Bioinformatics Software Engineer

 CDI · IE   Bac+5 / Master   Scienta Lab · Paris (France)


Bioinformatics Software Engineering Data Engineering



Scienta Lab is a French deeptech startup harnessing artificial intelligence to solve unmet medical needs of patient living with immune conditions.

Scienta Lab develops a foundation model for immune-mediated inflammatory diseases. The model leverages multimodal data (clinical notes, biology, biopsies, radiology, omics ...) to predict patient diagnosis, prognosis, and response to treatment across the immunology therapeutic area.

The company is partnering with top-tier academic research institutions such as Inserm, AP-HP, and the NECESSITY European Consortium to develop its model. Successful research pilots have been deployed in rheumatology with scientific publications in top-tier medical journals and conferences.


As a Software Engineer at Scienta Lab you will contribute to high-impact research projects at the interface of software engineering, bioinformatics, deep learning and drug discovery & development.

You will be part of the R&D team and will report to Scienta Lab’s CTO. You will collaborate with external collaborators (biologists, academic medical researchers / pharmaceutical companies) and internal AI Research Scientists to build structuration and normalization pipelines to make data usable by our foundation model.

We value high-level coding and research and aim to develop a culture of continuous improvement in the team. You will be exposed to good practices to deliver production-ready software and top-tier scientific publications in these areas.

Main Missions :

  • Build data structuration pipelines to normalize, control quality, filter, and reduce the noise of omics data coming from different sources and of different natures.
  • Collaborate with domain experts, biologists, and AI researchers to understand the specific needs and goals of the omics data analysis pipeline. Define the scope of the pipeline, including the types of omics data to be processed (genomics, transcriptomics, proteomics, etc.) and the analysis workflows to be implemented and design a modular and scalable pipeline architecture that accommodates different data formats, analysis tools, and potential future enhancements.
  • Contribute to the R&D team's processes and good practices. This entails actively participating in refining and optimizing the software development lifecycle, ensuring efficient and high-quality delivery of projects. We expect you to actively engage in code reviews, mentorship, and knowledge sharing, fostering a culture of continuous learning and growth within the team.

Who we are looking for

  • Degree (PhD/Master) in computer science, bioinformatics, computational biology, or a related field.
  • Strong understanding of biological concepts and familiarity with omics data types (genomics, transcriptomics, epigenomics, etc..).
  • Good command of coding in Python, and a strong grasp of programming best practices
  • Strong teamwork skills to collaborate with biologists, researchers, and other software engineers in a collaborative environment.

How to stand out

  • Familiarity with bioinformatics tools, libraries, and databases relevant to omics data analysis (e.g., Bioconductor, NCBI databases).
  • Experience in developing and optimizing pipelines using workflow management systems (e.g., Snakemake, Nextflow).
  • You have contributed to open-source software, preferably in bioinformatics.


  • Competitive salary and benefits package
  • Possibility to work partially remotely
  • Half of transportation costs covered by the company and half of health insurance (Alan)


Procédure : If you are interested, please send your resume and a cover letter to and we will contact you back shortly.

Date limite : None


Julien Duquesne

Offre publiée le 18 août 2023, affichage jusqu'au 16 octobre 2023