Post-Doctoral Research Visit F/M Postdoc positions in Mathematical Biology at Institut Pasteur and CentraleSupélec

Inria

France

October 31, 2022

Description

2022-05374 - Post-Doctoral Research Visit F/M Postdoc positions in Mathematical Biology at Institut Pasteur and CentraleSupélec

Contract type : Fixed-term contract

Renewable contract : Oui

Level of qualifications required : PhD or equivalent

Fonction : Post-Doctoral Research Visit

Context

The project is a partnership between Laurent Pfeiffer and Frederic Bonnans (DISCO team, located at CentraleSupélec and affiliated to Inria Saclay), and Jakob Ruess (InBio team, located at Institut Pasteur and affiliated to Institut Pasteur and Inria Paris). Inria is the French national institute for research in computer science, control, and applied mathematics promoting scientific excellence and technology transfer. The Pasteur Institute is a non- profit private foundation dedicated to biomedical research and the fight against infectious diseases.

InBio is an interdisciplinary research group, combining experimental and theoretical biology in the same lab. We use systems and synthetic biology approaches with control and active learning methods and 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. The group consists of scientists with diverse backgrounds (mathematics, physics, biology) and nationalities. The spoken language is English. We have a wet lab as well as a dry lab, both located on the Institut Pasteur campus in the heart of Paris.

DISCO is a research group gathering experts in control engineering and optimal control. We work on the theoretical analysis and the development of numerical tools for complex dynamical systems, such as delay systems and PDEs. Our activities around dynamical systems cover a broad range of topics: modeling, control, estimation, stabilization, and optimization. All group members are involved in interdisciplinary projects in various areas, such as life sciences, energy management, transportation systems.

Assignment

We are looking for two postdocs, for a duration of two years, to work on a starting collaborative ANR-project between Inria and Institut Pasteur. The goal is to develop and deploy mathematical approaches for modeling and controlling synthetic gene circuits in yeast cells that are being constructed at our biology laboratory at Institut Pasteur.

In the context of our collaborative project, we have positions available in both the InBio team (Inria Paris/Institut Pasteur) and the DISCO team (Inria Saclay/CentraleSupélec). Successful candidates are expected to work with both teams but, depending on skills and research interests, can either work primarily at CentraleSupélec or at Institut Pasteur.

Main activities

The Project:

Synthetic biology aims at engineering biochemical processes to supplement cells with artificial functionality. To this end, we design synthetic gene circuits that operate as dynamical systems inside cells and deploy methods from control engineering to regulate circuit functionality. A key problem in this is that biochemical processes inside single cells are inherently stochastic and create heterogeneity within cell populations that eventually leads to complex couplings between single-cell processes and population dynamics. It is thus difficult to quantitatively predict how exactly a constructed circuit will function in the context of a growing population and to design single-cell circuits such that desired dynamics emerge at the population scale.

At the single-cell scale, stochastic biochemical processes are typically represented as continuous-time Markov chains governed by a chemical master equation (Kolmogorov forward equations). Frequently, these discrete state processes are approximated on the continuum leading to a Fokker-Planck equation as an approximation of the original master equation. We have recently proposed a multi-scale modeling framework that augments models of single-cell processes with auxiliary processes at the population scale such as growth or selection and developed a method (the Flips solver) that can be used to numerically calculate the solution of the resulting Fokker-Planck partial differential equations (Lunz et al., PLoS Computational Biology, 2021).

Our multi-scale modeling framework gives us unprecedented opportunities to forward-simulate coupled dynamics of stochastic single-cell and population processes, which paves the way to model, design, and dynamically control synthetic gene circuits so as to create desired functionality within growing populations. Within this project, we thus aim to focus on the development of methods for reverse engineering and controlling multi-scale models and on applying this methodology in real applications for a collection of bio- production gene circuits that are available in our experimental laboratory at Institut Pasteur.

Links to publications:

https: // doi.org/10.1371/journal.pcbi.1009214

https: // doi.org/10.1073/pnas.2114438119

https: // doi.org/10.1016/j.mbs.2022.108866

https: // doi.org/10.23919/ECC.2019.8795858

https: // hal.inria.fr/hal-03445175

Skills

Candidates should have a PhD in a theoretical field, such as mathematics, physics, computer science, control engineering or similar, and be capable of using methods from these fields to study dynamical systems and stochastic processes in applications. Experience with either continuous-time Markov chains, stochastic differential equations, stochastic chemical kinetics or alternatively partial differential equations and numerical analysis is a plus. Specific expertise in biology is not required but candidates are expected to build up an understanding of our concrete applications throughout the course of the project. Candidates who expect to finish their PhD-studies in the near future are also encouraged to apply.

Benefits package
  • Subsidized meals
  • Partial reimbursement of public transport costs
  • Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
  • Possibility of teleworking (up to 90 per day for full time contract) and flexible organization of working hours
  • Professional equipment available (videoconferencing, loan of computer equipment, etc.)
  • Social, cultural and sports events and activities
  • General Information
  • Theme/Domain : Modeling and Control for Life Sciences Biologie et santé, Sciences de la vie et de la terre (BAP A)

  • Town/city : Paris

  • Inria Center : CRI de Paris
  • Starting date : 2023-01-01
  • Duration of contract : 2 years
  • Deadline to apply : 2022-10-31
  • Contacts
  • Inria Team : INBIO
  • Recruiter : Ruess Jakob / jakob.ruess@inria.fr
  • The keys to success

    Applications should include a CV, list of publications, and contact details of scientists willing to recommend the candidate.

    About Inria

    Inria is the French national research institute dedicated to digital science and technology. It employs 2,600 people. Its 200 agile project teams, generally run jointly with academic partners, include more than 3,500 scientists and engineers working to meet the challenges of digital technology, often at the interface with other disciplines. The Institute also employs numerous talents in over forty different professions. 900 research support staff contribute to the preparation and development of scientific and entrepreneurial projects that have a worldwide impact.

    Instruction to apply

    Defence Security : This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment.

    Recruitment Policy : As part of its diversity policy, all Inria positions are accessible to people with disabilities.

    Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed.

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