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Kushal K Dey, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, 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, Jané-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, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021 Apr 29. PMID: 33915569.
    Citations:    Fields:    
  2. 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. Genome-wide enhancer maps link risk variants to disease genes. Nature. 2021 Apr 07. PMID: 33828297.
    Citations:    Fields:    
  3. 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. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2. bioRxiv. 2021 Feb 25. PMID: 33655247.
    Citations:    
  4. White AE, Dey KK, Stephens M, Price TD. Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace's Line. Glob Ecol Biogeogr. 2021 Mar; 30(3):685-696. PMID: 33776580.
    Citations:    
  5. Kim SS, Dey KK, Weissbrod O, Márquez-Luna C, Gazal S, Price AL. Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease. Nat Commun. 2020 12 07; 11(1):6258. PMID: 33288751.
    Citations: 1     Fields:    Translation:Humans
  6. Amariuta T, Ishigaki K, Sugishita H, Ohta T, Koido M, Dey KK, Matsuda K, Murakami Y, Price AL, Kawakami E, Terao C, Raychaudhuri S. Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nat Genet. 2020 12; 52(12):1346-1354. PMID: 33257898.
    Citations: 1     Fields:    Translation:HumansCells
  7. Dey KK, van de Geijn B, Kim SS, Hormozdiari F, Kelley DR, Price AL. Evaluating the informativeness of deep learning annotations for human complex diseases. Nat Commun. 2020 09 17; 11(1):4703. PMID: 32943643.
    Citations: 2     Fields:    Translation:Humans
  8. Hsiao CJ, Tung P, Blischak JD, Burnett JE, Barr KA, Dey KK, Stephens M, Gilad Y. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome Res. 2020 04; 30(4):611-621. PMID: 32312741.
    Citations: 7     Fields:    
  9. 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. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nat Commun. 2020 02 24; 11(1):939. PMID: 32094358.
    Citations: 8     Fields:    Translation:HumansCells
  10. White AE, Dey KK, Mohan D, Stephens M, Price TD. Regional influences on community structure across the tropical-temperate divide. Nat Commun. 2019 06 14; 10(1):2646. PMID: 31201312.
    Citations: 3     Fields:    Translation:Animals
  11. Al-Asadi H, Dey KK, Novembre J, Stephens M. Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 2019 04 15; 35(8):1292-1298. PMID: 30192911.
    Citations: 1     Fields:    Translation:Humans
  12. Dey KK, Xie D, Stephens M. A new sequence logo plot to highlight enrichment and depletion. BMC Bioinformatics. 2018 Dec 10; 19(1):473. PMID: 30526486.
    Citations: 10     Fields:    Translation:HumansCells
  13. Dey KK, Hsiao CJ, Stephens M. Correction: Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet. 2017 May; 13(5):e1006759. PMID: 28549067.
    Citations: 1     Fields:    
  14. Dey KK, Hsiao CJ, Stephens M. Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet. 2017 Mar; 13(3):e1006599. PMID: 28333934.
    Citations: 23     Fields:    Translation:HumansAnimalsCells
  15. Pradhan S, Patra P, Mitra S, Dey KK, Basu S, Chandra S, Palit P, Goswami A. Copper nanoparticle (CuNP) nanochain arrays with a reduced toxicity response: a biophysical and biochemical outlook on Vigna radiata. J Agric Food Chem. 2015 Mar 18; 63(10):2606-17. PMID: 25686266.
    Citations: 2     Fields:    Translation:AnimalsCells
  16. Mitra S, Patra P, Pradhan S, Debnath N, Dey KK, Sarkar S, Chattopadhyay D, Goswami A. Microwave synthesis of ZnO@mSiO2 for detailed antifungal mode of action study: understanding the insights into oxidative stress. J Colloid Interface Sci. 2015 Apr 15; 444:97-108. PMID: 25585293.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  17. Pradhan S, Patra P, Mitra S, Dey KK, Jain S, Sarkar S, Roy S, Palit P, Goswami A. Manganese nanoparticles: impact on non-nodulated plant as a potent enhancer in nitrogen metabolism and toxicity study both in vivo and in vitro. J Agric Food Chem. 2014 Sep 03; 62(35):8777-85. PMID: 25126671.
    Citations: 5     Fields:    Translation:AnimalsCells
  18. Pradhan S, Patra P, Das S, Chandra S, Mitra S, Dey KK, Akbar S, Palit P, Goswami A. Photochemical modulation of biosafe manganese nanoparticles on Vigna radiata: a detailed molecular, biochemical, and biophysical study. Environ Sci Technol. 2013 Nov 19; 47(22):13122-31. PMID: 24144189.
    Citations: 8     Fields:    Translation:AnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.