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Results: 1 to 20 of 139

1.

Genomic standards consortium projects.

Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G.

Stand Genomic Sci. 2014 Feb 15;9(3):599-601. doi: 10.4056/sigs.5559680. eCollection 2014 Jun 15.

PMID:
25197446
[PubMed]
Free PMC Article
2.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium.

Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6.

PMID:
24997787
[PubMed - in process]
3.

Veillonella, Firmicutes: Microbes disguised as Gram negatives.

Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.

Stand Genomic Sci. 2013 Dec 15;9(2):431-48. doi: 10.4056/sigs.2981345. eCollection 2013 Dec 20.

PMID:
24976898
[PubMed]
Free PMC Article
4.

Vibrio chromosome-specific families.

Lukjancenko O, Ussery DW.

Front Microbiol. 2014 Mar 18;5:73. doi: 10.3389/fmicb.2014.00073. eCollection 2014.

PMID:
24672511
[PubMed]
Free PMC Article
5.

Benchmarking of methods for genomic taxonomy.

Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O.

J Clin Microbiol. 2014 May;52(5):1529-39. doi: 10.1128/JCM.02981-13. Epub 2014 Feb 26.

PMID:
24574292
[PubMed - in process]
Free PMC Article
6.

Sigma factors in a thousand E. coli genomes.

Cook H, Ussery DW.

Environ Microbiol. 2013 Dec;15(12):3121-9. doi: 10.1111/1462-2920.12236. Epub 2013 Aug 29.

PMID:
23992563
[PubMed - indexed for MEDLINE]
7.

Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes.

Bohlin J, Brynildsrud O, Vesth T, Skjerve E, Ussery DW.

PLoS One. 2013 Jul 26;8(7):e69878. doi: 10.1371/journal.pone.0069878. Print 2013.

PMID:
23922837
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

CMG-biotools, a free workbench for basic comparative microbial genomics.

Vesth T, Lagesen K, Acar Ö, Ussery D.

PLoS One. 2013;8(4):e60120. doi: 10.1371/journal.pone.0060120. Epub 2013 Apr 5.

PMID:
23577086
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart.

Holch A, Webb K, Lukjancenko O, Ussery D, Rosenthal BM, Gram L.

Appl Environ Microbiol. 2013 May;79(9):2944-51. doi: 10.1128/AEM.03715-12. Epub 2013 Feb 22.

PMID:
23435887
[PubMed - in process]
Free PMC Article
10.

Bayesian prediction of bacterial growth temperature range based on genome sequences.

Jensen DB, Vesth TC, Hallin PF, Pedersen AG, Ussery DW.

BMC Genomics. 2012;13 Suppl 7:S3. doi: 10.1186/1471-2164-13-S7-S3. Epub 2012 Dec 13.

PMID:
23282160
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

From essential to persistent genes: a functional approach to constructing synthetic life.

Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A.

Trends Genet. 2013 May;29(5):273-9. doi: 10.1016/j.tig.2012.11.001. Epub 2012 Dec 6.

PMID:
23219343
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Polyclonality of concurrent natural populations of Alteromonas macleodii.

Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F.

Genome Biol Evol. 2012;4(12):1360-74. doi: 10.1093/gbe/evs112.

PMID:
23212172
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes.

Kaas RS, Friis C, Ussery DW, Aarestrup FM.

BMC Genomics. 2012 Oct 31;13:577. doi: 10.1186/1471-2164-13-577.

PMID:
23114024
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Non-O1 Vibrio cholerae unlinked to cholera in Haiti.

Mekalanos JJ, Robins W, Ussery DW, Davis BM, Schadt E, Waldor MK.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):E3206; author reply E3207. doi: 10.1073/pnas.1212443109. Epub 2012 Oct 3. No abstract available.

PMID:
23035253
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli.

Snipen L, Wassenaar TM, Altermann E, Olson J, Kathariou S, Lagesen K, Takamiya M, Knøchel S, Ussery DW, Meinersmann RJ.

Microb Inform Exp. 2012 Aug 28;2(1):8. doi: 10.1186/2042-5783-2-8.

PMID:
22929701
[PubMed]
Free PMC Article
16.

Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains).

Zakham F, Aouane O, Ussery D, Benjouad A, Ennaji MM.

Microb Inform Exp. 2012 Aug 28;2(1):7. doi: 10.1186/2042-5783-2-7.

PMID:
22929624
[PubMed]
Free PMC Article
17.

Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets.

Ali A, Soares SC, Santos AR, Guimarães LC, Barbosa E, Almeida SS, Abreu VA, Carneiro AR, Ramos RT, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V.

Gene. 2012 Oct 25;508(2):145-56. doi: 10.1016/j.gene.2012.07.070. Epub 2012 Aug 6.

PMID:
22890137
[PubMed - indexed for MEDLINE]
Free Article
18.

LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium.

Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casadesús J, Dorman CJ.

Mol Microbiol. 2012 Sep;85(6):1072-89. doi: 10.1111/j.1365-2958.2012.08162.x. Epub 2012 Jul 23.

PMID:
22804842
[PubMed - indexed for MEDLINE]
19.

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.

Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC.

Proc Natl Acad Sci U S A. 2012 May 15;109(20):E1277-86. doi: 10.1073/pnas.1201061109. Epub 2012 Apr 25.

PMID:
22538806
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Two novel methods for using genome sequences to infer taxonomy.

Ussery DW, Gordon SV.

Microbiology. 2012 Jun;158(Pt 6):1414. doi: 10.1099/mic.0.059816-0. Epub 2012 Apr 13. No abstract available.

PMID:
22504434
[PubMed - indexed for MEDLINE]
Free Article

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