Pôle Interactions Biology

Contact: Thomas Nowak

Topics

We are working on computational methods to make bioengineering simpler with a focus on the modeling process. In particular, we have been developing predictive population-level models for bacterial and microalgal systems, mathematically analyzing stochastic effects among competing cell populations, and developing a simulation tool for microbiological systems.

Our group members and collaborators mainly come from AI, synthetic biology, distributed computing, and control theory. We were fortunate enough to be able to equip an experimental wet lab for our research group in the premises of ENS Paris-Saclay.

Our research agenda includes the study of quantitative and predictive modeling of intra-cellular and cell-population dynamics, simulation techniques, automated model discovery of bioprocesses, automated design of plasmids for bacterial hosts, optimization of bioproduction, and the design of synthetic circuits towards applications in bioproduction and medical diagnosis.

Some of our members are also affiliated with the Cellular Computing Group at ENS Paris-Saclay and INRAE Jouy-en-Josas: https://cellularcomputing.group/

Publications

A list of biology-related publications by lab members can be found at the following link: https://hal.science/LMF-BIO

Software

  • Bio-LBM: simulation of populations of biological species using the Lattice Boltzmann Method
  • estimAI: parametrization of chemical reaction networks
  • logicsponge: Python framework to compute with data streams
  • MobsPy: Python framework for modeling and simulation of chemical reaction networks

Current Projects

  • COSTXPRESS (ANR): Quantitative Models of Expression Costs of Synthetic Genetic Circuits.
  • DREAMY (ANR): Distributed Algorithms for Microbiological Systems.
  • MicroPILOTING (ANR): A Microfluidic System for Predictive Interaction Models of Bacteria and Microalgae Cells
  • RAMAN (PHC Maïmonide): Real-Time Raman Spectroscopy, Combined with Advanced Machine-Learning Algorithms, for Monitoring Production of Algal Protein in Photo-Bioreactors
  • SAIF (PEPR IA): Safe AI through Formal Methods
  • UnPlaD (GS LSH): Understanding Plant-pathogen Diversity

Meetings

We hold weekly meetings to discuss ongoing research and listen to talks about biology-related topics. The meetings take place every Monday at 10 am.

Members

Faculty

Emeritus

PhD Students

Mariapia D'Urso

Gaspard Fougea

Alexandra Loudières

Mélanie Pietri

Paul Zeinaty

Postdoctoral Researchers

Johannes Bund

Kerian Thuillier

Associated