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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: stevens rl. 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 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. 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.
The RAST Server: rapid annotations using subsystems technology.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. Aziz RK, et al. BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75. BMC Genomics. 2008. PMID: 18261238 Free PMC article.
Real time metagenomics: using k-mers to annotate metagenomes.
Edwards RA, Olson R, Disz T, Pusch GD, Vonstein V, Stevens R, Overbeek R. Edwards RA, et al. Bioinformatics. 2012 Dec 15;28(24):3316-7. doi: 10.1093/bioinformatics/bts599. Epub 2012 Oct 9. Bioinformatics. 2012. PMID: 23047562 Free PMC article.
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: stevens rl. 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.
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.
Seaver SM, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LM, Zallot R, Hasnain G, Niehaus TD, El Yacoubi B, Pasternak S, Olson R, Pusch G, Overbeek R, Stevens R, de Crécy-Lagard V, Ware D, Hanson AD, Henry CS. Seaver SM, et al. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9645-50. doi: 10.1073/pnas.1401329111. Epub 2014 Jun 9. Proc Natl Acad Sci U S A. 2014. PMID: 24927599 Free PMC article.
281 results