Computational Associate II - Xavier Lab

Broad Institute of MIT and Harvard; Cambridge (MA); On-site; USD 58,000 - 80,667; Full time

Job summary

The Broad Institute of MIT & Harvard seeks a Computational Associate II to support multi-omic analyses and develop novel methods within the Xavier Lab and Klarman Cell Observatory.

This role focuses on analyzing single-cell and spatial multi-omics data, developing pipelines, and collaborating with wet and dry-lab scientists. Opportunities to publish and present work across collaborating institutions exist.

Qualifications

• BS or MS with publication record or related experience; strong analytical skills.
• Proficiency in Python or R and ML/deep learning knowledge.
• Experience with biological data such as single-cell or spatial transcriptomics.

Responsibilities

• Analyze data across collaborations (e.g., single-cell RNA-Seq, spatial transcriptomics, proteomics, metabolomics).
• Develop, enhance, and maintain bioinformatics pipelines.
• Plan project requirements with leadership and execute tasks efficiently.
• Write maintainable, scalable code and learn new skills as needed.
• Present progress in group meetings and contribute to publications.
• Lead projects resulting in first-author publications.

Skills

Python

R

ML & deep learning

Single-cell data analysis

Spatial transcriptomics

Communication

Education

BS in related field

MS in Computer Science/Engineering or Biology/Bioinformatics

Job description

The Broad Institute of MIT & Harvard is seeking a highly motivated Computational Associate II to join the Xavier Lab and Klarman Cell Observatory to provide computational support to collaborative research projects. Our group utilizes multi-omic datasets—including single-cell and spatial transcriptomics, perturbation screens, metagenomics, and metabolomics—to study mechanisms driving health and disease. We are an interdisciplinary group with expertise in computational biology, functional genomics, microbiology, and immunology.

We are seeking a biologically curious individual with strong technical expertise who is driven to turn complex multi-omic datasets into biological insights. As a Computational Associate II you will work collaboratively with other lab members as well as lead independent analyses. In particular, we are seeking a candidate ready to analyze single cell and spatial multi-omics datasets and interested in the development of novel methods and workflows.

We offer a collaborative and rigorous research environment with strong connections between wet and dry labs. In this position you will work closely with computational and experimental biologists, including principal investigators, research scientists, postdocs, and graduate students. You will also have opportunities to publish and present your work and interact with our collaborators at MGH, MIT, Harvard, and the Broad Institute.

Responsibilities

• Analyze data across various internal and external collaborations (e.g., single-cell RNA-Seq, single-cell ATAC-Seq, spatial transcriptomics, proteomics, metabolomics, and/or microbiome data)
• Develop, enhance, and maintain current and new bioinformatics pipelines
• Work with other team members and leadership to plan project requirements and timelines, shift priorities as needed, and efficiently execute project tasks
• Write well-crafted, maintainable, scalable, and performant code
• Learn new technical skills and biological knowledge as needed
• Present project progress during group meetings
• Lead projects leading to first-author publications

Qualifications

• A BS degree and a minimum of 2+ years of related experience with a publication record, or an M.S. in Computer Science/Engineering, Biology, Bioinformatics, or a related field
• Python or R and knowledge of ML and deep learning methods
• Experience analyzing biological data, such as experience working with single cell and/or spatial transcriptomics data
• Independence, creativity, and attention to detail with excellent critical thinking, research, and analytical skills
• Excellent communication and interpersonal skills and the ability to work with biologists, computational biologists, data scientists, and software engineers in a fast-paced, highly collaborative environment
• Demonstrated ability to carry out a variety of tasks in parallel, recognize and solve problems effectively, and shift priorities rapidly

Selected Publications

• Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis https://pubmed.ncbi.nlm.nih.gov/31348891/
• The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon https://pubmed.ncbi.nlm.nih.gov/36720220/
• Bidirectional CRISPR screens decode a GLIS3-dependent fibrotic cell circuit https://pubmed.ncbi.nlm.nih.gov/41501466/
• Population-scale multiome immune cell atlas reveals complex disease drivers https://www.medrxiv.org/content/10.1101/2025.11.25.25340489v1
• A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions https://www.biorxiv.org/content/10.64898/2026.03.31.715361v2.full
• Bridging AI and biology: Foundation models meet human physiology and disease https://pubmed.ncbi.nlm.nih.gov/41519120/

Pay Range: $58,000.00/yr - $80,667.00/yr

The expected base pay range for this position as listed above is based on a 40 hour per week schedule. Broad provides pay ranges representing its reasonable and good faith estimate of what the organization reasonably expects to pay for a position at the time of posting. Actual compensation will vary based on factors including but not limited to, relevant skills, experience, education, qualifications, and other factors permissible by law.

At Broad, your base pay is just one part of a comprehensive total rewards package. From day one, this role offers a competitive benefits package including medical, dental, vision, life, and disability insurance; a 401(k) retirement plan; flexible spending and health savings accounts; at least 13 paid holidays; winter closure; paid time off; parental and family care leave; and an employee assistance program, among other Broad benefits.

The Broad Institute is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, national origin, religion, age, color, sex, disability, protected veteran status, or any other characteristic protected by local, state, or federal laws, rules, or regulations.

Should you need a reasonable accommodation to complete the application or interview process, please contact [e-mail] for assistance.