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:
Architect, develop, and maintain scalable, production-ready bioinformatics pipelines for next-generation sequencing data, with primary ownership of workflows implemented in Nextflow and WDL
Lead pipeline design decisions with a strong emphasis on modularity, reusability, robustness, scalability, and maintainability
Refactor and optimize existing pipelines to improve performance, cost efficiency, fault tolerance, and ease of extension
Establish and enforce best practices for workflow development, including parameterization, versioning, provenance tracking, and reproducibility
Design and implement comprehensive testing strategies for pipelines and supporting code, including unit, integration, and end-to-end tests
Deeply understand and troubleshoot complex sequencing data processing pipelines across multiple stages (QC, alignment, methylation calling, feature generation, etc.)
Partner closely with Research, Machine Learning, and Platform Engineering teams to transition research workflows into production-grade systems
Support training and evaluation of machine learning models by enabling efficient data generation and large-scale distributed execution on AWS
Participate in and lead code reviews and design reviews, mentoring other engineers and scientists on workflow and software engineering best practices
Contribute to pipeline documentation, onboarding materials, and internal standards
QUALIFICATIONS:
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:
Extensive hands-on experience developing bioinformatics pipelines using Nextflow and/or WDL, including complex multi-step NGS workflows
Proven track record of building and supporting production-level bioinformatics software in regulated or high-reliability environments
Deep understanding of software engineering best practices, including workflow design patterns, testing, version control, CI/CD, code review, and documentation
Strong experience with containerized workflows (Docker) and execution on cloud platforms; AWS experience strongly preferred
Expertise in distributed and parallel computing, including workflow execution engines and cloud-native scaling strategies
Experience profiling and optimizing pipelines and code for runtime, memory usage, and cost efficiency
Strong understanding of sequencing technologies and data types, particularly methylation and epigenomic assays
Advanced programming skills in Python, including experience with scientific and data-processing libraries (e.g., Pandas, NumPy, scikit-learn)
Expert-level proficiency with Linux, shell scripting, and command-line bioinformatics tools
Ability to work independently, lead technical initiatives, and manage multiple priorities in a fast-paced environment
Strong communication skills and a collaborative mindset
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
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What We Do
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. Where some set out to build a test, we set out to achieve a mission: change the management of disease worldwide by using DNA testing to proactively inform treatment. Through a cfDNA technology platform approach, we've pioneered noninvasive testing in unlimited applications—each with their own potential to revolutionize care for patients. #TeamNatera includes clinicians, scientists, biostatisticians, researchers, and laboratory professionals from around the world. Our diverse teams blend a passion for patients with deep clinical, scientific, and technological roots. Natera’s tests are validated by more than 100 peer-reviewed publications that demonstrate high accuracy.
