Computational Scientist II Position Available In Middlesex, Massachusetts

Computational Scientist II Broad Institute United States, Massachusetts, Burlington Jun 24, 2025 Description & Requirements The Translational Analysis Group (TAG) at the Broad Institute of MIT and Harvard, led by Dr. Mark Fleharty, is seeking a Computational Scientist II with extensive experience building and maintaining NGS pipelines. In this full-time, on-site role, you will design and implement next-generation workflows for liquid biopsy assays in pediatric oncology. You’ll collaborate with biologists, clinicians, data scientists, and software engineers to translate novel scientific insights into production-ready computational tools. TAG’s mission is to move liquid biopsy from proof-of-concept to clinically validated assays for sensitive cancer detection and monitoring in children.
Responsibilities
As a Computational Scientist II, you will:
Lead the design, implementation, and continuous improvement of robust, reproducible pipelines for analysis of liquid biopsy NGS data-encompassing sample QC, alignment, error correction, variant calling, annotation, and results delivery.
Develop and validate novel algorithms for ultra-sensitive detection of somatic variants, rare event calling, and multi-modal biomarker integration.
Drive performance benchmarking and analytical validation using both synthetic and clinical datasets; partner with wet lab and clinical teams to refine pipeline inputs and outputs.
Collaborate closely with software engineers to ensure scalable, production-ready workflows and with wet lab scientists to ensure computational methods fit experimental realities.
Champion best practices in version control, code review, automated testing, and documentation (e.g., GitHub, containerization, CI/CD pipelines)
Mentor and advise junior computational team members; foster a culture of knowledge sharing, curiosity, and continual learning.
Present findings and methods to internal and external stakeholders, contribute to publications, grants, and regulatory submissions.
Remain at the forefront of new technologies and methods in the liquid biopsy and bioinformatics space, actively shaping our analytical strategy and scientific vision.
Qualifications
PhD in Bioinformatics, Computational Biology, Computer Science, Engineering, or related quantitative discipline.
Proven expertise developing, optimizing, and maintaining advanced bioinformatics pipelines for NGS data, preferably in liquid biopsy, minimal residual disease, or somatic variant detection contexts.
Mastery of at least two programming languages, including one higher-level language such as Python or R, and one lower-level language such as C++ or Rust, for data analysis and pipeline development; experience with workflow orchestration tools (e.g., Nextflow, Cromwell) and cloud or distributed computing environments.
Deep understanding of molecular biology underlying liquid biopsy technologies-cfDNA/ctDNA biology, error suppression, and the statistical and technical nuances of ultra-low-frequency variant detection.
Demonstrated experience benchmarking analytical methods, using gold-standard truth sets and orthogonal validation, and familiarity with clinical assay validation requirements (e.g., CLIA, CAP, frameworks)
Excellence in scientific communication-clear, actionable reporting, documentation, and team-wide dissemination of best practices.
Strong track record of cross-functional teamwork, mentoring, and capacity-building in computational teams.
Self-motivated, adaptable, detail-oriented; able to manage multiple priorities in a fast-evolving environment.
Commitment to scientific rigor, reproducibility, and open, collaborative problem-solving.