Senior Data Scientist, Predictive Immune Biomarker Foundation Models

The Precision Genetics group within the Data, AI and Genome Sciences Department is seeking a Senior Scientist to join our Computational Precision Immunology team in Cambridge, MA. We are looking for a skilled data scientist with extensive experience to develop predictive biomarkers in immunology based on multi-modal and multi-scale data analyses.

• Foundation Models:
  Build, fine-tune, troubleshoot, and benchmark foundation models for predictive immune biomarker discovery.
• Multi-omics Analysis:
  Perform quality control (QC) and analysis of different molecular data types including bulk and single-cell RNA-seq (e.g., Limma, Seurat, scanpy), spatial transcriptomics (e.g., Cos Mx, 10x Visium), and proteomics (e.g., OLINK, mass spectrometry-based approaches).
• Multi-omics Integration:
  Integrate multi-omics datasets, including gene/protein expression, spatial transcriptomics, and genotype data.
• Documentation:
  Prepare detailed documentation of analysis methods and results in a timely manner.

• Ph.D. in Computational Biology or a related field.
• A proven track record in multi-omics analysis.
• Hands‑on experience with building, fine‑tuning, benchmarking foundation models, preferably for patient stratification related downstream tasks.
• Fundamental understanding of AI/ML methods, multi‑omics data analysis, and omics integration (e.g., RNA‑Seq, single‑cell RNA‑Seq, genotype, spatial transcriptomics, OLINK).
• Proficiency in R, Python, and Bash, with the ability to establish best practices for reproducible data analyses.
• Experience with high‑performance computing (HPC) systems and AWS Cloud Services (e.g., IAM, S3 buckets).
• A collaborative and self‑motivated individual with a strong work ethic, capable of managing multiple objectives in a dynamic environment and adapting to changing priorities.
• Excellent written and verbal communication skills.

• Good understanding of autoimmune disease biology.
• Experience in processing and analyzing real‑world data.
• Familiarity with spatial transcriptomics analysis.
• Knowledge of statistical and population genetics principles.

Autoimmune Diseases, Biomarkers, Cellular Immunology, Computational Biology, Data Science, Genetic Analysis, High Performance Computing (HPC), Immunology Research, Machine Learning (ML), Omics, RNA-Seq, Stratification, Transcriptomics

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The salary range for this role is $ - $

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…