Computational & Systems Biology Program

The Kushal Dey Lab

Research

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.

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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).

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People

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

Members

Thahmina Ali
Thahmina Ali

WGS Student

Xuewei Cao

Postdoc

Elizabeth Dorans

Collaborator

Tabassum Fabiha

Research Technician

Ru Feng

Collaborator

Karthik Guruvayurappan
Karthik Guruvayurappan

WGS Student

Hanbyul Lee

Postdoc

Louis Liu

WGS Student

Margo Morse
Margo Morse

SKI Administrative Assistant

Haochen Sun
Haochen Sun

Research Technician

Sarthak Tiwari
Sarthak Tiwari

WGS Student

Berk Turhan
Berk Turhan

WGS Student

Harry Zhang
Harry Zhang

WGS Student

Lab Alumni
Deenan He

Per-Diem Research Technician

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

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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.

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].


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