Associate Director of Bioinformatics (Women's Health and Organ Health)

Natera is seeking an Associate Director to lead a team of Bioinformatics Scientists in our Women's Health and Organ Health research organization. This role oversees the scientific planning and execution of research and assay-development for diagnostic projects, including creating production-ready pipeline components.

Responsibilities

• Lead and mentor a team of Bioinformatics Scientists, owning their professional growth and team standards.
• Own the research strategy for new product development, from scoping through execution, collaborating with cross-functional stakeholders.
• Lead bioinformatics analysis for assay development and optimization, troubleshooting experiments alongside laboratory scientists. This includes multi-omic approaches (methylation, fragmentomics) and both short-read and long-read sequencing (hybrid-capture and amplicon target enrichment).
• Partner with laboratory teams on study design at the research and feasibility stage, ensuring data quality before further development.
• Advise and prototype improvements to analysis pipelines, including variant detection, quality control, and modality-specific processing (e.g., methylation calling, fragment-size analysis, structural-variant calling).
• Transition research prototypes into stable production workflows, enforcing software engineering best practices (version control, testing, CI/CD, containerization).
• Automate routine aspects of research data management, pipeline execution, and reporting to maximize scientific productivity.
• Set standards for AI-assisted work, defining when agent-driven conclusions require scientist sign-off.
• Act as a cross-functional subject-matter expert, partnering with data science, molecular biology, pipeline engineering, biostatistics, quality assurance, and laboratory operations on new products and research-to-production transitions.

What Success Looks Like After a Year

• The team has a visible research roadmap you own, with measurable progress.
• You independently advise and guide research strategies in cross-functional settings.
• New analysis methods from your team are implemented in production code and demonstrate expected performance on benchmark studies.
• You and your team members are trusted experts consulted for complex decision-making.
• AI agent-assisted work is normalized on the team, with standards you establish.

Requirements

• Ph.D. in Bioinformatics, Computational Biology, Computer Science, Mathematics, Engineering, Biostatistics, or a related field (M.S. with equivalent experience considered).
• 7+ years in bioinformatics, including 3+ years leading scientists and working across functions.
• Demonstrated ownership of a team that transitioned scientific research into real clinical use.
• Experience developing or scientifically guiding diagnostic sequencing assays.

Skills

• Deep expertise in next-generation sequencing analysis: hybrid-capture/amplicon target enrichment, sequencing QC, secondary analysis, and variant calling.
• Experience with cell-free DNA sequencing and multiomics data (e.g., methylation, fragmentomics) in a diagnostics setting.
• Working knowledge of diagnostic product development in regulated (CLIA) environments, including applicable standards and practices.
• Strong Python, programming, and data analysis skills.
• Fluency in exploratory data analysis and visualization, translating complex findings into actionable recommendations.
• Understanding of sequencing workflows from sample extraction to instrument output, distinguishing biology from analysis issues.
• Proven ability to assess new platforms, assays, or methods against benchmarks.
• Clear communication of technical details to non-expert audiences.
• Ability to manage multiple objectives and timelines independently.

Preferred Qualifications

• Long-read sequencing (PacBio HiFi, Oxford Nanopore) alongside short-read (Illumina).
• Proficiency in R, shell scripting, or Java.
• Cloud computing (AWS, GCP) and workflow orchestration (Snakemake, WDL, Nextflow, Cromwell).
• Containerization (Docker, Kubernetes) for reproducible, production-grade analyses.
• Record of conference presentations or peer-reviewed publications.
• Desire to work in a fast-paced, high-impact environment.

Pay

Remote USA: $166,600—$202,000 USD. Actual compensation is based on factors like skill set, experience, certifications, and location.

Benefits

• Comprehensive medical, dental, vision, life, and disability plans for eligible employees and dependents.
• Free genetic testing for employees and immediate family members.
• Fertility care benefits.
• Pregnancy and baby bonding leave.
• 401k benefits.
• Commuter benefits.
• Generous employee referral program.

About Natera

Natera is a global leader in cell-free DNA (cfDNA) testing, focused on oncology, women’s health, and organ health. Our mission is to integrate personalized genetic testing and diagnostics into standard care, enabling earlier and more targeted interventions for healthier lives. The team includes highly dedicated professionals from world-class institutions, working collaboratively to advance genetic disease management.