Associate Scientist, Post Doc Fellow- Immunology Analytics

MSD; Cambridge (MA); On-site; USD 65,000 - 90,000; Full time

Job summary

MSD in Cambridge, MA is seeking a Postdoctoral Research Fellow to join a cross-functional translational team focusing on immune-mediated inflammatory diseases. You will analyze large-scale single-cell and spatial transcriptomics data from human cohorts to identify cellular programs and translational biomarkers.

The role spans computational biology, immunology, and translational medicine, with opportunities to publish, present at conferences, and develop multi-omics frameworks to support

Qualifications

• PhD in Computational Biology, Bioinformatics, Systems Biology, Genomics or related field.
• Strong programming skills in R and Python with genomics data experience.
• Experience analyzing large-scale single-cell, spatial transcriptomics or multi-omics datasets.
• Demonstrated publication record in computational biology or related areas.
• Excellent communication and collaboration skills.

Responsibilities

• Analyze large-scale single-cell RNA-seq and spatial transcriptomics datasets.
• Develop computational methods for data integration and interpretation.
• Apply machine learning and network biology to generate biological insights.
• Collaborate with immunologists, clinicians, and computational researchers.
• Lead publication-quality analyses and contribute to peer-reviewed manuscripts.

Skills

R

Python

Genomics data analysis

Machine learning

Statistical modeling

Data visualization

Education

PhD in Computational Biology / Bioinformatics / Systems Biology / Genomics

Tools

Seurat

Scanpy

scVI

CellChat

MultiNicheNet

Xenium

CosMx

Visium

Job description

Postdoctoral Research Fellow, Single-Cell and Spatial Transcriptomics in Immune-Mediated Inflammatory Diseases

We are seeking a highly motivated Postdoctoral Research Fellow to join a cross-functional translational research team focused on understanding the cellular and tissue mechanisms underlying chronic immune-mediated inflammatory diseases. The successful candidate will leverage large-scale single-cell and spatial transcriptomics datasets from human tissue cohorts to identify disease-driving cellular programs, tissue microenvironments, and translational biomarkers.

This position offers a unique opportunity to work at the interface of computational biology, immunology, spatial genomics, and translational medicine while contributing to high-impact research programs spanning multiple therapeutic areas. The project aims to transform emerging multi-omics datasets into biological insights, biomarker hypotheses, disease-mechanism models, and translational strategies relevant to immune-mediated inflammatory diseases, including hidradenitis suppurativa (HS) and related disorders.

Career Development Opportunities

• Receive mentorship from experts across computational biology, immunology, translational medicine, and drug discovery.
• Publish first-author manuscripts in leading scientific journals.
• Present at major international scientific conferences.
• Develop expertise in cutting-edge single-cell, spatial, and multi-omics technologies.
• Build a strong interdisciplinary network across academia and industry.
• Gain experience translating complex biological datasets into actionable therapeutic insights.

Scientific Impact

The successful candidate will contribute to the development of comprehensive cellular and spatial atlases of chronic immune-mediated inflammatory diseases, generating insights into disease circuits, tissue microenvironments, biomarker biology, and translational mechanisms. The work is expected to result in multiple high-impact publications and presentations while providing foundational knowledge to support therapeutic discovery and development.

This research will help advance our understanding of how cellular programs and tissue organization contribute to disease pathogenesis and therapeutic response, enabling more precise approaches to target discovery, biomarker identification, and patient stratification.

Research Objectives

Build Cellular Atlases of Immune-Mediated Inflammatory Diseases

• Develop comprehensive single-cell transcriptomic references from diseased and comparator tissues.
• Identify disease-associated immune, epithelial, stromal, and vascular cell states.
• Harmonize and annotate cellular populations across cohorts and studies.
• Characterize molecular pathways and regulatory programs that drive disease heterogeneity.
• Define shared and disease-specific cellular mechanisms across inflammatory conditions.

Define Spatial Tissue Niches and Cellular Interactions

• Analyze spatial transcriptomics datasets to localize disease-associated cell states within tissue architecture.
• Characterize cellular neighborhoods and multicellular interaction networks in situ.
• Identify tissue microenvironments associated with inflammation, remodeling, fibrosis, and disease progression.
• Develop computational frameworks for spatial niche discovery and tissue organization analysis.
• Integrate spatial and single-cell datasets to generate mechanistic hypotheses regarding disease biology.

Mechanism of Action and Biomarker Discovery

• Evaluate target expression and pathway activity across cellular and spatial contexts.
• Identify biomarkers associated with disease biology, therapeutic response, and patient stratification.
• Characterize disease endotypes and molecular signatures linked to clinical heterogeneity.
• Integrate multimodal datasets to construct disease-mechanism and translational biology models.
• Generate hypotheses supporting therapeutic target evaluation and precision medicine approaches.

Key Responsibilities

• Analyze large-scale single-cell RNA-seq, spatial transcriptomics, and related multi-omics datasets.
• Develop and implement computational methods for data integration, annotation, and interpretation.
• Apply advanced bioinformatics, statistical modeling, machine learning, and network biology approaches.
• Integrate transcriptomic, spatial, proteomic, and clinical data to generate biological insights.
• Collaborate closely with immunologists, translational scientists, clinicians, and computational researchers.
• Lead publication-quality analyses and prepare manuscripts for peer-reviewed journals.
• Present findings at internal scientific forums and external conferences.
• Contribute to the development of innovative analytical methods and reusable computational resources.
• Collaborate across Data, AI and Genome Sciences (DAGS), Immunology Discovery, and Translational Medicine teams.

Qualifications

Education Minimum Requirement

• Must currently hold a PhD OR
• Receive a Ph.D. no later than spring 2027
• Ph.D. in Computational Biology, Bioinformatics, Systems Biology, Genomics, Computer Science, Statistics, or a related discipline.

Required Skills and Experience

• Strong programming skills in R and/or Python.
• Experience analyzing large-scale genomics or multi-omics datasets.
• Hands-on experience with GPU computing, HPC clusters, and AWS cloud environments for large-scale single-cell and spatial omics analyses.
• Ability to develop and optimize scalable computational pipelines for scRNA-seq, spatial transcriptomics, and multimodal biological data.
• Demonstrated publication record in computational biology, genomics, immunology, or related fields.
• Strong scientific communication, presentation, and collaborative skills.

Preferred Skills and Experience

• Single-cell omics analysis workflows (e.g., Seurat, Scanpy, scVI, CellChat, MultiNicheNet, or related tools).
• Spatial transcriptomics platforms such as Xenium, CosMx, Visium, MERFISH, or related technologies.
• Background in immunology, inflammatory diseases, tissue biology, or translational research.
• Machine learning, network analysis, systems biology, or multimodal data integration.
• Familiarity with cloud computing and high-performance computing environments.
• Working with large-scale human cohort datasets.

Preferred Skills

Bioinformatics, Biomarkers, Disease Research, High Performance Computing (HPC), Machine Learning, Researching, Signaling Pathways, Systems Biology, Transcriptomics, Translational Medicine

Required Skills