Computational Scientist - MDL

Overview

The Broad Institute of MIT & Harvard is seeking an outstanding and innovative Computational Scientist to join the Methods Development Lab. The core mission is the development of novel, scalable computational methods and robust analytical pipelines for the interrogation of ultra high-throughput single-cell multiomic data, including analyses of transcriptomics, proteomics, epigenomics, and large-scale perturbation datasets (e.g., Perturb-seq). The successful candidate will critically and creatively dissect complex single-cell datasets across multiple technology platforms, collaborate with experimental research scientists, contribute to methods innovation and open-source software development, execute rigorous data analysis, and communicate results to contribute to high-impact manuscripts.

This role emphasizes shared success, team-based problem solving, and the ability to guide experimental protocol development through computational insights.

Must be able to work onsite in Cambridge, MA five days per week.

Pay Range: 88,000 – 124,000 USD annually. The Broad Institute provides a comprehensive benefits package in addition to base pay.

• Innovate and engineer novel computational methods and algorithms to address analytical challenges in ultra high-throughput single-cell multiomic datasets.
• Design, build, optimize, and maintain robust analytical pipelines for processing massive single-cell datasets, ensuring scalability, performance, and reproducibility across HPC and cloud environments.
• Contribute significantly to open-source software development by documenting and packaging novel methods and software for community use and future projects.
• Develop and apply specialized analytical techniques for the quantitative assessment of Perturb-seq and related single-cell perturbation screens, including accurate gRNA assignment and on-target knockdown efficiency evaluation.
• Execute in-depth, creative analyses on complex single-cell datasets, leveraging established best practices and newly developed methods to extract critical biological insights.
• Collaborate seamlessly with experimental teams, leveraging computational results to guide and optimize the development of novel experimental protocols.
• Present results, methodology, and insights clearly at group meetings, and contribute substantively to writing and preparation of manuscripts and publications.

• Ph.D. in Computational Biology, Computer Science, or a related quantitative field with 2+ years of relevant work experience.
• Proven expertise in analyzing single-cell RNA-seq and related sequencing modalities, with strong emphasis on computational methods development and innovation.
• Direct experience in designing and analyzing single-cell perturbation screens (e.g., Perturb-seq), including gRNA assignment and on-target efficiency evaluation.
• Experience developing computational strategies for identification, quantification, and functional interpretation of alternatively spliced RNA isoforms from single-cell long-read sequencing data.
• Publication history in single-cell RNA-seq computational methodology is strongly preferred.
• Expert proficiency in Python and R for statistical analysis, algorithm development, and data visualization; experience designing, building, and deploying scalable and reproducible analytic pipelines in a cloud computing environment.
• Strong foundational knowledge of statistical and machine learning techniques applied to high-dimensional biological data, including data integration, batch correction, and dimensionality reduction.
• Ability to work both independently and collaboratively; experience across research groups with bench-to-analysis collaboration.
• Ability to critically read and discuss scientific publications, especially on novel computational methodologies; excellent written and verbal communication skills.
• Ability to thrive in a fast-paced, rapidly changing environment.

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