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Items: 1 to 20 of 426

1.

Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.

Bryant JM, Thibault VC, Smith DG, McLuckie J, Heron I, Sevilla IA, Biet F, Harris SR, Maskell DJ, Bentley SD, Parkhill J, Stevenson K.

BMC Genomics. 2016 Jan 26;17(1):79. doi: 10.1186/s12864-015-2234-5.

2.

The Kinetic Energy of Hydrocarbons as a Function of Electron Density and Convolutional Neural Networks.

Yao K, Parkhill J.

J Chem Theory Comput. 2016 Jan 26. [Epub ahead of print]

PMID:
26812530
3.

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.

Barquist L, Mayho M, Cummins C, Cain AK, Boinett C, Page AJ, Langridge GC, Quail MA, Keane JA, Parkhill J.

Bioinformatics. 2016 Jan 21. pii: btw022. [Epub ahead of print]

4.

Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168.

Anjum A, Brathwaite KJ, Aidley J, Connerton PL, Cummings NJ, Parkhill J, Connerton I, Bayliss CD.

Nucleic Acids Res. 2016 Jan 18. pii: gkw019. [Epub ahead of print]

5.

Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network.

Brodrick HJ, Raven KE, Harrison EM, Blane B, Reuter S, Török ME, Parkhill J, Peacock SJ.

Genome Med. 2016 Jan 12;8(1):4. doi: 10.1186/s13073-015-0259-7.

6.

Modulation of the human gut microbiota by dietary fibres occurs at the species level.

Chung WS, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, Duncan SH, Flint HJ.

BMC Biol. 2016 Jan 11;14(1):3. doi: 10.1186/s12915-015-0224-3.

7.

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water.

Karkey A, Jombart T, Walker AW, Thompson CN, Torres A, Dongol S, Tran Vu Thieu N, Pham Thanh D, Tran Thi Ngoc D, Voong Vinh P, Singer AC, Parkhill J, Thwaites G, Basnyat B, Ferguson N, Baker S.

PLoS Negl Trop Dis. 2016 Jan 6;10(1):e0004346. doi: 10.1371/journal.pntd.0004346. eCollection 2016 Jan.

8.

Circlator: automated circularization of genome assemblies using long sequencing reads.

Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR.

Genome Biol. 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0.

9.

Genomic perspectives on the evolution and spread of bacterial pathogens.

Bentley SD, Parkhill J.

Proc Biol Sci. 2015 Dec 22;282(1821). pii: 20150488. doi: 10.1098/rspb.2015.0488. Review.

10.

Genome-Based Infection Tracking Reveals Dynamics of Clostridium difficile Transmission and Disease Recurrence.

Kumar N, Miyajima F, He M, Roberts P, Swale A, Ellison L, Pickard D, Smith G, Molyneux R, Dougan G, Parkhill J, Wren BW, Parry CM, Pirmohamed M, Lawley TD.

Clin Infect Dis. 2015 Dec 18. pii: civ1031. [Epub ahead of print]

PMID:
26683317
11.

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

Reuter S, Török ME, Holden MT, Reynolds R, Raven KE, Blane B, Donker T, Bentley SD, Aanensen DM, Grundmann H, Feil EJ, Spratt BG, Parkhill J, Peacock SJ.

Genome Res. 2016 Feb;26(2):263-70. doi: 10.1101/gr.196709.115. Epub 2015 Dec 15.

12.

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid.

Duncan SH, Russell WR, Quartieri A, Rossi M, Parkhill J, Walker AW, Flint HJ.

Environ Microbiol. 2015 Dec 4. doi: 10.1111/1462-2920.13158. [Epub ahead of print]

PMID:
26636660
13.

Whole genome investigation of a divergent clade of the pathogen Streptococcus suis.

Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MT, Parkhill J, Langford PR, Rycroft AN, Wren BW, Tucker AW, Maskell DJ.

Front Microbiol. 2015 Nov 4;6:1191. doi: 10.3389/fmicb.2015.01191. eCollection 2015.

14.

Nonadiabatic Dynamics for Electrons at Second-Order: Real-Time TDDFT and OSCF2.

Nguyen TS, Parkhill J.

J Chem Theory Comput. 2015 Jul 14;11(7):2918-24. doi: 10.1021/acs.jctc.5b00262. Epub 2015 Jun 24.

PMID:
26575729
15.

Erratum for Kulohoma et al., Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome.

Kulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR, Gray KJ, Kiran AM, Molyneux E, French N, Parkhill J, Faragher BE, Everett DB, Bentley SD, Heyderman RS.

Infect Immun. 2015 Dec;83(12):4896. doi: 10.1128/IAI.01156-15. No abstract available.

16.

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

Cuthbertson L, Rogers GB, Walker AW, Oliver A, Green LE, Daniels TW, Carroll MP, Parkhill J, Bruce KD, van der Gast CJ.

ISME J. 2015 Nov 10. doi: 10.1038/ismej.2015.198. [Epub ahead of print]

PMID:
26555248
17.

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.

Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP.

Sci Data. 2015 Oct 27;2:150058. doi: 10.1038/sdata.2015.58. eCollection 2015.

18.

Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study.

Hill DM, Lucidarme J, Gray SJ, Newbold LS, Ure R, Brehony C, Harrison OB, Bray JE, Jolley KA, Bratcher HB, Parkhill J, Tang CM, Borrow R, Maiden MC.

Lancet Infect Dis. 2015 Dec;15(12):1420-8. doi: 10.1016/S1473-3099(15)00267-4. Epub 2015 Oct 27.

19.

Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis.

Howell KJ, Peters SE, Wang J, Hernandez-Garcia J, Weinert LA, Luan SL, Chaudhuri RR, Angen Ø, Aragon V, Williamson SM, Parkhill J, Langford PR, Rycroft AN, Wren BW, Maskell DJ, Tucker AW.

J Clin Microbiol. 2015 Dec;53(12):3812-21. doi: 10.1128/JCM.01991-15. Epub 2015 Sep 30.

PMID:
26424843
20.

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

Sun Z, Harris HM, McCann A, Guo C, Argimón S, Zhang W, Yang X, Jeffery IB, Cooney JC, Kagawa TF, Liu W, Song Y, Salvetti E, Wrobel A, Rasinkangas P, Parkhill J, Rea MC, O'Sullivan O, Ritari J, Douillard FP, Paul Ross R, Yang R, Briner AE, Felis GE, de Vos WM, Barrangou R, Klaenhammer TR, Caufield PW, Cui Y, Zhang H, O'Toole PW.

Nat Commun. 2015 Sep 29;6:8322. doi: 10.1038/ncomms9322.

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