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Items: 1 to 20 of 24

1.

Hidden diversity and evolution of viruses in market fish.

Geoghegan JL, Di Giallonardo F, Cousins K, Shi M, Williamson JE, Holmes EC.

Virus Evol. 2018 Oct 31;4(2):vey031. doi: 10.1093/ve/vey031. eCollection 2018 Jul.

2.

The phylogenomics of evolving virus virulence.

Geoghegan JL, Holmes EC.

Nat Rev Genet. 2018 Dec;19(12):756-769. doi: 10.1038/s41576-018-0055-5. Review.

PMID:
30305704
3.

Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia.

Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan JL, Dwyer DE, Holmes EC, Eden JS.

Viruses. 2018 Sep 6;10(9). pii: E476. doi: 10.3390/v10090476.

4.

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.

5.

Virological Sampling of Inaccessible Wildlife with Drones.

Geoghegan JL, Pirotta V, Harvey E, Smith A, Buchmann JP, Ostrowski M, Eden JS, Harcourt R, Holmes EC.

Viruses. 2018 Jun 2;10(6). pii: E300. doi: 10.3390/v10060300.

6.

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.

7.

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.

8.

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.

9.

Predicting virus emergence amid evolutionary noise.

Geoghegan JL, Holmes EC.

Open Biol. 2017 Oct;7(10). pii: 170189. doi: 10.1098/rsob.170189. Review.

10.

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.

11.

Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence.

Geoghegan JL, Senior AM, Holmes EC.

Proc Biol Sci. 2016 Aug 31;283(1837). pii: 20160727. doi: 10.1098/rspb.2016.0727.

12.

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
13.

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.

14.

Virological factors that increase the transmissibility of emerging human viruses.

Geoghegan JL, Senior AM, Di Giallonardo F, Holmes EC.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4170-5. doi: 10.1073/pnas.1521582113. Epub 2016 Mar 21.

15.

Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment.

Di Giallonardo F, Geoghegan JL, Docherty DE, McLean RG, Zody MC, Qu J, Yang X, Birren BW, Malboeuf CM, Newman RM, Ip HS, Holmes EC.

J Virol. 2015 Oct 28;90(2):862-72. doi: 10.1128/JVI.02305-15. Print 2016 Jan 15.

16.

Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam.

Geoghegan JL, Tan le V, Kühnert D, Halpin RA, Lin X, Simenauer A, Akopov A, Das SR, Stockwell TB, Shrivastava S, Ngoc NM, Uyen le TT, Tuyen NT, Thanh TT, Hang VT, Qui PT, Hung NT, Khanh TH, Thinh le Q, Nhan le NT, Van HM, Viet do C, Tuan HM, Viet HL, Hien TT, Chau NV, Thwaites G, Grenfell BT, Stadler T, Wentworth DE, Holmes EC, Van Doorn HR.

J Virol. 2015 Sep;89(17):8871-9. doi: 10.1128/JVI.00706-15. Epub 2015 Jun 17.

17.

A generic assay for whole-genome amplification and deep sequencing of enterovirus A71.

Tan le V, Tuyen NT, Thanh TT, Ngan TT, Van HM, Sabanathan S, Van TT, Thanh le TM, Nguyet LA, Geoghegan JL, Ong KC, Perera D, Hang VT, Ny NT, Anh NT, Ha do Q, Qui PT, Viet do C, Tuan HM, Wong KT, Holmes EC, Chau NV, Thwaites G, van Doorn HR.

J Virol Methods. 2015 Apr;215-216:30-6. doi: 10.1016/j.jviromet.2015.02.011. Epub 2015 Feb 19.

18.

Seasonal drivers of the epidemiology of arthropod-borne viruses in Australia.

Geoghegan JL, Walker PJ, Duchemin JB, Jeanne I, Holmes EC.

PLoS Negl Trop Dis. 2014 Nov 20;8(11):e3325. doi: 10.1371/journal.pntd.0003325. eCollection 2014 Nov.

19.

Contact heterogeneity, rather than transmission efficiency, limits the emergence and spread of canine influenza virus.

Dalziel BD, Huang K, Geoghegan JL, Arinaminpathy N, Dubovi EJ, Grenfell BT, Ellner SP, Holmes EC, Parrish CR.

PLoS Pathog. 2014 Oct 23;10(10):e1004455. doi: 10.1371/journal.ppat.1004455. eCollection 2014 Oct.

20.

Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV).

Lopes AM, Capucci L, Gavier-Widén D, Le Gall-Reculé G, Brocchi E, Barbieri I, Quéméner A, Le Pendu J, Geoghegan JL, Holmes EC, Esteves PJ, Abrantes J.

Virology. 2014 Nov;468-470:104-112. doi: 10.1016/j.virol.2014.08.002. Epub 2014 Aug 23.

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