Staff Bioinformatics Engineer, Clinical Applications

Helix; United States; Remote; USD 134,000 - 179,000; Full time

Benefits offered by this job

Health insurance

Parental leave

401(k) matching

Well-being benefits

Flexible PTO

Remote work options

Job summary

Helix is transforming healthcare by making genomics a standard of care. We are seeking Senior/Staff Bioinformatics Engineers to productionize curation workflows and automate evidence integration from ClinVar, gnomAD, and PubMed.

You will work with scientists and product leaders to scale AI/ML–driven variant curation and guide architecture decisions across the stack. Ideal candidates have 7+ years (Senior) or 9+ years (Staff) of software development, strong Python and AWS skills, and experience

Qualifications

• Production-quality Python, relational databases and AWS cloud platforms.
• Experience productionizing and scaling AI/ML software, especially agentic systems.
• Experience collaborating with scientists to integrate bioinformatics/NGS tools into workflows.
• Strong judgment evaluating AI-generated code and pipeline logic for production readiness.

Responsibilities

• Productionize curation workflows for variant classification.
• Automate evidence integration from ClinVar, gnomAD and PubMed.
• Collaborate with scientists, product and clinical stakeholders to meet requirements.
• Direct AI coding agents to accelerate pipeline development with emphasis on correctness and security.

Skills

Python

AWS

Relational databases

AI/ML

LangChain/LangGraph

Bioinformatics collaboration

Education

Bachelor's degree in Science or related field

Master's or Ph.D. in related field

Tools

LangChain

LangGraph

ClinVar

gnomAD

PubMed

Job description

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 partner with scientists and product leaders to turn promising prototypes into production systems that scale. Your code will power how Helix automates gene and variant curation for real patients. We have openings for both Senior and Staff level Engineers. You may apply at either level, and we’ll consider your experience, qualifications and demonstrated scope when determining the right level.

As a Senior/Staff Bioinformatics Engineer, Clinical Applications, you will:

• Productionize curation workflows that support both classical and modern AI/ML approaches to variant classification.
• Automate evidence integration from sources such as ClinVar, gnomAD, and PubMed.
• Collaborate closely with scientists, product, and clinical stakeholders to ensure software solutions meet scientific and product requirements.
• Direct AI coding agents to accelerate development of curation pipelines, applying engineering judgment to 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 that affect broader systems.
• At Staff level, independently frame ambiguous problems, set technical direction, and make consequential architecture and prioritisation decisions across the product area.

About you:

• Bachelor's degree in Science or related field with 7+ years (Senior) or 9+ years (Staff) of professional software development experience. Or, a Master's or Ph.D. with 3+ years (Senior) or 5+ years (Staff) of professional software development experience.
• 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 it reaches production.

Pluses:

• 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, the role may have the opportunity to take on people leadership responsibilities. 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: $161,500 - $219,625
• 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 ourPrivacy Notice (https://www.helix.com/privacy-policy).

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.

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Compensation

The base pay range for this role is $134,000 – $179,000 per year.