Associate Principal Scientist, Biomarker Discovery Automation & Engineering, Multi-omics

Job Description

We are seeking a dedicated and highly motivated automation engineer/scientist to join the Data, AI & Genome Sciences (DAGS) group at our Research Laboratories in Cambridge, MA. The successful candidate will focus on the development, implementation, operation, and optimization of automated systems and associated instrumentation supporting single-cell, spatial, and molecular omics workflows, with particular impact in Immunology Biomarker Discovery. This individual will join the Spatial and Single Cell Multiomics (SSM) Team within DAGS, a creative and highly collaborative group that leverages cutting-edge automation and advanced multiomics technologies to drive Biomarker Discovery and innovation across the drug development pipeline, from pre-clinical to clinical stages. Our team applies Spatial Multiomics platforms including CosMx WTx, Xenium, COMET mIF, Digital Pathology, and MSI as multi-omics single-cell approaches including REAP-seq/CITE-seq, CROP-seq/Perturb-seq, immune profiling, and Multiome ATAC-seq. SSM collaborates closely with therapeutic areas including Oncology, Immunology, Neuroscience, and Cardiometabolic Disease, as partner functions across Data, AI & Genome Sciences, Data Science & Scientific Informatics, Quantitative Bioscience, and ChemBio within the Discovery, Preclinical and Translational Medicine (DPTM) organization.

Key Responsibilities

• Collaborate closely with experimental biologists, automation engineers, data scientists, and therapeutic area subject matter experts to develop and implement scalable automation workflows that enable high-quality, reproducible data generation in a timely manner.

• Develop, implement, optimize, and validate automated workflows for single-cell, spatial, and molecular omics assays, including Parse-seq, 10x Flex, CROP-seq/Perturb-seq, immune profiling, Multiome ATAC-seq, spatial workflows, Olink HT, high-throughput CRISPR screens, and complex cell-based model systems.

• Integrate instrumentation, process controls, and QC metrics into automated workflows to improve robustness, reduce variability, and enable scalable laboratory operations.

• Monitor automated systems during workflow execution and perform system- and instrument-level troubleshooting, coordinate maintenance, and drive error recovery as needed.

• Support technology transfer, workflow scale-up, and deployment of new automated methods into routine laboratory operations.

• Prepare, document, and maintain automation methods, workflow parameters, SOPs, and experimental records to support reproducibility, compliance, and operational rigor.

• Partner proactively with cross-functional teams across DAGS, Therapeutic Areas, and RaDS-IT to accelerate impact on biomarker discovery and early drug discovery efforts.

• Clearly communicate workflow designs, protocols, performance metrics, and experimental results through presentations, technical documentation, and reports to stakeholders and senior leadership.

Required Education

• Ph.D. in engineering, molecular biology, cell biology, genomics, computational biology or a related STEM discipline, with 3–5+ years of post-graduate industry experience.

Required Skills and Experience

• Strong experience developing, implementing, and supporting automated workflows for single-cell, spatial, and/or multi-omics assays.

• Experience with automated systems and associated instrumentation used in omics workflow execution.

• Experience supporting technology transfer, assay scale-up, and deployment of new automated workflows into routine laboratory operations.

• Experience driving workflow standardization, operational excellence, and continuous improvement initiatives.

• Experience integrating instrumentation, process controls, assay monitoring, and quality control metrics into automated laboratory workflows.

• Strong experience troubleshooting automated workflows, monitoring instrument performance, and managing error recovery during execution.

• Strong understanding of experimental design principles, with excellent organizational and documentation skills, including preparation of SOPs, protocols, and technical summaries.

• Demonstrated problem-solving ability, critical thinking, and analytical skills.

• Excellent written and verbal communication skills, with the ability to train and mentor scientists with levels of experience.

• Ability to manage multiple projects simultaneously in a fast-paced, highly collaborative, matrixed environment.

• Experience working in Linux/Unix environments and high-performance computing (HPC) clusters.

Preferred Skills and Experience

• Experience applying automation to biomarker discovery, translational research, and/or Immunology and Oncology research settings.

• Experience with automation platforms, scripting, or workflow control tools relevant to high-throughput biology laboratories.

• Fluency in scripting and data visualization tools such as Basic HSL, R, R Shiny, Python, and/or MATLAB.

• Familiarity with matrixed collaboration across functional areas including therapeutic areas, data science, engineering, and IT.

• A strong publication, patent, or technical contribution record in relevant areas

What We Are Looking For

If you are passionate about leveraging cutting-edge technologies to drive scientific discovery and have the skills and experience outlined above, we encourage you to apply for this exciting opportunity to join our team at our Research Laboratories.

#EligibleforERP

Required Skills:

Automation, Cell-Based Assays, Genomics, High-Performance Computing (HPC) Systems, High-Throughput Screening, Laboratory Automation, Linux, Molecular Biology, Omics, Omics Technologies, Single Cell Analysis, Transcriptomics, Unix

Preferred Skills:

Current Employees apply HERE

Current Contingent Workers apply HERE

US and Puerto Rico Residents Only:

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.

As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics.  As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

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We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.

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The salary range for this role is

$144,800.00 - $227,900.00

This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee’s position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.

The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits.  Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits.

You can apply for this role through https://jobs.merck.com/us/en (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.

San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles’ Fair Chance Initiative for Hiring Ordinance

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Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company.  No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails. 

Employee Status:

Regular

Relocation:

Domestic

VISA Sponsorship:

Yes

Travel Requirements:

10%

Flexible Work Arrangements:

Not Applicable

Shift:

Not Indicated

Valid Driving License:

No

Hazardous Material(s):

BSL2, human biospecimens

Job Posting End Date:

06/8/2026

*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.