Principal Scientist – GEM Molecular Validation & Technologies

Amgen • South San Francisco, CA

4d • $165,637 - $224,097

About The Position

Amgen is seeking an experienced Principal Scientist to support and advance the Amgen Comparative Medicine Genetically Engineered Models (GEM) Program. This role will provide scientific and technical expertise in the molecular characterization and qualification of genetically engineered models, supporting model integrity from generation through colony establishment and experimental use. The individual will also contribute to building scalable GEM capabilities through sequencing, automation, computational approaches, and emerging AI-enabled tools. The ideal candidate will bring extensive experience with genetically engineered models, genome engineering, and molecular validation, with the scientific judgment to evaluate complex engineered alleles and troubleshoot unexpected molecular or genotype findings. Strong hands-on expertise in CRISPR-based model generation and characterization, qPCR/ddPCR, long-read sequencing, NGS, automation, bioinformatics, and computational analysis is highly desirable. Experience with engineered cell systems, including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), would be an additional strength. A major focus will be developing fit-for-purpose GEM molecular characterization strategies, including orthogonal genotyping, allele and structural integrity, copy number and zygosity, mosaicism, off-target analysis, and sequencing. The role will also advance scalable automation, computational, and AI-enabled approaches for model design, sequence analysis, data interpretation, and workflow integration to improve GEM quality, efficiency, and scientific decision-making. This is a highly hands-on Principal Scientist role requiring deep technical expertise, independent scientific judgment, innovation, and strong problem-solving skills. The individual will collaborate across internal and external teams to resolve complex model questions and ensure GEMs are appropriately characterized for their intended scientific use.

Requirements

• Doctorate degree [and relevant post-doc where applicable] in Molecular Biology, Genetics, Cell Biology, Bioinformatics, or a related scientific discipline and 2 years of relevant research and industry experience
• Master’s degree in Molecular Biology, Genetics, Cell Biology, Bioinformatics, or a related scientific discipline and 5 years of relevant research and industry experience
• Bachelor’s degree in Molecular Biology, Genetics, Cell Biology, Bioinformatics, or a related scientific discipline and 7 years of relevant research and industry experience

Nice To Haves

• Extensive experience with genetically engineered models, genome engineering, and molecular characterization, including knockout, knock-in, conditional, transgenic, humanized, and/or complex engineered models.
• Strong hands-on expertise in qPCR, multiplex ddPCR, Oxford Nanopore long-read sequencing, NGS, and sequencing-based characterization.
• Experience with CRISPR/Cas9 model design and generation, engineered-allele validation, and off-target assessment.
• Experience developing or implementing bioinformatics and computational workflows for sequencing analysis; programming experience, particularly Python, is highly desirable.
• Experience with automation and high-throughput molecular workflows and quantitative expression approaches such as RT-ddPCR.
• Experience with in vivo GEMs and engineered cell systems, including ESCs, iPSCs, HSPCs, or related systems, is preferred.
• Experience evaluating or implementing AI-enabled approaches for scientific analysis, model design, data interpretation, or workflow automation is desirable.
• Strong scientific judgment, experimental problem-solving, communication, and cross-functional collaboration skills, with the ability to translate complex molecular data into actionable scientific conclusions.

Responsibilities

• Develop and execute fit-for-purpose molecular characterization strategies for newly generated and existing genetically engineered models, including knockout, knock-in, conditional, transgenic, humanized, and complex multi-allelic models.
• Design, develop, validate, and troubleshoot qPCR, multiplex ddPCR, long-read sequencing, NGS, and other orthogonal molecular assays.
• Characterize engineered alleles for sequence and structural integrity, copy number, zygosity, mosaicism, insertion sites, off-target effects, and unintended editing events.
• Resolve complex or inconclusive molecular and genotyping results by integrating complementary analytical approaches.
• Establish reproducible QC standards and workflows for internal GEM characterization.
• Develop and optimize Oxford Nanopore long-read sequencing and NGS workflows to characterize engineered alleles, structural variants, insertion sites, and complex genome-editing outcomes.
• Develop quantitative expression approaches, including RT-ddPCR and related assays, to assess the molecular consequences and expression of engineered alleles.
• Integrate genotype, sequence, and expression data to provide high-confidence characterization and interpretation of GEMs.
• Evaluate emerging molecular and sequencing technologies that improve scientific rigor, scalability, and turnaround time.
• Develop and implement scalable computational workflows for sequencing analysis, QC, visualization, interpretation, and reporting.
• Apply programming, bioinformatics, and AI-enabled approaches to model design, sequence and off-target analysis, molecular data interpretation, troubleshooting, and workflow automation.
• Partner with computational and bioinformatics scientists to integrate molecular characterization data and develop standardized analytical pipelines.
• Identify opportunities to use AI and automation to improve scientific decision-making, efficiency, and scalability across the GEM lifecycle.
• Develop automated and high-throughput workflows for genotyping, sequencing, and molecular characterization.
• Optimize laboratory instrumentation and automation to improve throughput, reproducibility, data quality, and efficiency.
• Evaluate and implement new technologies that expand GEM characterization capabilities.
• Contribute to scalable GEM laboratory, data, and analytical infrastructure, including SOPs, QC checkpoints, documentation, and traceability standards.
• Work closely with the GEM Lead, Comparative Medicine, Therapeutic Area scientists, computational teams, Functional Genomics, and external partners to resolve complex model questions.
• Serve as a scientific and technical resource for GEM molecular characterization, genome engineering, sequencing, and genotype interpretation.
• Communicate complex molecular findings clearly to support model selection, troubleshooting, and scientific decision-making, and contribute to training and knowledge transfer.
• Apply rigorous early molecular characterization to identify model issues before unnecessary colony expansion or downstream experimental investment.
• Ensure work aligns with animal-welfare considerations and the 3Rs principles of Replacement, Reduction, and Refinement.
• Contribute to continuous improvement of GEM technologies, workflows, and scientific standards.

Benefits

• A comprehensive employee benefits package, including a Retirement and Savings Plan with generous company contributions, group medical, dental and vision coverage, life and disability insurance, and flexible spending accounts
• A discretionary annual bonus program, or for field sales representatives, a sales-based incentive plan
• Stock-based long-term incentives
• Award-winning time-off plans
• Flexible work models where possible.

What This Job Offers

• Job Type: Full-time
• Career Level: Principal
• Education Level: Ph.D. or professional degree