Kushal K Dey

Genome-wide enhancer maps link risk variants to disease genes.

Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM.

Nature. 2021 Apr 07. PMID: 33828297

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2.

Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jane-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Gordon Jiang Z, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A.

bioRxiv. 2021 Feb 25. PMID: 33655247

Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace's Line.

White AE, Dey KK, Stephens M, Price TD.

Glob Ecol Biogeogr. 2021 Mar. 30(3):685-696. PMID: 33776580

Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease.

Kim SS, Dey KK, Weissbrod O, Márquez-Luna C, Gazal S, Price AL.

Nat Commun. 2020 12 07. 11(1):6258. PMID: 33288751

Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements.

Amariuta T, Ishigaki K, Sugishita H, Ohta T, Koido M, Dey KK, Matsuda K, Murakami Y, Price AL, Kawakami E, Terao C, Raychaudhuri S.

Nat Genet. 2020 12. 52(12):1346-1354. PMID: 33257898

Evaluating the informativeness of deep learning annotations for human complex diseases.

Dey KK, van de Geijn B, Kim SS, Hormozdiari F, Kelley DR, Price AL.

Nat Commun. 2020 09 17. 11(1):4703. PMID: 32943643

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis.

Hsiao CJ, Tung P, Blischak JD, Burnett JE, Barr KA, Dey KK, Stephens M, Gilad Y.

Genome Res. 2020 04. 30(4):611-621. PMID: 32312741

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.

Marcus JH, Posth C, Ringbauer H, Lai L, Skeates R, Sidore C, Beckett J, Furtwängler A, Olivieri A, Chiang CWK, Al-Asadi H, Dey K, Joseph TA, Liu CC, Der Sarkissian C, Radzeviciute R, Michel M, Gradoli MG, Marongiu P, Rubino S, Mazzarello V, Rovina D, La Fragola A, Serra RM, Bandiera P, Bianucci R, Pompianu E, Murgia C, Guirguis M, Orquin RP, Tuross N, van Dommelen P, Haak W, Reich D, Schlessinger D, Cucca F, Krause J, Novembre J.

Nat Commun. 2020 02 24. 11(1):939. PMID: 32094358

Regional influences on community structure across the tropical-temperate divide.

White AE, Dey KK, Mohan D, Stephens M, Price TD.

Nat Commun. 2019 06 14. 10(1):2646. PMID: 31201312

Inference and visualization of DNA damage patterns using a grade of membership model.

Al-Asadi H, Dey KK, Novembre J, Stephens M.

Bioinformatics. 2019 04 15. 35(8):1292-1298. PMID: 30192911