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 Rezo Therapeutics, Genentech, Amgen, Denali Therapeutics, Anthropic, 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
Principal Scientist, Integrated Computational and Experimental Inflammation Discovery
Scientist 3 - Translational Medicine (Ophthalmology- Glaucoma)
Principal Translational Scientist & Team Leader, Oncology Biomarkers & Translational Research
Senior Translational Scientist, Oncology Biomarkers & Translational Research
Senior Scientist, Analytical Development - Stem Cell & Metabolomics
Associate Director, Scientific Computing and AI Engineer
Sr. Data Expert, Data Engineer (Clinical & Multimodal Data Integration)
Scientist/Engineer, Machine Learning / Bioinformatics
Postdoctoral Fellow, Translational Genomics and Proteomics Center, Ye Lab
Machine Learning / Senior Machine Learning Scientist / Engineer
Machine Learning Scientist / Senior Machine Learning Scientist
Senior / Principal Scientist Lung Modeling, Complex in vitro Systems (CiS) Laboratory
Scientist 3- Translational Medicine (Multiple Sclerosis & TR focused)
Senior Machine Learning Scientist, Foundational ML, AI for Biology & Translation (AIBT)
Senior Principal Statistician, Early Development (Senior Director Level)
Principal Scientist, Translational Genomics and Proteomics Center
Scientist 3 Translational Medicine (Cardiovascular and Metabolism)
Senior/Principal Machine Learning Scientist, Perturbation Biology, AI Biology & Translation (AIBT)
Senior Scientist, Computational Biology (Multimodal Data Integration)
Senior/Principal Machine Learning Scientist, Structure and Simulation (AI for Drug Discovery)
Principal Scientist – Translational Medicine (Tumor/Epigenetic Signaling)
2026 Fall Intern - Frontier Research, Prescient Design (AI for Drug Discovery)
Postdoctoral Fellow, Computational Biology & Medicine/Neuroscience
AI Scientist/Senior, Clinical & Molecular Genomics Modeling, BRAID
Computational Scientist 3, Spatial Omics & Computational Pathology
Associate Director - Computational Biology (Cardiovascular, Metabolic, Obesity and Related)
Senior Scientist, Stem Cell Product Attribute Sciences (Allogeneic Cell Therapy)
Sr. Principal / Distinguished ML Scientist, Autonomous Science for Cell Biology
Senior / Principal Scientist, AI for Protein Engineering
ML Scientist I / II, Foundation Models for Life Sciences
Senior/ Principal Scientist, Synthetic Molecule Analytical Chemistry
Senior/Principal Scientist - Synthetic Molecule Analytical Chemistry, Genentech Research and Early Development
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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.