Associate Scientist, Postdoctoral Research Fellow, AI-Guided Functional Immunology

Merck & Co.; Cambridge (MA); Hybrid; USD 82,000 - 92,000; Full time

Job summary

Merck & Co. is seeking a Postdoctoral Research Fellow in Cambridge to advance AI-guided functional immunology.

You will develop perturbation modeling integrating single-cell transcriptomics, functional genomics, and organoid models to uncover immunological disease mechanisms and generate experimentally validated insights. The role emphasizes designing active learning strategies, interpretable ML models, and collaboration with data science, immunology, and translational teams.

Qualifications

• PhD in Computational Biology, Bioinformatics, AI/ML, CS, Immunology, or related quantitative discipline.
• Proven research productivity: publications/preprints.
• Ability to communicate complex concepts to multidisciplinary teams.

Responsibilities

• Advance AI/ML methods linking single-cell foundation models with functional perturbation data.
• Develop interpretable, reproducible approaches to predict perturbation effects on cell states.
• Design perturbation designs with experimental groups and feed data back into models.
• Develop active learning or Bayesian optimization for perturbation testing strategies.
• Evaluate out-of-distribution generalization and model benchmarks.

Skills

Machine learning

Deep learning

Data science

Python

PyTorch

Single-cell omics

Communication

Education

PhD in Computational Biology or related field

Tools

PyTorch

CRISPR

Organoid models

Job description

Job Description

Postdoctoral Research Fellow, AI-Guided Functional Immunolog"y

Our AI/ML team develops biologically grounded and interpretable machine learning methods to accelerate target discovery across immunology. We are seeking a highly motivated Postdoctoral Research Fellow to develop next-generation perturbation modeling approaches that integrate single-cell transcriptomics, functional genomics, and human organoid models to elucidate immunological disease mechanisms and generate experimentally validated biological insightsf.

What You'll Do:

• Advance AI/ML methods that connect single-cell foundation models with functional perturbation data.
• Develop interpretable and reproducible computational approaches to predict how genetic and chemical perturbation of immune cells reshape cell states.
• Design and interpret perturbation designs together with experimental groups and feed the resulting data back into the models.
• Develop experiment-selection strategies (active learning, Bayesian optimization) that decide which knockouts the next round tests and characterize how a model-chosen training set biases its own evaluation.
• Design evaluations for out-of-distribution generalization held-out cell contexts, matched-decoy nulls, and the linear and mean baselines a foundation model must beat to earn trust.
• Collaborate with multidisciplinary teams across data science, immunology, functional genomics, and translational research.
• Communicate scientific findings through presentations, publications, and cross-functional discussions.

You Should Have:

• Strong expertise in machine learning, deep learning, and data science.
• Demonstrated research productivity through publications, preprints, or conference presentations.
• Ability to communicate complex technical concepts to multidisciplinary scientific teams.

Educational Requirement:

• Must currently hold a PhD OR
• Receive a Ph.D. no later than spring 2027
• Ph.D. in Computational Biology, Bioinformatics, AI/ML, Computer Science, Immunology, Bioengineering, Statistics, or a related quantitative discipline

Required Experience Skills:

• Experience with single-cell omics analysis, representation learning, or biomedical data analysis.
• Strong expertise in machine learning, deep learning, and data science.
• Proficiency in Python and deep learning frameworks such as PyTorch.
• Experience applying and evaluating deep models on high-dimensional biological data (single-cell, imaging, or similar).
• Proficiency in Foundation Models, Perturbation Modeling, and/or Organoid Models.
• Experience with CRISPR and target discovery.

Preferred Skills and Experience:

• Single-cell foundation models, transformers, and representation learning.
• Genetic perturbation modeling: CRISPR screens, Perturb-seq, or arrayed knockouts.
• Wet-lab experience, especially involving organoid, iPSC, or immune co-culture model systems.
• Background understanding of, or experience working in, immunology.
• Experimental design, active learning, or model benchmarking and evaluation.
• Publications in venues such as NeurIPS, ICML, ISMB/RECOMB, Cell Systems, Nature Methods, or related journals.

The salary range for this role is: $82,000-$92,000

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.

Required Skills: Biology, Computational Biology, Data Analysis, Design of Experiments (DOE), Image Analysis, Immunology Research, Programming Languages, Single-Cell Genomics, Statistical Analysis

Preferred Skills:

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.

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

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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:

Hybrid

Shift:

Not Indicated

Valid Driving License:

No

Hazardous Material(s):

N/A

Job Posting End Date:

10/19/2026

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:

R420884