Computational Associate II - Xavier Lab

Broad Institute; Cambridge (MA); On-site; USD 90,000 - 120,000; Full time

Benefits offered by this job

Medical insurance

401(k) retirement plan

Paid holidays

Job summary

The Broad Institute of MIT and Harvard seeks a Computational Associate II to provide computational support for cross-disciplinary, multi-omic projects in the Xavier Lab and Klarman Cell Observatory. You will analyze single-cell and spatial datasets, develop pipelines, and collaborate with wet and dry lab scientists to translate data into biological insights.

Ideal candidates have 2+ years of related experience, strong Python/R skills, and familiarity with ML/deep learning.

Qualifications

• A BS degree and a minimum of 2+ years of related experience with a publication record, or an MS 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 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

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

Skills

Python

R

ML

Single-cell data

Education

BS degree in Computer Science / Biology / Bioinformatics or related

MS in CS/Engineering/Biology/Bioinformatics or related

Tools

Jupyter

Git

RStudio

Job description

Description & Requirements

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/

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.