Principal Scientist
Amgen
5 hours ago
On-site
South San Francisco, CA
Clinical Research and Development
Principal Scientist
What You Will Do
Build, optimize, and scale the molecular characterization engines behind the GEM platform, providing rigor, innovation, and technical leadership for the research pipeline.
Key Responsibilities
- Design, develop, and execute genotyping and characterization assays using ddPCR, qPCR, long-read sequencing (ONT), and NGS platforms.
- Develop and implement validation strategies, including:
- Off-target analysis (e.g., CRISPR specificity, rhAmpSeq or similar approaches)
- Copy number variation (CNV) and zygosity determination
- Structural variant and insertion site mapping
- Allele configuration confirmation across model types
- Perform comprehensive characterization of GEMs, including CRISPR-engineered knockout, knock-in, conditional, large insertions, and complex multi-gene models.
- Integrate molecular and sequencing data to generate high-confidence conclusions and support delivery of fully characterized, high-quality models.
- Drive implementation and optimization of high-throughput workflows (liquid handling automation and integrated genotyping pipelines).
- Evaluate and implement emerging technologies to enhance characterization, throughput, and data quality.
- Contribute to continuous improvement of genotyping pipelines and sequencing-based workflows.
- Apply technical expertise to setup, optimize, and troubleshoot instrumentation platforms (e.g., ddPCR, ONT, fragment analyzers, automation systems).
- Develop and maintain SOPs, instrument logs, and performance tracking.
- Build scalable lab infrastructure to support increasing GEM portfolio complexity.
- Collaborate with the GEM Lead and cross-functional teams (Comparative Medicine, Therapeutic Areas, Functional Genomics) and external CROs.
- Serve as a scientific resource for model validation strategies and risk assessment.
- Support implementation of sample tracking, data management, and reporting systems (e.g., Benchling or equivalent ELN).
- Ensure documentation and traceability from experimental design through model validation; define QC checkpoints.
- Share expertise, train lab personnel, develop best practices/standardized workflows, and contribute to scientific/technical documentation.
- Ensure work aligns with animal welfare and 3Rs principles (Replacement, Reduction, Refinement).
Basic Qualifications
- PhD/PharmD/MD plus 2 years of experience in genetically engineered models (GEM), genotyping, and molecular characterization
OR
- Master’s plus 5 years of experience in GEMs, genotyping, and molecular characterization
OR
- Bachelor’s plus 7 years of experience in GEMs, genotyping, and molecular characterization
Preferred Qualifications / Skills
- Hands-on expertise in CRISPR genome engineering and complex model generation
- ddPCR, qPCR, and long-read sequencing (e.g., Oxford Nanopore Technologies)
- NGS workflows and genomic analysis
- Experience characterizing complex GEM models (KO, KI, conditional, multi-allelic, transgenic) using CRISPR and/or ES cell-based approaches
- Experience with automation platforms and high-throughput screening (e.g., Beckman, Tecan, acoustic dispensing)
- Proven ability to contribute to lab workflow development, infrastructure setup, and process optimization
- Experience working with CROs and cross-functional teams
- Proficiency with Benchling or similar ELN/LIMS platforms
- Strong communication, collaboration, and problem-solving skills
Benefits (explicitly stated)
- Retirement and Savings Plan with company contributions; group medical, dental, and vision; life and disability insurance; flexible spending accounts
- Discretionary annual bonus (or sales-based incentive for field sales reps)
- Stock-based long-term incentives
- Time-off plans
- Flexible work models where possible
Application Instructions
- Apply at careers.amgen.com
- Anticipated application deadline: April 22, 2026 (applications may continue beyond this date)
- Sponsorship for this role is not guaranteed
What You Will Do
Build, optimize, and scale the molecular characterization engines behind the GEM platform, providing rigor, innovation, and technical leadership for the research pipeline.
Key Responsibilities
- Design, develop, and execute genotyping and characterization assays using ddPCR, qPCR, long-read sequencing (ONT), and NGS platforms.
- Develop and implement validation strategies, including:
- Off-target analysis (e.g., CRISPR specificity, rhAmpSeq or similar approaches)
- Copy number variation (CNV) and zygosity determination
- Structural variant and insertion site mapping
- Allele configuration confirmation across model types
- Perform comprehensive characterization of GEMs, including CRISPR-engineered knockout, knock-in, conditional, large insertions, and complex multi-gene models.
- Integrate molecular and sequencing data to generate high-confidence conclusions and support delivery of fully characterized, high-quality models.
- Drive implementation and optimization of high-throughput workflows (liquid handling automation and integrated genotyping pipelines).
- Evaluate and implement emerging technologies to enhance characterization, throughput, and data quality.
- Contribute to continuous improvement of genotyping pipelines and sequencing-based workflows.
- Apply technical expertise to setup, optimize, and troubleshoot instrumentation platforms (e.g., ddPCR, ONT, fragment analyzers, automation systems).
- Develop and maintain SOPs, instrument logs, and performance tracking.
- Build scalable lab infrastructure to support increasing GEM portfolio complexity.
- Collaborate with the GEM Lead and cross-functional teams (Comparative Medicine, Therapeutic Areas, Functional Genomics) and external CROs.
- Serve as a scientific resource for model validation strategies and risk assessment.
- Support implementation of sample tracking, data management, and reporting systems (e.g., Benchling or equivalent ELN).
- Ensure documentation and traceability from experimental design through model validation; define QC checkpoints.
- Share expertise, train lab personnel, develop best practices/standardized workflows, and contribute to scientific/technical documentation.
- Ensure work aligns with animal welfare and 3Rs principles (Replacement, Reduction, Refinement).
Basic Qualifications
- PhD/PharmD/MD plus 2 years of experience in genetically engineered models (GEM), genotyping, and molecular characterization
OR
- Master’s plus 5 years of experience in GEMs, genotyping, and molecular characterization
OR
- Bachelor’s plus 7 years of experience in GEMs, genotyping, and molecular characterization
Preferred Qualifications / Skills
- Hands-on expertise in CRISPR genome engineering and complex model generation
- ddPCR, qPCR, and long-read sequencing (e.g., Oxford Nanopore Technologies)
- NGS workflows and genomic analysis
- Experience characterizing complex GEM models (KO, KI, conditional, multi-allelic, transgenic) using CRISPR and/or ES cell-based approaches
- Experience with automation platforms and high-throughput screening (e.g., Beckman, Tecan, acoustic dispensing)
- Proven ability to contribute to lab workflow development, infrastructure setup, and process optimization
- Experience working with CROs and cross-functional teams
- Proficiency with Benchling or similar ELN/LIMS platforms
- Strong communication, collaboration, and problem-solving skills
Benefits (explicitly stated)
- Retirement and Savings Plan with company contributions; group medical, dental, and vision; life and disability insurance; flexible spending accounts
- Discretionary annual bonus (or sales-based incentive for field sales reps)
- Stock-based long-term incentives
- Time-off plans
- Flexible work models where possible
Application Instructions
- Apply at careers.amgen.com
- Anticipated application deadline: April 22, 2026 (applications may continue beyond this date)
- Sponsorship for this role is not guaranteed