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System-wide transcriptome damage and tissue identity loss in COVID-19 patients.
Park J, Foox J, Hether T, Danko DC, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshin EE, MacKay M, Rendeiro AF, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti NP, Shapira S, Salvatore M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Rice CM, Borczuk AC, Meydan C, Schwartz RE, Mason CE. Park J, et al. Among authors: danko dc. Cell Rep Med. 2022 Jan 24;3(2):100522. doi: 10.1016/j.xcrm.2022.100522. eCollection 2022 Feb 15. Cell Rep Med. 2022. PMID: 35233546 Free PMC article.
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.
McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE. McIntyre ABR, et al. Genome Biol. 2017 Sep 21;18(1):182. doi: 10.1186/s13059-017-1299-7. Genome Biol. 2017. PMID: 28934964 Free PMC article.
Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.
McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE. McIntyre ABR, et al. Genome Biol. 2019 Apr 5;20(1):72. doi: 10.1186/s13059-019-1687-2. Genome Biol. 2019. PMID: 30953547 Free PMC article.
Illuminating Genetic Mysteries of the Dead Sea Scrolls.
Anava S, Neuhof M, Gingold H, Sagy O, Munters A, Svensson EM, Afshinnekoo E, Danko D, Foox J, Shor P, Riestra B, Huchon D, Mason CE, Mizrahi N, Jakobsson M, Rechavi O. Anava S, et al. Cell. 2020 Jun 11;181(6):1218-1231.e27. doi: 10.1016/j.cell.2020.04.046. Epub 2020 Jun 2. Cell. 2020. PMID: 32492404 Free article.
Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions.
Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, Mason CE. Butler DJ, et al. bioRxiv [Preprint]. 2020 May 1:2020.04.20.048066. doi: 10.1101/2020.04.20.048066. bioRxiv. 2020. Update in: Nat Commun. 2021 Mar 12;12(1):1660. doi: 10.1038/s41467-021-21361-7. PMID: 32511352 Free PMC article. Updated. Preprint.
Obesity and ethnicity alter gene expression in skin.
Walker JM, Garcet S, Aleman JO, Mason CE, Danko D, Butler D, Zuffa S, Swann JR, Krueger J, Breslow JL, Holt PR. Walker JM, et al. Sci Rep. 2020 Aug 21;10(1):14079. doi: 10.1038/s41598-020-70244-2. Sci Rep. 2020. PMID: 32826922 Free PMC article.
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.
Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR Jr, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Butler D, et al. Nat Commun. 2021 Mar 12;12(1):1660. doi: 10.1038/s41467-021-21361-7. Nat Commun. 2021. PMID: 33712587 Free PMC article.
31 results