[Remote] Research Scientist I - The Shalek Lab

Note: The job is a remote job and is open to candidates in USA. The Broad Institute of MIT and Harvard is hiring a Research Scientist I to lead computational analysis and data integration for a cell-state engineering platform. The role involves analyzing perturbation screens and large-scale single-cell and multi-omic datasets, building reproducible workflows, collaborating with experimental and machine learning teams, and mentoring junior researchers.

Responsibilities

• Lead the computational design and analysis of pooled TF-ORF and other perturbation screens with scRNA-seq readouts, including benchmarking, quality-control frameworks, and end-to-end analysis pipelines, to map transcriptional states to fitness and functional phenotypes
• Build, document, and maintain scalable, reproducible workflows for large-scale single-cell data processing on high-performance and cloud computing infrastructure, including multiplexed sample demultiplexing and batch-effect correction
• Integrate large, heterogeneous datasets (perturbation screens, bulk and single-cell RNA-seq, public cell atlases, spatial and other multi-omic data, and genomic data) to identify gene programs and regulators of cancer cell-state transitions, immune tolerance, and drug resistance
• Collaborate closely with machine learning scientists to generate structured, well-annotated datasets for model training, evaluate model performance, and design experiments to validate model predictions
• Communicate study findings efficiently and present data at lab, institute, and external meetings as projects progress; contribute to manuscripts and preprints
• Collaborate extensively with colleagues across disciplines within the group and with external partners, including experimental biologists, computational scientists, clinicians, and industry scientists
• Train, mentor, and supervise junior computational and experimental researchers, rotation students, and visiting scholars

Skills

• Ph.D. in Bioengineering, Computational Biology, Bioinformatics, Medical Engineering, Data Science, or related quantitative fields
• 4+ years of relevant research experience applying computational approaches to large-scale single-cell and multi-omic data to solve biomedical problems
• Demonstrated experience analyzing pooled genetic perturbation screens (e.g., ORF/TF overexpression, CRISPR) with scRNA-seq readouts, including quality control, normalization, batch correction, and benchmarking
• Strong time management and communication skills to balance multiple analyses between several collaborators in a remote work environment
• Ability to multi-task and work independently under pressure
• Ability to work in a team environment, meet deadlines, and prioritize and balance work from multiple individuals
• Experience mentoring junior researchers
• Extensive experience integrating and analyzing multi-omics data (e.g., genetics, bulk RNA-seq, single-cell RNA-seq, spatial omics, public atlases) for biomedical research
• Proficient coding/scripting in Python and R, with experience in the scientific Python ecosystem (e.g., scanpy, pandas, scikit-learn) and sound software engineering practices (version control, reproducible workflows)
• Experience with Linux environments, high-performance computing and/or cloud computing, and broad experience with open-source bioinformatics tools to generate biological insight from large datasets
• High productivity, evidenced by high-quality collaborative science and research publications in peer-reviewed journals on which they are named co-authors
• Familiarity with perturbation screen design and the experimental workflows that generate the data is a plus
• Experience collaborating with machine learning scientists, such as preparing training datasets, benchmarking predictive models, or applying ML methods to biological data, is highly desirable

Benefits

• 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
• An employee assistance program

Company Overview

• The Broad Institute brings together a diverse group of individuals from across its partner institutions — undergraduate and graduate students, postdoctoral fellows, professional scientists, administrative professionals, and academic faculty. It was founded in 2003, and is headquartered in Cambridge, Massachusetts, USA, with a workforce of 1001-5000 employees. Its website is http://www.broadinstitute.org.

Company H1B Sponsorship

• Broad Institute of MIT and Harvard has a track record of offering H1B sponsorships, with 68 in 2026, 106 in 2025, 59 in 2024, 73 in 2023, 68 in 2022, 70 in 2021, 93 in 2020. Please note that this does not guarantee sponsorship for this specific role.