Lead Bioinformatics & Machine Learning Scientist (Epigenomics) New US Remote

Natera, Inc.; United States; Remote; USD 146,000 - 180,000; Full time

Job summary

Natera, Inc. is seeking a Lead Bioinformatics & Machine Learning Scientist to advance Epigenomics in Oncology within our Bioinformatics R&D team. You will develop ML methods for early cancer detection from cfDNA methylation data and provide technical leadership in a highly collaborative setting.

The role emphasizes mentoring, design reviews, and collaboration with molecular biologists to ensure data integrity and impactful biomarkers. Remote-friendly with competitive benefits.

Qualifications

• PhD with 4–8+ years post-PhD experience in relevant quantitative field.
• Hands-on cancer genomics/epigenomics experience; cfDNA or methylation data is a plus.
• Strong quantitative reasoning and applied ML background; deep learning a plus.
• Proven track record developing computational methods for high-throughput sequencing data.
• Strong programming in Python and scientific libraries (pandas, NumPy, scikit-learn).
• Experience with Linux, shell scripting, Git, and workflow managers; cloud/HPC exposure.
• Ability to perform hypothesis-driven research and present results clearly.
• Experience mentoring or leading scientists.

Responsibilities

• Drive technical workstreams from problem definition to classifier delivery.
• Design, implement, and validate ML/statistical methods for cancer diagnostics.
• Promote best practices in interpretability, uncertainty, and reproducibility.
• Design robust pipelines for cfDNA methylation and sequencing data.
• Collaborate with molecular biologists on experimental design and QC.
• Mentor scientists and participate in code/design reviews.

Skills

PhD in Bioinformatics/CompSci/ML

Machine learning & statistics

Genomics/epigenomics analysis

cfDNA methylation data analysis

Python & scientific stack

Linux CLI & scripting

Workflow managers (Nextflow/Snakemake)

Git/version control

Cloud/HPC compute experience

Mentoring/technical leadership

Education

PhD in Bioinformatics, Computer Science, ML, Statistics or related field

Tools

Nextflow

Snakemake

Git

Python (NumPy, pandas, scikit-learn)

Linux shell

Job description

US Remote

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

The pay range is listed and actual compensation packages are based on a wide array of factors unique to each candidate, including but not limited to skill set, years & depth of experience, certifications and specific office location. This may differ in other locations due to cost of labor considerations.

Remote USA

$146,000 - $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.

Voluntary Self-Identification

For government reporting purposes, we ask candidates to respond to the below self-identification survey.Completion of the form is entirely voluntary. Whatever your decision, it will not be considered in the hiringprocess or thereafter. Any information that you do provide will be recorded and maintained in aconfidential file.

As set forth in Natera’s Equal Employment Opportunity policy,we do not discriminate on the basis of any protected group status under any applicable law.

If you believe you belong to any of the categories of protected veterans listed below, please indicate by making the appropriate selection.As a government contractor subject to the Vietnam Era Veterans Readjustment Assistance Act (VEVRAA), we request this information in order to measurethe effectiveness of the outreach and positive recruitment efforts we undertake pursuant to VEVRAA. Classification of protected categoriesis as follows:

A "disabled veteran" is one of the following: a veteran of the U.S. military, ground, naval or air service who is entitled to compensation (or who but for the receipt of military retired pay would be entitled to compensation) under laws administered by the Secretary of Veterans Affairs; or a person who was discharged or released from active duty because of a service-connected disability.

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