Computational & Systems Biology Program

The Kushal Dey Lab


Kushal Dey
Kushal Dey, PhD

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.

View Lab Overview

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 Genomics2(7), p.100145.

Delorey, T.M.*, .., Dey, K.K.* et al,  2021. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature595(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).

View All Publications


Kushal Dey

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


Thahmina Ali

Computational Biologist

Xuewei Cao


Elizabeth Dorans


Tabassum Fabiha

Research Technician

Ru Feng


Karthik Guruvayurappan

WGS Student

Hanbyul Lee


Louis Liu

WGS Student

Margo Morse

SKI Administrative Assistant

Haochen Sun

Research Technician

Sarthak Tiwari

WGS Student

Berk Turhan

WGS Student

Harry Zhang

WGS Student

Lab Alumni
Deenan He

Per-Diem Research Technician

Lab Affiliations


  • 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)
Read more

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

Graduate and Undergraduate Students

The Dey Lab welcomes graduate and undergraduate students interested in developing statistical and machine learning models in the interface of disease genetics and genomics, as well as their applications to state-of-the-art data.

Apply now

MSK AI & Machine Learning Postdoctoral Fellow Opportunity

The Dey Lab in Computational & Systems Biology program at Memorial Sloan Kettering Cancer Center is seeking postdoctoral fellow in machine learning/artificial intelligence and applied statistics to lead inter-disciplinary collaborative projects in biological sciences supervised by Dr. Dey, in collaboration with Dr. Rahul Mazumder, MIT Sloan School of Management.

Apply now

Postdoctoral Fellow

The Dey Lab in Computational & Systems Biology program at Memorial Sloan Kattering Cancer Center is seeking a postdoctoral fellow to lead inter-disciplinary collaborative projects jointly supervised by Dr. Dey and Dr. Gao Wang, Assistant Professor of Neurological Sciences, Columbia University, Department of Neurology.

Apply now

View All Open Positions

Get in Touch


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 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, 2022 through disclosure submission in spring 2023). This data reflects interests that may or may not still exist. This data is updated annually.

Learn more about MSK’s COI policies here. For questions regarding MSK’s COI-related policies and procedures, email MSK’s Compliance Office at [email protected].

View all disclosures