Staff Bioinformatics Scientist, Clinical Applications
About The Position
Helix is seeking a Staff Bioinformatics Scientist, Clinical Applications, to help connect genomic variants with clinically useful answers and support the integration of genomics into healthcare. The role will serve as a scientific authority on automation and AI for gene and variant curation, working closely with product, clinical, and engineering leaders. The position focuses on designing and prototyping automated approaches for annotation, evidence synthesis, and pre-classification of germline variants; evaluating AI/ML methods for production pipelines; and monitoring their performance against real-world outcomes. The scientist will collaborate with engineers on APIs and data interfaces connecting secondary NGS outputs to internal clinical reporting tools, and lead analytical validation studies supporting CLIA/CAP compliance and LDT filings. The expected first 90 days include onboarding and training, contributing to projects and learning company processes, then developing OKRs with a manager and taking ownership of team projects and initiatives.
Requirements
- Ph.D. in Bioinformatics, Computational Biology, Human Genetics, or a related field.
- At least 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.
- Skill communicating technical tradeoffs to non-technical and cross-functional stakeholders.
- Strong judgment in evaluating AI-generated analyses and recommendations for scientific validity and regulatory defensibility.
Nice To Haves
- Experience in a regulated environment, such as under CLIA/CAP or FDA.
- Experience building production-quality software.
- Experience mentoring or managing others, or interest in developing as a people leader.
Responsibilities
- Design and prototype automated approaches to annotation, evidence synthesis, and pre-classification of germline variants for clinical applications at scale.
- Evaluate and integrate AI/ML approaches, including literature evidence extraction, disease-to-gene mapping, and application of ACMG/AMP evidence guidelines, into production pipelines.
- Monitor and benchmark automated pipeline performance against real-world outcomes, such as ClinVar reclassifications.
- Work cross-functionally with engineers to build APIs and data interfaces connecting 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.
- Communicate technical tradeoffs to non-technical and cross-functional stakeholders.
- Evaluate AI-generated analyses and recommendations for scientific validity and regulatory defensibility before they inform clinical decisions in production.
Benefits
- Comprehensive health insurance with eligibility from date of hire and above-average employer-paid premium coverage.
- 12 weeks of Helix paid parental leave.
- 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.
- Annual discretionary bonus of 15% of annual salary.
- Equity.
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What This Job Offers
Job Type
Full-time
Career Level
Senior
Education Level
Ph.D. or professional degree
