Publication Supplements

2021

• Factors influencing estimates of HIV-1 infection timing using BEAST
  Dearlove B, et al. Factors influencing estimates of HIV-1 infection timing using BEAST. PLoS Comput Biol. 2021 Feb 1;17(2):e1008537. doi: 10.1371/journal.pcbi.1008537. PMID: 33524022.

• RV144 Vaccine Imprinting Constrained HIV-1 Evolution Following Breakthrough Infection
  Lewitus E, et al. RV144 Vaccine Imprinting Constrained HIV-1 Evolution Following Breakthrough Infection, Virus Evolution, 2021;, veab057, https://doi.org/10.1093/ve/veab057

2020

• A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants
  Dearlove B, et al. A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Proc Natl Acad Sci U S A. 2020 Sep 22;117(38):23652-23662. doi: 10.1073/pnas.2008281117. Epub 2020 Aug 31. PMID: 32868447; PMCID: PMC7519301
   
• Late boosting of the RV144 regimen with AIDSVAX B/E and ALVAC-HIV in HIV-uninfected Thai volunteers: a double-blind, randomised controlled trial
  Pitisuttithum P, et al. Late boosting of the RV144 regimen with AIDSVAX B/E and ALVAC-HIV in HIV-uninfected Thai volunteers: a double-blind, randomised controlled trial. Lancet HIV. 2020 Apr;7(4):e238-e248. doi: 10.1016/S2352-3018(19)30406-0. Epub 2020 Feb 6. PMID: 32035516; PMCID: PMC7247755.

2019

• The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes
  Bai H, Li Y, Michael NL, Robb ML, Rolland M. The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes. PLoS Comput Biol. 2019 Jun 6;15(6):e1007056. doi: 10.1371/journal.pcbi.1007056. PMID: 31170145; PMCID: PMC6581281.

• Safety and efficacy of VRC01 broadly neutralising antibodies in adults with acutely treated HIV (RV397): a phase 2, randomised, double-blind, placebo-controlled trial
  Crowell TA, et al. Safety and efficacy of VRC01 broadly neutralising antibodies in adults with acutely treated HIV (RV397): a phase 2, randomised, double-blind, placebo-controlled trial. Lancet HIV. 2019 May;6(5):e297-e306. doi: 10.1016/S2352-3018(19)30053-0. Epub 2019 Apr 15. PMID: 31000477.

• A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity
  Lewitus E, Rolland M. A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity. Virus Evol. 2019 Nov 4;5(2):vez044. doi: 10.1093/ve/vez044. PMID: 31700680; PMCID: PMC6826062.

• Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand
  Rolland M, et al. Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand. PLoS Pathog. 2020 Feb 6;16(2):e1008179. doi: 10.1371/journal.ppat.1008179. PMID: 32027734; PMCID: PMC7004303.

2013

• Nautilus: A Bioinformatics Package for the Analysis of HIV Type 1 Targeted Deep Sequencing Data
  Kijak, Gustavo H et al. “Nautilus: a bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data.” AIDS research and human retroviruses vol. 29,10 (2013): 1361-4. doi:10.1089/AID.2013.0175

2010

• RecDraw: a software package for the representation of HIV-1 recombinant structures
  Kijak, Gustavo H et al. “RecDraw: a software package for the representation of HIV-1 recombinant structures.” AIDS research and human retroviruses vol. 26,12 (2010): 1317-21. doi:10.1089/aid.2010.0127