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

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

Job summary

MSD in Cambridge, MA seeks a Postdoctoral Research Fellow to advance AI-guided functional immunology. You will connect single‑cell foundation models with perturbation data and design experiment selections using active learning and Bayesian optimization.

The role emphasizes interpretable, reproducible computational approaches and collaboration across immunology, genomics, and translational research, with opportunities for publications and presentations.

Qualifications

• PhD in a quantitative field with strong computational biology or AI/ML breadth.
• PhD must be by Spring 2027 or already held.
• Experience in single‑cell omics or related biomedical data analysis required.

Responsibilities

• Advance AI/ML methods linking single‑cell foundation models with perturbation data.
• Develop interpretable computational approaches to predict perturbation effects on cell states.
• Design perturbation designs with experimental groups and feed data back into models.
• Develop active learning and Bayesian optimization strategies for knockouts and training sets.
• Evaluate out‑of‑distribution generalization and baseline comparisons.
• Collaborate with data science, immunology, functional genomics, and translational teams.
• Communicate findings via presentations and publications.

Skills

Machine learning

Deep learning

Data science

Python

PyTorch

Single‑cell analysis

Biomedical data analysis

Experiment design

Active learning

Bayesian optimization

Education

PhD in Computational Biology or related field

PhD expected by Spring 2027

Tools

PyTorch

Python

Job description

Postdoctoral Research Fellow, AI-Guided Functional Immunology

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:

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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*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.