Section of Molecular Systems Biology

Our research

Our trans-disciplinary research activities cover all aspects of modern molecular 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.

Research areas

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.

Youngchan Kim applies protein engineering and optical spectroscopy approaches to investigate biological molecules and systems that exploit quantum phenomena under physiological conditions. He is also interested in developing and applying optical sensing and imaging techniques to biomedical research.

Bingxin Lu develops computational methods and models to address important biological challenges related to human health. She aims to facilitate knowledge discovery from massive biological data, especially genomics and multi-omics data. Her work bridges software engineering, machine learning, algorithms, statistics, phylogenetics, and population genetics.

Sneha M. Pinto employs mass spectrometry-based quantitative proteomic and post-translational modifications (PTM)-omics approaches to identify signalling dynamics and biomarkers associated with human health and disease. She is also interested in developing integrated approaches to investigate epithelial-immune crosstalk in zoonotic diseases.

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. 

Yashwanth Subbannayya integrates multiple -omics methodologies - such as proteomics, PTMomics, metabolomics, and transcriptomics - to study the biological mechanisms of cancers, innate immunity, and infectious diseases. He is particularly interested in the post-translational regulation of pattern recognition receptor pathways in immune cells, and he develops resources for research, including biological databases and analysis tools.