Lead Scientist / Associate Director, Bioinformatics and Data Science

Profluent Bio; Emeryville (CA); On-site; USD 205,000 - 246,000; Full time

Benefits offered by this job

Equity participation

401(k) with employer match

Health/dental/vision insurance

Generous PTO

Professional development

High-growth opportunity

Job summary

Profluent Bio in Emeryville, CA seeks a senior computational scientist to lead the design, development, and operation of an NGS analysis platform powering gene editing and therapeutic programs.

You will guide interdisciplinary teams, translate sequencing data into biological insights, and establish reproducible analytic practices while mentoring a growing bioinformatics group. This is a leadership role at the frontier of AI and biology.

Qualifications

• PhD or MS in Bioinformatics, Computational Biology, Computer Science, or a related quantitative field.
• 5+ years (PhD) or 7+ years (MS) of industry experience applying NGS and computational analysis to gene/cell therapy.
• Deep expertise in design, analysis, and interpretation of high-throughput sequencing assays.
• Strong Python programming and quantitative analysis skills.
• Experience partnering with experimental scientists to guide assay design and follow-up studies.
• Demonstrated scientific leadership and mentoring experience.

Responsibilities

• Lead development and operation of the NGS analysis platform for gene editing and therapeutic programs.
• Develop scalable pipelines and analytical methods for new sequencing assays.
• Partner with wet-lab teams to design, test, troubleshoot, and validate new assays.
• Lead computational characterization of on-target activity, specificity and off-target effects.
• Translate sequencing data into actionable insights and program decisions.
• Collaborate to curate high-quality datasets for model training and evaluation.
• Establish rigorous, reproducible practices for validation, testing, and documentation.
• Recruit, mentor, and develop a high-performing bioinformatics and data science team.

Skills

Python

Data interpretation

Scientific leadership

Education

PhD or MS in Bioinformatics/Computational Biology/CS

Tools

Benchling

SQL

Job description

Profluent is the frontier AI lab for biology. Profluent builds powerful foundation models for all of life's molecules, unlocking solutions that transform medicine, agriculture, and beyond. Founded in 2022 and headquartered in Emeryville, CA, Profluent is backed by leading investors including Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, and Convergent Ventures and has 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, protein design, and therapeutic 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.

This is a high-impact leadership role at the intersection of computational biology, experimental science, and software engineering. You’ll define how Profluent characterizes the activity and specificity of novel gene editors, establish rigorous and reproducible practices across bioinformatics and data science, and mentor and grow a team as our platform and therapeutic programs scale.

Responsibilities

• Lead the development and operation of Profluent’s NGS analysis platform for gene editing, protein design, and therapeutic programs
• Develop scalable pipelines and analytical methods for new sequencing assays
• Partner with wet-lab teams to design, test, troubleshoot, and validate new assays
• Lead computational characterization of gene-editor on-target activity, specificity, and off-target effects
• Translate sequencing data into clear biological insights, program decisions, and regulatory-ready analyses
• Collaborate with computational teams to curate high-quality datasets for model training and evaluation
• Establish rigorous, reproducible practices for analytical validation, testing, documentation, and code review
• Recruit, mentor, and develop a high-performing bioinformatics and data science team

Qualifications

• PhD or MS in Bioinformatics, Computational Biology, Computer Science, or a related quantitative field
• PhD with 5+ years or MS with 7+ years of industry experience applying NGS and computational analysis to gene or cell therapy development
• Deep expertise in the design, analysis, and interpretation of high-throughput sequencing assays
• Strong programming and quantitative analysis skills, particularly in Python
• Proven ability to translate complex sequencing data into clear biological insights and program decisions
• Experience partnering closely with experimental scientists to guide assay design, troubleshoot results, and define follow-up studies
• Demonstrated scientific leadership, including setting analytical strategy, leading complex cross-functional projects, and mentoring computational scientists
• Experience developing scalable, reproducible, and well-validated computational workflows

Preferences

• Experience with CRISPR-based gene editing data and analysis
• 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 and 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

$205,379 — $245,632 USD