Bioinformatics Analyst III

Overview

The successful candidate will work closely with stakeholders across the IPSI (Immune Profiling & Systems Immunology in Immunology Discovery) organization to advance the Single-Cell Fibroblast Atlas initiative. The role focuses on applying AI/ML and advanced computational methods to large-scale single-cell transcriptomic, proteomics, and spatial datasets to define fibroblast states, map tissue-specific niches, and uncover their roles in health and disease.

• Curate, harmonize, and analyze large-scale single-cell and spatial omics datasets (internal and public) with emphasis on fibroblast biology.
• Develop and optimize predictive AI/ML models to classify fibroblast states, identify regulatory networks, and generate disease-relevant insights.
• Integrate multi-modal data (scRNA-seq, spatial, etc.) to construct a comprehensive fibroblast atlas.
• Collaborate with other stakeholders.
• Build the Fibroblast Atlas to enable target discovery while driving cross-functional projects at the interface of data science, immunology, and translational medicine impacting the portfolio.
• Support senior analysts and scientists in implementing, training, and troubleshooting AI/ML models tailored to single-cell and spatial omics data.
• Ingest, clean, and preprocess large-scale single-cell transcriptomic and spatial datasets for single-cell atlas workflows.
• Collaborate with immunology and computational teams to translate biological questions on fibroblast states, niches, and disease roles into computational solutions.
• Document data curation, processing, and modeling pipelines to ensure reproducibility and transparency across the atlas project.
• Assist in interpreting model outputs to generate insights into fibroblast heterogeneity and tissue-specific function.
• Contribute to time-sensitive projects with critical deliverables, supporting target discovery and prioritization within the fibroblast atlas framework.

• MS degree (5+ years of experience) or PhD (0+ years of experience) in a quantitative field (Bioinformatics, Computational Biology, Computer Science, Computational Genetics, Biostatistics, AI/Machine Learning, or related discipline).
• Proficiency in Python and standard ML/data science libraries.
• Experience working on HPC or cloud environments for large-scale omics and imaging datasets.
• Domain knowledge in single-cell analysis, spatial omics, or systems immunology, ideally with exposure to fibroblast or stromal cell biology.
• Strong attention to detail, documentation, and communication skills.
• Ability to independently design, execute, and troubleshoot computational workflows.

• Experience with Num Py, Pandas, Scikit-learn, Matplotlib, and Seaborn.
• Familiarity with deep learning frameworks (Tensor Flow and/or PyTorch).
• Proficiency with Git for version control and collaboration.
• Hands-on experience with single-cell data analysis tools (e.g., Scanpy, Seurat, Bioconductor, or equivalent).
• Exposure to multi-modal integration methods (e.g., CITE-seq, ATAC-seq, proteomics, imaging mass cytometry, spatial transcriptomics).
• Experience with OpenCV, Scikit-image, or computer vision models for imaging datasets.
• Knowledge of cell type annotation, clustering, and trajectory inference methods.
• Experience building multi-modal AI/ML models that link transcriptomic, proteomic, and imaging data.

• Implementing, training AI/ML models.
• Data pre-processing for AI compatibility.
• Domain knowledge of bioinformatics.
• Experience working with single cell and spatial data (transcriptomics, proteomics, epigenomics, etc.).
• Ability to communicate results clearly.

• Mid-Senior level

• Contract

• Research, Analyst, and Information Technology

• Pharmaceutical Manufacturing

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