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Items: 1 to 20 of 94

1.

Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications.

Jolley KA, Bray JE, Maiden MCJ.

Wellcome Open Res. 2018 Sep 24;3:124. doi: 10.12688/wellcomeopenres.14826.1. eCollection 2018.

2.

BIGSdb: Scalable analysis of bacterial genome variation at the population level.

Jolley KA, Maiden MC.

BMC Bioinformatics. 2010 Dec 10;11:595. doi: 10.1186/1471-2105-11-595.

3.

A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter.

Sheppard SK, Jolley KA, Maiden MC.

Genes (Basel). 2012 Apr 12;3(2):261-77. doi: 10.3390/genes3020261.

4.

Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods.

Jolley KA, Hill DM, Bratcher HB, Harrison OB, Feavers IM, Parkhill J, Maiden MC.

J Clin Microbiol. 2012 Sep;50(9):3046-53. doi: 10.1128/JCM.01312-12. Epub 2012 Jul 11.

5.

MLSTar: automatic multilocus sequence typing of bacterial genomes in R.

Ferrés I, Iraola G.

PeerJ. 2018 Jun 15;6:e5098. doi: 10.7717/peerj.5098. eCollection 2018.

6.

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.

Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MC.

BMC Genomics. 2014 Dec 18;15:1138. doi: 10.1186/1471-2164-15-1138.

7.

Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis.

Forsythe SJ, Dickins B, Jolley KA.

BMC Genomics. 2014 Dec 16;15:1121. doi: 10.1186/1471-2164-15-1121.

8.

Bayesian semi-supervised classification of bacterial samples using MLST databases.

Cheng L, Connor TR, Aanensen DM, Spratt BG, Corander J.

BMC Bioinformatics. 2011 Jul 26;12:302. doi: 10.1186/1471-2105-12-302.

9.

Identification of Novel Sequence Types among Staphylococcus haemolyticus Isolated from Variety of Infections in India.

Panda S, Jena S, Sharma S, Dhawan B, Nath G, Singh DV.

PLoS One. 2016 Nov 8;11(11):e0166193. doi: 10.1371/journal.pone.0166193. eCollection 2016.

10.

mlstdbNet - distributed multi-locus sequence typing (MLST) databases.

Jolley KA, Chan MS, Maiden MC.

BMC Bioinformatics. 2004 Jul 1;5:86.

11.

Short read sequence typing (SRST): multi-locus sequence types from short reads.

Inouye M, Conway TC, Zobel J, Holt KE.

BMC Genomics. 2012 Jul 24;13:338.

12.

Accessing the SEED genome databases via Web services API: tools for programmers.

Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA.

BMC Bioinformatics. 2010 Jun 14;11:319. doi: 10.1186/1471-2105-11-319.

13.

A database and API for variation, dense genotyping and resequencing data.

Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F.

BMC Bioinformatics. 2010 May 11;11:238. doi: 10.1186/1471-2105-11-238.

14.

Population and Functional Genomics of Neisseria Revealed with Gene-by-Gene Approaches.

Maiden MC, Harrison OB.

J Clin Microbiol. 2016 Aug;54(8):1949-55. doi: 10.1128/JCM.00301-16. Epub 2016 Apr 20. Review.

15.

AgdbNet - antigen sequence database software for bacterial typing.

Jolley KA, Maiden MC.

BMC Bioinformatics. 2006 Jun 21;7:314.

16.

MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms.

Tomasini N, Lauthier JJ, Llewellyn MS, Diosque P.

Infect Genet Evol. 2013 Dec;20:188-96. doi: 10.1016/j.meegid.2013.08.029. Epub 2013 Sep 8.

PMID:
24025589
17.

Establishment of the European meningococcal strain collection genome library (EMSC-GL) for the 2011 to 2012 epidemiological year.

Bratcher HB, Brehony C, Heuberger S, Pieridou-Bagatzouni D, Křížová P, Hoffmann S, Toropainen M, Taha MK, Claus H, Tzanakaki G, Erdôsi T, Galajeva J, van der Ende A, Skoczyńska A, Pana M, Vaculíková A, Paragi M, Maiden MC, Caugant DA.

Euro Surveill. 2018 May;23(20). doi: 10.2807/1560-7917.ES.2018.23.20.17-00474.

18.

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.

19.

Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus.

Gonzalez-Escalona N, Jolley KA, Reed E, Martinez-Urtaza J.

J Clin Microbiol. 2017 Jun;55(6):1682-1697. doi: 10.1128/JCM.00227-17. Epub 2017 Mar 22.

20.

A RESTful API for accessing microbial community data for MG-RAST.

Wilke A, Bischof J, Harrison T, Brettin T, D'Souza M, Gerlach W, Matthews H, Paczian T, Wilkening J, Glass EM, Desai N, Meyer F.

PLoS Comput Biol. 2015 Jan 8;11(1):e1004008. doi: 10.1371/journal.pcbi.1004008. eCollection 2015 Jan.

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