Computational Scientist I – MDL Full Time

The core mission of this role is the development of novel, scalable computational methods and robust analytical pipelines for the interrogation of ultra high-throughput single-cell multiomic data. This includes, but is not limited to, advanced analyses of transcriptomics, proteomics, epigenomics, and large-scale perturbation (e.g., Perturb-seq) datasets.

The successful candidate will be responsible for critically and creatively dissecting complex single-cell datasets across multiple technology platforms and modalities. We are seeking a highly motivated, collaborative, and strategically minded individual to drive scientific discovery in close partnership with experimental research scientists, who prioritizes shared success and team-based problem solving. The role requires a candidate who can contribute significantly to methods innovation and open-source software development, execute rigorous data analysis, and clearly communicate cutting-edge results to contribute substantively to high-impact manuscripts.

Responsibilities

• Innovate and engineer novel computational methods and algorithms to address critical analytical challenges in ultra high-throughput single-cell multiomic datasets.
• Design, build, optimize, and rigorously maintain robust analytical pipelines for processing massive single-cell datasets, ensuring scalability, high performance, and reproducibility across HPC and cloud environments.
• Contribute significantly to open-source software development by documenting and packaging all 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 both established best practices and newly developed methods to extract critical biological insights.
• Collaborate seamlessly with experimental teams, leveraging computational results to strategically guide and optimize the development of novel experimental protocols.
• Present results, methodology, and insights clearly at group meetings, and contribute substantively to the writing and preparation of manuscripts and publications.

Qualifications

• Ph.D. degree 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 a strong emphasis on computational methods development and innovation.
• Direct experience in the design and analysis of single-cell perturbation screens (e.g., Perturb-seq), including gRNA assignment and on-target efficiency evaluation.
• Experience developing computational strategies for the 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 & R for statistical analysis, algorithm development, and data visualization, including demonstrated experience designing, building, and deploying scalable and reproducible analytical 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.
• Strong ability to work both independently and collaboratively. Proven experience working across research groups, with close collaboration in a bench-to-analysis lab setting.
• Ability to critically read and discuss scientific research publications, especially those focused on novel computational methodologies.Excellent written and verbal communication skills, especially for describing complex methods and algorithms.
• Ability to thrive in a fast-paced, rapidly changing environment.

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

Pay Range: 88,000 – 124,000 Usd Annual

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 recruiting@broadinstitute.org for assistance.