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2017 1
2018 2
2019 2
2020 2
2021 4
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Page 1
American Gut: an Open Platform for Citizen Science Microbiome Research.
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium, Knight R. McDonald D, et al. Among authors: meleshko d. mSystems. 2018 May 15;3(3):e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun. mSystems. 2018. PMID: 29795809 Free PMC article.
metaSPAdes: a new versatile metagenomic assembler.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. Nurk S, et al. Among authors: meleshko d. Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15. Genome Res. 2017. PMID: 28298430 Free PMC article.
Using SPAdes De Novo Assembler.
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Prjibelski A, et al. Among authors: meleshko d. Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102. Curr Protoc Bioinformatics. 2020. PMID: 32559359
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. Among authors: meleshko d. bioRxiv. 2020 May 1:2020.04.20.048066. doi: 10.1101/2020.04.20.048066. Preprint. bioRxiv. 2020. PMID: 32511352 Free PMC article. Updated.
A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology-Radiology Fusion.
Khosravi P, Lysandrou M, Eljalby M, Li Q, Kazemi E, Zisimopoulos P, Sigaras A, Brendel M, Barnes J, Ricketts C, Meleshko D, Yat A, McClure TD, Robinson BD, Sboner A, Elemento O, Chughtai B, Hajirasouliha I. Khosravi P, et al. Among authors: meleshko d. J Magn Reson Imaging. 2021 Mar 14. doi: 10.1002/jmri.27599. Online ahead of print. J Magn Reson Imaging. 2021. PMID: 33719168
A global metagenomic map of urban microbiomes and antimicrobial resistance.
Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE; International MetaSUB Consortium. Danko D, et al. Among authors: meleshko d. Cell. 2021 May 22:S0092-8674(21)00585-7. doi: 10.1016/j.cell.2021.05.002. Online ahead of print. Cell. 2021. PMID: 34043940 Free 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. Among authors: meleshko d. Nat Commun. 2021 Mar 12;12(1):1660. doi: 10.1038/s41467-021-21361-7. Nat Commun. 2021. PMID: 33712587 Free PMC article.