Cathrine Scheepers, Ram K. Shrestha, Bronwen E. Lambson, Katherine J. L. Jackson, Imogen A. Wright, Dshanta Naicker, Mark Goosen, Leigh Berrie, Arshad Ismail, Nigel Garrett, Quarraisha Abdool Karim, Salim S. Abdool Karim, Penny L. Moore, Simon A. Travers and Lynn Morris (2015)  Ability To Develop Broadly Neutralizing HIV-1 Antibodies Is Not Restricted by the Germline Ig Gene Repertoire.  The Journal of Immunology.  194(9):4371-8

Wright IA and Travers SA (2014) RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.  Nucleic Acids Research doi: 10.1093/nar/gku473


Ram Krishna Shrestha, Baruch Lubinsky, Vijay B Bansode, Mónica B. J. Moinz, Grace P McCormack and Simon A Travers (2014).  QTrim: A novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform.  BMC Bioinformatics 2014, 15:33  doi:10.1186/1471-2105-15-33  (PDF)


Seager I, Travers SA, Leeson MD, Crampin AC, French N, Glynn JR, McCormack GP (2014)  Coreceptor Usage, Diversity, and Divergence in Drug-Naive and Drug-Exposed Individuals from Malawi, Infected with HIV-1 Subtype C for More Than 20 Years.  AIDS Research and Human Retroviruses 30(10)


Kharsany ABM, Buthelezi TJ, Frohlich JA, Yende-Zuma N, Samsunder N, Mahlase G, Williamson C, Travers SA, Marais JC, Dellar R, Abdool Karim SS, Abdool Karim Q (2014). HIV Infection in High School Students in Rural South Africa: Role of Transmissions Among Students.  AIDS Research and Human Retroviruses 30(10)


Natasha T. Wood, Elisa Fadda,  Robert Davis, Oliver C. Grant, Joanne C. Martin,  Robert J. Woods,  Simon A. Travers. The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop. PLOS One. 8(11) e80301.  doi:10.1371/journal.pone.0080301.g001  (PDF)  


van Zyl GU, Liy TF, Classen M, Engelbrecht S, de Oliveira T, Preiser W, Wood NT, Travers SA, Shafer RW. (2013) Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens. PLoS One 8(6): e67188. doi:10.1371/journal.pone.0067188 (PDF) 


Bansode V, McCormack GP, Crampin AC, Ngwira B, Shrestha RK, French N, Glynn JR and Travers SA (2013).  Characterizing the emergence and persistence of drug resistant mutations in HIV-1 cubtype C infections using 454 ultra deep pyrosequencing.  BMC Infectious Diseases 13 (52) (PDF)


Crous S, Shrestha RK, Travers SA (2012) Appraising the performance of genotyping tools in the prediction of coreceptor tropism in HIV-1 subtype C virusesBMC Infectious Diseases, 12(1):203-2334-12-203. (PDF)


Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, Scheffler K, Smith D. (2012)  Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. Journal of Virology 86(11):6231-7 (PDF). 


Seager I, Leeson MD, Crampin A, Mulawa D, French D, Glynn J, Travers S.A.A., McCormack GP (2012) HIV-1 mutational patterns in HIV-1 subtype C infected long-term survivors in Karonga District Malawi: correction and further analysis.  AIDS Research and Human Retroviruses 28(3):308-313 (PDF)


Travers SA (2012) Conservation, Compensation, and Evolution of N-Linked Glycans in the HIV-1 Group M Subtypes and Circulating Recombinant Forms, doi:10.5402/2012/823605. (PDF)


Vijay B Bansode, Simon A A Travers, Amelia C Crampin, Bagrey Ngwira, Neil French, Judith R Glynn and Grace P McCormack (2011) Reverse Transcriptase drug resistance mutations in HIV-1 Subtype C infected patients on ART in Karonga District, Malawi.  AIDS Research and Therapy 8(38) doi:10.1186/1742-6405-8-38


Redmond N. E., Raleigh J, van Soest R.W.M., Kelly M., Travers S.A.A., Bradshaw B., Vartia S., McCormack G.P. (2011)   Molecular Systematics of the Order Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (mtCOI, NAD1) Gene Sequence Data. Plos One. 6(9) e24344


Meehan CJ, Hedge JA, Robertson DL, McCormack GP, Travers S.A.A Emergence, dominance, and possible decline of CXCR4 chemokine receptor usage during the course of HIV infection. J Med Virol. 2010 Dec;82(12):2004-12 


Vijay Bansode, Zuzanna J. Drebert, Simon A.A. Travers, Emmanuel Banda, Anna Molesworth,Amelia Crampin, Bagrey Ngwira, Neil French, Judith R. Glynn and Grace P. McCormack. Drug Resistance Mutations in Drug-Naive HIV Type 1 Subtype C-Infected Individuals from Rural Malawi. AIDS Res Hum Retroviruses. 2010 Oct ;26 


Travers, S. A. A., Tully D. C., McCormack G. P. and Fares, M. A. (2007) A study of the coevolutionary patterns operating within the env gene of the HIV-1 group M subtypes. Molecular Biology and Evolution 24 (12) 2787-2801. (PDF)


Travers, S. A. A. and Fares, M. A. (2007) Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses. Molecular Biology and Evolution 24 (4) 1032-1044. (PDF)


Redmond N. E., van Soest R. W. M., Kelly M., Raleigh J., Travers S. A. A. and McCormack G.P. (2007) Reassessment of the classification of the Order Haplosclerida (Class Demospongiae, Phylum Porifera) using 18S rRNA gene sequence data. Molecular Phylogenetics and Evolution 43(1): 344-52. (PDF 


Fares, M. A. and Travers, S. AA. (2006) A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.  Genetics 173: 9-23. (PDF)


McCormack G. P., Glynn, J. R., Clewley, J. P., Crampin, A. C., Travers, S. A. A., Redmond, N, Keane T. M., Sibande, F., Mulawa D. and Fine P. E. M. (2006) Emergence of a three codon deletion in gag p17 in HIV type 1 subtype C long-term survivors, and general population spread. Aids Research and Human Retroviruses 22: 195-201. (PDF)


Keane, T. M., Naugton, T. J., Travers, S. A. A., McInerney, J. O (2006) Building large phylogenetic trees on coarse-grained parallel machinesAlgorithmica 45: 285-300. (PDF) 


Travers, S. A. A., O’Connell, M, McCormack, G. P., McInerney, J. O., (2005) Evidence for heterogeneous selective pressures in the evolution of the env gene in different HIV-1 subtypesJournal of Virology 79 (3) 1836-1841. (PDF)


Keane, T. M., Naugton, T. J., Travers, S. A. A., McInerney, J. O., McCormack, G. P. (2005) DPRml: Distributed Phylogenetic Reconstruction by Maximum LikelihoodBioinformatics 21 (7) 969-974. (PDF)


Travers, S. A. A., Clewley, J. P., Glynn, J. R., Fine, P. E., Crampin, A. C., Sibande, F., Mulawa, D., McInerney, J. O., McCormack, G. P. (2004) Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1.  Journal of Virology 78 (19) 10501-6. (PDF)


Creevey, C. J., Fitzpatrick, D. A., Philip, G. K., Kinsella, R. J., O’Connell, M. J., Pentony, M. M.,Travers, S. AA., Wilkinson, M. and McInerney, J. O. (2004) Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings of the Royal Society B Series: Biological Sciences 271 (1557) 2551-2558. (PDF)