In our journey to impact on patients lifes, we are looking for a Senior Bioinformatician (Data Scientist) based in Bordeaux or Bidart. 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 Tertiary analysis team is transversal across the main business lines of SOPHiA: Genomics, Oncology and Clinical Trials. The primary focus of the team is the exploitation of expert knowledge and predictive models to enrich the annotation and interpretation of variants in patients.
On a daily basis, this expands from identifying and processing new available data sources, translating expert knowledge into algorithms and applications and integrating these resources into SOPHiA’s analysis products.
The Tertiary analysis team identifies, handles and validates the annotation of genomic variants and 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 approaches, mainly covering the latter aspect for somatic diseases. More specifically, you will be involved in:
- The identification and handling of biological metadata (with focus on somatic diseases)
- Contributions to the creation, population and maintenance of SOPHiA knowledge base about variants and their annotations.
- Ramp;D of knowledge integration and consensus systems to harmonize conflictual knowledge.
Responsibilities:
- Annotation of somatic variants with predictive models and expert knowledge.
- Conception and development of the backend solutions for the management and integration of expert knowledge and SOPHiA knowledge base (KB).
- Scientific and technical management of our extensive bioinformatics knowledge base, including pipelines for the automatic update of our variants database and integration of new knowledge.
- SOPHiA Trial Match enables clinicians to match patients to clinical trials based on their genomic profiles. The development and maintenance of SOPHiA Trial Match is also part of our responsibilities, were we work as scientific experts, coordinating data between the BioPharma and the IT teams. In this role, your tasks will include the harmonized annotation and interpretation of relevant alterations across thousands of patients for different somatic diseases.
Requirements
- PhD related to bioinformatics or computational biology fields or a Master Degree with several years of experience.
- Working knowledge of genomics, molecular biology and/or clinical aspects in somatic (cancer) contexts.
- Competence in a widely used bioinformatics programming language (e.g. Python, R, Julia) and Bash scripting.
- Experience with semantic knowledge representation systems, such as ontologies and their representation standards (e.g. OWL, RDF) and their querying language (e.g. SPARQL) is a strong advantage.
- Knowledge of relational databases and SQL query language is an advantage.
- Excellent communication skills, including experience in communicating complex scientific principles in simple terms.
- English is required.
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?
Location: Position is based in Bordeaux or Bidart (France)
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.?