Natera · 4 hours ago
Senior/Lead Bioinformatics Engineer
San Carlos, CA
Full-time
Hybrid
Senior Level, Lead/Staff
$144K/yr - $180K/yrNatera is seeking a Senior/Lead Bioinformatics Engineer to join the Bioinformatics Research team focused on Epigenomics in Oncology. This role will provide technical leadership in the design, development, and maintenance of large-scale, production-grade bioinformatics pipelines.
BiotechnologyGeneticsHealth DiagnosticsMedicalWomen's
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
Qualification
Required
MS or PhD in Computer Science, Bioinformatics, Computational Biology, or a related field, with a strong focus on cancer genomics or epigenomics
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
Preferred
AWS experience strongly preferred
Benefits
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
Comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents
Free testing in addition to fertility care benefits
Pregnancy and baby bonding leave
Commuter benefits
Generous employee referral program
Company
Natera
Natera specializes in cell-free DNA testing to provide a more targeted interventions to oncology, women's health, and organ health.
Founded in 2004
5001-10000 employees
H1B Sponsorship
Natera has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (90)
2024 (72)
2023 (37)
2022 (71)
2021 (64)
2020 (40)
Funding
Current Stage
Public CompanyTotal Funding
$1.16BKey Investors
Sofinnova InvestmentsLightspeed Venture PartnersSequoia Capital
2023-09-07Post Ipo Equity· $250M
2022-11-15Post Ipo Equity· $400.05M
2022-03-16Post Ipo Equity· $5M
Leadership Team
Steve Chapman
CEO
Jonathan Sheena
Co-Founder, Board Member
Recent News
2026-01-22
Business Wire
2026-01-22
Company data provided by crunchbase