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.

#LI-Hybrid

The final salary offered to a successful candidate will be dependent on several factors that may include but are not limited to years of experience, skillset, geographic location, industry, education, etc. Base pay is one part of the Total Package that is provided to compensate and recognize employees for their work, and this role may be eligible for additional discretionary bonuses/incentives, and restricted stock units.

Pay range

$184,000-$210,000 USD