PublicationsPublications are divided in topics: bioinformatics software application, virus and pathogen evolution and medical virology and molecular evolution of others organisms. |
Assessment of Automated Genotyping Protocols as Tools for Surveillance of HIV-1 Genetic Diversity. Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme A, Kellam P, and D. Pillay. (2006) AIDS, 20(11):1521-9. |
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Out of Africa: The BioAfrica website. de Oliveira T (2006) BioTechniques 41, 129. |
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An
automated
genotyping system for analysis of HIV-1 and other microbial sequences. de Oliveira T, K. Deforche, S. Cassol, M. Salminen, R. Camacho, D. Pavareskevis, C. Seebregts, J. Snoeck, A.M. VanDamme. (2005) Bioinformatics, 21: 3797-3800. |
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Scourge of a Continent: The BioAfrica website de Oliveira T, Cassol S (edited by M. Leslie) (2005) Science 310, 1877. |
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BioAfrica’s
HIV-1 Proteomics Resource: Combining protein data with bioinformatics
tools. Doherty RS, de Oliveira T, Seebregts C, Danaviah S, Gordon M, Cassol S. (2005) Retrovirology, 9;2(1):18. |
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An
Integrated
Genetic Data Environment (GDE)-Based LINUX Interface for Analysis of
HIV-1 and Other Microbial Sequences. de Oliveira T, Miller R, Tarin M, Cassol S. (2003) Bioinformatics, 19(1): 153-4. |
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Conserved footprints of APOBEC3G on hypermutated HIV-1 and HERV-K(HML2) sequences. Journal of Virology (2008) In press Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A & Iversen AKN |
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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. (2008) Jun 10. [Epub ahead of print] Salemi M, Goodenow MM, Montieri S, de Oliveira T, Santoro MM, Beshkov D, Alexiev I, Elenkov I, Elenkov I, Yakimova T, Varleva T, Rezza G, Ciccozzi M. |
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High-Resolution Molecular
Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania.
PLoS ONE.
2008 Jan 2;3(1):e1390. Salemi M, de Oliveira T, Ciccozzi M, Rezza G, Goodenow MM. |
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Phylogenetic
Surveillance of Viral Genetic Diversity and the Evolving Molecular
Epidemiology of HIV-1. Journal of Virology.
(2007) Sep 26; de Oliveira T/Gifford RJ, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D. |
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Mapping
the
molecular
characteristics of Brazilian human T-cell lymphotropic virus type 1 Env
(gp46) and Pol amino acid sequences for vaccine design. Mem Inst Oswaldo Cruz.
(2007); 102(6):741-9. Mota-Miranda AC, de Oliveira T, Moreau DR, Bomfim C, Galvao-Castro B, Alcantara LC. |
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Libya
should
stop denying scientific evidence on HIV. Nature (2007);
448(7157):992. Colizzi V, de Oliveira T, Roberts RJ. |
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Recombination
is confounding the early evolutionary history of HIV-1: subtype G is a
circulating recombinant form. Journal of Virology.
(2007);81(16):8543-51. Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme AM. |
| An
outbreak
of HIV-1 subtype G among Italian injecting drug users. AIDS (2007) May
31;21(9):1213-1215. Ciccozzi M, Montieri S, Salemi M,de Oliveira T, Dorrucci M, Sinicco A, De Luca A, Giuliani M, Balotta C, Rezza G. |
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Evidence
for
recombination in natural populations of porcine circovirus type 2 in
Hong Kong and mainland China. J Gen Virol. (2007)
;88(Pt 6):1733-7. Ma CM, Hon CC, Lam TY, Li VY, Wong CK, de Oliveira T, Leung FC. |
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Re-mapping
the molecular
features of the human immunodeficiency virus type 1 and human T-cell
lymphotropic virus type 1 Brazilian sequences. Mem Inst Oswaldo Cruz.
(2007); 102(2):133-9. Queiroz AT, Mota-Miranda AC, de Oliveira T, Moreau DR, Urpia Cde C, Carvalho CM, Galvao-Castro B, Alcantara LC. |
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Sequential
Broadening of CTL Responses in Early HIV-1 Infection is Associated With
Viral Escape.
PLoS ONE. (2007); 2:e225. Karlsson AC, Iversen AK, Chapman JM, de Oliveira T, Spotts G, McMichael AJ, Davenport MP, Hecht FM, Nixon DF. |
| Genetic
and
Biologic Characterization of HIV Type 1 Subtype C Isolates from South
Brazil. AIDS
Res Hum Retroviruses. (2007); 23(1):135-43. Monteiro JP, Ferraro GA, de Oliveira T, Goldani LZ, Kashima S, Alcantara LC, Morgado MG, Bou-Habib DC, Galvao-Castro B. |
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Molecular
epidemiology: HIV-1 and HCV sequences from Libyan outbreak.
Nature
(2006) 444(7121):836-7. de Oliveira T, Pybus OG, Rambaut A, Salemi M, Cassol S, Ciccozzi M, Rezza G, Gattinara GC, D’Arrigo R, Amicosante M, Perrin L, Colizzi V, Perno CF; Benghazi Study Group. |
| Tracing
the
origin of Brazilian HTLV-1 as determined by analysis of host and viral
genes. AIDS
(2006), 20(5):780-782. Alcantara LC, de Oliveira T, Gordon M, Pybus O, Mascarenhas RE, Seixas MO, Goncalves M, Hlela C, Cassol S, Galvao-Castro B. |
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Phylodynamic
analysis
of human immunodeficiency virus type 1 in distinct brain compartments
provides a model for the neuropathogenesis of AIDS. Journal of Virology
(2005), 79(17):11343-11352. Salemi M, Lamers SL, Yu S, de Oliveira T, Fitch WM, McGrath MS. |
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Different
Epidemic Potentials of the HIV-1B and C Subtypes. J Mol Evol. (2005),
60(5):598-605. Salemi M, de Oliveira T, Soares MA, Pybus O, Dumans AT, Vandamme AM, Tanuri A, Cassol S, Fitch WM. |
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Codon-Substitutions
Models as Indicators of Positive Selection and Amino Acid
Diversification: An Alternative Approach to HIV-1Vaccine Development?
Genetics
(2004), 167(3):1047-58. de Oliveira T, Salemi M, Gordon M, Vandamme A-M, van Rensburg EJ, Engelbrecht S, and Cassol S |
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Variability
at HIV-1 Subtype C Protease Cleavage Sites: An Indication of Viral
Fitness? Journal
of Virology (2003), 77(17): 9422-30 de Oliveira T, Engelbrecht S, van Rensburg EJ, Gordon M, Bishop K, Megede Jz, Barnett SW, Cassol S. |
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Mosaic
genomes of the six major Primate lentivirus lineages revealed by
phylogenetic and split-decomposition analyses. Journal of Virology
(2003), 77(13): 7202-7213. Salemi M, de Oliveira T, Courgnaud V, Moulton V, Holland B, Cassol S, Peeters M, and Vandamme A-M. |
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Molecular
Characteristics
of HIV-1 Subtype C Viruses from KwaZulu-Natal, South Africa:
Implications for Vaccine and Antiretroviral Control Strategies.
Journal of
Virology (2003), 77(4): 2587-2599. Gordon M, de Oliveira T, Bishop K, Coovadia HM, Madurai L, Engelbrecht S, Janse van Rensburg E, Mosam A, Smith A, Cassol S. |
| A
Specific
subtype C of human immunodeficiency virus type 1 circulates in Brazil.
AIDS
(2003), 17: 11-22. Soares M, de Oliveira T, Brindeiro R, Diaz R, Sabino E, Brigido L, Pires I, Morgado M, Dantas M, Barreira D, Teixeira P, Cassol S, Tanuri A. |
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| Novel
Evolutionary Analysis of Full-lenght HIV-1 Subtype C Molecular Clones
from Cape Town, South Africa. AIDS Research and Human
Restroviruses (2002), 18(17): 1327-32. Zur Megede J, Engelbrecht S, de Oliveira T, Cassol S, Scriba T, van Rensburg E, Barnett S. |
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Molecular dating and biogeography of the neritic krill Nyctiphanes. D’Amato ME, Harkins GW, de Oliveira T, Teske PR, Gibbons MJ. (2008) Marine Biology in press. |
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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. Palmarini M, Hallwirth C, York D, Murgia C, de Oliveira T, Spencer T, Fan H. (2000) Journal of Virology, 74(17):8065-76. |
Revised 15 of May 2008 - Tulio de Oliveira. |