Scientist III, Bioinformatics (Companion Diagnostics)

Thermo Fisher Scientific • Austin, TX

8d

About The Position

At Thermo Fisher Scientific, the CDx Bioinformatics team supports development of next-generation sequencing companion diagnostics that help guide cancer treatment. The Scientist III, Bioinformatics applies knowledge of biology, oncology, and genomic data analysis to active diagnostic development programs. The role prepares study datasets, investigates sequencing results, and develops tools to improve the quality and efficiency of scientific analysis. It works collaboratively with Research and Development, Program Management, Clinical Affairs, Biostatistics, Quality, Regulatory Affairs, and Software Development colleagues. The position offers opportunities to contribute across multiple programs, build expertise in regulated diagnostic development, and use computational approaches, including AI-assisted tools, with sound scientific judgment.

Requirements

• Bachelor’s degree with at least five years of relevant experience, or an advanced degree with at least three years of relevant experience, in bioinformatics, computational biology, molecular biology, or a related field.
• Hands-on experience analyzing NGS data in oncology, molecular diagnostics, or a closely related setting.
• Experience preparing and reviewing scientific datasets for use by other teams or external collaborators.
• Strong understanding of molecular biology, cancer genomics, and the relationship between genomic alterations and diagnostic assay design.
• Working knowledge of NGS data processing, variant calling, sequencing quality metrics, and sources of technical error.
• Experience with Linux/Unix, Git, and common sequencing data formats such as BAM and VCF.
• Experience interpreting relevant variant classes, such as SNVs, indels, copy-number alterations, gene fusions, and splice variants.
• Proficiency in Python or another suitable analysis language, including the ability to write, troubleshoot, and review code independently.
• Ability to reconcile data from multiple sources and build reproducible analyses with documented assumptions and quality checks.
• Practical familiarity with AI-assisted tools and their limitations, including the ability to identify and correct unsupported or incorrect outputs.
• Ability to explain technical findings clearly, distinguish evidence from assumptions, and recognize when further analysis or specialist input is needed.

Nice To Haves

• Companion diagnostic development or analytical and clinical validation studies.
• Targeted oncology sequencing of FFPE tissue or plasma specimens.
• Work in a regulated or quality-controlled environment, including documented analysis methods, version control, and review requirements.
• Preparation of partner data transfers, study-report datasets, or analyses supporting regulatory submissions.

Responsibilities

• Prepare, curate, and review study datasets, including variant and quality-control line listings, sample metadata, and data transfer packages.
• Reconcile source data and resolve missing, inconsistent, or unexpected results before delivery.
• Analyze DNA and RNA sequencing results in the context of assay design, oncology biomarkers, and study requirements.
• Assess variant coverage, reporting eligibility, and differences between assays or analysis configurations.
• Investigate discordant results, unexpected variant calls, no-calls, and quality-control findings.
• Review sequencing evidence and analysis settings, document findings, and explain what the evidence does and does not support.
• Prepare program-specific assay definition inputs, including hotspot and variant content files, and perform reanalyses using defined software and configuration versions.
• Provide analyses and technical documentation for study reports, regulatory questions, and partner requests.
• Maintain traceability to source data, methods, and analysis versions.
• Develop and improve scripts and tools for recurring tasks such as dataset curation, variant comparison, quality checks, and reporting.
• Test changes, participate in code review, and document methods so others can use and maintain them.
• Use approved AI-assisted tools where useful for coding, troubleshooting, data exploration, and documentation; independently verify generated code and content before use and protect confidential data appropriately.
• Manage assigned deliverables across multiple programs, clarify requirements with collaborators, and communicate findings, dependencies, and delivery risks.

Benefits

• Variable annual bonus may be available based on company, team, and/or individual performance results in accordance with company policy.
• Choice of national medical and dental plans and a national vision plan, including health incentive programs.
• Employee assistance and family support programs, including commuter benefits and tuition reimbursement.
• At least 120 hours of paid time off (PTO) and 10 paid holidays annually.
• Paid parental leave: 3 weeks for bonding and 8 weeks for caregiver leave.
• Accident and life insurance, and short- and long-term disability in accordance with company policy.
• Competitive 401(k) U.S. retirement savings plan.
• Employees’ Stock Purchase Plan (ESPP) offers eligible colleagues the opportunity to purchase company stock at a discount.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior