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John Archer

Principal Researcher

Publications

28 Publications

Lorenzo-Redondo R, Fryer HR, Bedford T, Kim EY, Archer J, Pond SLK, Chung YS, Penugonda S, Chipman JG, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR, Wolinsky SM (2017) Re-evaluating evolution in the HIV reservoir Reply. Nature, 551(7681): E10-E10. doi: 10.1038/nature24635 Open publication

Lorenzo-Redondo R, Fryer HR, Bedford T, Kim EY, Archer J, Pond SLK, Chung YS, Penugonda S, Chipman JG, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR, Wolinsky SM (2015) Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature, 530: 51-56. doi: 10.1038/nature16933 Open publication

Archer JP, Whiteley G, Casewell NR, Harrison RA, Wagstaff SC (2014) VTBuilder: a tool for the assembly of multi isoform transcriptomes. BMC Bioinformatics, 15(1):389. doi: 10.1186/s12859-014-0389-8 Open publication

Gibson RM, Meyer AM, Winner D, Archer J, Feyertag F, Ruiz-Mateos E, Leal M, Robertson DL, Schmotzer CL, Quiñones-Mateu ME (2014) Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism. Antimicrob Agents Chemother, 58(4):2167-85. doi: 10.1128/AAC.02710-13 Open publication

Kim EY, Lorenzo-Redondo R, Little SJ, Chung YS, Phalora PK, Maljkovic Berry I, Archer J, Penugonda S, Fischer W, Richman DD, Bhattacharya T, Malim MH, Wolinsky SM (2014) Human APOBEC3 induced mutation of human immunodeficiency virus type-1 contributes to adaptation and evolution in natural infection. PLoS Pathog, 10(7):e1004281. doi: 10.1371/journal.ppat.1004281 Open publication

Weber J, Vazquez AC, Winner D, Gibson RM, Rhea AM, Rose JD, Wylie D, Henry K, Wright A, King K, Archer J, Poveda E, Soriano V, Robertson DL, Olivo PD, Arts EJ, Quiones-Mateu ME (2013) Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism. Jornal Clinical Microbiology, 51(5):1517-1527. doi: 10.1128/JCM.00092-13 Open publication

Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A, Robertson DL (2012) Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics, 13(1):47. doi: 10.1186/1471-2105-13-47 Open publication

Archer J, Weber J, Henry K, Winner D, Gibson R, Lee L, Paxinos E, Arts EJ, Robertson DL, Mimms L, Quiñones-Mateu ME (2012) Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism. PLoS ONE, 7(11): e49602. doi: 10.1371/journal.pone.0049602 Open publication

Williams SG, Madan R, Norris MG, Archer J, Mizuguchi K, Robertson DL, Lovell, SC (2011) Using knowledge of protein structural constraints to predict the evolution of HIV-1. Journal of Molecular Biology, 410(5):1023-1034. doi: 10.1016/j.jmb.2011.04.037 Open publication

Archer J, Rambaut A, Taillon B, Harrigan P, Lewis M, Robertson D (2010) The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time-An Ultra-Deep Approach. PLoS computational biology, 6(12),:e1001022. doi: 10.1371/journal.pcbi.1001022 Open publication

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