Section of Systems Biology
Using a combination of experimental, computational, and theoretical approaches, we aim to understand, predict, and ultimately control biological systems.
Our trans-disciplinary research activities cover all aspects of modern Systems Biology: We perform experiments to investigate, quantify and characterise the response/status/output of molecular systems at global and specific levels (experimental systems biology). Through computational and mathematical modelling, we gain maximal benefit from the experimental data and frame models for further experimental testing (theoretical and computational systems biology). Finally, we design and engineer biological systems in living organisms for the purpose of improving applications for industry or biological research (synthetic biology).
Overall, our research provides fundamental insights into molecular biological systems and opens new avenues for their design to underpin health and industrial biotechnology.
Our members work in the following research areas:
André Gerber investigates global and specific aspects of post-transcriptional gene regulation by RNA-binding proteins and non-coding RNAs. He uses baker’s yeast, nematodes, and mammalian cells to investigate the conservation of gene regulatory circuits, its connection to other levels of cellular control (metabolism), and the implications in health and disease.
Claudio Avignone Rossa uses genome-scale metabolic network models of bacteria and human cell lines to optimize conditions for the production of compounds of medical and industrial interest. He is also interested in the study of the metabolic and physiological interactions between species in natural and synthetic microbial ecosystems, and how these evolve and adapt to changes in their environment.
Matteo Barberis aims to unravel design principles of cellular organization by integrating computational modeling and molecular biology, in order to predict, test and validate experimentally molecular mechanisms underlying emergent properties of biological systems. He uses yeast and mammalian cells to investigate how dynamics switches timely control the eukaryotic cell division cycle. He is also interested to develop multi-scale frameworks and tools to understand how properties of biological systems emerge from the integration of multiple layers of cellular regulation.
Alex Couto Alves focuses on genetic association studies for mapping the loci controlling phenotypic changes across the life course. We integrate these genetic loci with data from laboratory studies to understand the molecular function of the mapped loci. This includes mapping regulatory regions controlling gene expression. For that, we develop software tools and data analysis strategies for the analysis of genetic and gene expression data.
Giuseppe Facchetti applies mathematical modelling for a quantitative understanding of biological processes. He is currently working on cell size homeostasis using fission yeast as a model system but aiming to use the findings in other organisms in order to look for the general principle underlying this fundamental cellular control. He is also interested in the interplay between cell metabolism and cell size control.
Jose Jimenez applies experimental evolution and systematic engineering in bacterial systems, combining simple genetic circuits to produce emergent properties that allow complex functions to be performed.
Andrea Rocco investigates noise propagation across molecular networks, and stochastic dynamics in cell differentiation. He aims to understand the balance between biological variability and individual robustness by adopting methodologies typical of theoretical physics and mathematics.