Kushal Dey: Publications

Kushal Dey: Publications


Featured 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

Gazal, S., Weissbrod, O., Hormozdiari, F., Dey, K.K., Nasser, J., Jagadeesh, K.A., Weiner, D.J., Shi, H., Fulco, C.P., O’Connor, L.J. and Pasaniuc, B., 2022. Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity. Nature Genetics, 54, pp.827-836.

Weiner, D.J., Nadig, A., Jagadeesh, K.A., Dey, K.K., Neale, B.M., Robinson, E.B., Karczewski, K.J. and O’Connor, L.J., 2023. Polygenic architecture of rare coding variation across 394,783 exomes. Nature614(7948), pp.492-499.

Zhang, M.J., Hou, K., Dey, K.K., Jagadeesh, K.A., Weinand, K., Sakaue, S., Taychameekiatchai, A., Rao, P., Pisco, A.O., Zou, J. and Wang, B., 2022. Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data. Nature Genetics, 54,  pp.1572-1580

Nasser, J.,…Dey, K.K., et al, 2021. Genome-wide enhancer maps link risk variants to disease genes. Nature593(7858), pp.238-243.

Kim, S.S., Dey, K.K., Weissbrod, O., Marquez-Luna, C., Gazal, S. and Price, A.L., 2020. Improving the informativeness of Mendelian disease pathogenicity scores for common disease. Nature Communications. 11(1): 6258.

Amariuta, T., .., Dey, K.K., et al, 2020. Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nature Genetics52(12), pp.1346-1354.

Hsiao, C.J., Tung, P., Blischak, J.D., Burnett, J.E., Barr, K.A., Dey, K.K., Stephens, M. and Gilad, Y., 2020. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome research30(4), pp.611-621.

White, A.E., Dey, K.K., Mohan, D., Stephens, M. and Price, T.D., 2019. Regional influences on community structure across the tropical-temperate divide. Nature Communications10(1), pp.1-8.

White, A.E., Dey, K.K., Stephens, M. and Price, T.D., 2021. Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace’s Line. Global Ecology and Biogeography30(3), pp.685-696.

Marcus, J.H., …Dey, K.K., et al. 2020. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nature communications11(1), pp.1-14.

Al-Asadi, H.*, Dey, K.K.*, Novembre, J. and Stephens, M., 2019. Inference and visualization

of DNA damage patterns using a grade of membership model. Bioinformatics, 35(8), pp.1292-1298.

Dey, K.K., Xie, D. and Stephens, M., 2018. A new sequence logo plot to highlight enrichment

and depletion. BMC bioinformatics, 19(1), pp.1-9.