Lead Bioinformatics Scientist, NGS

Profluent is an AI-first protein design company. Founded in 2022, we develop deep generative models to design and validate novel, functional proteins to revolutionize biomedicine. Based in Emeryville, CA, we are backed by leading investors including Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, and Convergent Ventures, and have raised over $150M to date. We’re seeking an experienced computational scientist to lead the design, development, and operation of the NGS analysis platform that powers Profluent’s gene editing and protein design programs. You’ll work at the intersection of computational biology, software engineering, and experimental biology to build scalable systems that extract clear, actionable insights from large-scale sequencing data. In this role, you’ll architect core bioinformatics infrastructure, define analytical strategy, and collaborate closely with experimental and ML teams to accelerate design-build-test-learn cycles. You’ll also mentor team members, promote software engineering best practices, and help shape the future of Profluent’s computational biology capabilities. Responsibilities Lead design and implementation of scalable NGS analysis pipelines supporting gene editing and protein engineering workflows Develop clear, intuitive visualizations and reports to communicate sequencing results and biological insights Manage cloud-based compute environments and data systems for large-scale datasets Partner with biology teams to analyze results, troubleshoot, and optimize experimental design Collaborate with machine learning teams to curate data for model training Establish best practices for code review, testing, and CI/CD in computational workflows Mentor junior scientists and foster a culture of rigor, reproducibility, and innovation Qualifications PhD or MS in Bioinformatics, Computational Biology, Computer Science, or a related quantitative field 5+ years of experience analyzing NGS datasets (e.g., amplicon sequencing, high-throughput editing, or screening experiments) Strong programming skills in Python (pandas, numpy, biopython, etc.) Expertise with workflow orchestration tools (Nextflow, Snakemake) and cloud environments (GCP, AWS) Experience with containerization (Docker, Kubernetes) and scalable compute infrastructure Deep understanding of Linux, git-based version control, and software engineering best practices Proven ability to transform complex sequencing data into actionable biological insights Preferences (but not required) Experience with gene editing technologies (CRISPR, base or prime editing; strongly preferred) Familiarity with SQL and data modeling for biological or experimental data Experience with LIMS platforms (e.g., Benchling) and lab data integration Track record of developing production-quality scientific software or open-source bioinformatics tools What We Offer High-growth opportunity with meaningful impact on the future of protein design Competitive compensation package with equity participation 401(k) with a strong employer match Comprehensive benefits including health/dental/vision insurance Generous PTO policy and commitment to work-life balance Professional development opportunities in a cutting-edge field at the intersection of AI and biology Profluent Bio, Inc is an equal opportunity employer promoting diversity and inclusion in the workspace. We do not discriminate on the basis of race, color, religion, marital status, age, national origin, ancestry, physical or mental disability, medical conditions, veteran status, sexual orientation, gender (including gender identity and gender expression), sex (which includes pregnancy, childbirth, and breastfeeding), genetic information, taking or requesting statutorily protected leave, or any other basis protected by law. Work Authorization Requirement Applicants must have ongoing work authorization in the United States that does not require employer sponsorship. Sponsorship