Job offer

Our team conducts translational research in pancreatic cancer, combining patient cohorts, patient-derived experimental models (primary cell cultures, organoids and xenografts), molecular profiling and therapeutic response studies.

Through the PaCaOmics programme and related research projects, we have generated extensive collections of clinical, genomic, transcriptomic, pharmacological and experimental data. These datasets originate from multiple cohorts, sequencing platforms and experimental protocols, with several samples and experimental models frequently associated with the same patient.

We are looking for a bioinformatics engineer to organise, integrate, quality-control and facilitate the scientific exploitation of these heterogeneous datasets., * Scientific data management: Design and maintain a structured, centralised data environment linking patients, biological samples, experimental models and molecular analyses, ensuring traceability, consistency and interoperability.

• NGS quality control: Develop and implement reproducible quality-control procedures for genomic and transcriptomic datasets, including bulk and single-cell RNA sequencing. Identify technical problems, sample inconsistencies, outliers and batch effects.
• Data integration and harmonisation: Develop project-specific approaches for data preprocessing, normalisation and integration across cohorts, technologies and experimental conditions, while preserving original data and documenting analytical limitations.
• R Shiny development: Design and maintain interactive applications allowing researchers to explore available datasets, visualise molecular profiles and quality-control results, identify relevant samples and select cohorts for scientific projects.
• Scientific collaboration: Work closely with researchers, clinicians and technological platforms to prepare validated datasets for analyses, publications and collaborative projects, following reproducibility, FAIR data and data protection principles.

The position requires strong expertise in R, R Shiny, Python, SQL, genomic and transcriptomic data analysis, and NGS quality control.

The successful candidate will join a multidisciplinary research team at the CRCM in Marseille, working closely with the Institut Paoli-Calmettes and national and international collaborators.

The position offers substantial technical autonomy and a central role in developing and maintaining the bioinformatics infrastructure supporting our pancreatic cancer research programme.

French is the primary working language, and professional proficiency in both French and English is required., Master Degree or equivalent, * Master’s degree (MSc, M2) or engineering degree in bioinformatics, computational biology, computer science applied to life sciences, or a related discipline. A PhD is an advantage but is not required.

• Excellent proficiency in R and R Shiny application development.
• Strong programming skills in Python.
• Solid knowledge of SQL, relational databases and scientific data management.
• Practical experience in genomic and transcriptomic data analysis, particularly NGS and RNA-seq.
• Experience in NGS quality control, including sequencing metrics, alignment assessment, sample consistency and identification of technical artefacts.
• Good understanding of data normalisation, batch effects and integration of heterogeneous molecular datasets.
• Proficiency in Linux, Git, scripting and reproducible bioinformatics workflows.
• Ability to structure, document and maintain complex scientific datasets, ensuring data integrity and traceability.
• Excellent command of French and good professional proficiency in English, both written and spoken, are mandatory.

Additional skills considered an advantage

• Experience with single-cell RNA-seq and multi-omics data integration.
• Familiarity with bioinformatics tools and workflows such as FastQC, MultiQC, Nextflow and Snakemake.
• Experience with REDCap, LIMS or biobank databases.
• Knowledge of biomedical imaging data management.
• Experience in quantitative proteomics.
• Knowledge of FAIR data principles, GDPR and biomedical data protection requirements.

Personal qualities

We are looking for an autonomous, rigorous and well-organised candidate with strong analytical and problem-solving skills. The successful applicant should be able to understand biological research questions, identify data quality issues and develop sustainable bioinformatics solutions in close collaboration with researchers, clinicians and technology platforms. Specific Requirements

The position requires a candidate capable of working autonomously on the organisation, quality control and integration of complex biomedical research datasets.

Specific requirements include:

• Ability to manage heterogeneous datasets generated from multiple patient cohorts, biological samples, experimental models and sequencing platforms.
• Practical experience in developing reproducible NGS quality-control procedures and identifying technical inconsistencies, sample identification errors and batch effects.
• Ability to design and maintain structured databases linking clinical, molecular and experimental information.
• Capacity to develop user-friendly R Shiny applications for researchers without bioinformatics expertise.
• Ability to implement project-specific data normalisation and integration strategies, taking into account differences in sequencing technologies, protocols and biological contexts.
• Strong organisational skills, scientific rigour, initiative and ability to work independently while collaborating with multidisciplinary research teams.
• French: Excellent written and spoken proficiency is mandatory, as French is the primary working language.
• English: Good professional proficiency, both written and spoken, is mandatory for scientific communication and international collaborations., * Hold a Master’s degree (MSc, M2), an engineering degree or an equivalent qualification in bioinformatics, computational biology, computer science or a related field.
• Demonstrate practical experience in bioinformatics, particularly genomic and transcriptomic data analysis, scientific data management and NGS quality control.
• Have strong programming skills in R, including R Shiny development, as well as proficiency in Python and SQL.
• Have excellent written and spoken French and good professional proficiency in English. Both languages are mandatory.
• Be able to work independently and collaborate with multidisciplinary research teams.
• Be available to work in Marseille, France, with an expected starting date of 1 December 2026.

A PhD is not required. Previous experience in biomedical research, data integration or scientific database development will be considered an advantage.

Applications will be evaluated on the basis of qualifications, technical expertise, professional experience and suitability for the position.

INSERM is committed to equal opportunities and welcomes applications from qualified candidates regardless of nationality, gender or background, in accordance with applicable employment regulations. Selection process

Candidates are invited to submit a CV and a cover letter outlining their relevant experience, technical skills and motivation for the position tu julie.roques@inserm.fr

Applications will be evaluated according to the following criteria:

• Academic qualifications and professional experience in bioinformatics.
• Technical expertise in R, R Shiny, Python, SQL and scientific database management.
• Experience in genomic and transcriptomic data analysis, NGS quality control and data integration.
• Ability to work independently, solve technical problems and interact with multidisciplinary research teams.
• Proficiency in French and English.

Shortlisted candidates will be invited to an interview with members of the research team to discuss their experience, technical expertise and suitability for the position.

A practical technical assessment may be requested if necessary.

The final selection will be based on the candidate’s qualifications, demonstrated competencies and suitability for the responsibilities of the position. Additional comments

Applicants are encouraged to provide concrete examples of previous work involving scientific database development, NGS quality control, data integration or R Shiny applications.

Links to relevant publications, software projects or GitHub repositories may be included where available, but are not mandatory.

• Salary: According to INSERM salary scales, taking into account the candidate’s qualifications and professional experience.
• Contract: 12-month fixed-term contract, renewable.
• Working environment: Integration into an INSERM research team at the Cancer Research Center of Marseille (CRCM), with close interactions with the Institut Paoli-Calmettes and national and international collaborators.
• Scientific environment: Access to extensive genomic, transcriptomic and experimental datasets generated from patient cohorts and patient-derived pancreatic cancer models.
• Professional development: Opportunities to develop expertise in scientific data management, bioinformatics infrastructure, multi-omics integration and interactive data exploration tools.
• Autonomy and responsibility: A central technical role in developing and maintaining the data infrastructure supporting a translational pancreatic cancer research programme.
• Employment benefits: Leave, social protection and other benefits in accordance with applicable INSERM regulations.