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

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

Job summary

Merck in Cambridge, MA invites applications for a Postdoctoral Research Fellow focused on AI-guided functional immunology. The project integrates single-cell transcriptomics, functional genomics, and human organoid models to uncover immunological disease mechanisms and generate experimentally validated insights.

You will develop perturbation modeling methods, design active-learning strategies, and collaborate across data science, immunology, and translational teams, communicating results through

Qualifications

• PhD in a quantitative field related to computational biology or AI/ML.
• PhD must be completed no later than spring 2027.
• Experience with single-cell omics or biomedical data analysis.
• Proficiency in Python and PyTorch.
• Experience applying deep models to high-dimensional biological data.

Responsibilities

• Advance AI/ML methods connecting single-cell models with perturbation data.
• Develop interpretable, reproducible computational approaches for perturbations in immune cells.
• Design perturbation experiments with experimental groups and map results to models.
• Create active learning and Bayesian optimization strategies for experimental design.
• Evaluate out-of-distribution generalization and model benchmarking.
• Collaborate with data science, immunology, and translational teams.
• Communicate findings via presentations and publications.

Skills

Machine learning

Publications / conference talks

Science communication

Education

PhD in Computational Biology / Bioinformatics / AI-ML / CS / Immunology

PhD by Spring 2027

Tools

Python

PyTorch

Job description

Job Description

Postdoctoral Research Fellow, AI-Guided Functional Immunology

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

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.

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

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:

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.

Learn more about your rights, including under California, Colorado and other US State Acts

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

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

Requisition ID: R420884