Bioinformatics Pipeline Developer

About Us

Owkin is an AI company on a mission to solve the complexity of biology. It is building the first Biology Super Intelligence (BASI) by combining powerful biological large language models, multimodal patient data, and agentic software. At the heart of this system is Owkin K, an AI copilot and its new LLM fine-tuned on biology called Owkin Zero, used by researchers, clinicians, and drug developers to better understand biology, validate scientific hypotheses, and deliver better diagnostics and therapies faster.

Please submit your CV in English

About The Role

We are seeking a detail-oriented and curious Bioinformatics Pipeline Developer to join our team. In this role, you will be at the intersection of biology and big data, helping to build and maintain the "highways" that process genomic, transcriptomic, clinical and other types of biological data. You won’t just be running scripts; you’ll be optimizing how we integrate diverse biological layers - from DNA sequencing to single-cell RNA-seq - to uncover clinical insights.

In Particular, You Will

• Build, test, benchmark, maintain and update automated workflows (AirFlow or Snakemake) for processing sequencing (WES/WGS, bulk and single-cell RNAseq, spatial transcriptomics) and other clinical, imaging and molecular data types.
• Implement strategies to ensure data quality, consistency and interoperability.
• Calculate, implement, benchmark and integrate biological information and scores based on biomedical scientist’s input.
• Maintain clear, version-controlled codebases (GitHub) and technical documentation.

About You

Required Skills \& Qualifications

• A relevant education in bioinformatics, computational biology, computer science, or a related field (Bachelor, Master or PhD), with proven experience gained in industry or academia.
• Proficiency in Python.
• Experience of developing bioinformatic pipelines.
• Experience working in cloud environments.
• Familiarity with orchestration tools and frameworks
• Experience with NGS tools such as variant calling and RNAseq analysis.
• Basic understanding of biological processes such as NGS library preparation (e.g., Illumina, RNA-seq) and the biological differences between tissue types (e.g., enterocytes vs. colonocytes).
• Comfortable using Git for collaborative development.

Nice-to-Haves

• Proficiency in R.
• Experience with Docker or Singularity containers.
• Familiarity with single-cell/spatial transcriptomic analysis (Scanpy).
• Knowledge of oncology-specific databases (TCGA, gnomAD, COSMIC).

Reference

What we offer

• Flexible work organization
• Friendly and informal working environment
• Opportunity to work with an international team with high technical and scientific backgrounds

Recruitment Process \& Security

• Please complete the form and submit your CV.
• Owkin is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, sex, gender, sexual orientation, age, color, religion, national origin, protected veteran status or on the basis of disability.
• Owkin is a great place to work. As a coveted workplace we are, unfortunately, vulnerable to recruitment phishing scams. We urge all job seekers and candidates to be wary of potential scams. Most of these have individuals posing as representatives of prominent companies, including Owkin, with the aim of obtaining personal, sensitive, or financial information from applicants. These scams prey upon an individual’s desire to obtain a job and can sometimes “feel” like a genuine recruitment process. Some red flags are identified below. Should you encounter a recruitment process that claims to be for Owkin but is not consistent with the below, please do not provide any personal or financial information:
• Legitimate Owkin recruitment processes include communication with candidates through recognized professional networks, such as LinkedIn.
• Communication is always through an official Owkin email address (from the @owkin.com domain), over the phone or through our applicant tracking system (Greenhouse).
• The Owkin talent team do use platforms such as LinkedIn and Job Teaser, however if you have any concern or doubt about this contact, please ask for them to send an email from @Owkin.com.
• The Owkin talent team will not solicit personal data from candidates during the application phase including, but not limited to, date of birth, social security numbers, or bank account information;
• Legitimate Owkin interviews may be conducted over the phone, in person, or via an approved enterprise videoconferencing service (Google Meets). They will not occur via Signal, Telegram or Messenger
• Owkin offers of employment are based on merit and only extended once a candidate has interviewed with members of the talent and hiring team. Offers will be extended both verbally and in written format.

If you think that you have been a victim of fraud,

• Check the identity of the talent team on LinkedIn
• Check our senior team on our website https://owkin.com/team/
• Check the existence of the position on our website: https://www.owkin.com/careers#current-opportunities
• Notify Owkin's recruitment unit at this address [email protected]
• contact the following authorities:

+ [FR] https://internet-signalement.gouv.fr/

+ [UK] https://www.actionfraud.police.uk/reporting-fraud-and-cyber-crime

+ [US] https://reportfraud.ftc.gov/