Lead Bioinformatics & Machine Learning Scientist (Epigenomics)

Natera is currently seeking a Lead Bioinformatics & Machine Learning Scientist to contribute to research and development within our Bioinformatics Research and Development team, focused on Epigenomics in Oncology. The team develops machine learning methods for early cancer detection from cell-free DNA methylation data. The ideal candidate will have a strong background in machine learning and statistical modeling, as well as genomics and sequencing data analysis. The successful candidate will be instrumental in developing and expanding state-of-the-art machine learning methods for early detection of cancer, and will provide technical leadership and mentorship within a highly collaborative team. PRIMARY RESPONSIBILITIES: • Drive technical workstreams within a collaborative team that takes methods from problem definition through delivery of final classifiers to downstream validation teams • Design, implement, and validate novel machine learning and statistical methods to solve problems in cancer diagnostics • Establish and promote best practices in model interpretability, uncertainty estimation, and reproducibility • Design robust feature engineering and extraction pipelines tailored to cfDNA methylation and sequencing data • Collaborate closely with molecular biologists on experimental design, ensuring data integrity and quality control • Mentor other scientists and foster a culture of innovation, collaboration, and scientific excellence • Lead and actively participate in code and design reviews QUALIFICATIONS: • PhD in Bioinformatics, Computer Science, Machine Learning, Statistics, or a related quantitative field, with 4 to 8+ years of post-PhD experience • Hands-on experience in cancer genomics or epigenomics; experience with cell-free DNA or methylation sequencing data is a plus • Strong foundation in quantitative reasoning, statistical analysis, and applied machine learning; experience with deep learning frameworks is a plus • Proven track record of developing computational methods for high-throughput sequencing data analysis • Strong programming skills, with hands-on experience in Python and its scientific library stack (pandas, NumPy, scikit-learn) • Experience with Linux command-line tools, shell scripting, version control (Git), workflow managers (e.g., Nextflow, Snakemake), and cloud or HPC compute environments • Ability to perform hypothesis-driven research, visualize findings, and summarize results in oral and written form • Experience mentoring or technically leading other scientists Compensation & Total Rewards This range reflects a good-faith estimate of the base pay we reasonably expect 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 • Comprehensive health benefits (medical, dental, vision) • 401(k) with company match • Generous paid time off and company holidays • Additional wellness and work-life benefits Compensation Range $172,000 — $214,000 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 eac