new bioinformatics tools to improve current annotations and facilitate gene prediction in newly sequenced genomes, and in metagenomics and RNA-seq reads.

· Natural history of specific gene families. Over the years we have been engaged in studies on the evolution of specific protein families of interest. Most recently, in collaboration with Dr. Thomas Bürglin (Karolinska Institute, Sweden), we have been involved in studies on the evolution of plant homeobox genes. In collaboration with Prof. Alberto J. L. Macario and Prof. Everly Conway de Macario, University of Maryland, MD, USA, we recently systematically identified human chaperones of the hsp70 and hsp60 gene families mining the human genome. We are currently interested in the evolutionary history of proteins involved in the developmental Bardet-Biedl Syndrome (BBS).