Genome-Scale Metabolic Modelling of Industrial Microbes Internship
Lesaffre
Genome-Scale Metabolic Modelling of Industrial Microbes Internship
Lesaffre
Fermentation specialist advancing food and health
At the heart of this dynamic, the BioData Department plays a strategic role supporting R&D through biological data engineering, management, and analysis. Within this department, this internship will be jointly supervised by a researcher from our Bioinformatics team (BioInfo), who is responsible for data management, code infrastructure, and pipeline development, and our Computational Biology team (BioAI), who is responsible for data analysis, modelling, and method development & application. As an innovative and multidisciplinary team, BioData develops software to efficiently handle large amounts of data, process data collected at different levels of biological organization using diverse experimental methods and provide timely analysis and interpretation of this data in the context of Lesaffre’s research activities.
The project will be part of ongoing initiatives to further develop methodologies and tools with the potential to bring insights to existing genomics data. At Lesaffre, as a result of our R&D activities, we house a large genomic collection of industrial yeasts and bacteria. Under the supervision of a bioinformatician and a computational biologist, you will leverage both biological and software development skill sets to develop new pipelines that mine this genomic data to bring value to our biological research teams, strengthening our methodology portfolio and improving our data analysis capabilities, while working in close collaboration with both dry- and wet-lab researchers.
More precisely, the prioritized objectives of the internship will be to:
Implement and improve methods for automated high-throughput metabolic network reconstruction and analysis.
Further develop and diversify our existing microorganism genomic annotation workflows.
Apply the developed methods by formalizing reproducible and efficient pipelines for large-scale application.
Successful completion of the objectives will result in the following expected deliverables:
Successful Reconstruction and QC of Metabolic Networks of Strains from Our Genomic Collection.
Versioned Nextflow pipeline.
Presentation of Results to R&D teams.
Final year master's or engineering student (Bioinformatics, Computational Biology, Systems Biology or related fields).
Good programming skills in Python.
Familiarity with pipeline tools (e.g., Nextflow).
Exposure to version control (Git/Gitlab) and reproducible research (e.g., Docker, Anaconda).
Solid knowledge of genomics, biochemistry, and microbial metabolism.
Knowledge of constraint-based reconstruction and analysis (COBRA) methods (coursework or project).
Analytical mindset, rigor, and autonomy.
Strong communication skills.
Fluency in English.
The position is open for a duration of 6 months starting between January and March 2027. This is a full-time position under a presential regime at the facilities of Lesaffre International in Marcq-en-Barœul in France.
What you will gain from this internship:
This internship offers a unique opportunity to work at the intersection of bioinformatics, computational biology, and industrial R&D within a global leader in fermentation and biotechnology. Furthermore, you can expect:
Dual supervision in interdisciplinary and dynamic teams.
Experience with real-life industrial data.
Strengthen your professional portfolio through contributions to production-grade pipelines.
Lesaffre is a global fermentation company with a long history and a turnover of €3.2 billion. It employs about 11,700 people from 100 nationalities and operates on all continents. The company develops and produces fermentation-derived ingredients and solutions for food, health, naturalness, and environmental sustainability, working with customers, partners, and researchers to harness the power of microorganisms. Its products come from fermentation processes that use microorganisms to transform raw materials into ingredients and additives for scale, safety, flavor, nutrition, and sustainability. Compared with competitors, Lesaffre combines global reach, large-scale production, and a deep, century-long expertise in fermentation, along with a strong network across customers, researchers, and regions. The company’s goal is to nourish 9 billion people in a healthy way by 2050 while making the most of the planet’s resources, using fermentation as a key solution to food and health challenges.
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