Lead Bioinformatician (cfDNA Algorithms and Pipelines)

About the role

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 focused on pulling reliable signals out of ambiguous sequencing data, particularly in low fraction (fetal, donor cfDNA) samples. You will build methodological foundations and implement algorithms for detecting variants (SNVs, Indels, CNVs, SVs) that are challenging to call accurately.

Responsibilities

• Panel and Assay Science: Provide genomics algorithm insights for our expanded panel roadmap, including gene selection rationale. Collaborate with Product, Laboratory Directors, and Research to define approaches for analytically difficult genes and assay edge cases, balancing scientific defensibility with technical feasibility.
• Caller Strategy and Method Development: Define computational strategies for new targeted and special-purpose callers. Decide when to develop new callers versus extending existing methods. Prototype and benchmark new methods, and work with engineering teams to deploy them into production.
• Scientific Investigation and Escalation: Serve as a genomics consultant for complex production escalations, distinguishing biological causes from analytical or pipeline issues. Turn one-off investigations into durable rules and design changes to reduce repeat work.
• Data Quality and Cross-functional Partnership: Act as the bioinformatics liaison with Variant Management, Reporting, and Laboratory Operations on data quality, variant representation, and system integration. Provide scientific rationale for Quality and Laboratory functions to assess method readiness for deployment.
• Ways of Working: Help define standards for AI-assisted scientific investigation, including when human sign-off is required for region-level findings.

What Success Looks Like After a Year

• Contributed to the scientific and bioinformatics rationale of product roadmaps.
• Established and utilized deployment-readiness criteria for new analysis methods, with at least one new or extended caller contributed.
• Proactively taken on bioinformatics aspects of complex production investigations.
• Recognized as a go-to resource for genomics questions about Natera’s assays across teams.

Qualifications

• Degree in Bioinformatics, Computational Biology, Human Genetics, or a related field. Equivalent work experience is fully considered.
• 4+ years of experience analyzing short-read sequencing data for screening or diagnostic applications, preferably in a regulated, accredited, or production-adjacent setting. Relevant experience is counted from the point your work became substantially independent.
• Experience contributing to the bioinformatics workflows behind a sequencing assay or panel.
• Experience resolving complex investigations across biological, analytical, and systems-level causes.

Skills and Abilities

• Experience developing, validating, or benchmarking bioinformatics methods (e.g., SNVs, CNVs, SVs), particularly for analytically difficult regions.
• Proficiency in Python with demonstrated experience prototyping bioinformatics tools or callers.
• Human genetics expertise to contribute to panel design, including variant spectrum, population frequency, and accuracy trade-offs.
• Familiarity with identifying regions where short reads cannot be placed confidently (e.g., homologous sequences, pseudogenes, low-complexity/repeat regions, copy-number-heavy regions).
• Experience contributing to study designs or performance criteria for bioinformatics analysis methods.
• Direct experience with non-invasive prenatal, reproductive, or carrier screening (preferred).
• Experience with cfDNA or applications where target molecules are a minority of sequenced data.
• Experience developing algorithms for 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.

Pay

Remote USA: $130,900—$163,600 USD. Actual compensation is based on factors unique to each candidate, including skill set, experience, certifications, and location.

Benefits

• Comprehensive medical, dental, vision, life, and disability plans for eligible employees and dependents.
• Free genetic testing for employees and their immediate families, including fertility care benefits.
• Pregnancy and baby bonding leave.
• 401k benefits and commuter benefits.
• Generous employee referral program.

About Natera

Natera™ is a global leader in cell-free DNA (cfDNA) testing, dedicated to oncology, women’s health, and organ health. Our mission is to make personalized genetic testing and diagnostics part of the standard of care to enable earlier and more targeted interventions. The Natera team consists of highly dedicated professionals from world-class institutions, working collaboratively to change the landscape of genetic disease management.