Senior/Lead Bioinformatics Engineer

LOCATION: Position is available as a hybrid position in San Carlos, California as well as a remote position within the US.

Natera is seeking a Senior/Lead Bioinformatics Engineer to join the Bioinformatics Research team focused on Epigenomics in Oncology. Natera’s mission is to transform disease management worldwide by leveraging information from a simple blood draw to enable early detection and guide treatment decisions.

This role will provide technical leadership in the design, development, and maintenance of large-scale, production-grade bioinformatics pipelines, with a strong emphasis on workflow orchestration using Nextflow and WDL. The ideal candidate brings deep hands-on experience building, optimizing, and operating NGS pipelines in cloud environments, and is comfortable bridging research and production engineering.

PRIMARY RESPONSIBILITIES:

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Architect, develop, and maintain scalable, production-ready bioinformatics pipelines for next-generation sequencing data, with primary ownership of workflows implemented in Nextflow and WDL

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Lead pipeline design decisions with a strong emphasis on modularity, reusability, robustness, scalability, and maintainability

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Refactor and optimize existing pipelines to improve performance, cost efficiency, fault tolerance, and ease of extension

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Establish and enforce best practices for workflow development, including parameterization, versioning, provenance tracking, and reproducibility

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Design and implement comprehensive testing strategies for pipelines and supporting code, including unit, integration, and end-to-end tests

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Deeply understand and troubleshoot complex sequencing data processing pipelines across multiple stages (QC, alignment, methylation calling, feature generation, etc.)

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Partner closely with Research, Machine Learning, and Platform Engineering teams to transition research workflows into production-grade systems

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Support training and evaluation of machine learning models by enabling efficient data generation and large-scale distributed execution on AWS

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Participate in and lead code reviews and design reviews, mentoring other engineers and scientists on workflow and software engineering best practices

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Contribute to pipeline documentation, onboarding materials, and internal standards

QUALIFICATIONS:

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MS or PhD in Computer Science, Bioinformatics, Computational Biology, or a related field, with a strong focus on cancer genomics or epigenomics

KNOWLEDGE, SKILLS, AND ABILITIES:

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Extensive hands-on experience developing bioinformatics pipelines using Nextflow and/or WDL, including complex multi-step NGS workflows

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Proven track record of building and supporting production-level bioinformatics software in regulated or high-reliability environments

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Deep understanding of software engineering best practices, including workflow design patterns, testing, version control, CI/CD, code review, and documentation

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Strong experience with containerized workflows (Docker) and execution on cloud platforms; AWS experience strongly preferred

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Expertise in distributed and parallel computing, including workflow execution engines and cloud-native scaling strategies

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Experience profiling and optimizing pipelines and code for runtime, memory usage, and cost efficiency

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Strong understanding of sequencing technologies and data types, particularly methylation and epigenomic assays

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Advanced programming skills in Python, including experience with scientific and data-processing libraries (e.g., Pandas, NumPy, scikit-learn)

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Expert-level proficiency with Linux, shell scripting, and command-line bioinformatics tools

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Ability to work independently, lead technical initiatives, and manage multiple priorities in a fast-paced environment

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Strong communication skills and a collaborative mindset

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:

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Annual performance incentive bonus

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Long-term equity awards

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Comprehensive health benefits (medical, dental, vision)

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401(k) with company match

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Generous paid time off and company holidays

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Additional wellness and work-life benefits

Compensation Range
$144,000—$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!

For more information, visit www.natera.com.

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.

Link: https://www.natera.com/notice-of-data-collection-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.

For more information:
- BBB announcement on job scams
- FBI Cyber Crime resource page