Lead Bioinformatician (cfDNA Algorithms and Pipelines)

Natera; San Carlos (CA); On-site; USD 144,000 - 180,000; Full time

Benefits offered by this job

Annual incentive bonus

Long-term equity awards

401(k) with match

Generous paid time off

Wellness and work-life benefits

Job summary

Natera is seeking a Lead Bioinformatician to advance algorithmic foundations for cfDNA diagnostics. This individual contributor role focuses on developing scalable, clinically impactful computational tools for detecting variants in low-fraction samples.

You will shape analytic strategy, prototype and benchmark methods, and collaborate with Product, Laboratory Directors, and Research to deploy robust solutions in production.

Qualifications

• Degree in Bioinformatics, Computational Biology, Bioinformatics, Human Genetics, or related field; no MS/PhD required if depth is demonstrated.
• 4+ years analyzing short-read sequencing data for screening or diagnostic use in regulated environments.
• Experience contributing to bioinformatics workflows behind a sequencing assay or panel.
• Ability to resolve complex investigations across biological, analytical, and systems levels.

Responsibilities

• Panel and Assay Science: advise on genes for the panel roadmap and analytical edge cases.
• Caller Strategy and Method Development: define and benchmark new callers and productionize methods.
• Scientific Investigation and Escalation: distinguish biological vs analytical causes in escalations.
• Data Quality and Cross-functional Partnership: liaise with VMR and Lab Ops on data quality and variant representation.
• Ways of Working: define acceptable AI-assisted conclusions with appropriate human sign-off.

Skills

Python programming

Algorithm development

Genomics analysis

Cross-functional communication

Data interpretation

Education

Degree in Bioinformatics or related field

Tools

Python (pandas/numpy)

Job description

Lead Bioinformatician (cfDNA Algorithms and Pipelines)

Natera is seeking a Lead Bioinformatician to advance the algorithmic foundations of our diagnostic assays supporting Women’s and Organ health. This is an individual contributor role. You will bring the genomics expertise the team needs to pull reliable signals out of sequencing data that is often ambiguous.

You will build the methodological foundations and implement the algorithms needed for detecting variants (SNVs, Indels, CNVs, SVs) that are hard to call accurately in low fraction (fetal, donor cfDNA) samples. The ideal candidate will have deep experience in algorithmic genomics, strong programming skills, and a passion for developing scalable, clinically impactful computational tools.

Primary Responsibilities:

Panel and Assay Science: Provide genomics algorithm insights to our expanded panel roadmap, including which genes are worth considering and why, working with Product, the Laboratory Directors, and Research, who own that decision jointly. Help define the approach for analytically difficult genes and assay edge cases, and weigh what is scientifically defensible against what is technically possible.

Caller Strategy and Method Development: Define the computational strategy for new targeted and special-purpose callers. Help decide when a new caller is justified and when an existing method should be extended instead. Prototype and benchmark new methods, and work with the engineering team to get methods into production.

Scientific Investigation and Escalation: Serve as a genomics consultant on complex production escalations, separating biological causes from analytical and pipeline ones. Recognize when a result looks suspicious because of where the reads came from and not because the analysis went wrong. Turn one-off investigations into durable rules and design changes that reduce repeat work.

Data Quality and Cross-functional Partnership: Act as bioinformatics liaison with Variant Management, Reporting, and Laboratory Operations on data quality, variant representation, and system integration. Provide the scientific rationale that the accountable Quality and Laboratory functions rely on when they decide a method is ready to deploy.

Ways of Working: Help define what correct looks like for AI-assisted scientific investigation, for example what an agent may and may not conclude from a region-level finding without a human signing off. We do not screen for prior experience with these tools, and many strong candidates come from environments where they were restricted; we provide the tooling and the ramp time.

What success looks like after a year:

• Contributed to the scientific and bioinformatics rationale of product roadmaps.
• Deployment-readiness criteria for new analysis methods exist and are in use, and you have contributed to at least one new or extended caller yourself.
• You take on the bioinformatics aspects inside complex production investigations without waiting to be assigned them.
• Other groups know they can bring genomics questions about our assays to you.

Qualifications:

• Degree in Bioinformatics, Computational Biology, Bioinformatics, Human Genetics, or a related field. We do not require a Ph.D. or M.S.: equivalent depth built through work counts fully.
• 4+ years analyzing short-read sequencing data for screening or diagnostic applications, preferably in a regulated, accredited, or production-adjacent setting. We count relevant experience from the point your work became substantially independent, however you got there.
• Experience contributing to the bioinformatics workflows behind a sequencing assay or panel.
• Experience seeing a complex investigation through to resolution across biological, analytical, and systems-level causes.

Knowledge, Skills, and Abilities:

What we are screening for

• Experience developing, validating, or benchmarking bioinformatics methods (e.g. SNVs, CNVs, SVs), particularly for analytically difficult regions.
• Proficient in Python with demonstrated experience prototyping bioinformatics tools or callers.
• Enough human genetics depth to contribute to the panel design: variant spectrum, population frequency, and where compromises on accuracy can (and cannot) be made.
• Familiarity with identifying regions where short reads cannot be placed with confidence: homologous sequence and pseudogenes, low-complexity and repeat structure, and copy-number-heavy regions.
• Experience contributing to study designs or performance criteria for a bioinformatics analysis method.

Strong candidates may also have

• Direct non-invasive prenatal, reproductive, or carrier screening experience.
• Experience with cfDNA, or with another application where the molecules you care about are a small minority of what was sequenced.
• Experience developing algorithms for both short-read and long-read sequencing platforms (e.g., Illumina, ONT, PacBio).
• Cross-functional credibility with genetic counseling, variant management, reporting, and production-adjacent groups.
• Experience in an accredited or high-complexity laboratory, or familiarity with production support or escalation processes.

Compensation & Total Rewards

This range reflects a good-faith estimate of the base pay we reasonablyexpect to offer at the time of hire. Final compensation will vary based on experience, qualifications, and internal equity considerations.

This position is also eligible for additional compensation and benefits through Natera’s robust Total Rewards program, including:

• Annual performance incentive bonus
• Long-term equity awards
• 401(k) with company match
• Generous paid time off and company holidays
• Additional wellness and work-life benefits

Compensation Range

$144,000 - $180,000 USD

OUR OPPORTUNITY

Natera™ is a global leader in cell-free DNA (cfDNA) testing, dedicated to oncology, women’s health, and organ health. Our aim is to make personalized genetic testing and diagnostics part of the standard of care to protect health and enable earlier and more targeted interventions that lead to longer, healthier lives.

The Natera team consists of highly dedicated statisticians, geneticists, doctors, laboratory scientists, business professionals, software engineers and many other professionals from world-class institutions, who care deeply for our work and each other. When you join Natera, you’ll work hard and grow quickly. Working alongside the elite of the industry, you’ll be stretched and challenged, and take pride in being part of a company that is changing the landscape of genetic disease management.

WHAT WE OFFER

Competitive Benefits - Employee benefits include comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents. Additionally, Natera employees and their immediate families receive free testing in addition to fertility care benefits. Other benefits include pregnancy and baby bonding leave, 401k benefits, commuter benefits and much more. We also offer a generous employee referral program!

Natera is proud to be an Equal Opportunity Employer. We are committed to ensuring a diverse and inclusive workplace environment, and welcome people of different backgrounds, experiences, abilities and perspectives. Inclusive collaboration benefits our employees, our community and our patients, and is critical to our mission of changing the management of disease worldwide.

All qualified applicants are encouraged to apply, and will be considered without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, age, veteran status, disability or any other legally protected status. We also consider qualified applicants regardless of criminal histories, consistent with applicable laws.

If you are based in California, we encourage you to read this important information for California residents.