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Brocchieri, Luciano: Assistant Professor

Research Interests

My main interest is in identifying the biological processes underlying the evolution of genes and proteins. 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. In the process, we develop bioinformatic tools for the analysis of molecular sequences. These interests reflect in the following current research projects:

  • 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 bioinformatics tools to improve current annotations and to facilitate gene prediction in newly sequenced genomes, and for graphical representation of sequence compositional properties (frame-analysis) and sequence expression data (RNA-seq).
  • 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. In particular, we are interested in the role of alternative DNA structures, such as G4 DNA, in generating adaptive variation throughout the genome of P. aeruginosa.
  • Models of protein evolution. We are investigating new approaches to the determination of phylogenetic relations of homologous protein/gene sequences. We developed a model of functionally-constrained protein evolution and we are using this model as a conceptual framework for investigating patterns of protein evolution and for the reconstruction of phylogenetic trees.
  • 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 and animal 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).

Teaching

GMS6233: Quantitative models of protein evolution and phylogenetics

Spring Semester. A two-unit course emphasizing theoretical principles and application of models of protein evolution in phylogenetic analysis.

 

Software:

Gene identification in prokaryotes using compositional contrasts:  N-PACT N-Profile Analysis Computational Tool

Brocchieri Lab

For a more comprehensive overview of Dr. Brocchieri’s work, please visit Brocchieri Lab.

Education:

Ph.D. University of Parma, Italy. 1992, Environmental Sciences. Thesis in theoretical population genetics.  B.A. University of Parma, Italy, 1984, Biology (Highest Honors).

Professional Service:

Senior Research Scientist at Stanford University, Department of Mathematics.  Post-doctoral Research Associate at Stanford University, Department of Mathematics.  Fellowship of the Italian Ministry of Public Education for a PhD program in Environmental Sciences.