Principal Bioinformatics Scientist I

At Roche you can show up as yourself, embraced for the unique qualities you bring. Our culture encourages personal expression, open dialogue, and genuine connections,  where you are valued, accepted and respected for who you are, allowing you to thrive both personally and professionally. This is how we aim to prevent, stop and cure diseases and ensure everyone has access to healthcare today and for generations to come. Join Roche, where every voice matters.

The Position

A healthier future. It’s what drives us to innovate. To continuously advance science and ensure everyone has access to the healthcare they need today and for generations to come. Creating a world where we all have more time with the people we love. That’s what makes us Roche.

This role is a vital part of our Bioinformatics team, which is committed to advancing precision medicine by building cutting-edge computational tools for clinical diagnostics. As a member of this team, you will sit at the dynamic intersection of computational biology, assay development, and software engineering to translate complex genomic data into actionable health insights. You will have the opportunity to collaborate closely with cross-functional partners across Wet-Lab Assay Development, Software Engineering, CLIA Operations, and Quality to design, validate, and operationalize next-generation diagnostic tests.

The Opportunity

As a Bioinformatics Scientist, you will lead the design, optimization, and clinical validation of innovative NGS data processing pipelines and algorithms. You will serve as the technical bridge between wet-lab innovation and production-grade software engineering, leveraging advanced statistical modeling and modern AI coding tools to deliver high-accuracy molecular diagnostics for patient care.

• Pipeline & Algorithm Development: Design, benchmark, and optimize scalable, reproducible NGS bioinformatics pipelines using Nextflow, Docker/Singularity, and cloud environments.

• Analytical Validation: Partner with Assay Development and CLIA lab teams to establish statistical analysis plans and validate novel diagnostic assays (ensuring high sensitivity, specificity, and precision).

• AI-Accelerated Engineering: Routinely integrate AI coding tools and automated workflows to accelerate algorithm development, refactoring, and data analysis.

• Production Translation: Draft clear functional and technical specifications to guide software engineering teams in transitioning research prototypes into robust clinical software.

• Quality & Regulatory Compliance: Implement sample- and run-level statistical QC metrics while maintaining thorough QMS-compliant documentation for CAP/CLIA audits.

• Best Practices: Enforce high-standard software engineering practices, including Git version control, continuous integration, unit testing, and modular architecture.

Who You Are

• Education & Experience: Bachelor’s degree with 9+ years of related experience; OR Master’s degree with 7+ years of related experience; OR Ph.D. with 4+ years of related experience (work experience can be prior or post-grad; relevant post-grad academic lab training will be considered).

• Matrixed Collaboration & Stakeholder Management: Proven ability to partner seamlessly across multidisciplinary teams—including wet-lab scientists, software engineers, lab directors, and Quality assurance—to align technical specs with clinical goals.

• Clinical Diagnostic Expertise: Demonstrated track record supporting or working within a CAP/CLIA-certified laboratory environment with direct experience in diagnostic test development and analytical validation.

• Technical Mastery: Deep understanding of high-throughput sequencing data analysis across various modalities (targeted panels, WGS/WES, transcriptomics, or liquid biopsy/ctDNA).

• Proficient in Python/R/C++ and Linux/Bash alongside hands-on experience using workflow managers (Nextflow) and containerized software deployments.

• Modern Workflow Adaptability: Proven ability to leverage AI development tools to maximize productivity, alongside excellent communication skills suited for navigating complex, cross-functional organizational environments.

Relocation benefits are not being offered for this position

The expected salary range for this position based on the primary location of Santa Clara, CA  is $121,400 - $225,400 USD Annual. Actual pay will be determined based on experience, qualifications, geographic location, and other job-related factors permitted by law.  A discretionary annual bonus may be available based on individual and Company performance. 

This position also qualifies for the benefits detailed at the link provided below.

Benefits

Who we are

A healthier future drives us to innovate. Together, more than 100’000 employees across the globe are dedicated to advance science, ensuring everyone has access to healthcare today and for generations to come. Our efforts result in more than 26 million people treated with our medicines and over 30 billion tests conducted using our Diagnostics products. We empower each other to explore new possibilities, foster creativity, and keep our ambitions high, so we can deliver life-changing healthcare solutions that make a global impact.

Let’s build a healthier future, together.

Roche is an equal opportunity employer. It is our policy and practice to employ, promote, and otherwise treat any and all employees and applicants on the basis of merit, qualifications, and competence. The company's policy prohibits unlawful discrimination, including but not limited to, discrimination on the basis of Protected Veteran status, individuals with disabilities status, and consistent with all federal, state, or local laws.

If you have a disability and need an accommodation in relation to the online application process, please contact us by completing this form Accommodations for Applicants.