Lead Bioinformatics Scientist, NGS

Profluent Bio; Emeryville (CA); On-site; USD 160,000 - 230,000; Full time

Benefits offered by this job

Competitive compensation package with equity

401(k) with employer match

Comprehensive health/dental/vision insurance

Generous PTO policy

Professional development opportunities

Job summary

Profluent Bio in Emeryville, CA is seeking an experienced computational scientist to lead the design and development of NGS analysis platforms for gene editing and protein design. This role involves collaboration with experimental biology and ML teams to extract actionable insights from large-scale sequencing data.

With a focus on mentoring and defining analytical strategies, you'll have a significant impact on Profluent's evolving computational biology capabilities, product development, and innovation.

Qualifications

• 5+ years of experience analyzing NGS datasets.
• Strong programming skills in Python.
• Deep understanding of Linux and software engineering best practices.

Responsibilities

• Lead design and implementation of scalable NGS analysis pipelines.
• Develop visualizations and reports to communicate sequencing results.
• Manage cloud-based compute environments and data systems.

Skills

Python (pandas, numpy, biopython)

NGS dataset analysis

Workflow orchestration tools (Nextflow, Snakemake)

Cloud environments (GCP, AWS)

Containerization (Docker, Kubernetes)

Linux

Git-based version control

Software engineering best practices

Education

PhD or MS in Bioinformatics, Computational Biology, or related field

Job description

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 will not be provided now or at any time in the future for this position.

Employment Eligibility Verification

Legal authorization to work in the United States is required. In compliance with federal law, all persons hired must verify their identity and work eligibility and complete the required employment verification form upon hire.

Hiring Salary Range

$160,000—$230,000 USD