Lead Bioinformatics & Machine Learning Scientist

Natera; San Carlos (CA); On-site; USD 172,000 - 214,000; Full time

Benefits offered by this job

Annual bonus

Equity awards

401(k) with match

Paid time off

Job summary

Natera is seeking a Lead Bioinformatics & Machine Learning Scientist to advance machine learning models behind our tissue-free, methylation-based cancer assay. You will lead end-to-end analyses, translate experimental design to computational workflows, and drive rigor in sequencing data processing across multiple cohorts.

The role requires a PhD with 4–8+ years post-PhD, deep sequencing analytics experience, and strong Python/Linux skills.

Qualifications

• PhD in CS/Bioinformatics/Computational Biology or related quantitative field with 4–8+ years post-PhD.
• Strong background in high-throughput DNA sequence data analysis and cancer epi/genomics.
• Experience in developing core ML models (GLMs, kernels, trees, neural nets) for biological data.
• Proficiency in Python and Linux, including shell scripting and data analysis libraries (NumPy, Pandas, Matplotlib).
• Familiarity with public databases such as TCGA, COSMIC, or OncoKB.

Responsibilities

• Develop, train, and evaluate ML models for cancer detection in MRD settings.
• Own end-to-end research analyses from ideation to implementation and evaluation.
• Bridge wet-lab design and computational analysis, ensuring QC across high-volume sequencing data.
• Communicate findings to technical and non-technical stakeholders and contribute to code quality standards.

Skills

High-throughput sequencing analysis

ML model development

Python

Linux

Shell scripting

NumPy/Pandas/Matplotlib

Data visualization

Education

PhD in Computer Science, Bioinformatics, Computational Biology or related field

Tools

TCGA

COSMIC

OncoKB

Job description

Lead Bioinformatics & Machine Learning Scientist

Natera is seeking a Lead Bioinformatics & Machine Learning Scientist to join our Bioinformatics Research team and help build the machine learning models behind Natera's tissue-free, methylation-based assay. These will be the models that detect cancer in the minimal residual disease (MRD) setting and help inform treatment selection. The ideal candidate brings a strong background in algorithm development, genomics, sequencing data processing, and applied machine learning.

Primary Responsibilities:

• Develop, train, and evaluate machine learning models, driving algorithm design decisions that support cancer detection in the MRD setting.
• Own end-to-end research analyses, from ideation through implementation (scripts and notebooks), troubleshooting, and performance evaluation, including developing new features within existing pipelines.
• Translate between wet-lab experimental design and computational analysis, navigating ambiguity as assay requirements evolve and maintaining rigorous quality control across high-volume sequencing data spanning multiple cohorts, vendors, and clinical protocols.
• Communicate findings and model performance to both technical and cross-functional stakeholders, and contribute to establishing standards for code quality and reproducibility.

Qualifications:

• PhD in Computer Science, Bioinformatics, Computational Biology, or a related quantitative field with a strong emphasis on cancer epi/genomics and 4 to 8+ years of experience post-PhD.

Knowledge, Skills, and Abilities:

• Deep theoretical and practical understanding of high-throughput DNA sequence data analysis, including mapping, sequence alignment, and variant calling workflows.
• Experience in algorithm development and data analysis, including applying and evaluating statistical methods.
• Demonstrated experience in developing core ML models, including generalized linear models, kernel methods, tree-based algorithms, and neural networks, with a focus on biological data (e.g., DNA sequencing data)
• Strong quantitative reasoning and data analysis skills, with a demonstrated ability to apply them effectively to relevant scientific problems.
• Experience with Python and Linux command-line tools, including writing shell scripts. Strong computational and programming skills, including thorough experience with Python statistical packages (NumPy, Matplotlib, Pandas).
• Familiarity with public databases such as TCGA, COSMIC, or OncoKB.
• Ability to visualize findings and summarize results in oral and written form for both technical and non-technical audiences.
• High scientific rigor, with eagerness to teach and learn new computational methods and biology.
• Ability to work on a cross-functional team in a highly collaborative environment, partnering with both computational and experimental scientists.

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 positionis also eligible for additional compensation and benefits throughNatera’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

$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 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.

Please be advised that Natera will reach out to candidates with a @ natera.com email domain ONLY. Email communications from all other domain names are not from Natera or its employees and are fraudulent. Natera does not request interviews via text messages and does not ask for personal information until a candidate has engaged with the company and has spoken to a recruiter and the hiring team. Natera takes cyber crimes seriously, and will collaborate with law enforcement authorities to prosecute any related cyber crimes.

Voluntary Self-Identification

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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