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Items: 1 to 50 of 63

1.

RADpainter and fineRADstructure: Population Inference from RADseq Data.

Malinsky M, Trucchi E, Lawson DJ, Falush D.

Mol Biol Evol. 2018 May 1;35(5):1284-1290. doi: 10.1093/molbev/msy023.

2.

Correction: Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.

Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, Mendez A, Rizzato C, Bravo MM, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D.

PLoS Genet. 2017 Apr 14;13(4):e1006730. doi: 10.1371/journal.pgen.1006730. eCollection 2017 Apr.

3.

Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.

Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, Mendez A, Rizzato C, Bravo MM, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D.

PLoS Genet. 2017 Feb 23;13(2):e1006546. doi: 10.1371/journal.pgen.1006546. eCollection 2017 Feb. Erratum in: PLoS Genet. 2017 Apr 14;13(4):e1006730.

4.

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation.

Koslicki D, Falush D.

mSystems. 2016 Jun 7;1(3). pii: e00020-16. eCollection 2016 May-Jun.

5.

Bacterial genomics: Microbial GWAS coming of age.

Falush D.

Nat Microbiol. 2016 Apr 26;1:16059. doi: 10.1038/nmicrobiol.2016.59. No abstract available.

PMID:
27572652
6.

The Kalash Genetic Isolate? The Evidence for Recent Admixture.

Hellenthal G, Falush D, Myers S, Reich D, Busby GB, Lipson M, Capelli C, Patterson N.

Am J Hum Genet. 2016 Feb 4;98(2):396-7. doi: 10.1016/j.ajhg.2015.12.025. No abstract available.

7.

The Landscape of Realized Homologous Recombination in Pathogenic Bacteria.

Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MC, Sheppard SK, Falush D.

Mol Biol Evol. 2016 Feb;33(2):456-71. doi: 10.1093/molbev/msv237. Epub 2015 Oct 29.

8.

Roary: rapid large-scale prokaryote pan genome analysis.

Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J.

Bioinformatics. 2015 Nov 15;31(22):3691-3. doi: 10.1093/bioinformatics/btv421. Epub 2015 Jul 20.

9.

The fine-scale genetic structure of the British population.

Leslie S, Winney B, Hellenthal G, Davison D, Boumertit A, Day T, Hutnik K, Royrvik EC, Cunliffe B; Wellcome Trust Case Control Consortium 2; International Multiple Sclerosis Genetics Consortium, Lawson DJ, Falush D, Freeman C, Pirinen M, Myers S, Robinson M, Donnelly P, Bodmer W.

Nature. 2015 Mar 19;519(7543):309-314. doi: 10.1038/nature14230.

10.

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.

PMID:
25605790
11.

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.

12.

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.

13.

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.

14.

A genetic atlas of human admixture history.

Hellenthal G, Busby GBJ, Band G, Wilson JF, Capelli C, Falush D, Myers S.

Science. 2014 Feb 14;343(6172):747-751. doi: 10.1126/science.1243518.

15.

Recent acquisition of Helicobacter pylori by Baka pygmies.

Nell S, Eibach D, Montano V, Maady A, Nkwescheu A, Siri J, Elamin WF, Falush D, Linz B, Achtman M, Moodley Y, Suerbaum S.

PLoS Genet. 2013;9(9):e1003775. doi: 10.1371/journal.pgen.1003775. Epub 2013 Sep 19.

16.

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter.

Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, Bentley SD, Maiden MC, Parkhill J, Falush D.

Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11923-7. doi: 10.1073/pnas.1305559110. Epub 2013 Jul 1.

17.

Progressive genome-wide introgression in agricultural Campylobacter coli.

Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJ, Ogden ID, Forbes K, French NP, Carter P, Miller WG, McCarthy ND, Owen R, Litrup E, Egholm M, Affourtit JP, Bentley SD, Parkhill J, Maiden MC, Falush D.

Mol Ecol. 2013 Feb;22(4):1051-64. doi: 10.1111/mec.12162. Epub 2012 Dec 20.

18.

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis.

Cui Y, Yu C, Yan Y, Li D, Li Y, Jombart T, Weinert LA, Wang Z, Guo Z, Xu L, Zhang Y, Zheng H, Qin N, Xiao X, Wu M, Wang X, Zhou D, Qi Z, Du Z, Wu H, Yang X, Cao H, Wang H, Wang J, Yao S, Rakin A, Li Y, Falush D, Balloux F, Achtman M, Song Y, Wang J, Yang R.

Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):577-82. doi: 10.1073/pnas.1205750110. Epub 2012 Dec 27.

19.

Phylogenetic distribution of traits associated with plant colonization in Escherichia coli.

Méric G, Kemsley EK, Falush D, Saggers EJ, Lucchini S.

Environ Microbiol. 2013 Feb;15(2):487-501. doi: 10.1111/j.1462-2920.2012.02852.x. Epub 2012 Aug 30.

PMID:
22934605
20.

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli.

Didelot X, Méric G, Falush D, Darling AE.

BMC Genomics. 2012 Jun 19;13:256. doi: 10.1186/1471-2164-13-256.

21.

Population identification using genetic data.

Lawson DJ, Falush D.

Annu Rev Genomics Hum Genet. 2012;13:337-61. doi: 10.1146/annurev-genom-082410-101510. Epub 2012 Jun 11. Review.

PMID:
22703172
22.

Inference of population structure using dense haplotype data.

Lawson DJ, Hellenthal G, Myers S, Falush D.

PLoS Genet. 2012 Jan;8(1):e1002453. doi: 10.1371/journal.pgen.1002453. Epub 2012 Jan 26.

23.

Recombination and population structure in Salmonella enterica.

Didelot X, Bowden R, Street T, Golubchik T, Spencer C, McVean G, Sangal V, Anjum MF, Achtman M, Falush D, Donnelly P.

PLoS Genet. 2011 Jul;7(7):e1002191. doi: 10.1371/journal.pgen.1002191. Epub 2011 Jul 28.

24.

Helicobacter pylori genome evolution during human infection.

Kennemann L, Didelot X, Aebischer T, Kuhn S, Drescher B, Droege M, Reinhardt R, Correa P, Meyer TF, Josenhans C, Falush D, Suerbaum S.

Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):5033-8. doi: 10.1073/pnas.1018444108. Epub 2011 Mar 7.

25.

Inference of homologous recombination in bacteria using whole-genome sequences.

Didelot X, Lawson D, Darling A, Falush D.

Genetics. 2010 Dec;186(4):1435-49. doi: 10.1534/genetics.110.120121. Epub 2010 Oct 5.

26.

Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families.

Morelli G, Didelot X, Kusecek B, Schwarz S, Bahlawane C, Falush D, Suerbaum S, Achtman M.

PLoS Genet. 2010 Jul 22;6(7):e1001036. doi: 10.1371/journal.pgen.1001036.

27.

Composition, variability, and temporal stability of the intestinal microbiota of the elderly.

Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O'Connor M, Harnedy N, O'Connor K, Henry C, O'Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O'Toole PW.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4586-91. doi: 10.1073/pnas.1000097107. Epub 2010 Jun 22.

28.

A draft sequence of the Neandertal genome.

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.

Science. 2010 May 7;328(5979):710-722. doi: 10.1126/science.1188021.

29.

Ethnic and geographic differentiation of Helicobacter pylori within Iran.

Latifi-Navid S, Ghorashi SA, Siavoshi F, Linz B, Massarrat S, Khegay T, Salmanian AH, Shayesteh AA, Masoodi M, Ghanadi K, Ganji A, Suerbaum S, Achtman M, Malekzadeh R, Falush D.

PLoS One. 2010 Mar 22;5(3):e9645. doi: 10.1371/journal.pone.0009645.

30.

Haplotype background, repeat length evolution, and Huntington's disease.

Falush D.

Am J Hum Genet. 2009 Dec;85(6):939-42. doi: 10.1016/j.ajhg.2009.11.002. No abstract available.

31.

Toward the use of genomics to study microevolutionary change in bacteria.

Falush D.

PLoS Genet. 2009 Oct;5(10):e1000627. doi: 10.1371/journal.pgen.1000627. Epub 2009 Oct 26. Review.

32.

Inferring weak population structure with the assistance of sample group information.

Hubisz MJ, Falush D, Stephens M, Pritchard JK.

Mol Ecol Resour. 2009 Sep;9(5):1322-32. doi: 10.1111/j.1755-0998.2009.02591.x. Epub 2009 Apr 1.

33.

Genealogical typing of Neisseria meningitidis.

Didelot X, Urwin R, Maiden MC, Falush D.

Microbiology. 2009 Oct;155(Pt 10):3176-86. doi: 10.1099/mic.0.031534-0. Epub 2009 Jul 30.

34.

SimMLST: simulation of multi-locus sequence typing data under a neutral model.

Didelot X, Lawson D, Falush D.

Bioinformatics. 2009 Jun 1;25(11):1442-4. doi: 10.1093/bioinformatics/btp145. Epub 2009 Mar 13.

PMID:
19286834
35.

Natural transformation of helicobacter pylori involves the integration of short DNA fragments interrupted by gaps of variable size.

Lin EA, Zhang XS, Levine SM, Gill SR, Falush D, Blaser MJ.

PLoS Pathog. 2009 Mar;5(3):e1000337. doi: 10.1371/journal.ppat.1000337. Epub 2009 Mar 13.

36.

Campylobacter genotyping to determine the source of human infection.

Sheppard SK, Dallas JF, Strachan NJ, MacRae M, McCarthy ND, Wilson DJ, Gormley FJ, Falush D, Ogden ID, Maiden MC, Forbes KJ.

Clin Infect Dis. 2009 Apr 15;48(8):1072-8. doi: 10.1086/597402.

37.

Evolution of pathogenicity in the Bacillus cereus group.

Didelot X, Barker M, Falush D, Priest FG.

Syst Appl Microbiol. 2009 Apr;32(2):81-90. doi: 10.1016/j.syapm.2009.01.001. Epub 2009 Feb 5.

PMID:
19200684
38.

Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori.

Kulick S, Moccia C, Didelot X, Falush D, Kraft C, Suerbaum S.

PLoS One. 2008;3(11):e3797. doi: 10.1371/journal.pone.0003797. Epub 2008 Nov 24.

39.

Inferring genomic flux in bacteria.

Didelot X, Darling A, Falush D.

Genome Res. 2009 Feb;19(2):306-17. doi: 10.1101/gr.082263.108. Epub 2008 Nov 17.

40.

Inference of population structure using multilocus genotype data: dominant markers and null alleles.

Falush D, Stephens M, Pritchard JK.

Mol Ecol Notes. 2007 Jul 1;7(4):574-578.

41.

Inferring human colonization history using a copying model.

Hellenthal G, Auton A, Falush D.

PLoS Genet. 2008 May 23;4(5):e1000078. doi: 10.1371/journal.pgen.1000078. Erratum in: PLoS Genet. 2008 Jun;4(6). doi: 10.1371/annotation/da6e20fe-f8eb-4e44-8669-6c20c7102b3d.

42.

Convergence of Campylobacter species: implications for bacterial evolution.

Sheppard SK, McCarthy ND, Falush D, Maiden MC.

Science. 2008 Apr 11;320(5873):237-9. doi: 10.1126/science.1155532.

43.

Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation.

Levine SM, Lin EA, Emara W, Kang J, DiBenedetto M, Ando T, Falush D, Blaser MJ.

FASEB J. 2007 Nov;21(13):3458-67. Epub 2007 Jun 12.

PMID:
17567566
44.

Host-associated genetic import in Campylobacter jejuni.

McCarthy ND, Colles FM, Dingle KE, Bagnall MC, Manning G, Maiden MC, Falush D.

Emerg Infect Dis. 2007 Feb;13(2):267-72.

45.

An African origin for the intimate association between humans and Helicobacter pylori.

Linz B, Balloux F, Moodley Y, Manica A, Liu H, Roumagnac P, Falush D, Stamer C, Prugnolle F, van der Merwe SW, Yamaoka Y, Graham DY, Perez-Trallero E, Wadstrom T, Suerbaum S, Achtman M.

Nature. 2007 Feb 22;445(7130):915-918. doi: 10.1038/nature05562. Epub 2007 Feb 7.

46.

Inference of bacterial microevolution using multilocus sequence data.

Didelot X, Falush D.

Genetics. 2007 Mar;175(3):1251-66. Epub 2006 Dec 6.

47.

A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?

Didelot X, Achtman M, Parkhill J, Thomson NR, Falush D.

Genome Res. 2007 Jan;17(1):61-8. Epub 2006 Nov 7.

48.

Mismatch induced speciation in Salmonella: model and data.

Falush D, Torpdahl M, Didelot X, Conrad DF, Wilson DJ, Achtman M.

Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):2045-53.

49.

Genome-wide association mapping in bacteria?

Falush D, Bowden R.

Trends Microbiol. 2006 Aug;14(8):353-5. Epub 2006 Jun 19.

PMID:
16782339
50.

Germs, genomes and genealogies.

Wilson DJ, Falush D, McVean G.

Trends Ecol Evol. 2005 Jan;20(1):39-45. Epub 2004 Nov 2.

PMID:
16701339

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