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

About

Our main long-term goal is to develop a comprehensive methodological framework supporting the development of a quantitative understanding of cellular processes.

Our research rests on three pillars:

  • Lab automation – engineer experimental platforms and develop computational pipeline for strain construction and data analysis,
  • Bioengineering – use synthetic biology and standardized cloning approaches to probe the functioning of natural systems and construct novel systems,
  • Quantitative modeling and real-time control – develop deterministic and stochastic models of cell processes to explain observations and guide designs.

Recent contributions include:

  • Software supporting lab automation and real-time control of cellular processes: ReacSight (Bertaux et al, Nat Commun, 2022) and MicroMator (Fox et al, Nat Commun, 2022),
  • Strategies to optimize bioproduction using regulation and control to preserve cell physiology: engineering microbial consortia (Aditya et al, Nat Commun, 2021, Aditya et al, PNAS, 2022) and applying cybergenetic principles (Sosa-Carrillo et al, Nature Commun, 2023),
  • Quantifying resistance and tolerance of bacterial clinical isolates to antimicrobial treatments (Andreani et al, bioRxiv, 2021).

InBio is an Inria – Institut Pasteur joint research group combining wet and dry biology in the same lab. It is hosted at Institut Pasteur and affiliated to the Inria Paris research center.

New: We would like to hire a research scientist on a Inria permanent position to join our team. Inria and other French institutions offer chargé de recherche positions that are quite unique in the academic world. Several Inria researchers and engineers join forces in a small team to tackle together a grand challenge over a 10 year horizon. Our long term goal is to understand how to better engineer microbial systems by combining wet and dry biology approaches. We are located at Institut Pasteur and benefit from a truly outstanding work environment. Do not hesitate to contact us for more information.

Former Members

We are grateful to former InBio members:

  • Eléa Greugny (Intern, INSA Lyon, Summer 2017; now PhD student in Computational Biology at Johnson & Johnson and Inria Saclay),
  • Laura Guyot (R & D Technology Engineer at Dassault Systems, May 2017 – Aug 2017 part time; permanent position),
  • Matthieu Pichené (Postdoc, ANR, Inria, Apr 2018 – Jul 2018),
  • Shuang Li (Intern, CRI, Spring 2018),
  • Elise Weill (PhD candidate, Paris-Saclay Univ, Sep 2018 – Aug 2019; now High school teacher),
  • Maxim Kryukov (Intern, Amgen program, MIPT, Summer 2018; now 4th year at MIPT),
  • Martin Larralde (Intern, ENS Saclay, Summer 2018; now PhD candidate at EMBL Heidelberg),
  • Albin Salazar (Intern, CRI, Spring 2019; now PhD candidate at ENS Paris),
  • Mariela Furstenheim (Intern, CRI, Spring 2019; now PhD candidate at Institut Curie),
  • Andjela Davidovic (Engineer, Hub Pasteur, Jun 2018 – Apr 2020 part time; permanent position)
  • Thomas Wahl (Intern, Medical Doctor student, Master 1, Summer 2020)
  • Sacha Maire (Intern, Biomedical engineering, Imperial College, Summer 2020)
  • Steven Fletcher (Engineer, Feb 2017 – Aug 2020, now Software engineer at )
  • Zach Fox (Postdoc, Jul 2019 – Oct 2020, now Postdoctoral researcher, Los Alamos National Lab, link)
  • Virgile Andreani (PhD student and postdoc, Sept 2016 – June 2021, now Postdoctoral researcher, Boston University, link)
  • Chetan Aditya (PhD student, Feb 2018 – Sept 2021, now Postdoctoral researcher, Princeton University, link)
  • Olivier Borkowski (Postdoc, Oct 2019 – Oct 2021, now Research scientist, INRAE, link)
  • François Bertaux (Permanent engineer, Apr 2018 – Nov 2021, now head of
  • Arthur Carcano (PhD student, Oct 2018 – Dec 2021, now R&D engineer, OCamlPro)
  • Davin Lunz (Postdoc, Nov 2019 – Dec 2021, with Commands team at Inria Saclay, now Software engineer, Kodiak Robotics)
  • Achille Fraisse (Engineer, Sep 2020 – Jan 2022, now PhD student at Edinburgh University, link)
  • Hélène Philippe (Intern, Sep 2021 – Mar 2022, now M2 University Paris Saclay, link)
  • Sebastián Sosa Carrillo (PhD Student and Postdoc, Feb 2018 – Jul 2022, now Postdoctoral researcher, University of Basel, link)
  • Jakob Ruess (Inria Research scientist, Feb 2017 – Dec 2022, permanent research position, ERC starting grant recipient, Inria Saclay, link)
  • Allyson Holmes (Research scientists, Feb 2022 – Jun 2023, link)
  • Ngô Hồng Dương (Intern, Feb 2023 – Aug 2023)
  • Konstantin Achkasov (Intern, March 2023 – Aug 2023, now Master student at Sorbonne Université & Institut Pasteur)

Fundings

Featured publications

Download

Lab Equipment

Our lab is equipped with state-of-the-art instruments that enable us to construct experimental platforms to investigate cellular processes at the population and single cell level:

  • a diverse range of small-volume bioreactors: a 16-reactor eVOLVER system, 8 Chi.Bio reactors, and a home-made 16-reactor array,
  • two opentrons OT-2 liquid handler robots, equipped with temperature and magnetic modules,
  • two table-top Guava easyCyte flow cytometers (HT BGV) with auto-sampler for 96-well plates,
  • two Tecan Spark multimode plate readers,
  • a Leica DMi8 fully-automated microscope with an Andor Mosaic 3 DMD system and two CoolLED pE-4000 light sources, together with a cellAsic Onix2 system and a set of Fluigent Flow EZ flow controllers for microfluidics,
  • lab equipment for molecular biology and microbiology (biosafety level 2),
  • two 96-core compute nodes and access to the Maestro cluster (15k cores, 70 GPU, 1PB rapid storage).


 

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. Credit: C. Morel
Scientific interactions between members of the InBio team (Inria/Institut Pasteur). Credit: C. Morel

Contact

Address
4th floor @ Yersin building (main room: 24-04-05) & 2nd floor @ Lwoff building (main room: 22-02-17) 28 rue du Docteur Roux 75015 Paris
Email & Tel
Gregory.Batt_at_inria.fr +33 1 40 61 39 99
Assistant (Inria)
Nelly Maloisel nelly.maloisel_at_inria.fr +33 1 80 49 40 49
Assistant (Pasteur)
Melanie Ridel melanie.ridel_at_pasteur.fr +33 1 44 38 93 71