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PATRIC, the bacterial bioinformatics database and analysis resource.
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW. Wattam AR, et al. Among authors: overbeek r. Nucleic Acids Res. 2014 Jan;42(Database issue):D581-91. doi: 10.1093/nar/gkt1099. Epub 2013 Nov 12. Nucleic Acids Res. 2014. PMID: 24225323 Free PMC article.
Antimicrobial Resistance Prediction in PATRIC and RAST.
Davis JJ, Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR, Will R, Xia F, Stevens R. Davis JJ, et al. Among authors: overbeek r. Sci Rep. 2016 Jun 14;6:27930. doi: 10.1038/srep27930. Sci Rep. 2016. PMID: 27297683 Free PMC article.
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL. Wattam AR, et al. Among authors: overbeek r. Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29. Nucleic Acids Res. 2017. PMID: 27899627 Free PMC article.
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.
Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, Chlenski P, Conrad N, Dickerman A, Dietrich EM, Gabbard JL, Gerdes S, Guard A, Kenyon RW, Machi D, Mao C, Murphy-Olson D, Nguyen M, Nordberg EK, Olsen GJ, Olson RD, Overbeek JC, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomas C, VanOeffelen M, Vonstein V, Warren AS, Xia F, Xie D, Yoo H, Stevens R. Davis JJ, et al. Among authors: overbeek r. Nucleic Acids Res. 2020 Jan 8;48(D1):D606-D612. doi: 10.1093/nar/gkz943. Nucleic Acids Res. 2020. PMID: 31667520 Free PMC article.
Enabling comparative modeling of closely related genomes: example genus Brucella.
Faria JP, Edirisinghe JN, Davis JJ, Disz T, Hausmann A, Henry CS, Olson R, Overbeek RA, Pusch GD, Shukla M, Vonstein V, Wattam AR. Faria JP, et al. Among authors: overbeek ra. 3 Biotech. 2015 Feb;5(1):101-105. doi: 10.1007/s13205-014-0202-4. Epub 2014 Mar 8. 3 Biotech. 2015. PMID: 28324362 Free PMC article.
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. Overbeek R, et al. Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. doi: 10.1093/nar/gki866. Print 2005. Nucleic Acids Res. 2005. PMID: 16214803 Free PMC article.
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R. McNeil LK, et al. Among authors: overbeek r. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53. doi: 10.1093/nar/gkl947. Epub 2006 Dec 1. Nucleic Acids Res. 2007. PMID: 17145713 Free PMC article.
91 results