Browsing South African National Bioinformatics Institute (SANBI) by Author "Travers, Simon A."
Now showing items 1-5 of 5
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Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing
Bansode, Vijay; McCormack, Grace P.; Shrestha, Ram K.; Travers, Simon A.; Crampin, Amelia C.; Ngwira, Bagrey; French, Neil; Glynn, Judith R. (BioMed Central -The Open Access Publisher, 2013)BACKGROUND: The role of HIV-1 RNA in the emergence of resistance to antiretroviral therapies (ARTs) is well documented while less is known about the role of historical viruses stored in the proviral DNA. The primary ... -
The Influence of N-Linked Glycans on the MolecularDynamics of the HIV-1 gp120 V3 Loop
Wood, Natasha T.; Fadda, Elisa; Davis, Robert; Grant, Oliver C.; Martin, Joanne C.; Woods, Robert J.; Travers, Simon A. (PLoS ONE, 2013)N-linked glycans attached to specific amino acids of the gp120 envelope trimer of a HIV virion can modulate the binding affinity of gp120 to CD4, influence coreceptor tropism, and play an important role in neutralising ... -
RAMICS: Trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA
Wright, Imogen A.; Travers, Simon A. (Oxford University Press, 2014)The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly ... -
Structural rearrangements maintain the Glycan Shield of an HIV-1 envelope trimer after the loss of a glycan
Ferreira, Roux-Cil; Grant, Oliver C.; Moyo, Thandeka; Dorfman, Jeffrey R.; Woods, Robert J.; Travers, Simon A.; Wood, Natasha T. (Nature Research, 2018)The HIV-1 envelope (Env) glycoprotein is the primary target of the humoral immune response and a critical vaccine candidate. However, Env is densely glycosylated and thereby substantially protected from neutralisation. ... -
Trends in Genotypic HIV-1 Antiretroviral resistance between 2006 and 2012 in South African Patients receiving first- and second line antiretroviral treatment regimens
Van Zyl, Gert U.; Liu, Tommy F.; Claassen, Mathilda; Engelbrecht, Susan; de Oliveira, Tulio; Preiser, Wolfgang; Wood, Natasha T.; Travers, Simon A.; Shafer, Robert W. (University of the Western CapePublic Library of Science -- PLoS, 2013)South Africa's national antiretroviral (ARV) treatment program expanded in 2010 to include the nucleoside reverse transcriptase (RT) inhibitors (NRTI) tenofovir (TDF) for adults and abacavir (ABC) for children. We ...