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Items: 1 to 20 of 257

1.

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.

Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53. Epub 2006 Dec 1.

2.

In silico Reconstruction of the Metabolic and Pathogenic Potential of Bacterial Genomes Using Subsystems.

McNeil LK, Aziz RK.

Genome Dyn. 2009;6:21-34. doi: 10.1159/000235760. Epub 2009 Aug 19. Review.

PMID:
19696491
3.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D206-14. doi: 10.1093/nar/gkt1226. Epub 2013 Nov 29.

4.

ITEP: an integrated toolkit for exploration of microbial pan-genomes.

Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND.

BMC Genomics. 2014 Jan 3;15:8. doi: 10.1186/1471-2164-15-8.

5.

MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.

Cruveiller S, Le Saux J, Vallenet D, Lajus A, Bocs S, Médigue C.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W471-9.

6.

The comprehensive microbial resource.

Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, Madupu R, Goetz P, Galinsky K, White O, Sutton G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D340-5. doi: 10.1093/nar/gkp912. Epub 2009 Nov 5.

7.

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.

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005.

8.

MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.

Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D636-47. doi: 10.1093/nar/gks1194. Epub 2012 Nov 27.

9.

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.

Podell S, Gaasterland T, Allen EE.

BMC Bioinformatics. 2008 Oct 7;9:419. doi: 10.1186/1471-2105-9-419.

10.

The mouse genome database (MGD): new features facilitating a model system.

Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; Mouse Genome Database Group.

Nucleic Acids Res. 2007 Jan;35(Database issue):D630-7. Epub 2006 Nov 29.

11.

Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.

Chang S, Zhang J, Liao X, Zhu X, Wang D, Zhu J, Feng T, Zhu B, Gao GF, Wang J, Yang H, Yu J, Wang J.

Nucleic Acids Res. 2007 Jan;35(Database issue):D376-80. Epub 2006 Oct 25.

12.

Curation of viral genomes: challenges, applications and the way forward.

Kulkarni-Kale U, Bhosle SG, Manjari GS, Joshi M, Bansode S, Kolaskar AS.

BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S12.

13.

PGAT: a multistrain analysis resource for microbial genomes.

Brittnacher MJ, Fong C, Hayden HS, Jacobs MA, Radey M, Rohmer L.

Bioinformatics. 2011 Sep 1;27(17):2429-30. doi: 10.1093/bioinformatics/btr418. Epub 2011 Jul 15.

14.

GenoList: an integrated environment for comparative analysis of microbial genomes.

Lechat P, Hummel L, Rousseau S, Moszer I.

Nucleic Acids Res. 2008 Jan;36(Database issue):D469-74. Epub 2007 Nov 21.

15.

Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research.

Stover NA, Krieger CJ, Binkley G, Dong Q, Fisk DG, Nash R, Sethuraman A, Weng S, Cherry JM.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D500-3.

16.

LeishCyc: a biochemical pathways database for Leishmania major.

Doyle MA, MacRae JI, De Souza DP, Saunders EC, McConville MJ, Likić VA.

BMC Syst Biol. 2009 Jun 5;3:57. doi: 10.1186/1752-0509-3-57.

17.

MycoDB: an online database for comparative genomics of the mycobacteria and related organisms.

Chaudhuri RR.

Methods Mol Biol. 2009;465:419-31. doi: 10.1007/978-1-59745-207-6_27.

PMID:
20560061
18.

VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics.

Yang J, Chen L, Sun L, Yu J, Jin Q.

Nucleic Acids Res. 2008 Jan;36(Database issue):D539-42. Epub 2007 Nov 4.

19.

Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource.

Lefkowitz EJ, Upton C, Changayil SS, Buck C, Traktman P, Buller RM.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D311-6.

20.

Megx.net--database resources for marine ecological genomics.

Lombardot T, Kottmann R, Pfeffer H, Richter M, Teeling H, Quast C, Glöckner FO.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D390-3.

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