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Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area.
Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Long SW, et al. Among authors: shukla m. mBio. 2020 Oct 30;11(6):e02707-20. doi: 10.1128/mBio.02707-20. mBio. 2020. PMID: 33127862 Free PMC article.
Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area.
Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Long SW, et al. Among authors: shukla m. medRxiv [Preprint]. 2020 Sep 29:2020.09.22.20199125. doi: 10.1101/2020.09.22.20199125. medRxiv. 2020. PMID: 33024977 Free PMC article. Updated. Preprint.
Predicting antimicrobial resistance using conserved genes.
Nguyen M, Olson R, Shukla M, VanOeffelen M, Davis JJ. Nguyen M, et al. Among authors: shukla m. PLoS Comput Biol. 2020 Oct 19;16(10):e1008319. doi: 10.1371/journal.pcbi.1008319. eCollection 2020 Oct. PLoS Comput Biol. 2020. PMID: 33075053 Free PMC article.
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes.
VanOeffelen M, Nguyen M, Aytan-Aktug D, Brettin T, Dietrich EM, Kenyon RW, Machi D, Mao C, Olson R, Pusch GD, Shukla M, Stevens R, Vonstein V, Warren AS, Wattam AR, Yoo H, Davis JJ. VanOeffelen M, et al. Among authors: shukla m. Brief Bioinform. 2021 Nov 5;22(6):bbab313. doi: 10.1093/bib/bbab313. Brief Bioinform. 2021. PMID: 34379107 Free PMC article.
Defining the risk of SARS-CoV-2 variants on immune protection.
DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Fischer WM, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli … See abstract for full author list ➔ DeGrace MM, et al. Among authors: shukla m. Nature. 2022 May;605(7911):640-652. doi: 10.1038/s41586-022-04690-5. Epub 2022 Mar 31. Nature. 2022. PMID: 35361968 Free PMC article. Review.
Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance.
Wattam AR, Bowers N, Brettin T, Conrad N, Cucinell C, Davis JJ, Dickerman AW, Dietrich EM, Kenyon RW, Machi D, Mao C, Nguyen M, Olson RD, Overbeek R, Parrello B, Pusch GD, Shukla M, Stevens RL, Vonstein V, Warren AS. Wattam AR, et al. Among authors: shukla m. Methods Mol Biol. 2024;2802:547-571. doi: 10.1007/978-1-0716-3838-5_18. Methods Mol Biol. 2024. PMID: 38819571
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. Overbeek R, et al. Among authors: shukla m. Nucleic Acids Res. 2014 Jan;42(Database issue):D206-14. doi: 10.1093/nar/gkt1226. Epub 2013 Nov 29. Nucleic Acids Res. 2014. PMID: 24293654 Free PMC article.
836 results