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Results: 1 to 20 of 69

1.

Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence.

Achtman M, Zhou Z, Didelot X.

PLoS One. 2015 Aug 14;10(8):e0134435. doi: 10.1371/journal.pone.0134435. eCollection 2015.

2.

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori.

Montano V, Didelot X, Foll M, Linz B, Reinhardt R, Suerbaum S, Moodley Y, Jensen JD.

Genetics. 2015 Jul;200(3):947-63. doi: 10.1534/genetics.115.176404. Epub 2015 May 20.

PMID:
25995212
3.

Measurably evolving pathogens in the genomic era.

Biek R, Pybus OG, Lloyd-Smith JO, Didelot X.

Trends Ecol Evol. 2015 Jun;30(6):306-13. doi: 10.1016/j.tree.2015.03.009. Epub 2015 Apr 14. Review.

PMID:
25887947
4.

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

Nandi T, Holden MT, Didelot X, Mehershahi K, Boddey JA, Beacham I, Peak I, Harting J, Baybayan P, Guo Y, Wang S, How LC, Sim B, Essex-Lopresti A, Sarkar-Tyson M, Nelson M, Smither S, Ong C, Aw LT, Hoon CH, Michell S, Studholme DJ, Titball R, Chen SL, Parkhill J, Tan P.

Genome Res. 2015 Apr;25(4):608. No abstract available.

5.

Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance.

Ezewudo MN, Joseph SJ, Castillo-Ramirez S, Dean D, Del Rio C, Didelot X, Dillon JA, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD.

PeerJ. 2015 Mar 5;3:e806. doi: 10.7717/peerj.806. eCollection 2015.

6.

The role of china in the global spread of the current cholera pandemic.

Didelot X, Pang B, Zhou Z, McCann A, Ni P, Li D, Achtman M, Kan B.

PLoS Genet. 2015 Mar 13;11(3):e1005072. doi: 10.1371/journal.pgen.1005072. eCollection 2015 Mar.

7.

ClonalFrameML: efficient inference of recombination in whole bacterial genomes.

Didelot X, Wilson DJ.

PLoS Comput Biol. 2015 Feb 12;11(2):e1004041. doi: 10.1371/journal.pcbi.1004041. eCollection 2015 Feb.

8.

Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus.

Cui Y, Yang X, Didelot X, Guo C, Li D, Yan Y, Zhang Y, Yuan Y, Yang H, Wang J, Wang J, Song Y, Zhou D, Falush D, Yang R.

Mol Biol Evol. 2015 Jun;32(6):1396-410. doi: 10.1093/molbev/msv009. Epub 2015 Jan 19.

9.

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing.

Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, Didelot X, Turner SD, Sebra R, Kasarskis A, Peto T, Crook D, Sifri CD.

Antimicrob Agents Chemother. 2015 Mar;59(3):1656-63. doi: 10.1128/AAC.04292-14. Epub 2015 Jan 5.

10.

The application of genomics to tracing bacterial pathogen transmission.

Croucher NJ, Didelot X.

Curr Opin Microbiol. 2015 Feb;23:62-7. doi: 10.1016/j.mib.2014.11.004. Epub 2014 Nov 22. Review.

PMID:
25461574
11.

The complexity and diversity of the Pathogenicity Locus in Clostridium difficile clade 5.

Elliott B, Dingle KE, Didelot X, Crook DW, Riley TV.

Genome Biol Evol. 2014 Nov 8;6(12):3159-70. doi: 10.1093/gbe/evu248.

12.

Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting.

Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, Didelot X, Bashir A, Sebra R, Kasarskis A, Sthapit B, Shakya M, Kelly D, Pollard AJ, Peto TE, Crook DW, Donnelly P, Thorson S, Amatya P, Joshi S.

Antimicrob Agents Chemother. 2014 Dec;58(12):7347-57. doi: 10.1128/AAC.03900-14. Epub 2014 Sep 29.

13.

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

Nandi T, Holden MT, Didelot X, Mehershahi K, Boddey JA, Beacham I, Peak I, Harting J, Baybayan P, Guo Y, Wang S, How LC, Sim B, Essex-Lopresti A, Sarkar-Tyson M, Nelson M, Smither S, Ong C, Aw LT, Hoon CH, Michell S, Studholme DJ, Titball R, Chen SL, Parkhill J, Tan P.

Genome Res. 2015 Jan;25(1):129-41. doi: 10.1101/gr.177543.114. Epub 2014 Sep 18. Erratum in: Genome Res. 2015 Apr;25(4):608. Holden, Mathew T G [corrected to Holden, Matthew T G].

14.

Bidirectional genomic exchange between Helicobacter pylori strains from a family in Coventry, United Kingdom.

Krebes J, Didelot X, Kennemann L, Suerbaum S.

Int J Med Microbiol. 2014 Nov;304(8):1135-46. doi: 10.1016/j.ijmm.2014.08.007. Epub 2014 Aug 17.

PMID:
25218701
15.

Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis.

Cao Q, Didelot X, Wu Z, Li Z, He L, Li Y, Ni M, You Y, Lin X, Li Z, Gong Y, Zheng M, Zhang M, Liu J, Wang W, Bo X, Falush D, Wang S, Zhang J.

Gut. 2015 Apr;64(4):554-61. doi: 10.1136/gutjnl-2014-307345. Epub 2014 Jul 9.

16.

OutbreakTools: a new platform for disease outbreak analysis using the R software.

Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N.

Epidemics. 2014 Jun;7:28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.

17.

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.

Everitt RG, Didelot X, Batty EM, Miller RR, Knox K, Young BC, Bowden R, Auton A, Votintseva A, Larner-Svensson H, Charlesworth J, Golubchik T, Ip CL, Godwin H, Fung R, Peto TE, Walker AS, Crook DW, Wilson DJ.

Nat Commun. 2014 May 23;5:3956. doi: 10.1038/ncomms4956.

18.

A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data.

O'Brien JD, Didelot X, Iqbal Z, Amenga-Etego L, Ahiska B, Falush D.

Genetics. 2014 Jul;197(3):925-37. doi: 10.1534/genetics.114.161299. Epub 2014 May 1.

19.

Bayesian inference of infectious disease transmission from whole-genome sequence data.

Didelot X, Gardy J, Colijn C.

Mol Biol Evol. 2014 Jul;31(7):1869-79. doi: 10.1093/molbev/msu121. Epub 2014 Apr 8.

20.

Efficient inference of recombination hot regions in bacterial genomes.

Yahara K, Didelot X, Ansari MA, Sheppard SK, Falush D.

Mol Biol Evol. 2014 Jun;31(6):1593-605. doi: 10.1093/molbev/msu082. Epub 2014 Feb 27.

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