Computational Scientist SMaHT Project

Overview

The Broad Institute, as one of five Genome Characterization Centers (GCCs), is part of a NIH-funded effort to catalog somatic genetic variation across human tissues. The SMaHT Network aims to enable downstream analyses such as mutation rates and burdens across tissues, mutational signature analysis, driver mutations and clonal expansions, and lineage tracing. We seek a highly motivated individual with a computational background to lead data curation and analyses for this project.

Some of our recent work includes Coorens et al., Nature 2025.

The successful candidate will join an interdisciplinary team working with a multimodal dataset from a wide range of human tissues and donors, including deep short- and long-read genomics, transcriptomics, epigenomics, and duplex sequencing data. The project offers opportunities to develop novel analytical methods for data QC, integration, detection of somatic mutations, multi-tissue analyses, and integration with transcriptomic data.

• Oversee the implementation of experimental work plans, pipelines for data processing, data organization, submission timelines, and analysis; contribute to budgetary and operational considerations.
• Communicate scientific details, results, and strategic considerations clearly to team members and the SMaHT network at large.
• Coordinate strategically across multiple groups at the Broad Institute and within the SMaHT Network; serve as a key contact for project leaders, collaborators (specifically the Data Analysis Center), and other staff.
• Design and execute data QC and analysis strategies involving multimodal human tissue datasets, and lead whole-genome short- and long-read DNA sequencing data, RNA sequencing, and somatic mutation analyses. Prior experience with long-read genomics and transcriptomics data is required.
• Apply and develop state-of-the-art computational tools and pipelines to assess data quality, integrate diverse data types and metadata, and detect somatic mutations and downstream analyses.
• Collaborate with internal technology development efforts for novel strategies to detect somatic mutations; develop new methodologies and evaluate methods for integrative analysis of genomic data types.
• Present ideas and results to the multidisciplinary SMaHT Network; prepare written reports and presentations for internal use and external conferences.

• PhD in Genomics, Bioinformatics, Computational Biology, Computer Science, Statistics, Math, or related quantitative field; 2+ years of industry experience preferred.
• Experience with computational analysis, algorithm development, and statistics is expected.
• Proven track record of leading complex data curation or analysis projects, ideally within large-scale consortia, is a strong plus.

• Deep Sequencing Expertise:
  Extensive experience with high-throughput biological data, including long-read genomic (Pac Bio/Oxford Nanopore) and transcriptomic data (RNA-seq).
• Pipeline Development:
  Proficiency in developing and maintaining reproducible computational pipelines using Python, R, or C++, and workflow managers like WDL, Nextflow, or Snakemake.
• Cloud Computing:
  Experience in cloud-based environments (e.g., Google Cloud Platform/Terra, AWS) for managing and processing petabyte-scale datasets.
• Somatic Mutation Analysis:
  Strong background in detecting and interpreting SNVs, indels, and SVs in human samples.
• Multimodal Data Integration:
  Demonstrated ability to integrate and analyze diverse data types, including transcriptomics, epigenomics, and duplex sequencing is a strong plus.

• Strategic Coordination:
  Ability to manage timelines and deliverables across multiple interdisciplinary groups within the Broad Institute and external collaborators (e.g., Data Analysis Center).
• Scientific Communication:
  Excellent verbal and written communication skills to present complex technical results to both specialist and general audiences.
• Adaptability:
  Motivated to work in a fast-paced, evolving research environment on a high-stakes, NIH-funded initiative.

Pay Range: 88, USD annual. The expected base pay range is based on a 40-hour week. Compensation varies by skills, experience, education, and other factors. Broad provides a comprehensive benefits package, including medical/dental/vision, 401(k), flexible spending and health savings accounts, paid holidays, paid time off, parental and family care leave, and an employee assistance program.

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 law. If you need a reasonable accommodation to complete the application or interview process, please contact recruiting for assistance.