Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 14

1.

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.

PMID:
24293654
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D581-91. doi: 10.1093/nar/gkt1099. Epub 2013 Nov 12.

PMID:
24225323
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

PMID:
23110173
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Real time metagenomics: using k-mers to annotate metagenomes.

Edwards RA, Olson R, Disz T, Pusch GD, Vonstein V, Stevens R, Overbeek R.

Bioinformatics. 2012 Dec 15;28(24):3316-7. doi: 10.1093/bioinformatics/bts599. Epub 2012 Oct 9.

PMID:
23047562
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model.

Boissy R, Ahmed A, Janto B, Earl J, Hall BG, Hogg JS, Pusch GD, Hiller LN, Powell E, Hayes J, Yu S, Kathju S, Stoodley P, Post JC, Ehrlich GD, Hu FZ.

BMC Genomics. 2011 Apr 13;12:187. doi: 10.1186/1471-2164-12-187.

PMID:
21489287
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75.

PMID:
18261238
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The genome of non-O1 Vibrio cholerae NRT36S demonstrates the presence of pathogenic mechanisms that are distinct from those of O1 Vibrio cholerae.

Chen Y, Johnson JA, Pusch GD, Morris JG Jr, Stine OC.

Infect Immun. 2007 May;75(5):2645-7. Epub 2007 Feb 5.

PMID:
17283087
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
17145713
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
16214803
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus.

Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P.

Nat Biotechnol. 2004 Dec;22(12):1554-8. Epub 2004 Nov 14.

PMID:
15543133
[PubMed - indexed for MEDLINE]
11.

Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method.

Farahi K, Pusch GD, Overbeek R, Whitman WB.

J Mol Evol. 2004 May;58(5):615-31.

PMID:
15170264
[PubMed - indexed for MEDLINE]
12.

Use of contiguity on the chromosome to predict functional coupling.

Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N.

In Silico Biol. 1999;1(2):93-108.

PMID:
11471247
[PubMed - indexed for MEDLINE]
13.

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.

Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E.

Nucleic Acids Res. 2000 Jan 1;28(1):123-5.

PMID:
10592199
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The use of gene clusters to infer functional coupling.

Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N.

Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2896-901.

PMID:
10077608
[PubMed - indexed for MEDLINE]
Free PMC Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Loading ...
Write to the Help Desk