Staff Bioinformatics Engineer, Clinical Applications

Helix • United States - Remote,

3d • $161,500 - $219,625 • Remote

About The Position

Helix is hiring a Senior or Staff Bioinformatics Engineer, Clinical Applications, to help make genomics a standard of care. The role bridges genomic variants and clinical answers that help patients act on their DNA, partnering with scientists and product leaders to turn prototypes into production systems that scale. The engineer’s work will support the automation of gene and variant curation for real patients.

The role focuses on productionizing curation workflows that use classical and modern AI/ML approaches to variant classification, automating evidence integration, and ensuring software meets scientific and product requirements. The position may be filled at the Senior or Staff level, with scope and level determined based on the candidate’s experience, qualifications, and demonstrated scope. Senior-level engineers own defined projects and make technical decisions within established priorities and architecture. Staff-level engineers independently frame ambiguous problems, set technical direction, and make consequential architecture and prioritization decisions across the product area; people leadership may also be possible at Staff level.

The position involves working with production-quality Python, relational databases, cloud platforms such as AWS, AI/ML software and agentic systems, and bioinformatics/NGS tools and databases. Helix offers remote options for many roles and a home office stipend. Compensation includes a base salary of $161,500–$219,625, a discretionary annual bonus of 15% of annual salary, and equity.

Requirements

• Bachelor’s degree in Science or a related field and at least 7 years of professional software development experience for Senior level or 9 years for Staff level; alternatively, a Master’s or Ph.D. and at least 3 years for Senior level or 5 years for Staff level.
• 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 production.

Nice To Haves

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

Responsibilities

• Productionize curation workflows supporting classical and modern AI/ML approaches to variant classification.
• Automate evidence integration from sources such as ClinVar, gnomAD, and PubMed.
• Collaborate with scientists, product teams, and clinical stakeholders to ensure software solutions meet scientific and product requirements.
• Direct AI coding agents to accelerate development of curation pipelines, and 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 affecting broader systems.
• At Staff level, independently frame ambiguous problems, set technical direction, and make consequential architecture and prioritization decisions across the product area.
• At Staff level, potentially take on people leadership responsibilities.

Benefits

• Comprehensive health insurance with eligibility from date of hire and above-average employer-paid premium coverage.
• 12 weeks of Helix paid parental leave option.
• 401(k) with employer matching of up to 3% and 100% vesting on date of hire.
• Comprehensive well-being benefits.
• Flexible PTO.
• Remote options for many roles.
• Home office stipend.
• Discretionary annual bonus of 15% of annual salary.
• Equity.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior