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Items: 1 to 50 of 79

1.

The molecular clock of Mycobacterium tuberculosis.

Menardo F, Duchêne S, Brites D, Gagneux S.

PLoS Pathog. 2019 Sep 12;15(9):e1008067. doi: 10.1371/journal.ppat.1008067. [Epub ahead of print]

2.

Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Aug;51(8):1295. doi: 10.1038/s41588-019-0482-z.

PMID:
31324894
3.

Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia.

Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Telfer B, Cooper C, Price K, Selvey C, Holden J, Bachmann N, Lee FJ, Dwyer DE, Duchêne S, Holmes EC, Grulich AE, Kelleher AD.

Viruses. 2019 May 27;11(5). pii: E482. doi: 10.3390/v11050482.

4.

Genome Analysis of Coxsackievirus A4 Isolates From Hand, Foot, and Mouth Disease Cases in Shandong, China.

Wang M, Li J, Yao MX, Zhang YW, Hu T, Carr MJ, Duchêne S, Zhang XC, Zhang ZJ, Zhou H, Tong YG, Ding SJ, Wang XJ, Shi WF.

Front Microbiol. 2019 May 7;10:1001. doi: 10.3389/fmicb.2019.01001. eCollection 2019.

5.

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Jun;51(6):1035-1043. doi: 10.1038/s41588-019-0417-8. Epub 2019 May 27. Erratum in: Nat Genet. 2019 Jul 19;:.

PMID:
31133745
6.

Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?

Holmes EC, Duchêne S.

MBio. 2019 Apr 16;10(2). pii: e00289-19. doi: 10.1128/mBio.00289-19. No abstract available.

7.

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae.

Wyres KL, Wick RR, Judd LM, Froumine R, Tokolyi A, Gorrie CL, Lam MMC, Duchêne S, Jenney A, Holt KE.

PLoS Genet. 2019 Apr 15;15(4):e1008114. doi: 10.1371/journal.pgen.1008114. eCollection 2019 Apr.

8.

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ.

PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650. eCollection 2019 Apr.

9.

Tracing Ancient Human Migrations into Sahul Using Hepatitis B Virus Genomes.

Yuen LKW, Littlejohn M, Duchêne S, Edwards R, Bukulatjpi S, Binks P, Jackson K, Davies J, Davis JS, Tong SYC, Locarnini S.

Mol Biol Evol. 2019 May 1;36(5):942-954. doi: 10.1093/molbev/msz021.

PMID:
30856252
10.

Evolutionary stasis of viruses?

Holmes EC, Duchêne S.

Nat Rev Microbiol. 2019 May;17(5):329. doi: 10.1038/s41579-019-0168-7. No abstract available.

PMID:
30814682
11.

The Asian Lineage of Zika Virus: Transmission and Evolution in Asia and the Americas.

Hu T, Li J, Carr MJ, Duchêne S, Shi W.

Virol Sin. 2019 Feb;34(1):1-8. doi: 10.1007/s12250-018-0078-2. Epub 2019 Jan 25. Review.

12.

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Park SE, Pham DT, Boinett C, Wong VK, Pak GD, Panzner U, Espinoza LMC, von Kalckreuth V, Im J, Schütt-Gerowitt H, Crump JA, Breiman RF, Adu-Sarkodie Y, Owusu-Dabo E, Rakotozandrindrainy R, Soura AB, Aseffa A, Gasmelseed N, Keddy KH, May J, Sow AG, Aaby P, Biggs HM, Hertz JT, Montgomery JM, Cosmas L, Olack B, Fields B, Sarpong N, Razafindrabe TJL, Raminosoa TM, Kabore LP, Sampo E, Teferi M, Yeshitela B, El Tayeb MA, Sooka A, Meyer CG, Krumkamp R, Dekker DM, Jaeger A, Poppert S, Tall A, Niang A, Bjerregaard-Andersen M, Løfberg SV, Seo HJ, Jeon HJ, Deerin JF, Park J, Konings F, Ali M, Clemens JD, Hughes P, Sendagala JN, Vudriko T, Downing R, Ikumapayi UN, Mackenzie GA, Obaro S, Argimon S, Aanensen DM, Page A, Keane JA, Duchene S, Dyson Z, Holt KE, Dougan G, Marks F, Baker S.

Nat Commun. 2018 Nov 30;9(1):5094. doi: 10.1038/s41467-018-07370-z.

13.

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.

Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill FX, Ho SYW, Gilbert MTP, Achtman M.

Curr Biol. 2018 Aug 6;28(15):2420-2428.e10. doi: 10.1016/j.cub.2018.05.058. Epub 2018 Jul 19.

14.

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination.

Lam MMC, Wyres KL, Duchêne S, Wick RR, Judd LM, Gan YH, Hoh CH, Archuleta S, Molton JS, Kalimuddin S, Koh TH, Passet V, Brisse S, Holt KE.

Nat Commun. 2018 Jul 13;9(1):2703. doi: 10.1038/s41467-018-05114-7.

15.

Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

Duchene S, Bouckaert R, Duchene DA, Stadler T, Drummond AJ.

Syst Biol. 2019 Mar 1;68(2):358-364. doi: 10.1093/sysbio/syy048.

16.

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

Duchene S, Duchene DA, Geoghegan JL, Dyson ZA, Hawkey J, Holt KE.

BMC Evol Biol. 2018 Jun 19;18(1):95. doi: 10.1186/s12862-018-1210-5.

17.

Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy.

Duchêne DA, Duchêne S, Ho SYW.

Genome Biol Evol. 2018 Jun 1;10(6):1375-1388. doi: 10.1093/gbe/evy094.

18.

A comparison of methods for estimating substitution rates from ancient DNA sequence data.

Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW.

BMC Evol Biol. 2018 May 16;18(1):70. doi: 10.1186/s12862-018-1192-3.

19.

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development.

Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG.

Infect Genet Evol. 2018 Aug;62:279-295. doi: 10.1016/j.meegid.2018.04.032. Epub 2018 Apr 25. Review.

20.

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy.

Britto CD, Dyson ZA, Duchene S, Carter MJ, Gurung M, Kelly DF, Murdoch DR, Ansari I, Thorson S, Shrestha S, Adhikari N, Dougan G, Holt KE, Pollard AJ.

PLoS Negl Trop Dis. 2018 Apr 23;12(4):e0006408. doi: 10.1371/journal.pntd.0006408. eCollection 2018 Apr.

21.

Estimating evolutionary rates in giant viruses using ancient genomes.

Duchêne S, Holmes EC.

Virus Evol. 2018 Feb 27;4(1):vey006. doi: 10.1093/ve/vey006. eCollection 2018 Jan.

22.

PhyloMAd: efficient assessment of phylogenomic model adequacy.

Duchêne DA, Duchêne S, Ho SYW.

Bioinformatics. 2018 Jul 1;34(13):2300-2301. doi: 10.1093/bioinformatics/bty103.

PMID:
29481585
23.

Correction: The paradox of HBV evolution as revealed from a 16th century mummy.

Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN.

PLoS Pathog. 2018 Feb 9;14(2):e1006887. doi: 10.1371/journal.ppat.1006887. eCollection 2018 Feb.

24.

Correction: Continental synchronicity of human influenza virus epidemics despite climactic variation.

Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC.

PLoS Pathog. 2018 Feb 7;14(2):e1006903. doi: 10.1371/journal.ppat.1006903. eCollection 2018 Feb.

25.

Continental synchronicity of human influenza virus epidemics despite climatic variation.

Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC.

PLoS Pathog. 2018 Jan 11;14(1):e1006780. doi: 10.1371/journal.ppat.1006780. eCollection 2018 Jan. Erratum in: PLoS Pathog. 2018 Feb 7;14 (2):e1006903.

26.

The paradox of HBV evolution as revealed from a 16th century mummy.

Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN.

PLoS Pathog. 2018 Jan 4;14(1):e1006750. doi: 10.1371/journal.ppat.1006750. eCollection 2018 Jan. Erratum in: PLoS Pathog. 2018 Feb 9;14 (2):e1006887.

27.

Bayesian molecular dating: opening up the black box.

Bromham L, Duchêne S, Hua X, Ritchie AM, Duchêne DA, Ho SYW.

Biol Rev Camb Philos Soc. 2018 May;93(2):1165-1191. doi: 10.1111/brv.12390. Epub 2017 Dec 15. Review.

PMID:
29243391
28.

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families.

Duchêne DA, Bragg JG, Duchêne S, Neaves LE, Potter S, Moritz C, Johnson RN, Ho SYW, Eldridge MDB.

Syst Biol. 2018 May 1;67(3):400-412. doi: 10.1093/sysbio/syx076.

PMID:
29029231
29.

The impacts of drift and selection on genomic evolution in insects.

Tong KJ, Duchêne S, Lo N, Ho SYW.

PeerJ. 2017 Apr 27;5:e3241. doi: 10.7717/peerj.3241. eCollection 2017.

30.

Genome-scale rates of evolutionary change in bacteria.

Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC.

Microb Genom. 2016 Nov 30;2(11):e000094. doi: 10.1099/mgen.0.000094. eCollection 2016 Nov.

31.

New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity.

Duchêne DA, Duchêne S, Ho SYW.

Mol Biol Evol. 2017 Jun 1;34(6):1529-1534. doi: 10.1093/molbev/msx092.

PMID:
28333201
32.

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, Morris AG, Alt KW, Caramelli D, Dresely V, Farrell M, Farrer AG, Francken M, Gully N, Haak W, Hardy K, Harvati K, Held P, Holmes EC, Kaidonis J, Lalueza-Fox C, de la Rasilla M, Rosas A, Semal P, Soltysiak A, Townsend G, Usai D, Wahl J, Huson DH, Dobney K, Cooper A.

Nature. 2017 Apr 20;544(7650):357-361. doi: 10.1038/nature21674. Epub 2017 Mar 8.

PMID:
28273061
33.

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families.

Geoghegan JL, Duchêne S, Holmes EC.

PLoS Pathog. 2017 Feb 8;13(2):e1006215. doi: 10.1371/journal.ppat.1006215. eCollection 2017 Feb.

34.

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C, Vignuzzi M, Duchene S, Holmes EC, Bourhy H.

PLoS Pathog. 2016 Dec 15;12(12):e1006041. doi: 10.1371/journal.ppat.1006041. eCollection 2016 Dec.

35.

17th Century Variola Virus Reveals the Recent History of Smallpox.

Duggan AT, Perdomo MF, Piombino-Mascali D, Marciniak S, Poinar D, Emery MV, Buchmann JP, Duchêne S, Jankauskas R, Humphreys M, Golding GB, Southon J, Devault A, Rouillard JM, Sahl JW, Dutour O, Hedman K, Sajantila A, Smith GL, Holmes EC, Poinar HN.

Curr Biol. 2016 Dec 19;26(24):3407-3412. doi: 10.1016/j.cub.2016.10.061. Epub 2016 Dec 8.

36.

Highly Divergent Dengue Virus Type 2 in Traveler Returning from Borneo to Australia.

Liu W, Pickering P, Duchêne S, Holmes EC, Aaskov JG.

Emerg Infect Dis. 2016 Dec;22(12):2146-2148. doi: 10.3201/eid2212.160813.

37.

Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives.

Mahar JE, Nicholson L, Eden JS, Duchêne S, Kerr PJ, Duckworth J, Ward VK, Holmes EC, Strive T.

J Virol. 2016 Sep 29;90(20):9317-29. doi: 10.1128/JVI.01212-16. Print 2016 Oct 15.

38.

Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods.

Duchêne S, Geoghegan JL, Holmes EC, Ho SY.

Bioinformatics. 2016 Nov 15;32(22):3375-3379. Epub 2016 Jul 13.

PMID:
27412094
39.

Cross-validation to select Bayesian hierarchical models in phylogenetics.

Duchêne S, Duchêne DA, Di Giallonardo F, Eden JS, Geoghegan JL, Holt KE, Ho SY, Holmes EC.

BMC Evol Biol. 2016 May 26;16(1):115. doi: 10.1186/s12862-016-0688-y.

40.

Evolution, Expression, and Function of Nonneuronal Ligand-Gated Chloride Channels in Drosophila melanogaster.

Remnant EJ, Williams A, Lumb C, Yang YT, Chan J, Duchêne S, Daborn PJ, Batterham P, Perry T.

G3 (Bethesda). 2016 Jul 7;6(7):2003-12. doi: 10.1534/g3.116.029546.

41.

Time-dependent estimates of molecular evolutionary rates: evidence and causes.

Ho SY, Duchêne S, Molak M, Shapiro B.

Mol Ecol. 2015 Dec;24(24):6007-12. doi: 10.1111/mec.13450.

PMID:
26769402
42.

Estimating the number and assignment of clock models in analyses of multigene datasets.

Duchêne S, Foster CS, Ho SY.

Bioinformatics. 2016 May 1;32(9):1281-5. doi: 10.1093/bioinformatics/btw005. Epub 2016 Jan 6.

PMID:
26743512
43.

Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales.

Duchêne S, Di Giallonardo F, Holmes EC.

Mol Biol Evol. 2016 Jan;33(1):255-67. doi: 10.1093/molbev/msv207. Epub 2015 Sep 28.

PMID:
26416981
44.

INSECT PHYLOGENOMICS. Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

Tong KJ, Duchêne S, Ho SY, Lo N.

Science. 2015 Jul 31;349(6247):487. doi: 10.1126/science.aaa5460.

45.

Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods.

Duchêne S, Lanfear R.

J Exp Zool B Mol Dev Evol. 2015 Sep;324(6):517-24. doi: 10.1002/jez.b.22638. Epub 2015 Jul 14.

PMID:
26173578
46.

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations.

Duchêne DA, Duchêne S, Holmes EC, Ho SY.

Mol Biol Evol. 2015 Nov;32(11):2986-95. doi: 10.1093/molbev/msv154. Epub 2015 Jul 10.

PMID:
26163668
47.

Geographic and temporal dynamics of a global radiation and diversification in the killer whale.

Morin PA, Parsons KM, Archer FI, Ávila-Arcos MC, Barrett-Lennard LG, Dalla Rosa L, Duchêne S, Durban JW, Ellis GM, Ferguson SH, Ford JK, Ford MJ, Garilao C, Gilbert MT, Kaschner K, Matkin CO, Petersen SD, Robertson KM, Visser IN, Wade PR, Ho SY, Foote AD.

Mol Ecol. 2015 Aug;24(15):3964-79. doi: 10.1111/mec.13284. Epub 2015 Jul 17.

PMID:
26087773
48.

Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes.

Caballero S, Duchêne S, Garavito MF, Slikas B, Baker CS.

PLoS One. 2015 May 6;10(5):e0123543. doi: 10.1371/journal.pone.0123543. eCollection 2015.

49.

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models.

Duchêne S, Ho SY, Holmes EC.

BMC Evol Biol. 2015 Mar 11;15:36. doi: 10.1186/s12862-015-0312-6.

50.

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data.

Duchêne S, Duchêne D, Holmes EC, Ho SY.

Mol Biol Evol. 2015 Jul;32(7):1895-906. doi: 10.1093/molbev/msv056. Epub 2015 Mar 13.

PMID:
25771196

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