The Laboratory for Bioinformatics, Mathematical Modelling and Synthetic Biology (BMS) of the Department of Electrical, Computer and Biomedical Engineering at the University of Pavia arose in December 2013 from the Laboratory for Biomedical Informatics (BMI) on initiative of Prof. Riccardo Bellazzi (BMI Director) and Prof. Paolo Magni (BMS Director) with the aim to increase autonomy, importance and visibility to the large number of successfully started and conducted activities in the fields of Bioinformatics, Mathematical Modelling of biological systems (in particular, pharmacokinetic and pharmacodynamic models) and Synthetic Biology. These are the three main research areas of the laboratory, which is strongly committed on research activities and on the training of high-profile researchers in the Bioengineering and Bioinformatics PhD program.
The first activities in the Bioinformatics field started in 2002 and focused on the analysis of DNA microarrays, mainly to develop advanced methods for the analysis of time series data. The activities proceeded with works in the proteomics area (analysis of mass-spectrometry data) and in the definition of methods for the construction of gene regulatory networks from expression data and from annotations in different biological databanks. In the last few years, the activities focused on the definition of analysis pipelines for Next Generation Sequencing (NGS) data, with particular attention on the problems linked with cloud computing, also with the help of Biomeris s.r.l., a startup established in 2012. In this field, BMS aims to play a crucial role in the national scene.
The activities in the field of mathematical models of biological systems started in the 80s in the BMI lab, when compartmental models were used to study the iron kinetics with data acquired through radioactive tracers. Then, in the 90s, the methodological activities focused on Bayesian estimation, the use of Markov Chain Monte Carlo (MCMC) algorithms and population approaches. Since the end of the 90s, the application field of these studies focused on the support of all the activities required for drug development and registration (in vitro, preclinical, clinical studies). The gained experience in this area brought the research team to take a leading part in Europe, also thanks to the collaborations with modelling groups in several pharmaceutical industries.
The Synthetic Biology activities started in the BMI lab and at the University of Pavia with a pilot project in 2008, by taking part to the main international Synthetic Biology competition called International Genetically Engineered Machine (iGEM), organized by the MIT in Boston. Following this successful experience, this topic grew in importance, supported by a numerous research team developed, also thanks to the participation to the subsequent iGEM competition editions until 2011. The role of the group in the national and international research panorama was also reinforced by the high visibility given by the national and international press to some successful research studies (see press review-link). Currently, this team represents one of the few active groups in the emergent field of Synthetic Biology in Italy, as also demonstrated by a review article appeared on Nature (link), where the main challenges and successes of the first 10 years of Synthetic Biology life were described and commented, and by a report on Synthetic Biology by the French Parliament (link). The main basic research topics under study include the characterization of biological components via experimental measurements and mathematical models and the predictability of bottom-up designed synthetic genetic circuits. The results are transferred and exploited in different applied studies, such as the construction of novel libraries of genetic components, the realization of complex circuits (e.g., kill switches for programmed cell death or systems for the genomic integration of synthetic circuits) and, most importantly, the development and optimization of a bio-process for the production of ethanol from dairy waste. This latter study brought to several awards that include the “Best Food or Energy” special prize, obtained at the MIT at the iGEM 2009 competition, and the “Benemerenza di S. Siro” prize in Pavia given to Prof. Paolo Magni and his research team.