Publication Supplements

2022

• Optimal sequence-based design for multi-antigen HIV-1 vaccines using minimally distant antigens

• Design of a pan-betacoronavirus vaccine candidate through a phylogenetically-informed approach

• HIV-1 infections with multiple founders associate with the development of neutralization breadth
  Lewitus E, Townsley SM, Li Y, Donofrio GC, Dearlove BL, Bai H, Sanders-Buell E, O'Sullivan AM, Bose M, Kibuuka H, Maganga L, Nitayaphan S, Sawe FK, Eller LA, Michael NL, Polonis VR, Ake JA, Vasan S, Robb ML, Tovanabutra S, Krebs SJ, Rolland M. HIV-1 infections with multiple founders associate with the development of neutralization breadth. PLoS Pathog. 2022 Mar 18;18(3):e1010369. doi: 10.1371/journal.ppat.1010369. PMID: 35303045; PMCID: PMC8967031.

• Acute HIV-1 infection viremia associate with rebound upon treatment interruption
  Mdluli T, Li Y, Pinyakorn S, Reeves DB, Cardozo-Ojeda EF, Yates A, Intasan J, Tipsuk S, Phanuphak N, Sacdalan C, Colby DJ, Kroon E, Crowell TA, Thomas R, Robb ML, Ananworanich J, de Souza M, Phanuphak P, Stieh DJ, Tomaka FL, Trautmann L, Ake JA, Hsu DC, Francisco LV, Vasan S, Rolland M. Acute HIV-1 infection viremia associate with rebound upon treatment interruption. Med (N Y). 2022 Jul 20:S2666-6340(22)00276-8. doi: 10.1016/j.medj.2022.06.009. Epub ahead of print. PMID: 35870446.

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