Featured Publications
IGVF Consortium. 2024. Deciphering the impact of genomic variation on function. Nature. Sep;633(8028):47-57. (Review)
Kaplan SJ, Wong W, Yan J, Pulecio J, Cho HS, Li Q, Zhao J, Leslie-Iyer J, Kazakov J, Murphy D, Luo R, Dey KK, Apostolou E, Leslie CS, Huangfu D. 2024. CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant. Cell Rep. Aug 27;43(8):114640.
Yao D, Binan L, Bezney J, Simonton B, Freedman J, Frangieh CJ, Dey K, Geiger-Schuller K, Eraslan B, Gusev A, Regev A, Cleary B. 2024. Scalable genetic screening for regulatory circuits using compressed Perturb-seq. Nat Biotechnol. Aug;42(8):1282-1295.
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. Nat Genet. Apr;56(4):627-636.
Sakaue S, Weinand K, Shakson I, Dey KK, Jagadeesh K, Kanai M, Watts GFM, Zhu Z; Accelerating Medicines Partnership RA/SLE Program and Network; Brenner MB, McDavid A, Donlin LT, Wei K, Price AL, Raychaudhuri S, Collaborators. 2024. Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nat Genet. Apr;56(4):615-626.
Kim SS, Truong B, Jagadeesh K, Dey KK, Shen AZ, Raychaudhuri S, Kellis M, Price AL. 2024. Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nat Commun. Jan 17;15(1):563.
Kang JB, Shen AZ, Gurajala S, Nathan A, Rumker L, Aguiar VRC, Valencia C, Lagattuta KA, Zhang F, Jonsson AH, Yazar S, Alquicira-Hernandez J, Khalili H, Ananthakrishnan AN, Jagadeesh K, Dey K; Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network; Daly MJ, Xavier RJ, Donlin LT, Anolik JH, Powell JE, Rao DA, Brenner MB, Gutierrez-Arcelus M, Luo Y, Sakaue S, Raychaudhuri S. 2023. Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. Nat Genet. Dec;55(12):2255-2268.
Weiner DJ, Nadig A, Jagadeesh KA, Dey KK., Neale BM, Robinson EB, Karczewski KJ, O’Connor LJ. 2023. Polygenic architecture of rare coding variation across 394,783 exomes. Nature. 614(7948):492-499.
Zhang MJ, Hou K, Dey KK, Jagadeesh KA, Weinand K, Sakaue S, Taychameekiatchai A, Rao P, Pisco AO, Zou J, Wang B. 2022. Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data. Nat Genet. 54:1572-1580
Jagadeesh KA*, Dey KK*, Montoro DT, Mohan R, Gazal S, Engreitz JM, Xavier RJ, Price AL, Regev A. 2022. Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics. Nat Genet. 54:1479-1492.
Gazal S, Weissbrod O, Hormozdiari F, Dey KK, Nasser J, Jagadeesh KA, Weiner DJ, Shi H, Fulco CP, O’Connor LJ, Pasaniuc B. 2022. Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity. Nat Genet. 54:827-836.
Dey KK, Gazal S, van de Geijn B, Kim SS, Nasser J, Engreitz JM, Price AL. 2022. SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease. Cell Genom. 2(7):100145.
Delorey TM*, .., Dey KK* et al. 2021. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 595(7865):107-113.
Nasser J,…Dey KK, et al. 2021. Genome-wide enhancer maps link risk variants to disease genes. Nature. 593(7858):238-243.
White AE, Dey KK, Stephens M, Price, TD. 2021. Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace’s Line. Glob Ecol Biogeogr. 30(3):685-696.
Marcus JH, …Dey KK, et al. 2020. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nat Commun. 11(1):1-14.
Dey KK, Van de Geijn B, Kim SS, Hormozdiari F, Kelley DR, Price AL. 2020. Evaluating the informativeness of deep learning annotations for human complex diseases. Nat Commun. 11:4703
Kim SS, Dey KK, Weissbrod O, Marquez-Luna C, Gazal S, Price AL. 2020. Improving the informativeness of Mendelian disease pathogenicity scores for common disease. Nat Commun. 11(1):6258.
Amariuta T,…, Dey KK, et al. 2020. Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nat Genet. 52(12):1346-1354.
Hsiao CJ, Tung P, Blischak JD, Burnett JE, Barr KA, Dey KK, Stephens M, Gilad Y. 2020. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome Res. 30(4):611-621.
White AE, Dey KK, Mohan D, Stephens M, Price TD. 2019. Regional influences on community structure across the tropical-temperate divide. Nat Commun. 10(1):1-8.
Al-Asadi H*, Dey KK*, Novembre J, Stephens M. 2019. Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 35(8):1292-1298.
Dey KK, Xie D, Stephens M. 2018. A new sequence logo plot to highlight enrichment and depletion. BMC Bioinformatics. 19(1):1-9.