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Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.
Timme RE, Karsch-Mizrachi I, Waheed Z, Arita M, MacCannell D, Maguire F, Petit Iii R, Page AJ, Mendes CI, Nasar MI, Oluniyi P, Tyler AD, Raphenya AR, Guthrie JL, Olawoye I, Rinck G, O'Cathail C, Lees J, Cochrane G, Cummins C, Brister JR, Klimke W, Feldgarden M, Griffiths E. Timme RE, et al. Microb Genom. 2023 Dec;9(12):001145. doi: 10.1099/mgen.0.001145. Microb Genom. 2023. PMID: 38085797 Free PMC article.
Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities.
Kocurek B, Ramachandran P, Grim CJ, Morin P, Howard L, Ottesen A, Timme R, Leonard SR, Rand H, Strain E, Tadesse D, Pettengill JB, Lacher DW, Mammel M, Jarvis KG. Kocurek B, et al. Among authors: timme r. Microbiol Spectr. 2023 Dec 12;11(6):e0148223. doi: 10.1128/spectrum.01482-23. Epub 2023 Oct 9. Microbiol Spectr. 2023. PMID: 37812012 Free PMC article.
Enterobacterales draft genome sequences: 15 historical (1998-2004) and 30 contemporary (2015-2016) clinical isolates from Pakistan.
Crawford MA, Lascols C, Lomonaco S, Timme RE, Fisher DJ, Anderson K, Hodge DR, Morse SA, Pillai SP, Sharma SK, Khan E, Allard MW, Hughes MA. Crawford MA, et al. Among authors: timme re. Microbiol Resour Announc. 2023 Sep 19;12(9):e0016323. doi: 10.1128/MRA.00163-23. Epub 2023 Jul 28. Microbiol Resour Announc. 2023. PMID: 37504519 Free PMC article.
Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States.
Stevens EL, Carleton HA, Beal J, Tillman GE, Lindsey RL, Lauer AC, Pightling A, Jarvis KG, Ottesen A, Ramachandran P, Hintz L, Katz LS, Folster JP, Whichard JM, Trees E, Timme RE, McDERMOTT P, Wolpert B, Bazaco M, Zhao S, Lindley S, Bruce BB, Griffin PM, Brown E, Allard M, Tallent S, Irvin K, Hoffmann M, Wise M, Tauxe R, Gerner-Smidt P, Simmons M, Kissler B, Defibaugh-Chavez S, Klimke W, Agarwala R, Lindsay J, Cook K, Austerman SR, Goldman D, McGARRY S, Hale KR, Dessai U, Musser SM, Braden C. Stevens EL, et al. Among authors: timme re. J Food Prot. 2022 May 1;85(5):755-772. doi: 10.4315/JFP-21-437. J Food Prot. 2022. PMID: 35259246 Free article. Review.
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Griffiths EJ, et al. Among authors: timme re. Gigascience. 2022 Feb 16;11:giac003. doi: 10.1093/gigascience/giac003. Gigascience. 2022. PMID: 35169842 Free PMC article.
Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria.
Mitchell PK, Wang L, Stanhope BJ, Cronk BD, Anderson R, Mohan S, Zhou L, Sanchez S, Bartlett P, Maddox C, DeShambo V, Mani R, Hengesbach LM, Gresch S, Wright K, Mor S, Zhang S, Shen Z, Yan L, Mackey R, Franklin-Guild R, Zhang Y, Prarat M, Shiplett K, Ramachandran A, Narayanan S, Sanders J, Hunkapiller AA, Lahmers K, Carbonello AA, Aulik N, Lim A, Cooper J, Jones A, Guag J, Nemser SM, Tyson GH, Timme R, Strain E, Reimschuessel R, Ceric O, Goodman LB. Mitchell PK, et al. Among authors: timme r. Microb Genom. 2022 Feb;8(2):000717. doi: 10.1099/mgen.0.000717. Microb Genom. 2022. PMID: 35113783 Free PMC article.
82 results