The Role
Design and validate automated bioinformatics and AI/ML approaches for germline variant annotation, evidence synthesis, and clinical classification. Integrate genomic data with clinical reporting systems, benchmark pipeline performance, and lead analytical validation supporting CLIA/CAP compliance and LDT filings. The role requires expertise in human genetics, ACMG/AMP guidelines, ClinVar, gnomAD, VCF, Python, and SQL, along with the ability to assess AI-generated analyses for scientific and regulatory validity.
Summary Generated by Built In
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 serve as the scientific authority on automation and AI for gene and variant curation. You'll work closely with product, clinical, and engineering leaders who are pushing genomic medicine forward.
As a Staff Bioinformatics Scientist, Clinical Applications, you will:
- Design and prototype automated approaches to annotation, evidence synthesis, and pre-classification of germline variants that can support clinical applications at scale.
- Evaluate and integrate AI/ML approaches, such as evidence extraction from literature, disease-to-gene mapping, and application of ACMG/AMP evidence guidelines, into production pipelines.
- Monitor and benchmark the performance of automated pipelines against real-world outcomes, such as ClinVar reclassifications, over time.
- Work cross-functionally with engineers to build APIs and data interfaces that connect secondary NGS outputs, such as VCFs and structural variant calls, to internal clinical reporting tools.
- Lead analytical validation studies, evaluating sensitivity, specificity, and reproducibility, to support CLIA/CAP compliance and LDT filings.
About you:
- Ph.D. in Bioinformatics, Computational Biology, Human Genetics, or a related field with 5+ years of clinical genomics industry experience.
- Deep expertise in human molecular genetics, ACMG/AMP variant interpretation guidelines, and clinical databases such as ClinVar and gnomAD.
- Advanced proficiency in genetic file formats, especially VCF, and data science tools such as SQL and Python.
- Demonstrated ability to evaluate emerging technical approaches, such as ML, LLMs, and novel bioinformatics methods, for feasibility and impact.
- Skilled at communicating technical tradeoffs to non-technical and cross-functional stakeholders.
- Strong judgment evaluating AI-generated analyses and recommendations for scientific validity and regulatory defensibility before they inform clinical decisions in production.
Pluses:
- Experience in a regulated environment, such as under CLIA/CAP or FDA.
- Experience building production-quality software.
- This role may have the opportunity to take on people leadership responsibilities in the future. 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: $146,000 - $196,250
- Expected Helix Discretionary Annual Bonus: 15% 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 $146,000 – $196,250 per year.
Skills Required
- Ph.D. in Bioinformatics, Computational Biology, Human Genetics, or a related field
- 5+ years of clinical genomics industry experience
- Deep expertise in human molecular genetics and ACMG/AMP variant interpretation guidelines
- Experience with clinical databases including ClinVar and gnomAD
- Advanced proficiency with genetic file formats, especially VCF
- Advanced proficiency with SQL and Python
- Ability to evaluate machine learning, LLM, and novel bioinformatics approaches
- Ability to communicate technical tradeoffs to non-technical and cross-functional stakeholders
- Strong judgment evaluating AI-generated analyses for scientific validity and regulatory defensibility
- Experience in a regulated environment such as CLIA, CAP, or FDA
- Experience building production-quality software
- Experience mentoring or managing others, or interest in developing as a people leader
Helix Compensation & Benefits Highlights
The following summarizes recurring compensation and benefits themes identified from responses generated by popular LLMs to common candidate questions about Helix and has not been reviewed or approved by Helix.
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Leave & Time Off Breadth — Feedback suggests generous PTO, flexible time away, unlimited vacation, paid sick days, and paid parental leave support work–life balance. These policies are frequently highlighted alongside flexible scheduling.
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Healthcare Strength — Feedback suggests medical, dental, and vision coverage are complemented by a wellness program. Access to health-focused initiatives contributes to a comprehensive core benefits package.
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Wellbeing & Lifestyle Benefits — Feedback suggests commuter benefits, free daily meals, and onsite parking enhance day‑to‑day experience. Such perks, combined with flexible work arrangements, add lifestyle value beyond base pay.
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The Company
What We Do
Helix is a rapidly growing startup focused on personal genomics. Helix has a simple but powerful mission: to empower every person to improve their life through DNA. We’re creating an ecosystem where people can explore diverse and uniquely personalized applications provided by high-quality partners.
Why Work With Us
We are collaborators—scientists, engineers, designers, marketers, and more—working across four offices to solve complex challenges locked within the human genome. We are biased toward action as we strive to uphold integrity in sequencing, science, and communication. At Helix, transparency, collaboration, and empowerment drive us in all that we do.
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