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About the Role

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.

Responsibilities

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.
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.
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.
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.

Requirements

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.
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.

Skills

NGS-based oncology assays
ctDNA biology
Python
SDLC best practices
CAP/CLIA LDT
IVD
AWS
R
Relational database technologies
Non-relational database technologies

Location

San Diego
South San Francisco

Work Type

Hybrid

Experience Level

Principal
Senior

Education Level

Ph.D.

Salary/Compensations

$184,000 - $204,000 USD
$190,000 - $210,000 USD

Benefits

Competitive compensation and benefits
Significant career opportunities
Eligible for additional discretionary bonuses/incentives
Eligible for restricted stock units

About the Company

Veracyte is a global diagnostics company whose vision is to transform cancer care for patients all over the world.
We empower clinicians with the high-value insights they need to guide and assure patients at pivotal moments in the race to diagnose and treat cancer.
Our Veracyte Diagnostics Platform delivers high-performing cancer tests that are fueled by broad genomic and clinical data, deep bioinformatic and AI capabilities, and a powerful evidence-generation engine, which ultimately drives durable reimbursement and guideline inclusion for our tests, along with new insights to support continued innovation and pipeline development.
For more information, please visit www.veracyte.com or follow us on LinkedIn or X (Twitter).

Equal Opportunity

Veracyte, Inc. is an Equal Opportunity Employer and will consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status or disability status.
Veracyte participates in E-Verify in the United States.
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