Bioinformatics Jobs in San Francisco
Where Tech Meets Biology - South San Francisco to Berkeley
Why Work in San Francisco?
The San Francisco Bay Area offers a unique blend of Silicon Valley tech culture and cutting-edge biotechnology. With major hubs in South San Francisco (biotech row), Emeryville, and Berkeley, the region is home to Genentech, UCSF, Berkeley, and hundreds of startups. The area excels in applying machine learning and AI to biological problems, making it ideal for computationally-minded scientists. Compensation packages often include significant equity, especially at startups.
Market Overview
- • Genentech (Roche) headquarters and massive bioinformatics team
- • Strong AI/ML in biology focus - ideal for computational scientists
- • UCSF and Berkeley provide world-class academic opportunities
- • South San Francisco 'biotech row' with 100+ companies
- • Tech-focused culture with generous equity compensation
- • Easy access to venture capital and startup funding
- • Growing computational pathology and precision medicine sectors
Top Biotech Companies in San Francisco
The San Francisco biotech ecosystem includes major companies like Genentech, Preventive, Achira, UCSF, Gladstone Institutes, and many emerging startups. Browse all companies →
Cost of Living
The Bay Area has the highest cost of living in the U.S., with median rent for a 1-bedroom apartment at $3,000-3,800/month in San Francisco proper, and $2,400-3,200 in South SF, Oakland, or Berkeley. Many bioinformatics professionals live in East Bay (Berkeley, Oakland) for affordability while commuting to South SF. Salaries are very high to compensate, and equity at startups can be life-changing.
Salary Ranges
Median posted minimum to median posted maximum for San Francisco postings that disclose annual pay in USD, by seniority. Levels with fewer than 6 such postings are not shown. See our Bioinformatics Salary Guide for national figures.
Mid level
$129K-$215K
59 postings · national $116K-$179K
Senior
$148K-$251K
59 postings · national $131K-$190K
Principal
$168K-$266K
53 postings · national $151K-$225K
Director
$204K-$285K
25 postings · national $178K-$269K
100 Bioinformatics Jobs in San Francisco
Vice President, Global Head of AI for Drug Discovery (AIDD)
ML Research Scientist (MLRS) - Representation Learning for Molecular AI
Machine Learning Research Engineer (MLRE) - Workflows/Systems
Scientist 3 Translational Medicine (Cardiovascular and Metabolism)
Senior Machine Learning Engineer, Agentic Science/Generative Models, AI for Biology & Translation (AIBT)
Associate Scientist, Postdoctoral Research Fellow - Translational Imaging
Senior Scientist Single Cell Assay and Technology Development
Principal Scientist, SOP & Workflow Automation Champion, AI for Drug Discovery (AIDD)
Machine Learning Scientist / Senior Machine Learning Scientist
Principal Scientist, Target Discovery & Portfolio Strategy
Senior Scientist, Computational Biology (Contractor)
Scientist /Senior Scientist, Multimodal & Relational Machine Learning Foundation Models
Senior Knowledge Engineer, Ontology and Data Standards (Contract)
Postdoctoral Fellow – Single-Cell Genomics & CRISPR Technology Development
Machine Learning Scientist/Senior Machine Learning Scientist - Synthesis Planning and Optimization, AI for Drug Discovery
Senior Machine Learning Scientist, Foundational ML, AI for Biology & Translation (AIBT)
Senior Principal Statistician, Early Development (Senior Director Level)
Machine Learning Scientist/Senior Machine Learning Scientist - Agents for Applied Small Molecule Drug Design, AI for Drug Discovery
Therapeutic Area Analytics & Insights Senior Manager - NI/AD/PD
Senior/Principal Machine Learning Scientist, Perturbation Biology, AI Biology & Translation (AIBT)
ML Scientist I / II, Foundation Models for Life Sciences
Scientist, Integrated Computational and Experimental Inflammation Discovery
Software Development Engineer/Senior Software Development Engineer, Agentic Systems, AI for Drug Discovery
2027 Future Talent Program - Quantitative Biosciences, Cellular Pharmacology & Lead Discovery - Intern
Principal Machine Learning Scientist, Frontier Research, AI for Drug Discovery (AIDD)
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Frequently Asked Questions
How does the Bay Area compare to Boston for bioinformatics?
The Bay Area offers higher base salaries and significant equity opportunities, especially at startups. It excels in AI/ML applications to biology and computational approaches. Boston has more traditional academic/pharma roles. Bay Area culture is more tech-focused, while Boston is more research-oriented. Both are top-tier markets.
What companies should I target in the Bay Area?
Top targets include Genentech/Roche (largest team), 10x Genomics, Invitae, Color Genomics, Natera, Tempus AI, GRAIL, Pacific Biosciences, and hundreds of AI-in-bio startups. UCSF and Berkeley offer academic positions. South SF biotech row has 100+ companies hiring.
Is equity compensation significant in Bay Area biotech?
Yes, especially at startups. Offers often include 0.1-1% equity for senior roles, which can be worth millions if the company succeeds. Even established companies like 10x Genomics offer RSUs. This is a key differentiator from Boston's more salary-focused compensation.
What's the commute like for bioinformatics jobs?
Most biotech companies are in South San Francisco, easily accessible via BART and Caltrain from SF, Oakland, and Berkeley. Traffic can be heavy for car commutes. Many companies offer shuttle services. Remote/hybrid work is common post-COVID, more so than Boston.
Is the Bay Area better for AI/ML in biology?
Absolutely. The Bay Area leads in applying deep learning, computer vision, and AI to biological problems. Companies like Insitro, Recursion Pharmaceuticals, and Freenome are headquartered here. The proximity to AI talent from Google, Meta, and OpenAI creates unique cross-pollination.