Staff Bioinformatics Scientist, Clinical Applications

Location: United States - Remote

Department: Bioinformatics

Location Type: REMOTE

Employment Type: FULL_TIME

• 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.

• 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.

• 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 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.

• 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 

• 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.