Computational & Systems Biology Program

The Kushal Dey Lab

Research

Kushal Dey
Kushal Dey, PhD

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 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 prioritizing 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

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).

Dey, K.K., Hsiao, C.J. and Stephens, M., 2017. Visualizing the structure of RNA-seq expression data using grade of membership models. PLOS Genetics,13(3):e1006599

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People

Kushal Dey

Kushal Dey, PhD

  • The Kushal Dey Lab builds computational 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.
Lab Affiliations

Achievements

Open Positions

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Computational Biologist

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Postdoctoral Researcher

The Kushal Dey Lab is seeking a highly motivated and successful individual with a background in statistical genetics and genomics.

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