Senior Bioinformatics Scientist

Location: Remote ; San Diego, California, United States; South San Francisco, California, United States

Department: 330 Bioinformatics & Data Science

The Position:

We are seeking a highly experienced and motivated Senior Bioinformatics Scientist to drive the design, and development of next‑generation minimal residual disease (MRD) laboratory‑developed tests (LDTs). This senior, independent scientist position is responsible for contributing to assay concepts, driving analytical development and validation, and partnering closely with wet‑lab, clinical, quality, regulatory, and software teams to deliver robust, clinically actionable MRD diagnostics for multiple indications.

The ideal candidate brings expertise in NGS‑based oncology assays, strong understanding of ctDNA biology and a proven track record of industry assay development under design control. This individual will lead technical execution of key scientific efforts, owning assay bioinformatics from concept through analytical validation and launch.

KEY RESPONSIBILITIES:

Scientific & Technical Expertise

• Contribute to bioinformatics strategy for MRD assay design, development, optimization, and lifecycle management for LDTs developed under CAP/CLIA quality systems.
• Lead and contribute to study design, data analysis, performance characterization, and decision‑making throughout development.
• Apply deep domain knowledge in cancer genomics, ctDNA biology, and NGS technologies to inform assay architecture, variant detection strategies, and error suppression approaches in collaboration with our data science and modeling teams.

Assay Development & Validation

• Design and execute analytical studies to evaluate assay performance, including accuracy, limit of detection, and reproducibility, in collaboration with wet‑lab and biostatistics partners.
• Develop, validate, and maintain scalable, production‑ready bioinformatics pipelines for MRD analysis, including QC, variant calling, MRD calling logic, and reporting.
• Lead benchmarking and optimization of computational methods, including background error modeling, and longitudinal MRD tracking.
• Ensure compliance with standards (CAP/CLIA, FDA, IVDR) throughout the bioinformatics development lifecycle, including rigorous testing and documentation.

Cross‑Functional Collaboration

• Partner closely with molecular biology, assay development, QA/RA, clinical, and software engineering teams to ensure bioinformatics solutions are aligned with assay design, regulatory expectations, and operational constraints.
• Contribute to regulatory submissions and audits by providing technical documentation and validation report, and responses to audits or regulatory inquiries.

Mentorship & Influence

• Provide technical mentorship and scientific guidance to junior scientists, helping raise the overall bar of assay development rigor and execution.
• Communicate complex analytical concepts and results clearly to both computational and non‑computational stakeholders, including senior leadership.

Who You Are:

REQUIRED EXPERIENCE:

• Ph.D. in Bioinformatics, Computational Biology, Genomics, Biostatistics, or a closely related quantitative field. (or M.Sc. plus 3 additional years industry experience).
• Minimum 6 years of total relevant experience in biotech, diagnostics, or regulated healthcare environments.
• Demonstrated experience in NGS‑based assay development for clinical diagnostics. Hands‑on experience with ctDNA‑based MRD assays, including personalized or tumor‑informed approaches.
• Strong programming skills in Python, with experience developing reproducible, production‑grade analysis pipelines, including experience with SDLC best practices.
• Proven experience working in design‑controlled, regulated environments (CAP/CLIA LDT, IVD, or equivalent).
• Proficiency in development of novel bioinformatics methodologies, and algorithms development, including benchmarking of computational methods.
• Track record of working with wet lab scientists on iterative experiment design, execution, analysis, and interpretation as a tightly integrated team.
• Demonstrated record of technical and scientific ownership, and independent work.

PREFERRED EXPERIENCE:

• Experience developing and deploying bioinformatics workflows in AWS (e.g., EC2, S3, Step Functions, Batch, Lambda, etc.).
• Strong understanding of germline and somatic mutation processes leading to complex variation and genome-wide biomarkers with potential clinical utility.
• Working knowledge of R.
• Experience with relational and non-relational database technologies is a plus.

#LI-Onsite, #LI-Hybrid, or #LI-Remote

For candidates based in our San Diego office, the salary (or hourly range is $170,000 - $187,000.

For candidates based in our South San Francisco office, the salary or hourly range is $177,000 - $207,000.

For candidates working remote (US), the salary or hourly range is $162,000 - $178,000