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Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C; BEEHIVE Collaboration. Wymant C, et al. Among authors: gall a. Virus Evol. 2018 May 18;4(1):vey007. doi: 10.1093/ve/vey007. eCollection 2018 Jan. Virus Evol. 2018. PMID: 29876136 Free PMC article.
Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis.
Baillie GJ, Galiano M, Agapow PM, Myers R, Chiam R, Gall A, Palser AL, Watson SJ, Hedge J, Underwood A, Platt S, McLean E, Pebody RG, Rambaut A, Green J, Daniels R, Pybus OG, Kellam P, Zambon M. Baillie GJ, et al. Among authors: gall a. J Virol. 2012 Jan;86(1):11-8. doi: 10.1128/JVI.05347-11. Epub 2011 Oct 19. J Virol. 2012. PMID: 22013031 Free PMC article.
IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD. Hunt M, et al. Among authors: gall a. Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28. Bioinformatics. 2015. PMID: 25725497 Free PMC article.
Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals.
Hoehn KB, Gall A, Bashford-Rogers R, Fidler SJ, Kaye S, Weber JN, McClure MO; SPARTAC Trial Investigators; Kellam P, Pybus OG. Hoehn KB, et al. Among authors: gall a. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676):20140241. doi: 10.1098/rstb.2014.0241. Philos Trans R Soc Lond B Biol Sci. 2015. PMID: 26194755 Free PMC article.
From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.
Cornelissen M, Gall A, Vink M, Zorgdrager F, Binter Š, Edwards S, Jurriaans S, Bakker M, Ong SH, Gras L, van Sighem A, Bezemer D, de Wolf F, Reiss P, Kellam P, Berkhout B, Fraser C, van der Kuyl AC; BEEHIVE Consortium. Cornelissen M, et al. Among authors: gall a. Virus Res. 2017 Jul 15;239:10-16. doi: 10.1016/j.virusres.2016.08.004. Epub 2016 Aug 4. Virus Res. 2017. PMID: 27497916 Free article.
HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.
Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C. Ratmann O, et al. Among authors: gall a. AIDS Res Hum Retroviruses. 2017 Nov;33(11):1083-1098. doi: 10.1089/AID.2017.0061. Epub 2017 May 25. AIDS Res Hum Retroviruses. 2017. PMID: 28540766 Free PMC article.
365 results