Principal Bioninformatics Scientist

Job Description:

We are seeking a highly experienced and motivated Principal Bioinformatics Scientist to lead the bioinformatics strategy, design, and development of next-generation minimal residual disease (MRD) laboratory-developed tests (LDTs). This role is a senior technical leadership position responsible for shaping 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 deep 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 serve as a scientific and technical leader, owning assay bioinformatics from concept through analytical validation and launch.

KEY RESPONSIBILITIES:

Scientific & Technical Leadership

• Lead bioinformatics strategy for MRD assay design, development, optimization, and lifecycle management for LDTs developed under CAP/CLIA quality systems.
• Serve as the bioinformatics owner, driving 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.

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.
• Facilitate successful production pipeline deployment by working closely with infrastructure and engineering teams
• Contribute to regulatory submissions and audits by providing technical documentation and validation report, and responses to audits or regulatory inquiries.

Mentorship & Influence

• Mentor junior scientists by providing technical and scientific guidance, 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.

REQUIRED EXPERIENCE:

• Ph.D. in Bioinformatics, Computational Biology, Genomics, Biostatistics, or a closely related quantitative field.
• Minimum 8 years of total relevant experience, with at least 5 years of direct industry experience in biotech, diagnostics, or regulated healthcare environments.
• Demonstrated experience leading 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 leadership, ownership, and independent work.

PREFERRED EXPERIENCE:

• 1-2 years management experience preferred
• 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.

For candidates based in our San Diego office, the range is $184,000 - $204,000.

For candidates based in our South San Francisco office, the range is $190,000- $210,000.

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