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Items: 26

1.

Immune Correlates of Disease Progression in Linked HIV-1 Infection.

Tuen M, Bimela JS, Banin AN, Ding S, Harkins GW, Weiss S, Itri V, Durham AR, Porcella SF, Soni S, Mayr L, Meli J, Torimiro JN, Tongo M, Wang X, Kong XP, Nádas A, Kaufmann DE, Brumme ZL, Nanfack AJ, Quinn TC, Zolla-Pazner S, Redd AD, Finzi A, Gorny MK, Nyambi PN, Duerr R.

Front Immunol. 2019 May 14;10:1062. doi: 10.3389/fimmu.2019.01062. eCollection 2019.

2.

Evidence for both Intermittent and Persistent Compartmentalization of HIV-1 in the Female Genital Tract.

Mabvakure BM, Lambson BE, Ramdayal K, Masson L, Kitchin D, Allam M, Abdool Karim S, Williamson C, Passmore JA, Martin DP, Scheepers C, Moore PL, Harkins GW, Morris L.

J Virol. 2019 May 1;93(10). pii: e00311-19. doi: 10.1128/JVI.00311-19. Print 2019 May 15.

PMID:
30842323
3.

The Westward Journey of Alfalfa Leaf Curl Virus.

Davoodi Z, Bejerman N, Richet C, Filloux D, Kumari SG, Chatzivassiliou EK, Galzi S, Julian C, Samarfard S, Trucco V, Giolitti F, Fiallo-Olivé E, Navas-Castillo J, Asaad N, Moukahel AR, Hijazi J, Mghandef S, Heydarnejad J, Massumi H, Varsani A, Dietzgen RG, Harkins GW, Martin DP, Roumagnac P.

Viruses. 2018 Oct 4;10(10). pii: E542. doi: 10.3390/v10100542.

4.

Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New Zealand.

Richet C, Kraberger S, Filloux D, Bernardo P, Harkins GW, Martin DP, Roumagnac P, Varsani A.

Arch Virol. 2019 Jan;164(1):237-242. doi: 10.1007/s00705-018-4031-3. Epub 2018 Sep 15.

PMID:
30220037
5.

From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study.

Claverie S, Bernardo P, Kraberger S, Hartnady P, Lefeuvre P, Lett JM, Galzi S, Filloux D, Harkins GW, Varsani A, Martin DP, Roumagnac P.

Adv Virus Res. 2018;101:55-83. doi: 10.1016/bs.aivir.2018.02.003. Epub 2018 May 7. Review.

PMID:
29908594
6.

Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages.

Tongo M, Harkins GW, Dorfman JR, Billings E, Tovanabutra S, de Oliveira T, Martin DP.

Virus Evol. 2018 Feb 19;4(1):vey003. doi: 10.1093/ve/vey003. eCollection 2018 Jan.

7.

Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.

Bernardo P, Charles-Dominique T, Barakat M, Ortet P, Fernandez E, Filloux D, Hartnady P, Rebelo TA, Cousins SR, Mesleard F, Cohez D, Yavercovski N, Varsani A, Harkins GW, Peterschmitt M, Malmstrom CM, Martin DP, Roumagnac P.

ISME J. 2018 Jan;12(1):173-184. doi: 10.1038/ismej.2017.155. Epub 2017 Oct 20.

8.

The role of Kenya in the trans-African spread of maize streak virus strain A.

Pande D, Madzokere E, Hartnady P, Kraberger S, Hadfield J, Rosario K, Jäschke A, Monjane AL, Owor BE, Dida MM, Shepherd DN, Martin DP, Varsani A, Harkins GW.

Virus Res. 2017 Mar 15;232:69-76. doi: 10.1016/j.virusres.2017.02.005. Epub 2017 Feb 9.

PMID:
28192163
9.

The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events.

Stainton D, Martin DP, Muhire BM, Lolohea S, Halafihi M, Lepoint P, Blomme G, Crew KS, Sharman M, Kraberger S, Dayaram A, Walters M, Collings DA, Mabvakure B, Lemey P, Harkins GW, Thomas JE, Varsani A.

Virus Evol. 2015 Sep 10;1(1):vev009. eCollection 2015.

10.

Ongoing geographical spread of Tomato yellow leaf curl virus.

Mabvakure B, Martin DP, Kraberger S, Cloete L, van Brunschot S, Geering ADW, Thomas JE, Bananej K, Lett JM, Lefeuvre P, Varsani A, Harkins GW.

Virology. 2016 Nov;498:257-264. doi: 10.1016/j.virol.2016.08.033. Epub 2016 Sep 15.

11.

Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar.

De Bruyn A, Harimalala M, Zinga I, Mabvakure BM, Hoareau M, Ravigné V, Walters M, Reynaud B, Varsani A, Harkins GW, Martin DP, Lett JM, Lefeuvre P.

BMC Evol Biol. 2016 Sep 6;16:182. doi: 10.1186/s12862-016-0749-2.

12.

Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa.

Bernardo P, Muhire B, François S, Deshoux M, Hartnady P, Farkas K, Kraberger S, Filloux D, Fernandez E, Galzi S, Ferdinand R, Granier M, Marais A, Monge Blasco P, Candresse T, Escriu F, Varsani A, Harkins GW, Martin DP, Roumagnac P.

Virology. 2016 Jun;493:142-53. doi: 10.1016/j.virol.2016.03.016. Epub 2016 Mar 31.

13.

Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains.

Kraberger S, Kumari SG, Hamed AA, Gronenborn B, Thomas JE, Sharman M, Harkins GW, Muhire BM, Martin DP, Varsani A.

Infect Genet Evol. 2015 Jan;29:203-15. doi: 10.1016/j.meegid.2014.11.024. Epub 2014 Nov 29.

PMID:
25444941
14.

The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates.

Cloete LJ, Tanov EP, Muhire BM, Martin DP, Harkins GW.

Virol J. 2014 Sep 16;11:166. doi: 10.1186/1743-422X-11-166.

15.

Towards inferring the global movement of beak and feather disease virus.

Harkins GW, Martin DP, Christoffels A, Varsani A.

Virology. 2014 Feb;450-451:24-33. doi: 10.1016/j.virol.2013.11.033. Epub 2013 Dec 20.

16.

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

Muhire BM, Golden M, Murrell B, Lefeuvre P, Lett JM, Gray A, Poon AY, Ngandu NK, Semegni Y, Tanov EP, Monjane AL, Harkins GW, Varsani A, Shepherd DN, Martin DP.

J Virol. 2014 Feb;88(4):1972-89. doi: 10.1128/JVI.03031-13. Epub 2013 Nov 27.

17.

Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East.

Kraberger S, Harkins GW, Kumari SG, Thomas JE, Schwinghamer MW, Sharman M, Collings DA, Briddon RW, Martin DP, Varsani A.

Virology. 2013 Sep;444(1-2):282-91. doi: 10.1016/j.virol.2013.06.024. Epub 2013 Jul 23.

18.

Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species.

Piasecki T, Harkins GW, Chrząstek K, Julian L, Martin DP, Varsani A.

Virology. 2013 Apr 10;438(2):98-105. doi: 10.1016/j.virol.2013.01.009. Epub 2013 Feb 12.

19.

Extensive recombination detected among beak and feather disease virus isolates from breeding facilities in Poland.

Julian L, Piasecki T, Chrzastek K, Walters M, Muhire B, Harkins GW, Martin DP, Varsani A.

J Gen Virol. 2013 May;94(Pt 5):1086-95. doi: 10.1099/vir.0.050179-0. Epub 2013 Jan 16.

PMID:
23324468
20.

East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus.

De Bruyn A, Villemot J, Lefeuvre P, Villar E, Hoareau M, Harimalala M, Abdoul-Karime AL, Abdou-Chakour C, Reynaud B, Harkins GW, Varsani A, Martin DP, Lett JM.

BMC Evol Biol. 2012 Nov 27;12:228. doi: 10.1186/1471-2148-12-228.

21.

NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments.

Semegni JY, Wamalwa M, Gaujoux R, Harkins GW, Gray A, Martin DP.

Bioinformatics. 2011 Sep 1;27(17):2443-5. doi: 10.1093/bioinformatics/btr417. Epub 2011 Jul 14.

22.

Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa.

Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, Shepherd DN, Oluwafemi S, Simuyandi M, Zinga I, Komba EK, Lakoutene DP, Mandakombo N, Mboukoulida J, Semballa S, Tagne A, Tiendrébéogo F, Erdmann JB, van Antwerpen T, Owor BE, Flett B, Ramusi M, Windram OP, Syed R, Lett JM, Briddon RW, Markham PG, Rybicki EP, Varsani A.

J Virol. 2011 Sep;85(18):9623-36. doi: 10.1128/JVI.00640-11. Epub 2011 Jun 29.

23.

Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome.

Lefeuvre P, Harkins GW, Lett JM, Briddon RW, Chase MW, Moury B, Martin DP.

PLoS One. 2011;6(5):e19193. doi: 10.1371/journal.pone.0019193. Epub 2011 May 16.

24.

Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe.

Dalai SC, de Oliveira T, Harkins GW, Kassaye SG, Lint J, Manasa J, Johnston E, Katzenstein D.

AIDS. 2009 Nov 27;23(18):2523-32. doi: 10.1097/QAD.0b013e3283320ef3.

25.

Dating the origins of the maize-adapted strain of maize streak virus, MSV-A.

Harkins GW, Martin DP, Duffy S, Monjane AL, Shepherd DN, Windram OP, Owor BE, Donaldson L, van Antwerpen T, Sayed RA, Flett B, Ramusi M, Rybicki EP, Peterschmitt M, Varsani A.

J Gen Virol. 2009 Dec;90(Pt 12):3066-74. doi: 10.1099/vir.0.015537-0. Epub 2009 Aug 19.

26.

Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts.

Harkins GW, Delport W, Duffy S, Wood N, Monjane AL, Owor BE, Donaldson L, Saumtally S, Triton G, Briddon RW, Shepherd DN, Rybicki EP, Martin DP, Varsani A.

Virol J. 2009 Jul 16;6:104. doi: 10.1186/1743-422X-6-104.

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