Research Interests

My main interest lies in the application of statistical and bioinformatics analysis of genetics and genomics data.

Plant genomics

I am involved in several aspects of plant genomics. Identification of genome-wide pattern of LD and nucleotide diversity, identification of structural variants, analysis of transcriptome, analysis of small RNAs.

Next generation ecotilling

I developed a fast method for the identification of rare variants in plants via next generation sequencing of pooled multiplexed PCR products. This method, that we named Next Generation Ecotilling, allowed the identifcation of several rare variants in a population of 768 poplar trees. This work was carried out in the framework of the EU-funded project EnergyPoplar.

QTL mapping

I also worked on QTL mapping. I estimated heritability of several quantitative traits and performed various genome-wide linkage and association studies.

Population isolates

I investigated the genetic structure of isolated populations from South Tyrol, Italy, with a focus on LD levels measured between seven STR markers on the X chromosome. I also investigated biodemographic structure (such as marriage patterns and consanguineity indices) of such populations.

Genetic epidemiology of colorectal and endometrial cancer (HNPCC)

Our work on HNPCC resulted in the AIFEG model (named after the "Associazione Italiana per lo studio della Familiarità ed Ereditarietà dei tumori Gastrointestinali", AIFEG) for predicting the probability of caryying mutations in MSH2 and MLH1. The model is somewhat similar to those already developed for BRCA1/2, but in addition we can exploit information on microsatellite instability which, in HNPCC, can help the discrimination between genetic and "sporadic" cases. You will find the AIFEG model and the relative documentation in the Downloads section.

Genetic epidemiology of breast and ovarian cancer

This is the main subject of my PhD research project, performed with the supervision of Silvano Presciuttini and in close collaboration with Giovanni Parmigiani. Also, Joan Bailey-Wilson always found some time to give me advice. The research involved several steps: evaluation of the different expressivity of BRCA1 and BRCA2, evaluation of models used for predicting the risk of carrying a mutation in BRCA1 or BRCA2, and the estimation of breast and ovarian cancer penetrances from genetic test results.

Geographic Distribution of HLA haplotypes

Knowledge of HLA haplotypic frequencies is crucial for a rational planning of a bone marrow donors strategy. In our study we showed that in Tuscany, HLA-A/B haplotypic frequencies may vary even at a smaller geographic scale, and showed how knowledge of geographic variation of haplotypic frequencies may be exploited for a more efficient recruitment effort.

Photobiology

In the early years of my career I was interested in photobiology. My research was focused on a ciliated protozoan (Ophryoglena flava), characterized by a peculiar motor pattern. In presence of a unidirectional source of light (a simple lamp is OK, too!), O. flava moves quickly towards it: this behavior is known as positive phototaxis. By means of behavioral studies we tried to define the photoreceptor involved in the phototaxis. We also were interested in assessing the effect of exposure to UV radiation on the efficiency of phototaxis.