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PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Wymant C, Hall M, Ratmann O, Bonsall D, Golubchik T, de Cesare M, Gall A, Cornelissen M, Fraser C; STOP-HCV Consortium, The Maela Pneumococcal Collaboration, and The BEEHIVE Collaboration. Wymant C, et al. Among authors: gall a. Mol Biol Evol. 2018 Mar 1;35(3):719-733. doi: 10.1093/molbev/msx304. Mol Biol Evol. 2018. PMID: 29186559 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.
Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C; BEEHIVE collaboration. Blanquart F, et al. Among authors: gall a. PLoS Biol. 2017 Jun 12;15(6):e2001855. doi: 10.1371/journal.pbio.2001855. eCollection 2017 Jun. PLoS Biol. 2017. PMID: 28604782 Free PMC article.
Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C; BEEHIVE collaboration. Blanquart F, et al. Among authors: gall a. PLoS Biol. 2017 Jul 13;15(7):e1002608. doi: 10.1371/journal.pbio.1002608. eCollection 2017 Jul. PLoS Biol. 2017. PMID: 28704367 Free PMC article.
Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes.
Cornelissen M, Gall A, van der Kuyl A, Wymant C, Blanquart F, Fraser C, Berkhout B. Cornelissen M, et al. Among authors: gall a. Methods Mol Biol. 2018;1746:55-61. doi: 10.1007/978-1-4939-7683-6_5. Methods Mol Biol. 2018. PMID: 29492886
The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012.
van der Kuyl AC, Vink M, Zorgdrager F, Bakker M, Wymant C, Hall M, Gall A, Blanquart F, Berkhout B, Fraser C, Cornelissen M; BEEHIVE Collaboration. van der Kuyl AC, et al. Among authors: gall a. Virus Res. 2018 May 2;250:51-64. doi: 10.1016/j.virusres.2018.04.008. Epub 2018 Apr 11. Virus Res. 2018. PMID: 29654800 Free article.
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.
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C; PANGEA Consortium and Rakai Health Sciences Program. Ratmann O, et al. Among authors: gall a. Nat Commun. 2019 Mar 29;10(1):1411. doi: 10.1038/s41467-019-09139-4. Nat Commun. 2019. PMID: 30926780 Free PMC article.
350 results