Bioinformatics Analyst III

Bioinformatics Analyst III - Single-Cell Fibroblast Atlas Initiative
Hybrid – Cambridge, MA
**Hourly Pay Rate: $60-64/hr

Contract Through end of year
Top 3 – 5 Skills Needed:**
1. Implementing, training AI/ML models

1. Data pre-processing for AI compatibility

2. Domain knowledge of bioinformatics

3. Experience working with single cell and spatial data (transcriptomics, proteomics, epigenomics etc.)

4. Ability to communicate results clearly

Job Description:
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 will focus on applying AI/ML and advanced computational methods to large-scale single-cell transcriptomic, proteomics and spatial etc. datasets to define fibroblast states, map tissue-specific niches, and uncover their roles in health and disease.

By building the Fibroblast Atlas, the candidate will enable target discovery while driving cross-functional projects at the interface of data science, immunology, and translational medicine impacting the portfolio.

Key Responsibilities

• 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.

• 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 (public and internal) 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, tissue-specific function.

• Contribute to time-sensitive projects with critical deliverables, supporting target discovery and prioritization within the fibroblast atlas framework.

Qualifications:

• 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.

Preferred Technical Skills:

• Experience with NumPy, Pandas, Scikit-learn, Matplotlib, and Seaborn.

• Familiarity with deep learning frameworks (TensorFlow 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).

Additional Technical Skills (a plus):

• 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.

Our role in supporting 
diversity
 and 
inclusion
As an international workforce business, we are committed to sourcing personnel that reflects the diversity and values of our client base but also that of Orion Group. We welcome the wide range of experiences and viewpoints that potential workers bring to our business and our clients, including those based on nationality, gender, culture, educational and professional backgrounds, race, ethnicity, sexual orientation, gender identity and expression, disability, and age differences, job classification and religion. In our inclusive workplace, regardless of your employment status as staff or contract, everyone is assured the right of equitable, fair and respectful treatment.