Computational & Systems Biology Program
The Kushal Dey Lab
Research
Assistant Professor
The Kushal Dey Lab builds statistical and machine learning models that integrate genetic and genomic data to prioritize variants, genes, and cell types, and to decode the causal functional architecture underlying heritable complex diseases — including immune-related diseases, like Alzheimer’s and inflammatory bowel disease, and heritable cancers, like breast cancer.
Nominating candidate risk genes and gene sets underlying disease-critical processes is of utmost importance for developing drug targets and informing CRISPR screening. The Kushal Dey Lab focuses on developing machine learning models and computational pipelines that integrate genomic and epigenomic data from RNA-seq, ChiP-seq, Perturb-seq and spatial transcriptomic experiments with genetic association studies (GWAS, WES) to enhance our understanding of the functional architecture of all heritable complex diseases, including immune-related diseases like Alzheimers’, IBD, Lupus and several heritable cancers like Breast and Prostate cancers.
Some of the research directions of interest include developing:
- Models to prioritize variants, genes and cell states for disease using a combination of genetic, genomic and perturbation data.
- Models to identify the causal directed graphs underlying gene and gene interaction models for disease.
- Benchmarking pipelines informed by disease genetics to validate and compare different genomic prediction models.
Publications Highlights
Mitra, S; Malik, R; Wong, W; Rahman, A; Hartemink AJ; Pritykin, Y; Dey, KK; Leslie, CS. 2024. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nature Genetics, 55, pp.627-636.
Jagadeesh, K.A.*, Dey, K.K.*, Montoro, D.T., Mohan, R., Gazal, S, Engreitz, J.M., Xavier, R.J., Price, A.L., and Regev, A., 2022. Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics. Nature Genetics, 54, pp. 1479-1492.
Dey, K.K., Gazal, S., van de Geijn, B., Kim, S.S., Nasser, J., Engreitz, J.M. and Price, A.L., 2022. SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease. Cell Genomics, 2(7), p.100145.
Delorey, T.M.*, .., Dey, K.K.* et al, 2021. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature, 595(7865), pp.107-113.
Dey, K.K., Van de Geijn, B., Kim, S.S., Hormozdiari, F., Kelley, D.R. and Price, A.L. 2020. Evaluating the informativeness of deep learning annotations for human complex diseases. Nature Communications, 11 (4703).
People
Kushal Dey, PhD
Assistant Professor
- The Kushal Dey lab focuses on developing machine learning models and computational pipelines that integrate genomic and epigenomic data.
- PhD, University of Chicago
- [email protected]
- Email Address
Members
Lab Alumni
Lab Affiliations
Achievements
- Josie Robertson Investigator (2023–2028)
- NCI P30 CCSG Developmental Award (2023-2024)
- NCI P30 CCSG supplement – “LLMs in cancer research” (2023-2024)
- Catalog Working Group Co-chair + Disease Focus Group Lead: IGVF consortium (2023-)
- K99/R00 Pathway to Independence Award (NIH/NHGRI) (2022–2026)
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Open Positions
To learn more about available postdoctoral opportunities, please visit our Career Center
To learn more about compensation and benefits for postdoctoral researchers at MSK, please visit Resources for Postdocs
Post-doctoral researcher in computational virology
Get in Touch
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Lab Head Email
Disclosures
Doctors and faculty members often work with pharmaceutical, device, biotechnology, and life sciences companies, and other organizations outside of MSK, to find safe and effective cancer treatments, to improve patient care, and to educate the health care community.
MSK requires doctors and faculty members to report (“disclose”) the relationships and financial interests they have with external entities. As a commitment to transparency with our community, we make that information available to the public.
Kushal Dey discloses the following relationships and financial interests:
No disclosures meeting criteria for time period
The information published here is a complement to other publicly reported data and is for a specific annual disclosure period. There may be differences between information on this and other public sites as a result of different reporting periods and/or the various ways relationships and financial interests are categorized by organizations that publish such data.
This page and data include information for a specific MSK annual disclosure period (January 1, 2023 through disclosure submission in spring 2024). This data reflects interests that may or may not still exist. This data is updated annually.
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