Build and scale production bioinformatics systems that automate genomic variant curation and classification. Integrate evidence from ClinVar, gnomAD, PubMed, and other sources while applying classical and AI/ML approaches. Collaborate with scientists, product leaders, and clinical stakeholders to develop reliable, secure, maintainable pipelines. Staff-level responsibilities include framing ambiguous problems, setting technical direction, and making architecture and prioritization decisions across the product area.
Who We Are & What We Do
At Helix, our mission is simple: to help everyone improve their lives through their DNA.
Ready to make a real-world impact with your skills? At Helix, we're transforming healthcare by making genomics a standard of care. We partner with health systems and life science companies to accelerate the integration of genomic data into clinical practice. Join us in building a future where healthcare is personalized, proactive, and powered by genomics.
What is special about this role?
You'll bridge the gap between genomic variants and the clinical answers that help patients act on their DNA. You'll partner with scientists and product leaders to turn promising prototypes into production systems that scale. Your code will power how Helix automates gene and variant curation for real patients.
We have openings for both Senior and Staff level Engineers. You may apply at either level, and we’ll consider your experience, qualifications and demonstrated scope when determining the right level.
As a Senior/Staff Bioinformatics Engineer, Clinical Applications, you will:
- Productionize curation workflows that support both classical and modern AI/ML approaches to variant classification.
- Automate evidence integration from sources such as ClinVar, gnomAD, and PubMed.
- Collaborate closely with scientists, product, and clinical stakeholders to ensure software solutions meet scientific and product requirements.
- Direct AI coding agents to accelerate development of curation pipelines, applying engineering judgment to validate correctness, security, and architectural fit before deployment.
- At Senior level, own defined projects end to end, make technical decisions within agreed priorities and architecture, and raise trade-offs that affect broader systems.
- At Staff level, independently frame ambiguous problems, set technical direction, and make consequential architecture and prioritisation decisions across the product area.
About you:
- Bachelor's degree in Science or related field with 7+ years (Senior) or 9+ years (Staff) of professional software development experience. Or, a Master's or Ph.D. with 3+ years (Senior) or 5+ years (Staff) of professional software development experience.
- Advanced proficiency in production-quality Python, relational databases, and cloud platforms such as AWS.
- Experience productionizing and scaling AI/ML software, especially agentic systems built with frameworks such as LangChain or LangGraph.
- Experience collaborating with scientists to integrate bioinformatics/NGS tools and databases into production workflows.
- Strong judgment evaluating AI-generated code and pipeline logic for correctness, security, and maintainability before it reaches production.
Pluses:
- Experience in clinical genomics, such as ACMG guidelines, clinical diagnostics, or Human Phenotype Ontology (HPO) terms.
- Experience developing regulated software, such as software as a medical device.
- At Staff level, the role may have the opportunity to take on people leadership responsibilities. Experience mentoring or managing others, or an interest in developing as a people leader, is a plus.
Expected Interview Process:
1) Recruiter Screen 2) Manager Screen/Tech Screen 3) Onsite 4) Offer
Expected Pay For This Role:
There are 3 distinct parts to your Helix offer: 1) Base Salary 2) Annual Bonus 3) Equity
- Expected Helix Base: $161,500 - $219,625 (Staff)
- Expected Helix Base: 134,000 - $179,000 (Senior)
- Expected Helix Discretionary Annual Bonus: 15% (Staff)/ 10% (Senior)of your annual salary
- Equity: We offer generous equity at Helix. If you receive a Helix offer your recruiter will book dedicated time with you to educate you on our equity model.
Aside from working alongside brilliant, dedicated, passionate, down-to-earth, curious, warm, and thoughtful people, we also provide great benefits:
- Comprehensive Health Insurance with Date of Hire eligibility
- Above average employer paid premium coverage
- 12 weeks Helix Paid Parental Leave option
- 401(k) with employer matching of up to 3% and 100% Vesting on the Date of Hire
- Comprehensive Well-Being Benefits
- Flexible PTO
- Remote options for many roles and a home office stipend
What To Expect During Your First 90 days:
- First 30 days: you’ll spend time learning the Helix way, completing training and onboarding for your roles, and getting introduced to your team and relevant stakeholders. You’ll also gain a deeper understanding of our customers, our products, the impact we make in the lives of our communities, and how to thrive at Helix through participation in Helix U.
- Day 30 - 60: you’ll spend time contributing to projects, deeply familiarizing yourself with team and company processes, and developing a deeper understanding of Helix’s products, services and capabilities.
- Day 60 - 90: you’ll build your OKRs with your manager, start to take ownership of projects and initiatives on your team, and begin to demonstrate your impact on the Helix mission.
To learn how Helix collects, uses, and protects your personal information during the recruitment process, please review our Privacy Notice.
Helix is proud to be an equal opportunity employer, and committed to providing employment opportunities regardless of race, religious creed, color, national origin, ancestry, physical disability, mental disability, medical condition, genetic information, marital status, sex, gender, gender identity, gender expression, pregnancy, childbirth and breastfeeding, age, sexual orientation, military or veteran status, or any other protected classification, in accordance with applicable federal, state, and local laws.
#LI-Remote
CompensationThe base pay range for this role is $134,000 – $219,000 per year.
Helix San Mateo, California, USA Office
101 S Ellsworth Ave #350, San Mateo, CA, United States, 94401
Similar Jobs
Beauty • Robotics • Design • Appliances • Manufacturing
Leads global, full-funnel media strategy and activation for Shark Home across North America and international markets. Owns media budgets, develops launch and category campaigns, optimizes investments using audience analytics and media mix modeling, and manages agency partnerships. Partners with Brand, Creative, Social, PR, Sales, and CX teams while driving media innovation, transformation, team leadership, and executive-level performance reporting.
Top Skills:
DspsGoogle AnalyticsMedia Mix ModelingMeta Ads
Artificial Intelligence • Fintech • Insurance • Marketing Tech • Software • Analytics
Handle inbound calls and warm leads, consult customers on insurance needs, recommend appropriate Property and Casualty coverages, and convert prospects into policyholders. The role includes paid licensing and sales training, customer communication, persuasion, remote work, and schedule flexibility across weekdays and weekends. Employees must obtain a Property and Casualty insurance license and maintain a dedicated home workspace with high-speed wired internet.
Top Skills:
High-Speed Wired InternetPc
Artificial Intelligence • Fintech • Insurance • Marketing Tech • Software • Analytics
Handle inbound calls and warm leads, consult customers on insurance needs, recommend appropriate coverages, and convert prospects into policyholders. The role provides paid training and Property and Casualty licensing, with no cold calling. Representatives must work a four-weekday and one-weekend schedule, meet remote workspace and internet requirements, and remain in their resident state for at least one year.
Top Skills:
PcWired High-Speed Internet
What you need to know about the San Francisco Tech Scene
San Francisco and the surrounding Bay Area attracts more startup funding than any other region in the world. Home to Stanford University and UC Berkeley, leading VC firms and several of the world’s most valuable companies, the Bay Area is the place to go for anyone looking to make it big in the tech industry. That said, San Francisco has a lot to offer beyond technology thanks to a thriving art and music scene, excellent food and a short drive to several of the country’s most beautiful recreational areas.
Key Facts About San Francisco Tech
- Number of Tech Workers: 365,500; 13.9% of overall workforce (2024 CompTIA survey)
- Major Tech Employers: Google, Apple, Salesforce, Meta
- Key Industries: Artificial intelligence, cloud computing, fintech, consumer technology, software
- Funding Landscape: $50.5 billion in venture capital funding in 2024 (Pitchbook)
- Notable Investors: Sequoia Capital, Andreessen Horowitz, Bessemer Venture Partners, Greylock Partners, Khosla Ventures, Kleiner Perkins
- Research Centers and Universities: Stanford University; University of California, Berkeley; University of San Francisco; Santa Clara University; Ames Research Center; Center for AI Safety; California Institute for Regenerative Medicine
