Genomic physics

The group combines different tools from theoretical physics (statistical mechanics, soft condensed matter, hydrodynamics), to study biological questions concerning genomes and the cells that carry them. We favor a bottom-up approach where simple models are gradually constructed from data analysis and experiments.

One of the main questions we are focusing on is how bacteria compute patterns of active genes in response to stimuli and cues using both the specific chemical binding of specialized proteins (the "regulatory network") and the physical organization of the bacterial genome as a complex polymer. 

We also study the architecture and evolution of regulatory networks, quantitative descriptions of bacterial growth, and the laws that determine the partitioning of genomes into functional and evolutionary elements.

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  • Organization of the E. coli nucleoid and transcription. We develop theoretical stochastic models for single-cell experiments probing chromosome organization in-vivo and in-vitro by use of both short-time loci tracking and single-cell expression reporters. Additionally, we consider polymer physics computational models and scaling arguments which can reproduce dynamic and static experimental data concerning the nucleoid. Finally, we integrate and analyze the many sources of data from bioinformatics and genomics containing clues regarding nucleoid organization.
  • Quantitative and single-cell physiology. We are interested in the role of single cells and replication kinetics in growth, focusing mainly on yeast and E. coli.
  • Gene-family statistics across genomes, species, strains and environments. A genome modulates its complexity by adding or expanding gene families, which are its elementary functional modules. We seek characterize the statistics of gene (protein domain) families across genomes, species, strains and environments, and to develop minimal models to account for the observed regularities. This allows to attack with a fresh perspective long-standing problems in evolutionary genomics, such as genome plasticity, the definition of bacterial species, and the reciprocal roles of horizontal and vertical gene acquisition.
  • Laboratory evolution. In collaboration with experimentalists, we seek to develop simple phenomenological descriptions of driven evolution experiments and use these tools to attempt to bridge the gap with « frozen » evolutionary genomics observations. One of our primary questions in this context is the dynamics of horizontal transfers and (large- and small-scale) duplications-losses.
  • Models of complex systems. The group has a general interest in developing physical models of complex systems, particularly, but not exclusively, if some analogies or parallels exist with some biological problems, systems or questions.

Collaborations

  • University of Cambridge 
  • Universities of Milan/ Pavia / Turin/ Como
  • University of Minnesota
  • ENS Paris
  • ENS Cachan
  • Brookhaven National Laboratories