[Remote] Senior/Lead Bioinformatics Engineer

Note: The job is a remote job and is open to candidates in USA. Natera is a global leader in cell-free DNA testing dedicated to oncology and women's health. They are seeking a Senior/Lead Bioinformatics Engineer to provide technical leadership in designing and maintaining bioinformatics pipelines focused on epigenomics in oncology.

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

Skills

• 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

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
• 401k benefits
• Commuter benefits
• Generous employee referral program

Company Overview

• Natera specializes in cell-free DNA testing to provide a more targeted interventions to oncology, women's health, and organ health. It was founded in 2004, and is headquartered in San Carlos, California, USA, with a workforce of 5001-10000 employees. Its website is https://www.natera.com/.

Company H1B Sponsorship

• Natera has a track record of offering H1B sponsorships, with 90 in 2025, 72 in 2024, 37 in 2023, 71 in 2022, 64 in 2021, 40 in 2020. Please note that this does not guarantee sponsorship for this specific role.

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