Genomics

Human genomics and personalized medicine

We are developing technology and expertise in the area of bioinformatics and molecular biology applied to personal genomics. In this context, we designed QueryOR, a web platform for human exome and genome variant analysis, and Scuba, a scalable kernel-based method for gene prioritization.

Common exomic and genomic variants
In human genetics the call of false-positive variants is a known issue in exome and genome analyses because of the inclusion of rare alleles and sequencing errors in the human reference genome.

Metagenomics

Microbial Analysis of the Venice Lagoon
Started as part of the OSD project, we are collecting and analyzing water and sediment samples at different time point and sites to characterize the microbial community by means of metagenetics and metagenomics approaches.

Microbial communities in the Ross Sea
Two PNRA projects, in collaboration with OGS, CNR Naples and Univ. of Parma, are aimed to understand prokaryotes interactions with antarctic phytodetritus and to identify cold adapted enzymes for PUFA biosynthesis.

Dynamics of the microbial community involved in anaerobic digestion
In collaboration with I. Agelidaki (DTU environment), P. G. Kougias (ELGO Demeter), we are performing a detailed characterization of the microbial community in methane-producing bioreactors by means of 16S rRNA sequencing and genome-centric metagenomics.

SYMBIO
Integration of biomass and wind power resulting in upgrading biogas to natural gas quality (i.e. methane) via hydrogen assisted anaerobic digestion. Genome-centric metatranscriptomics is the tool to decipher the complex microbial interactions driving the process.

Plant and food genomics

Plant Genomics
The aim of this initiative is to exploit our existing resources and expertise in Plant Genomics to create an integrated network of data, instruments and knowledge serving as a frame of reference for the scientific community and in the Agro-Food Sector.

Food Biotechnology
Projects in collaboration with DAFNAE (UniPD), with Biotechnology Department (UniVR) and DiSTAS, Università Cattolica del Sacro Cuore. Studies are focused on metagenomics, comparative genomics and transcriptomics to investigate crucial aspects of microbial process for food production.

Microbial genomics

Mapping of G-quadruplexes of M. tuberculosis (Mtb)
G-quadruplexes (G4s) are nucleic acids secondary structures that may form in single-stranded G-rich sequences to epigenetically regulate cellular functions. BRACO-19 is a well known G4 ligand that stabilizes G4s. Transcriptional profile investigation of Mtb treated with the G4 ligand BRACO-19 are ongoing using RNAseq.

The regulatory network of the M. tuberculosis SigE
Out of the 13 sigma factors encoded by M. tuberculosis (Mtb), SigE plays a very important role in virulence. We have constructed several mutants devoid of proteins required for SigE induction and activation to characterize the dynamics leading to SigE activation upon stress induction.