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.

Responsibilities

Advance the algorithmic foundations of diagnostic assays supporting Women's and Organ health; Build methodological foundations and implement algorithms for detecting variants (SNVs, Indels, CNVs, SVs) that are hard to call accurately in low fraction (fetal, donor cfDNA) samples; Panel and Assay Science: Provide genomics algorithm insights to expanded panel roadmap and help define approach for analytically difficult genes and assay edge cases; Caller Strategy and Method Development: Define computational strategy for new targeted and special-purpose callers, prototype and benchmark new methods, and work with engineering team to get methods into production; Scientific Investigation and Escalation: Serve as genomics consultant on complex production escalations, separating biological causes from analytical and pipeline ones, and turn one-off investigations into durable rules and design changes; 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; Ways of Working: Help define what correct looks like for AI-assisted scientific investigation

Requirements

Degree in Bioinformatics, Computational Biology, Human Genetics, or a related field (Ph.D. or M.S. not required; equivalent depth counts fully); 4+ years analyzing short-read sequencing data for screening or diagnostic applications, preferably in a regulated, accredited, or production-adjacent setting; 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; 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

Nice to 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

Benefits

Comprehensive medical, dental, vision, life and disability plans; Free testing for employees and their immediate families; Fertility care benefits; Pregnancy and baby bonding leave; 401k benefits; Commuter benefits; Employee referral program