Photo of Prof Tulio de Oliveira

Prof Tulio de Oliveira

Senior Researcher and Bioinformatics group leader: Africa Centre for Population Health Studies, University of KwaZulu Natal

Professor: School of Laboratory Medicine & Medical Sciences, College of Health Sciences, University of KwaZulu Natal

Director and Founding Member: Southern African Treatment and Resistance Network (SATuRN)

Prof Tulio de Oliveira
P.O. Box 198
Mtubatuba 3935
South Africa

E: This email address is being protected from spambots. You need JavaScript enabled to view it.
T: +27 (0)35 5507509

2016

  1. Druce, M., Hulo, C., Masson, P., Sommer, P., Xenarios, I., Le Mercier, P., & De Oliveira, T. (2016). Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. Database: The Journal of Biological Databases and Curation 2016. http://doi.org/10.1093/database/baw045

  2. Giovanetti, M., Faria, N. R., Nunes, M. R. T., de Vasconcelos, J. M., Lourenço, J., Rodrigues, S. G., … Alcantara, L. C. (2016). Zika virus complete genome from Salvador, Bahia, Brazil. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases 41 142–145. http://doi.org/10.1016/j.meegid.2016.03.030

  3. Manasa, J., Danaviah, S., Lessells, R. J., Elshareef, M., Tanser, F., Wilkinson, E., … de Oliveira, T. (2016). Increasing HIV-1 drug resistance between 2010 and 2012 in adults participating in population-based HIV surveillance in rural KwaZulu-Natal South Africa. AIDS Research and Human Retroviruses. http://doi.org/10.1089/AID.2015.0225

  4. Mulder, N. J., Christoffels, A., de Oliveira, T., Gamieldien, J., Hazelhurst, S., Joubert, F., … Tiffin, N. (2016). The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt. PLOS Computational Biology 12(2), e1004395. http://doi.org/10.1371/journal.pcbi.1004395

  5. Treffry-Goatley, A., Lessells, R., Sykes, P., Bärnighausen, T., de Oliveira, T., Moletsane, R., & Seeley, J. (2016). Understanding Specific Contexts of Antiretroviral Therapy Adherence in Rural South Africa: A Thematic Analysis of Digital Stories from a Community with High HIV Prevalence. PLOS ONE 11(2), e0148801. http://doi.org/10.1371/journal.pone.0148801

2015

1. Basson, A.E., Rhee, S.-Y., Parry, C.M., El-Khatib, Z., Charalambous, S., De Oliveira, T., Pillay, D., Hoffmann, C., Katzenstein, D., Shafer, R.W., Morris, L., 2015. Impact of drug resistance-associated amino acid changes in HIV-1 subtype C on susceptibility to newer nonnucleoside reverse transcriptase inhibitors. Antimicrob. Agents Chemother. 59, 960–971. doi:10.1128/AAC.04215-14

2. Danaviah, S., de Oliveira, T., Bland, R., Viljoen, J., Pillay, S., Tuaillon, E., Van de Perre, P., Newell, M.-L., 2015. Evidence of Long-Lived Founder Virus in Mother-to-Child HIV Transmission. PLoS ONE 10, e0120389. doi:10.1371/journal.pone.0120389

3. Pillay, D., Herbeck, J., Cohen, M.S., Oliveira, T. de, Fraser, C., Ratmann, O., Brown, A.L., Kellam, P., PANGEA-HIV Consortium, 2015. PANGEA-HIV: phylogenetics for generalised epidemics in Africa. Lancet Infect Dis 15, 259–261. doi:10.1016/S1473-3099(15)70036-8

4. Wilkinson, E., Holzmayer, V., Jacobs, G.B., de Oliveira, T., Brennan, C.A., Hackett, J., van Rensburg, E.J., Engelbrecht, S., 2015. Sequencing and Phylogenetic Analysis of Near Full-Length HIV-1 Subtypes A, B, G and Unique Recombinant AC and AD Viral Strains Identified in South Africa. AIDS Res. Hum. Retroviruses 31, 412–420. doi:10.1089/AID.2014.0230

2014

5. Basson, A.E., Rhee, S.-Y., Parry, C.M., El-Khatib, Z., Charalambous, S., Oliveira, T.D., Pillay, D., Hoffmann, C., Katzenstein, D., Shafer, R.W., Morris, L., 2014. The Impact of Drug Resistance Associated Amino Acid Changes on HIV-1 Subtype C on Susceptibility to Newer NNRTIs.

6. Brandt, P., Moodley, D., Pillay, A.W., Seebregts, C.J., Oliveira, T. de, 2014. An Investigation of Classification Algorithms for Predicting HIV Drug Resistance without Genotype Resistance Testing, in: Gibbons, J., MacCaull, W. (Eds.), Foundations of Health Information Engineering and Systems, Lecture Notes in Computer Science. Springer Berlin Heidelberg, pp. 236–253. Doi: 10.1007/978-3-642-53956-5_16

7. Dennis, A.M., Herbeck, J.T., Brown, A.L., Kellam, P., de Oliveira, T., Pillay, D., Fraser, C., Cohen, M.S., 2014. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest? JAIDS Journal of Acquired Immune Deficiency Syndromes. doi:10.1097/QAI.0000000000000271

8. Lessells, R.J., Stott, K.E., Manasa, J., Naidu, K.K., Skingsley, A., Rossouw, T., de Oliveira, T., Southern African Treatment and Resistance Network (SATuRN), 2014. Implementing antiretroviral resistance testing in a primary health care HIV treatment programme in rural KwaZulu-Natal, South Africa: early experiences, achievements and challenges. BMC Health Serv Res 14, 116. doi:10.1186/1472-6963-14-116

9. Lessells, R.J., Katzenstein, D.K., de Oliveira, T., 2012. Are subtype differences important in HIV drug resistance? Curr Opin Virol 2, 636–643. doi:10.1016/j.coviro.2012.08.006

10. Jacobs, G.B., Wilkinson, E., Isaacs, S., Spies, G., de Oliveira, T., Seedat, S., Engelbrecht, S., 2014. HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and Transmitted Drug Resistance Identified in the Western Cape Province, South Africa. PLoS One 9. doi:10.1371/journal.pone.0090845

11. Kiepiela, P., Manasa, J., Moosa, M.-Y., Moodley, P., Gordon, M., Parikh, U.M., Sunpath, H., de Oliveira, T., Ramjee, G., 2014. HIV Drug Resistance Patterns at the Epicentre of the HIV-1 Epidemic in Kwazulu-Natal, South Africa 2003-2013. Journal of AIDS & Clinical Research 05. doi:10.4172/2155-6113.1000299

12. Malherbe, G., Steel, H.C., Cassol, S., de Oliveira, T., Seebregts, C.J., Anderson, R., Cassol, E., Rossouw, T.M., 2014. Circulating Biomarkers of Immune Activation Distinguish Viral Suppression from Nonsuppression in HAART-Treated Patients with Advanced HIV-1 Subtype C Infection. Mediators Inflamm 2014. doi:10.1155/2014/198413

13. Manasa, J., Danaviah, S., Pillay, S., Padayachee, P., Mthiyane, H., Mkhize, C., Lessells, R.J., Seebregts, C., de Wit, T.F.R., Viljoen, J., Katzenstein, D., De Oliveira, T., 2014a. An affordable HIV-1 drug resistance monitoring method for resource limited settings. J Vis Exp. doi:10.3791/51242

14. Manasa, J., Lessells, R., Rossouw, T., Naidu, K., Van Vuuren, C., Goedhals, D., van Zyl, G., Bester, A., Skingsley, A., Stott, K., Danaviah, S., Chetty, T., Singh, L., Moodley, P., Iwuji, C., McGrath, N., Seebregts, C.J., de Oliveira, T., 2014b. Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa. Database (Oxford) 2014. doi:10.1093/database/bat082

15. Pillay, S., Bland, R.M., Lessells, R.J., Manasa, J., de Oliveira, T., Danaviah, S., 2014. Drug resistance in children at virological failure in a rural KwaZulu-Natal, South Africa, cohort. AIDS Res Ther 11. doi:10.1186/1742-6405-11-3

16. Tanser, F., de Oliveira, T., Maheu-Giroux, M., Bärnighausen, T., 2014. Concentrated HIV subepidemics in generalized epidemic settings. Curr Opin HIV AIDS 9, 115–125. doi:10.1097/COH.0000000000000034

17. Wilkinson, E., Engelbrecht, S., de Oliveira, T., 2014. Detection of Transmission Clusters of HIV-1 Subtype C over a 21-Year Period in Cape Town, South Africa. PLoS ONE 9, e109296. doi:10.1371/journal.pone.0109296

2013

18. Aitken, S.C., Kliphuis, A., Bronze, M., Wallis, C.L., Kityo, C., Balinda, S., Stevens, W., Spieker, N., de Oliveira, T., Rinke de Wit, T.F., Schuurman, R., 2013. Development and evaluation of an affordable real-time qualitative assay for determining HIV-1 virological failure in plasma and dried blood spots. J. Clin. Microbiology. 51, 1899–1905. doi:10.1128/JCM.03305-12

19. Chevenet, F., Jung, M., Peeters, M., de Oliveira, T., Gascuel, O., 2013. Searching for virus phylotypes. Bioinformatics 29, 561–570. doi:10.1093/bioinformatics/btt010

20. Frias, D., Monteiro-Cunha, J.P., Mota-Miranda, A.C., Fonseca, V.S., de Oliveira, T., Galvao-Castro, B., Alcantara, L.C.J., 2013. Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights. Bioinform Biol Insights 7, 335–345. doi:10.4137/BBI.S12093

21. Lessells, R.J., Avalos, A., de Oliveira, T., 2013. Implementing HIV-1 genotypic resistance testing in antiretroviral therapy programs in Africa: needs, opportunities, and challenges. AIDS Rev 15, 221–229.

22. Libin, P., Beheydt, G., Deforche, K., Imbrechts, S., Ferreira, F., Van Laethem, K., Theys, K., Carvalho, A.P., Cavaco-Silva, J., Lapadula, G., Torti, C., Assel, M., Wesner, S., Snoeck, J., Ruelle, J., De Bel, A., Lacor, P., De Munter, P., Van Wijngaerden, E., Zazzi, M., Kaiser, R., Ayouba, A., Peeters, M., de Oliveira, T., Alcantara, L.C.J., Grossman, Z., Sloot, P., Otelea, D., Paraschiv, S., Boucher, C., Camacho, R.J., Vandamme, A.-M., 2013. RegaDB: community-driven data management and analysis for infectious diseases. Bioinformatics 29, 1477–1480. doi:10.1093/bioinformatics/btt162

23. Manasa, J., Lessells, R.J., Skingsley, A., Naidu, K.K., Newell, M.-L., McGrath, N., de Oliveira, T., Southern African Treatment and Resistance Network, 2013. High-levels of acquired drug resistance in adult patients failing first-line antiretroviral therapy in a rural HIV treatment programme in KwaZulu-Natal, South Africa. PLoS ONE 8. doi:10.1371/journal.pone.0072152

24. Pineda-Peña, A.-C., Faria, N.R., Imbrechts, S., Libin, P., Abecasis, A.B., Deforche, K., Gómez-López, A., Camacho, R.J., de Oliveira, T., Vandamme, A.-M., 2013. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. Infect. Genet. Evol. 19, 337–348. doi:10.1016/j.meegid.2013.04.032

25. Rossouw, T., Lessells, R.J., de Oliveira, T., 2013. HIV & TB Drug Resistance & Clinical Management Case Book. BioAfrica and SATuRN.

26. Singh, L., Parboosing, R., Manasa, J., Moodley, P., de Oliveira, T., 2013. High level of HIV-2 false positivity in KwaZulu-Natal province: a region of South Africa with a very high HIV-1 subtype C prevalence. J. Med. Virol. 85, 2065–2071. doi:10.1002/jmv.23716

27. Stott, K.E., de Oliveira, T., Lessells, R.J., 2013. Combined antiretroviral and anti-tuberculosis drug resistance following incarceration. South Afr J HIV Med 14, 135–137. doi:10.7196/SAJHIVMED.957

28. Van Zyl, G.U., Liu, T.F., Claassen, M., Engelbrecht, S., de Oliveira, T., Preiser, W., Wood, N.T., Travers, S., Shafer, R.W., 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. doi:10.1371/journal.pone.0067188

2012

29.           Conradie, F., Wilson, D., Basson, A., de Oliveira, T., Hunt, G., Joel, D., Papathanosopoulos, M., Preiser, W., Klausner, J., Spencer, D., Stevens, W., Venter, F., van Vuuren, C., 2012. The 2012 southern African ARV drug resistance testing guidelines: guidelines. Southern African Journal of HIV Medicine 13, 162–167

30.           Goedhals, D., Rossouw, I., Hallbauer, U., Mamabolo, M., de Oliveira, T., 2012. The tainted milk of human kindness. The Lancet 380. doi:10.1016/S0140-6736(12)60957-X

31.           Manasa, J., Katzenstein, D., Cassol, S., Newell, M.-L., de Oliveira, T., Southern Africa Treatment And Resistance Network (SATuRN), 2012. Primary drug resistance in South Africa: data from 10 years of surveys. AIDS Res. Hum. Retroviruses 28, 558–565. doi:10.1089/AID.2011.0284

32.           Murrell, B., de Oliveira, T., Seebregts, C., Kosakovsky Pond, S.L., Scheffler, K., 2012. Modeling HIV-1 Drug Resistance as Episodic Directional Selection. PLoS Comput Biol 8. doi:10.1371/journal.pcbi.1002507

33.           Stott, K., Michel, J., Oliveira, T.D., 2012. Principles of HIV drug resistance for clinical management in South Africa. HIV Nursing Matters 3, 46–51.

34.           World Health Organization, W., WHO ResNet, De Oliveira, T., 2012. WHO | WHO HIV drug resistance report 2012 [WWW Document]. WHO. URL http://www.who.int/hiv/pub/drugresistance/report2012/en/ (accessed 3.31.15).

2011

1. Ajoge, H.O., Gordon, M.L., de Oliveira, T., Green, T.N., Ibrahim, S., Shittu, O.S., Olonitola, S.O., Ahmad, A.A., Ndung’u, T., 2011. Genetic Characteristics, Coreceptor Usage Potential and Evolution of Nigerian HIV-1 Subtype G and CRF02_AG Isolates. PLoS One 6. doi:10.1371/journal.pone.0017865

2010

2. Abecasis, A.B., Wang, Y., Libin, P., Imbrechts, S., de Oliveira, T., Camacho, R.J., Vandamme, A.-M., 2010. Comparative performance of the REGA subtyping tool version 2 versus version 1. Infect. Genet. Evol. 10, 380–385. doi:10.1016/j.meegid.2009.09.020

3. De Oliveira, T., Pillay, D., Gifford, R.J., UK Collaborative Group on HIV Drug Resistance, 2010a. The HIV-1 subtype C epidemic in South America is linked to the United Kingdom. PLoS ONE 5. doi:10.1371/journal.pone.0009311

4. De Oliveira, T., Shafer, R.W., Seebregts, C., 2010b. Public database for HIV drug resistance in southern Africa. Nature 464. doi:10.1038/464673c

2009

5. Alcantara, L.C.J., Cassol, S., Libin, P., Deforche, K., Pybus, O.G., Van Ranst, M., Galvão-Castro, B., Vandamme, A.-M., de Oliveira, T., 2009. A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res. 37, W634–642. doi:10.1093/nar/gkp455

6. Belshaw, R., de Oliveira, T., Markowitz, S., Rambaut, A., 2009. The RNA Virus Database. Nucleic Acids Res 37, D431–D435. doi:10.1093/nar/gkn729

7. Dalai, S.C., de Oliveira, T., Harkins, G.W., Kassaye, S.G., Lint, J., Manasa, J., Johnston, E., Katzenstein, D., 2009. Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe. AIDS 23, 2523–2532. doi:10.1097/QAD.0b013e3283320ef3

8. Huang, K.-H.G., Goedhals, D., Fryer, H., van Vuuren, C., Katzourakis, A., De Oliveira, T., Brown, H., Cassol, S., Seebregts, C., McLean, A., Klenerman, P., Phillips, R., Frater, J., Bloemfontein-Oxford Collaborative Group, 2009. Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa. Antivir. Ther. (Lond.) 14, 975–984. doi:10.3851/IMP1416

9. Lamers, S.L., Salemi, M., Galligan, D.C., de Oliveira, T., Fogel, G.B., Granier, S.C., Zhao, L., Brown, J.N., Morris, A., Masliah, E., McGrath, M.S., 2009. Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology. PLoS ONE 4. doi:10.1371/journal.pone.0005065

10. Monteiro, J.P., Alcantara, L.C.J., de Oliveira, T., Oliveira, A.M., Melo, M.A.G., Brites, C., Galvão-Castro, B., 2009. Genetic variability of human immunodeficiency virus-1 in Bahia state, Northeast, Brazil: high diversity of HIV genotypes. J. Med. Virol. 81, 391–399. doi:10.1002/jmv.21414

11. Walter, B.L., Armitage, A.E., Graham, S.C., de Oliveira, T., Skinhøj, P., Jones, E.Y., Stuart, D.I., McMichael, A.J., Chesebro, B., Iversen, A.K., 2009. Functional characteristics of HIV-1 subtype C compatible with increased heterosexual transmissibility. AIDS 23, 1047–1057. doi:10.1097/QAD.0b013e32832a1806

2008

12. Armitage, A.E., Katzourakis, A., de Oliveira, T., Welch, J.J., Belshaw, R., Bishop, K.N., Kramer, B., McMichael, A.J., Rambaut, A., Iversen, A.K.N., 2008. Conserved Footprints of APOBEC3G on Hypermutated Human Immunodeficiency Virus Type 1 and Human Endogenous Retrovirus HERV-K(HML2) Sequences. J Virol 82, 8743–8761. doi:10.1128/JVI.00584-08

13. Salemi, M., Goodenow, M.M., Montieri, S., de Oliveira, T., Santoro, M.M., Beshkov, D., Alexiev, I., Elenkov, I., Elenkov, I., Yakimova, T., Varleva, T., Rezza, G., Ciccozzi, M., 2008b. The HIV Type 1 Epidemic in Bulgaria Involves Multiple Subtypes and Is Sustained by Continuous Viral Inflow from West and East European Countries. AIDS Res Hum Retroviruses 24, 771–779. doi:10.1089/aid.2007.0181

14. Salemi, M., de Oliveira, T., Ciccozzi, M., Rezza, G., Goodenow, M.M., 2008a. High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania. PLoS ONE 3. doi:10.1371/journal.pone.0001390

2007

15. Abecasis, A.B., Lemey, P., Vidal, N., de Oliveira, T., Peeters, M., Camacho, R., Shapiro, B., Rambaut, A., Vandamme, A.-M., 2007. Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form. J Virol 81, 8543–8551. doi:10.1128/JVI.00463-07

16. Ciccozzi, M., Montieri, S., Salemi, M., De Oliveira, T., Dorrucci, M., Sinicco, A., De Luca, A., Giuliani, M., Balotta, C., Rezza, G., 2007. An outbreak of HIV-1 subtype G among Italian injecting drug users. AIDS 21, 1213–1215. doi:10.1097/QAD.0b013e32813aee1a

17. Colizzi, V., de Oliveira, T., Roberts, R.J., 2007. Libya should stop denying scientific evidence on HIV. Nature 448, 992. doi:10.1038/448992a

18. Gifford, R.J., de Oliveira, T., Rambaut, A., Pybus, O.G., Dunn, D., Vandamme, A.-M., Kellam, P., Pillay, D., 2007. Phylogenetic Surveillance of Viral Genetic Diversity and the Evolving Molecular Epidemiology of Human Immunodeficiency Virus Type 1. J Virol 81, 13050–13056. doi:10.1128/JVI.00889-07

19. Karlsson, A.C., Iversen, A.K.N., Chapman, J.M., de Oliveira, T., Spotts, G., McMichael, A.J., Davenport, M.P., Hecht, F.M., Nixon, D.F., 2007. Sequential Broadening of CTL Responses in Early HIV-1 Infection Is Associated with Viral Escape. PLoS ONE 2. doi:10.1371/journal.pone.0000225

20. Queiroz, A.T.L. de, Mota-Miranda, A.C.A., Oliveira, T. de, Moreau, D.R., Urpia, C. de C., Carvalho, C.M., Galvão-Castro, B., Alcantara, L.C.J., 2007. Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology studies. Memórias do Instituto Oswaldo Cruz 102, 133–139. doi:10.1590/S0074-02762007005000005

21. Ma, C.-M., Hon, C.-C., Lam, T.-Y., Li, V.Y.-Y., Wong, C.K.-W., de Oliveira, T., Leung, F.C.-C., 2007. Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China. J. Gen. Virol. 88, 1733–1737. doi:10.1099/vir.0.82629-0

22. Mota-Miranda, A.C., de Oliveira, T., Moreau, D.R., Bomfim, C., Galvão-Castro, B., Alcantara, L.C., 2007. Mapping the molecular characteristics of Brazilian human T-cell lymphotropic virus type 1 Env (gp46) and Pol amino acid sequences for vaccine design.

2006

23. Alcantara, L.C.J., de Oliveira, T., Gordon, M., Pybus, O., Mascarenhas, R.E., Seixas, M.O., Gonçalves, M., Hlela, C., Cassol, S., Galvão-Castro, B., 2006. Tracing the origin of Brazilian HTLV-1 as determined by analysis of host and viral genes. AIDS 20, 780–782. doi:10.1097/01.aids.0000216383.14808.13

24. De Oliveira, T., Pybus, O.G., Rambaut, A., Salemi, M., Cassol, S., Ciccozzi, M., Rezza, G., Gattinara, G.C., D’Arrigo, R., Amicosante, M., Perrin, L., Colizzi, V., Perno, C.F., Benghazi Study Group, 2006. Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature 444, 836–837.

25. De Oliveira, T., Salemi, M., Gordon, M., Vandamme, A.-M., van Rensburg, E.J., Engelbrecht, S., Coovadia, H.M., Cassol, S., 2004. Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design? Genetics 167, 1047–1058. doi:10.1534/genetics.103.018135

26. Gifford, R., de Oliveira, T., Rambaut, A., Myers, R.E., Gale, C.V., Dunn, D., Shafer, R., Vandamme, A.-M., Kellam, P., Pillay, D., UK Collaborative Group on HIV Drug Resistance, 2006. Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS 20, 1521–1529. doi:10.1097/01.aids.0000237368.64488.ae

2005

27. De Oliveira, T., Deforche, K., Cassol, S., Salminen, M., Paraskevis, D., Seebregts, C., Snoeck, J., van Rensburg, E.J., Wensing, A.M.J., van de Vijver, D.A., Boucher, C.A., Camacho, R., Vandamme, A.-M., 2005. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 21, 3797–3800. doi:10.1093/bioinformatics/bti607

28. Doherty, R.S., de Oliveira, T., Seebregts, C., Danaviah, S., Gordon, M., Cassol, S., 2005. BioAfrica’s HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools. Retrovirology 2. doi:10.1186/1742-4690-2-18

29. Salemi, M., de Oliveira, T., Soares, M.A., Pybus, O., Dumans, A.T., Vandamme, A.-M., Tanuri, A., Cassol, S., Fitch, W.M., 2005a. Different epidemic potentials of the HIV-1B and C subtypes. J. Mol. Evol. 60, 598–605. doi:10.1007/s00239-004-0206-5

30. Salemi, M., Lamers, S.L., Yu, S., De Oliveira, T., Fitch, W.M., McGrath, M.S., 2005b. Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS. J Virol 79, 11343–11352. doi:10.1128/JVI.79.17.11343-11352.2005

2003

31. De Oliveira, T., Engelbrecht, S., Janse van Rensburg, E., Gordon, M., Bishop, K., zur Megede, J., Barnett, S.W., Cassol, S., 2003a. Variability at Human Immunodeficiency Virus Type 1 Subtype C Protease Cleavage Sites: an Indication of Viral Fitness? J Virol 77, 9422–9430. doi:10.1128/JVI.77.17.9422-9430.2003

32. De Oliveira, T., Miller, R., Tarin, M., Cassol, S., 2003b. An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences. Bioinformatics 19, 153–154. doi:10.1093/bioinformatics/19.1.153

33. Gordon, M., de Oliveira, T., Bishop, K., Coovadia, H.M., Madurai, L., Engelbrecht, S., Janse van Rensburg, E., Mosam, A., Smith, A., Cassol, S., 2003. Molecular Characteristics of Human Immunodeficiency Virus Type 1 Subtype C Viruses from KwaZulu-Natal, South Africa: Implications for Vaccine and Antiretroviral Control Strategies. J Virol 77, 2587–2599. doi:10.1128/JVI.77.4.2587-2599.2003

34. Salemi, M., de Oliveira, T., Courgnaud, V., Moulton, V., Holland, B., Cassol, S., Switzer, W.M., Vandamme, A.-M., 2003. Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses. J. Virol. 77, 7202–7213. doi:10.1128/JVI.77.13.7202-7213.2003

35. Soares, M.A., de Oliveira, T., Brindeiro, R.M., Diaz, R.S., Sabino, E.C., Brigido, L., Pires, I.L., Morgado, M.G., Dantas, M.C., Barreira, D., Teixeira, P.R., Cassol, S., Tanuri, A., Brazilian Network for Drug Resistance Surveillance, 2003. A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS 17, 11–21. doi:10.1097/01.aids.0000042595.93174.a4

2002

36. Zur Megede, J., Engelbrecht, S., de Oliveira, T., Cassol, S., Scriba, T.J., van Rensburg, E.J., Barnett, S.W., 2002. Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town, South Africa. AIDS Res. Hum. Retroviruses 18, 1327–1332. doi:10.1089/088922202320886370

2000

37. Palmarini, M., Hallwirth, C., York, D., Murgia, C., de Oliveira, T., Spencer, T., Fan, H., 2000. 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 Sheep. Retrovirus. J Virol 74, 8065–8076.

1999

38. Bhigjee, A.I., Tarin, M.L., Bill, P.L., De Oliveira, T., York, D., 1999. Sequence of the env gene of some KwaZulu-Natal, South African strains of HTLV type I. AIDS Res. Hum. Retroviruses 15, 1229–1233. doi:10.1089/088922299310322

Bioinformatics

Professor Tulio de Oliveira is a bioinformatician and has worked on HIV genomics research since 1997 and is recognised as an expert on HIV genetic data and bioinformatics.  Tulio has published high-impact articles including the one that presents the Rega Subtyping tools (de Oliveira et al. Bioinformatics 2005), one that proves the innocence of the six foreign medical personnel condemned to death for infecting with HIV 438 children in a hospital in Libya (de Oliveira et al.Nature 2006), open access and public HIV drug resistance databases in Africa (de Oliveira et al. Nature 2010) and the first case of proven HIV surrogate transmission in South Africa (Goedhals et al. Lancet 2012). His group website (www.bioafrica.net) hosts popular open access bioinformatics tools and databases.