Principal Scientist – GEM Molecular Validation & Technologies

Amgen Inc. (IR); South San Francisco (CA); On-site; USD 166,000 - 224,000; Full time

Benefits offered by this job

Retirement and Savings Plan

Stock-based long-term incentives

Flexible work models

Job summary

Amgen is seeking a Principal Scientist to support and advance the GEM program, focusing on molecular characterization of genetically engineered models from generation to colony establishment. You will drive sequencing, validation, and AI-enabled analysis to improve model quality and decision-making.

The role requires deep hands-on expertise in CRISPR-based model generation, qPCR/ddPCR, long-read sequencing, and data integration with expression analyses across internal and external teams.

Qualifications

• PhD/MD or Master’s with strong research and industry experience in molecular biology or genetics.
• Experience with genetically engineered models and genome engineering.
• Proven ability to design and interpret molecular characterization assays.

Responsibilities

• GEM molecular characterization strategy design and execution.
• Develop sequencing and expression assays (qPCR, ddPCR, NGS, long-read).
• Build scalable computational workflows for data analysis and reporting.
• Advance automation and high-throughput workflows for GEMs.
• Collaborate across teams to interpret data and support model decisions.
• Ensure animal-welfare considerations and adherence to 3Rs principles.

Skills

CRISPR/Cas9

qPCR

ddPCR

NGS

Automation

Python

Education

Doctorate in Molecular Biology

Master's in Molecular Biology

Bachelor's in Molecular Biology

Tools

Oxford Nanopore sequencing

Long-read sequencing

RT-ddPCR

Job description

Career Category Scientific Job Description

Join Amgen’s Mission of Serving Patients At Amgen, if you feel like you’re part of something bigger, it’s because you are. Our shared mission—to serve patients living with serious illnesses—drives all that we do. Since 1980, we’ve helped pioneer the world of biotech in our fight against the world’s toughest diseases. With our focus on four therapeutic areas –Oncology, Inflammation, General Medicine, and Rare Disease– we reach millions of patients each year. Amgen is advancing a broad and deep pipeline of medicines to treat cancer, heart disease, inflammatory conditions, rare diseases, and obesity and obesity-related conditions. As a member of the Amgen team, you’ll help make a lasting impact on the lives of patients as we research, manufacture, and deliver innovative medicines to help people live longer, fuller happier lives. Our award-winning culture is collaborative, innovative, and science based. If you have a passion for challenges and the opportunities that lay within them, you’ll thrive as part of the Amgen team. Join us and transform the lives of patients while transforming your career.

Principal Scientist – GEM Molecular Validation & Technologies

What you will do Let’s do this. Let’s change the world. We are 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.

Key Responsibilities

• GEM Molecular Characterization & Validation 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.
• Advanced Sequencing & Expression 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.
• Computational, AI & Data Analysis 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.
• Automation & Technology Development 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.
• GEM Scientific Infrastructure & Collaboration 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.
• Scientific & Animal‑Welfare Stewardship 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.

What we expect of you

We are all different, yet we all use our unique contributions to serve patients. The dynamic professional we seek is a leader with these qualifications.

Basic Qualifications

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 OR Master’s degree in Molecular Biology, Genetics, Cell Biology, Bioinformatics, or a related scientific discipline and 5 years of relevant research and industry experience OR Bachelor’s degree in Molecular Biology, Genetics, Cell Biology, Bioinformatics, or a related scientific discipline and 7 years of relevant research and industry experience.

Preferred Qualifications

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.

What you can expect of us

As we work to develop treatments that take care of others, we also work to care for your professional and personal growth and well‑being. From our competitive benefits to our collaborative culture, we’ll support your journey every step of the way. The expected annual salary range for this role in the U.S. (excluding Puerto Rico) is posted. Actual salary will vary based on several factors including but not limited to, relevant skills, experience, and qualifications. In addition to the base salary, Amgen offers a Total Rewards Plan, based on eligibility, comprising of health and welfare plans for staff and eligible dependents, financial plans with opportunities to save towards retirement or other goals, work/life balance, and career development opportunities that may include:

• 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

Refer to the Work Location Type in the job posting to see if this applies.

Salary & Benefits

Salary Range 165,636.95USD -224,097.05 USD

Sponsorship

Sponsorship for this role is not guaranteed.

Equal Opportunity Employer

Amgen is an Equal Opportunity employer and will consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or any other basis protected by applicable law. We will ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation. Amgen will consider for employment qualified applicants with criminal histories in a manner consistent with the San Francisco Fair Chance Ordinance.

Application Process

Application deadline Amgen does not have an application deadline for this position; we will continue accepting applications until we receive a sufficient number or select a candidate for the position.

Additional Information

In any materials you submit, you may redact or remove age‑identifying information such as age, date of birth, or dates of school attendance or graduation. You will not be penalized for redacting or removing this information.

About Amgen

Amgen is committed to unlocking the potential of biology for patients suffering from serious illnesses by discovering, developing, manufacturing and delivering innovative human therapeutics. This approach begins by using tools like advanced human genetics to unravel the complexities of disease and understand the fundamentals of human biology. Amgen focuses on areas of high unmet medical need and leverages its biologics manufacturing expertise to strive for solutions that improve health outcomes and dramatically improve people’s lives. A biotechnology pioneer since 1980, Amgen has grown to be one of the world’s leading independent biotechnology companies, has reached millions of patients around the world and is developing a pipeline of medicines with breakaway potential. For more information, visit www.amgen.com and follow us on www.twitter.com/amgen