Staff Scientist-Bioinformatics

QuidelOrtho 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 QuidelOrtho, 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 QuidelOrtho'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 molecular assays.

The Key Working Relationships

Internal Partners:

• Molecular Assay Development Team - collaborative design, primer/probe review, troubleshooting recommendations.
• Virology & Microbiology Teams - input on organism selection and genomic real estate.
• Systems Engineering & Data Science - integration of computational tools, pipeline scaling, and systems compatibility.
• R&D Program Management - timeline alignment, risk mitigation, and feasibility assessments.
• Quality & Regulatory Affairs - documentation, traceability, and design history support.
• Software/IT Infrastructure - high-performance server maintenance, data storage, and workflow optimization.

External Partners:

• Bioinformatics tool vendors / software partners - coordination on licensed or optional computational tools (e.g., OMP engine).
• Academic collaborators / genome repositories - access to genomic/transcriptomic datasets.
• External sequencing partners or CROs - support additional data generation or large-scale analyses when needed.

The Work Environment

The work environment characteristics are representative of a laboratory/ BSL 2 environment and includes handling of viral and bacterial hazards, potentially hazardous chemicals, as well as infectious or potentially infectious bodily fluids, tissues, and samples. Up to 75% standing or sitting extended periods of time. Flexible work hours to meet project deadlines.

Physical Demands

Position requires ability to lift up to 20 lbs. on a regular basis. Walking, standing, and sitting for long periods of time (up to 75% of the day) are routine to accomplish tasks in this role. Specific vision abilities required by this job include close and distance vision and the ability to adjust focus. Personal protective equipment is required as posted.

Salary Transparency

The salary range for this position takes into account a wide range of factors including education, experience, knowledge, skills, geography, and abilities of the candidate, in addition to internal equity and alignment with market data. At QuidelOrtho, it is not typical for an individual to be hired at or near the top range for their role and compensation decisions are dependent on the facts and circumstances of each case. The salary range for this position is $125,000 to $150,000 and is bonus eligible. QuidelOrtho offers a comprehensive benefits package including medical, dental, vision, life, and disability insurance, along with a 401(k) plan, employee assistance program, Employee Stock Purchase Plan, paid time off (including sick time), and paid Holidays. All benefits are non-contractual, and QuidelOrtho may amend, terminate, or enhance the benefits provided, as it deems appropriate.

Equal Opportunity

QuidelOrtho believes in Equal Opportunity for all and is committed to ensuring all individuals, including individuals with disabilities, have an opportunity to apply for those positions that they are interested in and qualify for without regard to race, religion, color, national origin, citizenship, sex, sexual orientation, gender identity, age, veteran status, disability, genetic information, or any other protected characteristic. QuidelOrtho is also committed to providing reasonable accommodations to qualified individuals so that an individual can perform the duties. If you are interested in applying for an employment opportunity and require special assistance or an accommodation to apply due to a disability, please contact us at recruiting@quidelortho.com.