Senior Data Scientist, Predictive Immune Biomarkers

Merck; Cambridge (MA); On-site; USD 145,000 - 228,000; Full time

Job summary

Merck is seeking a Senior Scientist, Predictive Immune Biomarkers (R3) to lead the development of foundation models and multi-omics analyses for patient stratification. You will work on integrating RNA-seq, spatial transcriptomics, and proteomics to identify predictive immune biomarkers in a fast-paced environment.

The role requires a PhD in a STEM field, strong programming in R/Python/Bash, and experience with HPC/AWS. Excellent communication and collaboration skills are essential.

Qualifications

• PhD in a STEM field (listed) with strong research track record in multi-omics.
• Proven experience building, fine-tuning, and benchmarking foundation models for biomarker tasks.
• Strong programming in R, Python, and Bash; HPC and AWS experience.
• Experience with QC/analysis of RNA-seq, spatial transcriptomics, and proteomics.
• Excellent written and verbal communication; ability to document methods clearly.

Responsibilities

• Build, evaluate and benchmark foundation models for predictive immune biomarkers.
• Perform QC/analysis of bulk and single-cell RNA-seq, spatial transcriptomics and proteomics data.
• Document analysis workflows and results; collaborate across teams.

Skills

Multi-omics analysis

Foundation models

R

Python

Bash

HPC

AWS

Biomarker discovery

Genomics

Data science

Education

PhD in STEM field

Tools

Limma

Seurat

scanpy

CosMx

10x Visium

OLINK

Mass spectrometry

Job description

• Multi-omics Integration: Integrate multi-omics datasets, including gene/protein expression, spatial transcriptomics, and genotype data.

Job Description

Senior Scientist, Predictive Immune Biomarkers (R3)

Key Responsibilities

• Foundation Models: Build, fine-tune, troubleshoot, and benchmark foundation models for predictive immune biomarker discovery.


• Multi-omics Analysis: Perform quality control (QC) and analysis of different molecular data types including bulk and single-cell RNA-seq (e.g., Limma, Seurat, scanpy), spatial transcriptomics (e.g., CosMx, 10x Visium), and proteomics (e.g., OLINK, mass spectrometry-based approaches).


• Multi-omics Integration: Integrate multi-omics datasets, including gene/protein expression, spatial transcriptomics, and genotype data.


• Documentation: Prepare detailed documentation of analysis methods and results in a timely manner.

Required Qualifications

• Ph.D. in Computer Science, Engineering, Data Science, AI/ML, Bioinformatics, Computational Biology, Genetics & Genomics, Mathematics, Statistics, Physics, Pharmaceutical Science, or related STEM field.


• A proven track record in multi-omics analysis.


• Hands-on experience with building, fine-tuning, benchmarking foundation models, preferably for patient stratification related downstream tasks.


• Fundamental understanding of AI/ML methods, multi-omics data analysis, and omics integration (e.g., RNA-Seq, single-cell RNA-Seq, genotype, spatial transcriptomics, OLINK).


• Proficiency in R, Python, and Bash, with the ability to establish best practices for reproducible data analyses.


• Experience with high-performance computing (HPC) systems and AWS Cloud Services (e.g., IAM, S3 buckets).


• A collaborative and self-motivated individual with a strong work ethic, capable of managing multiple objectives in a dynamic environment and adapting to changing priorities.


• Excellent written and verbal communication skills.

Preferred Qualifications

• Good understanding of autoimmune disease biology.


• Experience in processing and analyzing real-world data.


• Familiarity with spatial transcriptomics analysis.


• Knowledge of statistical and population genetics principles.

Required Skills

Autoimmune Diseases, Biomarkers, Cellular Immunology, Computational Biology, Data Science, Genetic Analysis, High Performance Computing (HPC), Immunology Research, Machine Learning (ML), Omics, RNA-Seq, Stratification, Transcriptomics

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.

Requirements

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.

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.

Search Firm Representatives Please Read Carefully

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/International

VISA Sponsorship

Yes

Travel Requirements

10%

Flexible Work Arrangements

Not Applicable

Shift

Not Indicated

Valid Driving License

No

Hazardous Material(s)

n/a

Job Posting End Date

08/28/2026

• 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.

Requisition ID

R412803