Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method by Ghafari, M, Lumby, CK, Weissman, DB, Illingworth, CJR

A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection by Illingworth, CJR, Raghwani, J, Serwadda, D, Sewankambo, NK, Robb, ML, Eller, MA, Redd, AR, Quinn, TC, Lythgoe, KA

A2B-COVID: a tool for rapidly evaluating potential SARS-CoV-2 transmission events by Illingworth, CJR, Hamilton, WL, Jackson, C, Warne, B, Popay, A, Meredith, L, Hosmillo, M, Jahun, A, Fieldman, T, Routledge, M, Houldcroft, CJ, Caller, L, Caddy, S, Yakovleva, A, Hall, G, Khokhar, FA, Feltwell, T, Pinckert, ML, Georgana, I, Chaudhry, Y, Curran, M, Parmar, S, Sparkes, D, Rivett, L, Jones, NK, Sridhar, S, Forrest, S, Dymond, T, Grainger, K, Workman, C, Gkrania-Klotsas, E, Brown, NM, Weekes, MP, Baker, S, Peacock, SJ, Gouliouris, T, Goodfellow, I, Angelis, DD, Török, ME

SARS-CoV-2 evolution during treatment of chronic infection by Kemp, SA, Collier, DA, Datir, RP, Ferreira, IATM, Gayed, S, Jahun, A, Hosmillo, M, Rees-Spear, C, Mlcochova, P, Lumb, IU, Roberts, DJ, Chandra, A, Temperton, N, Sharrocks, K, Blane, E, Modis, Y, Leigh, KE, Briggs, JAG, van Gils, MJ, Smith, KGC, Bradley, JR, Smith, C, Doffinger, R, Ceron-Gutierrez, L, Barcenas-Morales, G, Pollock, DD, Goldstein, RA, Smielewska, A, Skittrall, JP, Gouliouris, T, Goodfellow, IG, Gkrania-Klotsas, E, Illingworth, CJR, McCoy, LE, Gupta, RK