Staff Bioinformatics Scientist, Clinical Applications

Helix; California; Remote; USD 146,000 - 196,000; Full time

Benefits offered by this job

Comprehensive Health Insurance with DQ

Above average employer-paid premium

12 weeks Helix Paid Parental Leave

401(k) with employer matching up to 3%

100% Vesting on Date of Hire

Comprehensive Well-Being Benefits

Flexible PTO

Remote options for many roles

Job summary

Helix is seeking a Staff Bioinformatics Scientist to bridge genomic variants and clinical answers, acting as the scientific authority on automation and AI for gene and variant curation. You will collaborate with product, clinical, and engineering leaders driving genomic medicine forward.

The role emphasizes design of automated annotation, integration of AI/ML, and conducting validation studies to support CLIA/CAP compliance and LDT filings, with cross-functional API work and scalable pipelines.

Qualifications

• 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.

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

Bioinformatics

Genomics

ACMG/AMP guidelines

SQL

Python

Communication

Education

Ph.D. in Bioinformatics/Computational Biology/Related field

Tools

SQL

Python

Job description

Who We Are & What We Do

At Helix, our mission is simple: to help everyone improve their lives through their DNA.

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 serve as the scientific authority on automation and AI for gene and variant curation. You’ll work closely with product, clinical, and engineering leaders who are pushing genomic medicine forward.

As a Staff Bioinformatics Scientist, Clinical Applications, You Will

• 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.

About You

• 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.

Pluses

• 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 Interview Process

• 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: $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.

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 our Privacy Notice.

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.

Compensation

The base pay range for this role is $146,000 – $196,250 per year.