Staff Scientist-Bioinformatics

The Opportunity

Quidel Ortho unites the strengths of Quidel Corporation and Ortho Clinical Diagnostics, creating a world-leading in vitro diagnostics company with award-winning expertise in immunoassay and molecular testing, clinical chemistry and transfusion medicine. We are more than 6,000 strong and do business in over 130 countries, providing answers with fast, accurate and consistent testing where and when they are needed most - home to hospital, lab to clinic.

Our culture puts our team members first and prioritizes actions that support happiness, inspiration and engagement. We strive to build meaningful connections with each other as we believe that employee happiness and business success are linked. Join us in our mission to transform the power of diagnostics into a healthier future for all.

The Role

At Quidel Ortho, we're advancing the power of diagnostics for a healthier future for all. Join our mission as our next Staff Scientist to support Bioinformatics.

The Staff Scientist, Bioinformatics is responsible for leading bioinformatics activities that support molecular assay development across Quidel Ortho's diagnostic portfolio. This role drives computational analysis, target selection, primer/probe design, and in-silico inclusivity and exclusivity evaluations to enable robust, high-performance assays. The individual will develop and optimize bioinformatics pipelines, manage large genomic databases, and provide scientific guidance to project teams during feasibility, design, and verification phases.

This position will be onsite full-time in San Diego, Ca (Sorrento Valley).

The Responsibilities

• Lead the end-to-end computational workflow for assaydesign, including target identification, region analysis,primer/probe evaluation, and in-silico validation workflows.
• Build, maintain, and optimize internal bioinformatics pipelines (Python, Biopython, YAML configurations, PostgreSQL) for inclusivity analysis, exclusivity analysis sequence slicing, alignment interpretation, variant identification, and reporting.
• Design and execute computational assessments of genomic and transcriptomic datasets (NCBI SRA, RNA-Seq expression data, high-coverage genomic databases) to support target selection and assay feasibility.
• Perform BLAST-based region screening against inclusivity/exclusivity databases (viral, bacterial, fungal, human genome/microbiome) to evaluate off-target interactions and identify high-confidence primer and probe binding sites.
• Generate curated datasets, alignment summaries, variant reports, and performance-impact analyses for use in assay optimization and troubleshooting.
• Conduct oligo interaction modeling using thermodynamic calculations (e.g., G analysis, melting temperature, longest contiguous window assessments) to evaluate primer/probe dimerization or secondary structure risks.
• Partner closely with Molecular Assay Development, R&D, Systems Engineering, and Data Science to ensure computational insights are integrated into experimental workflows and design decisions.
• Maintain high-performance compute environments and associated databases to support pipeline development (e.g., BLAST DBs, PostgreSQL storage, GPU-accelerated workflows).
• Prepare clear, traceable reports and documentation enabling reproducibility, regulatory support, cross-functional communication, and design history files.
• Perform other work-related duties as assigned.

The Individual

Required:

• Ph.D. in Bioinformatics, Computational Biology, Molecular Biology, or related field; or M.S. with 5+ years of relevant diagnostic industry experience.
• Expert-level experience in Python, Biopython, YAML, and shell-based environments for pipeline development.
• Strong knowledge of PostgreSQL, relational database structure, and genomic data storage/curation.
• Deep understanding of genomics, transcriptomics, and molecular assay design principles (primer/probe thermodynamics, secondary structure modeling, amplicon design).
• Demonstrated experience performing in-silico inclusivity/exclusivity analyses, BLAST-based real estate screening, variant interpretation, and sequence alignment.
• Familiarity with NGS datasets, RNA-Seq data analysis, and public repositories (NCBI, SRA).
• Strong ability to interpret complex genomic data and communicate actionable recommendations to laboratory scientists and cross-functional teams.
• Excellent documentation, reporting, and traceability practices aligned with regulated environments.
• Ability to work collaboratively in a fast-paced R&D environment.
• This position is not currently eligible for visa sponsorship.

Preferred:

• Experience with high-performance compute environments (GPU systems, multi-core servers, RAID storage).
• Knowledge of diagnostic assay chemistries (RT-PCR, TMA, Invader, qStar, or similar).
• Experience supporting Design History Files or regulatory submissions for diagnostic products.
• Familiarity with melting-temperature modeling and thermodynamic tools (e.g., MELTING5).
• Experience contributing to feasibility, verification, and validation of…