Senior Bioinformatician

 CDI · Autre   Bac+5 / Master   SOPHiA GENETICS · Bidart (France)


Senior Bioinformatician Data Engineer Bioinformatician


In our journey to impact on patients' lives, we are looking for a Senior Bioinformatician (Data Engineer), based in Bidart (France).

We are primarily looking for passionate people. Seize the opportunity to contribute to a great cause, improving the diagnosis and treatment of serious illnesses, from Cancer to Genetic Diseases, within an outstanding company.

The position is open in the Tertiary analysis, in the UpData team. The team is transversal working across the main business lines of: Genomics, Radiomics and Clinical Trials. The primary focus of the team is the annotation of genetic variants (and other clinically relevant features) of patients and diseases. As such, the Tertiary analysis team identifies, handles and validates the contextual information supporting the clinicians in their interpretation of results. This includes (1) the design, evaluation and integration of predictive models and algorithms to prioritize variants and their effects, and (2) the integration of expert knowledge from multiple data resources and repositories.

The tasks are varied and cover a large array of topics, mainly covering the latter aspect. 

More specifically, you will be involved in:

The identification and handling of biological metadata.

Contributions to the creation, population and maintenance of SOPHiA knowledge base for variants and their annotations.

Your main responsibilities include :

  • Conception and R&D of the backend solution for the management and integration of expert knowledge in the SOPHiA knowledge base (KB).
  • Scientific and technical management of our extensive bioinformatics databases
  • This will require the automation of variant database updating and integration of new data sources, including documentation and enabling design control of these processes.
  • This will additionally involve manipulating data within postgreSQL / mySQL and other database structures 
  • The aim is to supply data as a service to both internal and external clients.
  • This team coordinates with all data consumers to prioritize and organize accesses to - and maintenance of - external data services.
  • This requires collaboration with different departments across the company including; Sales; Marketing; IT; Quality; Project Management and Product Management.
  • The candidate will also participate in Bioinformatics based technical support, for our Alamut and SOPHiA DDM products.
  • The UpData Team is transversal involved numerous projects. Thus, the candidate would be required to document all activities and report developments in these projects to team leader, colleagues and project managers on a weekly basis.

Requirements :

  • PhD in a scientific field would be advantageous or a Masters with several years of experience.
  • Competence in a widely used bioinformatics programming language, Python, R and Snakemake workflows would be an advantage.
  • Linux bash scripting experience.
  • Database experience in MySQL and postgreSQL.
  • Ontologies development using tools such as SPARQL.
  • Knowledge of Data Warehouses, Data Lakes and Lakehouses would be advantageous.
  • Knowledge of Genetics and Molecular Biology. Experience in a clinical setting would be an advantage.
  • Knowledge of variant annotation software and or concepts would be advantageous.
  • Excellent communication skills, including experience in communicating complex scientific principles in simple terms.
  • English is required (fluent)

Benefits :

  • An exciting journey to facilitate patients' access to better treatment worldwide
  • Flexible, friendly and international working environment
  • A  stimulating technical environment
  • Continuous learning and trainings
  • Permanent exchanges with teams of experts within the company (AI, genomics, medicine, etc.)
  • A competitive salary (35h + 4 additional weekly hours contract)


Starting date: ASAP (or as agreed)

Contract type: Permanent full-time

Application process: If you think you fit this position, please send a CV and a cover letter. Please note that incomplete applications will not be considered.

After an initial screening process, candidates will be invited for remote interviews. You may be asked to perform a programming task as part of this process. Selected candidates will then be invited for personal interviews.

As committed employer, SOPHiA GENETICS offers everyone the same opportunities to access employment regardless of gender, ethnicity, religion, sexual orientation, social status, disability or age. SOPHiA GENETICS strives to develop an inclusive work environment that reflects the diversity of its employees. All information will be treated confidentially in accordance with the Employment Equity Act.


Procédure : please send a CV and a cover letter

Date limite : None


Raphaël Froment

Offre publiée le 17 août 2022, affichage jusqu'au 16 octobre 2022