Data Scientist – Immune Profiling & Multimodal AI

BostonGene; Waltham (MA); On-site; USD 111,000 - 176,000; Full time

Job summary

An innovative firm is seeking a Data Scientist to join their Digital Pathology and Multimodal Data Science team. This role focuses on analyzing high-dimensional immune datasets using computational biology and machine learning. The successful candidate will design pipelines for immune profiling analysis, collaborate with experts across disciplines, and contribute to groundbreaking research in precision immunology. This position offers a unique opportunity to work at the intersection of biology and technology, driving advancements in drug development and clinical decision-making.

Benefits

Medical insurance

Vision insurance

401(k)

Paid maternity leave

Paid paternity leave

Tuition assistance

Disability insurance

Qualifications

• PhD or MS with experience in immune system data analysis.
• Hands-on experience with immune profiling datasets.

Responsibilities

• Design and execute pipelines for immune-related data analysis.
• Integrate immune profiling data with clinical outcomes.

Skills

Python

R

Immunology

Data Analysis

Collaboration

Education

PhD in Immunology

MS with 2+ years experience

Tools

Flow Cytometry

CyTOF

CITE-seq

Single-cell RNA-seq

Job description

Direct message the job poster from BostonGene

BostonGene is redefining precision medicine with its AI-powered, multiomic approach to understanding and treating complex diseases. By integrating deep molecular profiling—including genomics, proteomics and the immune system—the platform delivers a systems biology view that accelerates drug development and clinical decision-making. With a CLIA-certified, CAP-accredited lab, BostonGene provides clinically validated insights that personalize care and support translational breakthroughs. Partnering with leading pharma, biotech and cancer centers, BostonGene drives innovation and advances transformative therapies.

Position Summary

We are seeking a Data Scientist with a focus on Immune Profiling and Immunology to join our growing Digital Pathology and Multimodal Data Science team. You will work at the interface of computational biology and machine learning to analyze high-dimensional immune datasets, including RNA-seq, flow cytometry, TCR/BCR sequencing, and spatial omics, and integrate them with pathology, transcriptomics, and clinical outcomes.

Key Responsibilities

• Immune Profiling Analysis: Design and execute pipelines to analyze immune-related data, including bulk and single-cell transcriptomics, flow cytometry, and immune repertoire sequencing (TCR/BCR).
• Multimodal Data Integration: Integrate immune profiling data with digital pathology, genomics, and clinical data to support AI model development and translational applications.
• Model Development Support: Collaborate with machine learning scientists to inform feature engineering, annotation strategies, and model interpretability based on immunological insights.
• Biomarker Discovery: Identify immune-related biomarkers of response, resistance, and disease subtypes using both hypothesis-driven and data-driven approaches.
• Collaborative Research: Partner with immunologists, pathologists, oncologists, and engineers to translate computational findings into biological and clinical insights.
• Innovation & Communication: Stay current on cutting-edge immune profiling and computational immunology tools, contribute to internal R&D initiatives, and support scientific publications and regulatory documentation.

Required Qualifications

• PhD (or MS with 2+ years experience) in Immunology, Computational Biology, Bioinformatics, or related field with a strong focus on immune system data analysis.
• Hands-on experience with immune profiling datasets (e.g., flow cytometry, CyTOF, CITE-seq, single-cell RNA-seq, TCR/BCR repertoire data).
• Proficiency in data analysis with Python and/or R; familiarity with immune deconvolution methods and immunophenotyping tools.
• Strong understanding of human immunology and its application in oncology or inflammatory diseases.
• Experience working with large patient datasets and integrating clinical metadata.
• Excellent collaboration and communication skills; ability to work across disciplines.

Preferred Qualifications

• Experience in multimodal data integration (e.g., linking immune data with spatial or histopathology data).
• Familiarity with AI/ML models and experience collaborating with ML teams.
• Industry or translational research experience in precision immunology or immuno-oncology.
• Knowledge of biomarker development and validation workflows.

What We Offer

• Work at the forefront of AI-enabled precision immunology
• Rich access to multimodal datasets across cancer and immune diseases
• A collaborative, fast-moving team at the intersection of biology and machine learning
• Competitive salary, equity, and full benefits package

Seniority level

• Seniority level

  Mid-Senior level

Employment type

• Employment type

  Full-time

Job function

• Job function

  Science

• Industries

  Biotechnology, Biotechnology Research, and Pharmaceutical Manufacturing

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Inferred from the description for this job

Medical insurance

Vision insurance

401(k)

Paid maternity leave

Paid paternity leave

Tuition assistance

Disability insurance

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