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 Merck (MSD), Chan Zuckerberg Biohub, Eli Lilly, Genentech, Xaira Therapeutics, 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
See our Bioinformatics Salary Guide for detailed compensation data across all locations.
Bioinformatics Scientist I
$110K - $145K
Median: $127K
Bioinformatics Scientist II
$140K - $180K
Median: $160K
Senior Bioinformatics Scientist
$175K - $230K
Median: $202K
Principal Bioinformatics Scientist
$210K - $280K
Median: $245K
Computational Biologist
$130K - $170K
Median: $150K
Machine Learning Scientist (Biology)
$160K - $220K
Median: $190K
Bioinformatics Engineer
$145K - $195K
Median: $170K
100 Bioinformatics Jobs in San Francisco
2027 Future Talent Program - Quantitative Biosciences, Cellular Pharmacology & Lead Discovery - Intern
Computational Biologist II, CellxState
2027 Future Talent Program - Quantitative Biosciences Cellular Pharmacology - Intern
Principal Machine Learning Scientist, Frontier Research, AI for Drug Discovery (AIDD)
Sr. Machine Learning Scientist, Foundation Models, AI for Drug Discovery
AI Scientist/Senior, Clinical & Molecular Genomics Modeling, BRAID
Associate Principal Scientist, Discovery Oncology, Reverse Translation
Associate Director - Computational Biology (Cardiovascular, Metabolic, Obesity and Related)
Senior Director of AI/ML Engineering – Head of Engineering for World Models
Senior Scientist II, Computational Pathology, Precision Medicine Pathology
Senior Scientific Software Engineer, Analytics and Workflows
Senior Machine Learning Scientist, Protein ML, AI for Drug Discovery (AIDD)
Senior/Principal Scientist, Computational Neuroscience, Computational Sciences Center of Excellence
Senior Machine Learning Engineer, Agentic Science/Generative Models, AI for Biology & Translation (AIBT)
Principal Scientist - Oligonucleotide Design and Chemistry
Executive Director, Research – Technology & Innovation for Inflammation Discovery
Postdoctoral Fellow- Machine Learning for Regulatory Genomics, Mostafavi Lab
Principal Scientist, Portfolio & gRED Interface-Biologics, AI for Drug Discovery (AIDD)
Principal Scientist, SOP & Workflow Automation Champion, AI for Drug Discovery (AIDD)
Senior Scientist, Antibody Developability/Biophysics & Portfolio Support, AI for Drug Discovery (AIDD)
Therapeutic Area Analytics & Insights Senior Manager - Cardiovascular, Renal, & Metabolism (CVRM)
Therapeutic Area Analytics & Insights Senior Manager - Ophthalmology
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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.