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© Inria / Photo C. Morel
Quantitative biology: numbers and fluorescent cells. InBio team (Inria/Institut Pasteur)

About

 

 

InBio is an interdisciplinary research group, combining wet and dry biology in the same lab. We employ systems and synthetic biology approaches with control and active learning methods, together with stochastic and statistical modeling frameworks.

Our main long-term goal is to develop a comprehensive methodological framework supporting the development of a quantitative understanding of cellular processes. Given a process of interest and current knowledge on the system, the problem is to decide iteratively which strain to construct and which experiment to run to characterize the process in an optimal manner.

More generally, we are interested in understanding, controlling and optimizing cellular processes from the single cell to the cell population levels. Past and current applications include (i) real-time control of gene expression using optogenetic and chemical stimulations in various systems (e.g. gene expression in yeast and bacteria, toggle switch in bacteria), (ii) understanding the origins of gene expression variability in response to Hog pathway induction in yeast, (iii) characterizing the dynamics of phenotypic heterogeneity in connection with reversible resistance to repeated anticancer treatments in Hela cells, and (iv) characterizing collective antibiotic resistance in ESBL-producing bacteria.

On the methodological side, we employ single cell models (mixed-effects models, stochastic processes) to represent the biological processes and develop methods for model reduction, sensitivity analysis, inference of model parameters, experimental design, and control, based on techniques such as global optimization, stochastic simulation, and moment closure, among others. In addition to software that support these methodological developments, we also develop software for videomicroscopy image analysis and for microscopy automation.

InBio is an Inria – Pasteur Institute joint research group. It is hosted at Institut Pasteur and affiliated to the Lifeware team at Inria Saclay – Ile-de-France.

Close collaborators include, in addition to Lifeware members, Eugenio Cinquemani (Inria Grenoble), Dirk Drasdo (Inria Paris), Calin Guet (IST Austria), Pascal Hersen (MSC lab, CNRS and Paris Diderot), Gasper Tkacik (IST Austria), Lingchong You (Duke University), and Christoph Zechner (Max-Planck Institute for Molecular Cell Biology & Genetics).

Internship proposal: Optimal design of parallelized light signals for optically controlled gene networks in single cells. [pdf]

Transversal Project

Fundings

Featured publications

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Pictures & Media

Analyzing the resistance of pathogenic bacteria to antibiotic treatments. Experimentation nurture modeling and optimization guides lab work. Sebastian Sosa Carrillo and Virgile Andréani, PhD students in the InBio team (Inria/Institut Pasteur). Credit: C. Morel
Microscopy platform: epifluorescence microscope with microfluidic system, image analysis and software to control the experiment. Steven Fletcher, engineer in the InBio team (Inria/Institut Pasteur). Credit: C. Morel
Quantitative biology: numbers and fluorescent cells. InBio team (Inria/Institut Pasteur). Credit: C. Morel
Engineering biological systems: reaction diagrams and differential equations. Elise Weill-Duflos, PhD student, Shuang Li, master student, and Virgile Andréani, PhD student, in the InBio team (Inria/Institut Pasteur). Credit: C. Morel
Scientific interactions between members of the InBio team (Inria/Institut Pasteur). Credit: C. Morel
Members of the InBio team (Inria/Institut Pasteur). From left to right: Shuang Li (master student), François Bertaux (engineer), Virgile Andréani (PhD student), Arthur Carcano (PhD student), Steven Fletcher (engineer), Chetan Aditya (PhD student), Elise Weill-Duflos (PhD Student), Gregory Batt (research scientist), Matthieu Pichené (postdoctoral researcher), and Sebastian Sosa Carrillo (PhD student). Missing that day: Andjela Davidovic (engineer) and Jakob Ruess (research scientist). Credit: C. Morel

Contact

Address
28 rue du Docteur Roux 75015 Paris
Email & Tel
Gregory.Batt_at_inria.fr +33 1 40 61 39 99
Assistant (Inria)
Corinne Petitot Corinne.Petitot_at_inria.fr +33 1 74 85 42 80
Assistant (Pasteur)
Denise Derhy denise.derhy_at_pasteur.fr +33 1 45 68 82 48