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Page 1
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: pusch gd. Methods Mol Biol. 2024;2802:547-571. doi: 10.1007/978-1-0716-3838-5_18. Methods Mol Biol. 2024. PMID: 38819571
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: pusch gd. 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.
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: pusch gd. 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: pusch gd. Nucleic Acids Res. 2020 Jan 8;48(D1):D606-D612. doi: 10.1093/nar/gkz943. Nucleic Acids Res. 2020. PMID: 31667520 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: pusch gd. Brief Bioinform. 2021 Nov 5;22(6):bbab313. doi: 10.1093/bib/bbab313. Brief Bioinform. 2021. PMID: 34379107 Free PMC article.
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.
Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, Kuscuoglu M, Lefkowitz EJ, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen GJ, Overbeek JC, Parrello B, Parrello V, Porter JS, Pusch GD, Shukla M, Singh I, Stewart L, Tan G, Thomas C, VanOeffelen M, Vonstein V, Wallace ZS, Warren AS, Wattam AR, Xia F, Yoo H, Zhang Y, Zmasek CM, Scheuermann RH, Stevens RL. Olson RD, et al. Among authors: pusch gd. Nucleic Acids Res. 2023 Jan 6;51(D1):D678-D689. doi: 10.1093/nar/gkac1003. Nucleic Acids Res. 2023. PMID: 36350631 Free PMC article.
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: pusch gd. 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.
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.
Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA 3rd, Stevens R, Vonstein V, Wattam AR, Xia F. Brettin T, et al. Among authors: pusch gd. Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365. Sci Rep. 2015. PMID: 25666585 Free PMC article.
32 results