Senior Bioinformatic Engineer, Method Development and Validation

Senior Bioinformatic Engineer, Method Development and Validation at PathoQuest

PathoQuest, a CRO spun out of Institut Pasteur, specializes in providing innovative Quality Control solutions for biological pharmaceutical products. We offer comprehensive expert services, from sample reception to analysis certificate production, leveraging proprietary sample processing protocols, a Next Generation Sequencing (NGS) platform, and specialized bioinformatic analysis pipelines. Currently in a scale-up phase, we have around fifty employees across France and the United States. We are currently looking to fill a newly created position for a Senior Bioinformatic Engineer, Method Development and Validation.

Missions

Under the hierarchical responsibility of the Chief Technical Officer (CTO), the Senior Bioinformatic Engineer will participate in monitoring development activities, validating pipelines, and transferring bioinformatic methods between the Tech Ops and Operations departments. This role also provides support to the Tech Ops biology team for method improvement or the development and validation of new NGS methods, ensuring the optimization of BFX data and contributing to overall method enhancement.

Responsibilities

• Monitors Bioinformatic projects at the Tech Ops stage.
• Proposes validation strategies (business and CSV) and transfer strategies for software.
• Independently drafts associated documentation (protocols and reports) for development, validation, and transfer.
• Acts as a proactive expert on NGS bioinformatic topics.
• Drafts procedures for new bioinformatic methods or modifies existing SOPs.
• Automates and optimizes analysis workflows.
• Provides training to enable personnel in the Operations department for new or optimized analytical methods.
• Ensures the life cycle management of BFX analytical methods, including identifying additional tools or functions to improve existing pipelines and optimizing parameters.
• Reviews code for the validation of analytical methods.
• Manages initial non-regulated client studies for new analytical methods to ensure their consistency.

Qualifications and Competencies

Qualifications and Experience

• Minimum Bac +5 in Bioinformatics.
• Minimum 5 years of experience in a similar bioinformatic development and validation role within the pharmaceutical industry, specifically in a GMP context.
• Proficiency in CSV and GMP guidelines (Annex 11, 21CFR Part 11), GAMP5.
• Significant experience in bioinformatics applied to NGS technologies.

Competencies

• English: B2 minimum.
• Project Management: Ability to manage priorities and meet deadlines.
• Knowledge of programming languages: Python, Shell, HTML, SQL, R.
• Familiarity with GitLab environment.
• Knowledge of Snakemake workflow manager.
• Understanding of good coding practices and code testing strategies.
• Experience in NGS data analysis (Illumina and Nanopore: assembly, mapping, variant calling, annotation, metagenomics).
• Experience in genomic data analysis (sequence comparison, phylogenetic analyses).
• Knowledge of microbial, viral, and mammalian genomics.
• Ability to work transversally and connect different departments within the company.
• Ability to evaluate the quality of computer code for use in a GMP context.
• Ability to anticipate, detect, and interpret technical difficulties.
• Ability to evaluate the efficiency of new pipelines for industrial use.
• Propose innovative and sustainable solutions for optimizing workflow for new assays.

Soft Skills

• Proactive and persuasive.
• Rigorous / Organized.
• Adaptability, ability to adjust communication based on the interlocutor.
• Analytical and synthesis skills.
• Team spirit.
• Client-oriented (internal and external).
• Results and performance-driven.
• Creativity.
• Solution-oriented mindset: Ability to find simple solutions to complex problems.

Location

This position is based in Paris (13th arrondissement), France.

Compensation

Based on the candidate's experience.

Project Benefits

• Fast-growing, dynamic, innovative, and ambitious scale-up environment.
• A company at the forefront of genetics, bioinformatics, and molecular biology.
• Attractive and globally significant client portfolio.

We thank those interested in this position who meet the above criteria to send their curriculum vitae to careers@pathoquest.com.

Key skills/competency

• Bioinformatics
• NGS Technologies
• Method Validation
• GMP Compliance
• CSV (Computer System Validation)
• Python Programming
• Snakemake
• Data Analysis
• Workflow Automation
• Project Management