Open Position (s)

 

1. Research Associate Position: Bioinformatics / Systems Biology

 

Context

We are seeking a motivated individual to join our research group within the MICALIS institute (INRAE & University of Paris-Saclay, website: https://www.micalis.fr), a leading research unit with over 350 researchers developing multidisciplinary approaches and promoting the development of synthetic biology for health and biotechnology.

The candidate will contribute to our ongoing efforts in developing cellular models, as highlighted in our recent publication (https://www.nature.com/articles/s41467-023-40380-0), which proposes combining AI-driven and mechanistic methods to better design strains and predict strain performance more effectively.

The candidate will participate in projects funded by the French funding research agency (ANR) and a European Project at MICALIS. Within MICALIS , the recruiting research team (~20 staff spread into wet and dry labs) specializes in developing computer-aided design tools for biotechnology (more details at https://jfaulon.com/). The candidate will closely collaborate with software developers and interact with Research and Data Scientists, Engineers, and Ph.D. fellows.

Mission(s)

Begin work with innovative AI-driven whole-cell models designed to facilitate studies of transcription, translation, and metabolism. In this role, the candidate will undertake the following tasks:

  • Participate in ANR-funded and European Project initiatives, aiming to enhance biotechnological applications through innovative cellular models.
  • Benchmark existing mechanistic methods to model the kinetics of transcription, translation and metabolism.
  • Contribute to the development of hybrid neural-mechanistic models based on physics-informed neural networks (PINNs) and/or graph neural networks (GNNs).
  • Benchmark the hybrid models with experimental measurements collected by project partners or generated in the hosting lab.
  • Develop strategies for applying hybrid models in cell engineering

Profile

  • D. degree in System Biology, Bioinformatics, Biophysics or a related field.
  • Prior knowledge in metabolic networks, metabolomics, metabolic flux analysis or kinetics of transcription and translation is desired.
  • Good programming skills in Python, testing practices, and Git versioning. Knowledge of continuous integration paradigms is a plus.
  • Excellent communication skills and the ability to work effectively in an interdisciplinary team.
  • Strong analytical skills and a keen interest in software development for biotechnological

Contract and Salary

  • Fixed-term contract of 12 months (renewable), in accordance with French legislation.
  • Salary will be commensurate with qualifications and experience.

To apply

Applicants should send a detailed curriculum vitae, a letter of intent explaining their motivations for the position, and contact details of at least two references.

Send your queries/applications to; Jean-Loup Faulon <jean-loup.faulon@inrae.fr>


 

2. Research Associate in Molecular Biology Laboratory Automation

We are happy to announce an opening for a Research Associate in molecular biology laboratory automation at the MICALIS Institute (INRAE, AgroParisTech, University of Paris-Saclay). This is an excellent opportunity to join a leading research group dedicated to advancing synthetic biology applications for health and biotechnology through innovative multidisciplinary approaches.

The MICALIS Institute is home to over 350 researchers pursuing research in microbiology. Within MICALIS, our group specializes in whole-cell and cell-free synthetic biology for metabolic pathway and biosensor engineering. We are currently engaged in a national project aimed at creating automated protocols for synthetic biology, with a strong emphasis on reproducibility.

Position Overview. The successful candidate will:

  • Participate in the development of automated protocols for synthetic biology applications.
  • Focus on reproducibility to ensure consistent and reliable results.
  • Engineer metabolic pathways using advanced automated protocols involving liquid handlers for gene assembly, strain transformation, strain cultivation, and spectrophotometer and high-performance liquid chromatography (HPLC) measurements.
  • Identify and optimize parameters affecting reproducibility and develop strategies to enhance it.

What We Offer:

  • A collaborative environment with experienced researchers and engineers.
  • Access to cutting-edge technologies and methodologies in metabolic pathway engineering and automation.
  • A chance to work closely with experts in using workflows and large language models for protocol automation.
  • For more information about our work and team, visit https://jfaulon.com/galaxy-synbiocad-portal/

Qualifications:

  • A Ph.D. degree, preferably with post-doctoral experience, in systems & synthetic biology, metabolic engineering, or molecular biology.
  • Proficiency in experimental protocols and analytical techniques used in synthetic biology, molecular biology, and biochemistry.
  • Experience with liquid handlers, pipetting robotic equipment, mass spectrometry, or HPLC is desirable, along with experience in designing and engineering metabolic pathways.
  • Ability to write high-quality research manuscripts, strong collaborative skills, and excellent communication skills in English are required.

Position Details:

  • Duration: the position is open for 12 months, with the possibility of renewal for two additional years.
  • Start Date: October 1st, 2024.
  • Contract: fixed-term, in accordance with French legislation.
  • Salary: competitive, based on qualifications and experience.

How to Apply:

Applicants should send a detailed curriculum vitae, a letter of intent explaining their motivations for the position, and contact details of at least two references. Please send your queries and applications to: jean-loup.faulon@inrae.fr

Join us at MICALIS and contribute to groundbreaking research that bridges the gap between biology and engineering. Apply today to become part of a dynamic team at the forefront of synthetic biology innovation.