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

Location: San Carlos, California, United States; onsite role

Salary: $177,800–$222,200 USD base pay, plus performance incentive bonus, equity awards, and benefits.

Company

Develops cell-free DNA testing and personalized genetic diagnostics for oncology, women's health, and organ health.

What you will do

• Lead, mentor, and develop a team of Bioinformatics Scientists while setting standards for scientific and engineering quality.
• Own research strategy and roadmaps for new diagnostic product development, from scoping through execution.
• Direct bioinformatics analysis for assay development, optimization, study design, and data-quality assessment across short-read, long-read, hybrid-capture, and amplicon workflows.
• Prototype and improve variant detection, quality control, methylation calling, fragmentomics, end-motif analysis, error suppression, and structural-variant calling.
• Move research prototypes into stable production workflows using version control, testing, CI/CD, containerization, and automation.
• Partner with data science, molecular biology, pipeline engineering, biostatistics, quality assurance, and laboratory operations.

Requirements

• Ph.D. in Bioinformatics, Computational Biology, Computer Science, Mathematics, Engineering, Biostatistics, or a related field; an M.S. with equivalent experience may be considered.
• At least 7 years of bioinformatics experience, including 3 or more years leading scientists and working cross-functionally.
• Experience taking scientific research into real clinical use and developing or guiding diagnostic sequencing assays.
• Deep expertise in NGS analysis, target enrichment, sequencing quality control, secondary analysis, and variant calling.
• Experience with cell-free DNA sequencing, omics data, Python, exploratory data analysis, visualization, and sequencing workflows from sample extraction through instrumentation.
• Working knowledge of diagnostic product development in a regulated, accredited setting, including CLIA-related practices and standards.

Nice to have

• Long-read sequencing with PacBio HiFi or Oxford Nanopore, alongside short-read Illumina sequencing.
• Experience with R, shell scripting, Java, AWS, GCP, or workflow orchestration tools such as Snakemake, WDL, Nextflow, or Cromwell.
• Experience with Docker or Kubernetes and reproducible production-grade analyses.
• Conference presentations or peer-reviewed publications.

Culture & Benefits

• Collaborative work with statisticians, geneticists, physicians, laboratory scientists, and software engineers.
• AI tools are part of routine work, with clear standards for agent autonomy and scientist sign-off.
• Medical, dental, vision, life, and disability benefits.
• 401(k) with company match, paid time off, company holidays, wellness, and work-life benefits.
• Annual performance incentive bonus, long-term equity awards, fertility care, pregnancy and baby bonding leave, and commuter benefits.