|An automated genotyping system for analysis of HIV-1 and other microbial sequences|
T De Oliveira, K Deforche, S Cassol, M Salminen, D Paraskevis, ...
Bioinformatics 21 (19), 3797-3800, 2005
|Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools|
AC Pineda-Peña, NR Faria, S Imbrechts, P Libin, AB Abecasis, ...
Infection, genetics and evolution 19, 337-348, 2013
|A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences|
LCJ Alcantara, S Cassol, P Libin, K Deforche, OG Pybus, M Van Ranst, ...
Nucleic acids research 37 (suppl_2), W634-W642, 2009
|HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression …|
RK Gupta, J Gregson, N Parkin, H Haile-Selassie, A Tanuri, LA Forero, ...
The Lancet infectious diseases 18 (3), 346-355, 2018
|Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study|
T De Oliveira, ABM Kharsany, T Gräf, C Cawood, D Khanyile, A Grobler, ...
The lancet HIV 4 (1), e41-e50, 2017
|Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study|
J Gregson, M Tang, N Ndembi, RL Hamers, SY Rhee, VC Marconi, ...
The Lancet infectious diseases 16 (5), 565-575, 2016
|HIV-1 and HCV sequences from Libyan outbreak|
T De Oliveira, OG Pybus, A Rambaut, M Salemi, S Cassol, M Ciccozzi, ...
Nature 444 (7121), 836-837, 2006
|Molecular cloning and functional analysis of three type D endogenous retroviruses of sheep reveal a different cell tropism from that of the highly related exogenous jaagsiekte …|
M Palmarini, C Hallwirth, D York, C Murgia, T De Oliveira, T Spencer, ...
Journal of Virology 74 (17), 8065-8076, 2000
|A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil|
MA Soares, T de Oliveira, RM Brindeiro, RS Diaz, EC Sabino, L Brigido, ...
Aids 17 (1), 11-21, 2003
|Renewing Felsenstein’s phylogenetic bootstrap in the era of big data|
F Lemoine, JBD Entfellner, E Wilkinson, D Correia, MD Felipe, ...
Nature 556 (7702), 452-456, 2018
|Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015–16: a modelling study|
MUG Kraemer, NR Faria, RC Reiner Jr, N Golding, B Nikolay, S Stasse, ...
The Lancet infectious diseases 17 (3), 330-338, 2017
|A predominantly HIV type 1 subtype C-restricted epidemic in South African urban populations|
JHV Harmelen, EVD Ryst, AS Loubser, D York, S Madurai, S Lyons, ...
AIDS research and human retroviruses 15 (4), 395-398, 1999
|Genomic and epidemiological monitoring of yellow fever virus transmission potential|
NR Faria, MUG Kraemer, SC Hill, JG De Jesus, RS Aguiar, FCM Iani, ...
Science 361 (6405), 894-899, 2018
|Universal test and treat and the HIV epidemic in rural South Africa: a phase 4, open-label, community cluster randomised trial|
CC Iwuji, J Orne-Gliemann, J Larmarange, E Balestre, R Thiebaut, ...
The lancet HIV 5 (3), e116-e125, 2018
|Microbial genome-wide association studies: lessons from human GWAS|
RA Power, J Parkhill, T de Oliveira
Nature reviews genetics 18 (1), 41, 2017
|Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form|
AB Abecasis, P Lemey, N Vidal, T de Oliveira, M Peeters, R Camacho, ...
Journal of virology 81 (16), 8543-8551, 2007
|Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004|
V Pillay, J Ledwaba, G Hunt, M Rakgotho, B Singh, L Makubalo, ...
Antiviral therapy 13, 101, 2008
|Concentrated HIV sub-epidemics in generalized epidemic settings|
F Tanser, T de Oliveira, M Maheu-Giroux, T Bärnighausen
Current Opinion in HIV and AIDS 9 (2), 115, 2014
|Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS|
M Salemi, SL Lamers, S Yu, T De Oliveira, WM Fitch, MS McGrath
Journal of virology 79 (17), 11343-11352, 2005
|Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies|
M Gordon, T De Oliveira, K Bishop, HM Coovadia, L Madurai, ...
Journal of virology 77 (4), 2587-2599, 2003