Our bioinformatics activities are mainly focused on the following topics:

1. Next Generation Sequencing: the emerging high-throughput sequencing technologies have led to an increasing need of bioinformatics pipelines able to accurately and efficiently process, interpret and manage sequencing data. Our activities are mainly focused on the design and implementation of ad hoc data analysis pipelines for several sequencing applications (e.g. DNA-seq, RNA-seq), their optimization on cluster and cloud environments and the development of new algorithms and procedures in order to overcome challanges proper to each different application.

2. Network-based pharmacology: given a biological process under study, network-based approaches integrate different data and knowledge sources to obtain a network where the molecules of interest are linked to other similar genes or proteins. Our strategies exploit the genomic data and the topological features of the networks to identify possible combinations of hit targets where it is desirable to act with a pharamacological therapy.

3. Tissue Engineering and Developmental Biology: tissue engineering and regenerative medicine are rapidly delivering products able to recover and improve the functionality of damaged tissues and organs. However, tools for monitoring the cellular pluripotency are needed for the design and implementation of devices that would reach the clinics. Our activities in this field are devoted to the extraction of quantitative measures of the cell status from their whole-genome expression profiles and to the identification of the links between stem cells and developing oocytes and embryos.

The working group:

Research fellows and PhD students: Federica De Paoli, Ivan Limongelli, Giovanna Nicora, Ettore Rizzo, Elisabetta Sauta, Susanna Zucca.

Supervisors: Riccardo Bellazzi, Paolo Magni