Note: The job is a remote job and is open to candidates in USA. Helix is hiring a Staff Bioinformatics Scientist, Clinical Applications to bridge genomic variants with clinically useful answers. The role develops and evaluates automated and AI/ML approaches for germline variant curation, connects genomic data to clinical reporting tools, and leads analytical validation for regulatory compliance.

Responsibilities

• 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

Skills

• 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
• Experience mentoring or managing others, or an interest in developing as a people leader

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

Company Overview

• Helix is a population genomics company that is working to advance genomics research and integrate genomic data into clinical care. It was founded in 2015, and is headquartered in San Mateo, California, USA, with a workforce of 201-500 employees. Its website is http://www.helix.com.

Company H1B Sponsorship

• Helix has a track record of offering H1B sponsorships, with 6 in 2026, 4 in 2025, 3 in 2024, 3 in 2023, 1 in 2022. Please note that this does not guarantee sponsorship for this specific role.