1.    D. Zella, A. Cavicchini, M. Salemi, C. Casoli, P. Ferrante, F. Lori, G. Achilli, E. Cattaneo, V. Landini, and U. Bertazzoni (1993). Molecular characterization of two isolates of Human T-cell leukemia virus type II from Italian drug abusers and comparison of genome structure with other isolates. J. Gen. Virol. 74: 437-444.
2.    Lamers SL, JW Sleasman, KA Barrie, SM Pomeroy, DJ Barrett, and MM Goodenow. Independent Variation and Positive Selection in env V1 and V2 Domains Within Maternal-Infant Strains of Human Immunodeficiency Virus Type 1 in vivo. J. Virol. 67:3951-3960, 1993.
3.    Lamers, SL., J.W. Sleasman, K.A. Barrie, S.M. Pomeroy, D.J. Barrett, and M.M. Goodenow.  Persistence of Multiple Maternal HIV-1 Genotypes in Infants Infected by Perinatal Transmission. J. Clin. Invest. 93:380-390, 1994.
4.    M. Salemi, E. Cattaneo, C. Casoli, and U. Bertazzoni (1995). Identification of IIa and IIb molecular subtypes of Human T-cell lymphotropic virus type II among Italian injecting drug users. J. Acquir. Immune Defic. Syndr. 8: 516-520.
5.    Barrie, K.A., E. Perez, S.L. Lamers, W.F. Farmerie, B.M. Dunn, J.W. Sleasman, and M.M. Goodenow. Natural Variation in HIV-1 Protease, Gag p7 and p6, and  Protease Cleavage Sites Within Gag/Pol Polyproteins: Amino Acid Substitutions in the Absence of Protease Inhibitors in Mothers and Children Infected by Human Immunodeficiency Virus Type 1. Virology. 219:407-416. 1996.
6.    Lamers S.L., J.W. Sleasman, and M.M. Goodenow.  A Model for Alignments of env V1 and V2 Hypervariable Domains from Human Immunodefiviency Viruses. Aids Research and Human Retroviruses. 12:1169-1177, 1996.

7.    M. Salemi, A-M. Vandamme, F. Guano, E. Cattaneo, C. Casoli, and U. Bertazzoni (1996). Complete nucleotide sequence of the Italian human T-cell lymphotropic virus type II (HTLV-II) isolate Gu and phylogenetic identification of a possible origin of South European epidemics. J. Gen. Virol. 77:1193-1201.
8.    Skinner, L.M., S.L. Lamers, J.C. Sanders, M.E. Eyster, M.M. Goodenow, and M. Katzman. Analysis of a large collection of natural HIV-1 Integrase Sequence, Including Those From Long-Term Nonprogressors. J. Acq. Imm. Def. Synd.and Hum. Ret. 19:99-110, 1998.
9.    White G.B., A. Pfahnl, S. Haddock, S.L. Lamers, Robert M. Greenberg, and P. Anderson.  Structure of a Putative Sodium Channel from the Sea Anenome Aiptasia pallida. Invertebrate Neuroscience 3, 317-326, 1998.
10.    M. Salemi, A-M Vandamme, C. Gradozzi, K Van Laethem, P. Ferrante, G. Taylor, C. Casoli, P. Goubau, J. Desmyter, and U. Bertazzoni (1998). Evolutionary rate and genetic heterogeneity of human T-cell lymphotropic virus type II (HTLV-II) using new isolates from European injecting drug users. J. Mol Evol.. 46:602-611.
11.    M. Salemi, S Van Dooren, E Audenaert, E Delaporte, P. Goubau, J Desmyter, and A-M Vandamme (1998). Two new Human T-lymphotropic virus type I subtypes in seroindeterminates, a Mbuti pygmy and a Gabonese, have closest relatives among African STLV-I strains. Virology 246:277-287
12.    M. Van Brussel, M. Salemi, H-F Liu, P; Goubau, J Desmyter, and A-M Vandamme (1998). The Simian T-lymphotropic virus  STLV-PP1664 from Pan paniscus is distinctly related to HTLV-2 but differs in genomic organization. Virology 243:366-379.
13.    A-M. Vandamme, M. Salemi, Van Brussel, H-F Liu,, K. Van Laethem, M. Van Ranst, L. Michels, J. Desmyter, and P. Goubau (1998). African origin of human T-lymphotropic virus type II (HTLV-II) supported by a new subtype HTLV-IId in Zairean Bambuti Efe pygmies. J. Virol. 72:4327-4340.
14.    H. Ellerbrok, C. Fleischer, M. Salemi, P. Reinhardt, W-D. Ludwig, A-M. Vandamme, and G Pauli (1998). Sequence analysis of the first HTLV-I infection in Germany without relations to endemic areas. AIDS Res. Hum. Retrovir.: 14:1199-1203.
15.    A-M Vandamme, M. Salemi, and J Desmyter (1998). The simian origins of the pathogenic human T-cell lymphotropic virus type I. Trends Microbiol.: 6:477-483.
16.    S. Van Dooren, E. Gotuzzo, M. Salemi, D. Watts, E. Audenaert, S. Duwe, H. Ellerbrok, R. Grassmann, J. Desmyter, and A-M Vandamme (1998). Evidence for a Post-Colombian introduction of human T-cell lymphotropic virus in Latin America. J. Gen. Virol.: 79:2695-2708.
17.    M. Van Brussel, M. Salemi, H-F Liu, P. Goubau, J. Desmyter, and A-M. Vandamme (1999). The discovery of two new divergent STLVs has implications for the evolution and epidemiology of HTLVs. Rev. Med. Virol. 9:155-170.
18.        M. Salemi, A-M. Vandamme, J. Desmyter, C. Casoli, and U. Bertazzoni. The origin and evolution of Human T-cell Lymphotropic virus type II (HTLV-II) and the relationship with its replication strategy (1999). Gene: 234:11-21.
19.    M. Salemi, M. J. Lewis, J. F. Egan, W. W. Hall, J. Desmyter, and A-M. Vandamme. Different population dynamics and evolutionary rates of Human T-cell lymphotropic virus type II (HTLV-II) in injecting drug users compared to in endemically infected Amerindian and Pygmy tribes (1999). Proc. Natl. Acad. Sci. USA 96:13253-13259.
20.    M. Salemi, S. Van Dooren, and A-M. Vandamme. Origin of human and simian T-cell lymphotropic viruses (1999). AIDS Reviews 3:131-139.
21.    Ping LH, Nelson JA, Hoffman IF, Schock J, Lamers SL, Goodman M, Vernazza P, Kazembe P, Maida M, Zimba D, Goodenow MM, Eron JJ Jr, Fiscus SA, Cohen MS, Swanstrom R. Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants. J Virol. 1999 Aug;73(8):6271-81.
22.    A.-M. Vandamme, W. W. Hall, M. Lewis, P. Goubau and M. Salemi. Origin of HTLV-I in South America (2000). Nature Med. 3:232-233.
23.    M. Salemi, J. Desmyter, and A-M. Vandamme. Tempo and mode of human and simian T-lymphotropic virus (HTLV/STLV) evolution revealed by analyses of full-genome sequences (2000). Mol. Biol. Evol. 3:374-386.
24.    J-P. Allain, Y. Dong, A-M. Vandamme, V. Moulton and M. Salemi. Evolutionary rate and genetic drift of hepatitis C virus are poorly correlated with the host immune response: studies of infected donor-recipient clusters (2000). J. Virol. 6:2541-2549.
25.    M. J. Lewis, P. Novoa, R. Ishak, M. Ishak, M. Salemi, A-M. Vandamme, M. K. Kaplan and W. W. Hall. Isolation, cloning, and complete nucleotide sequence of a phenotypically distinct Brazilian isolate of Human T-cell lymphotropic virus type 2 (HTLV-2) isolate (2000). Virology 271:142-154.
26.    Perez EP, Rose SL, Peyser B, Lamers SL, Burkhardt B, Dunn BM,  Hutson AD, Sleasman JW, Goodenow MM. Human Immunodeficiency Virus Type 1 Protease Genotype Predicts Immune and Viral Responses to Combination Therapy with Protease Inhibitors (Pis) in PI-Naïve Patients. J. Inf. Diseases 2001;183:579-88
27.    M. Salemi, K. Strimmer, W. W. Hall, M. Duffy, E. Delaporte, S. Mboup, M. Peeters, and A-M. Vandamme. Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution (2001). FASEB J. 15:267-268.
28.    A-M. Vandamme, U. Bertazzoni, M. Salemi. Evolutionary strategies of Human T-cell lymphotropic virus type II (HTLV-II) (2000). Gene 261: 171-180.
19.    M. Salemi. Controversy on the origin of HIV (2000). AIDS Reviews 2:119-120.
20.    S. Van Dooren, M. Salemi, and A-M. Vandamme. Dating the origin of the African Human T-cell lymphotropic virus type I (HTLV-I) subtypes (2001). Mol. Biol. Evol. 18:661-71.
21.    M. Salemi. Bioinformatics in Telemedicine Glossary 3rd eds (2001), European Commission Directorate General, 2001 Working Document, pp. 33-34.
22.    S. Van Dooren, M. Salemi, X. Pourrut, M. Peeters, M. van Ranst, E. Delaporte and A-M. Vandamme. Evidence for a second simian t-cell lymphotropic virus type 3 in Cercopithecus nictitans from Cameroon (2001). J. Virol.75,11939-11941.
23.    Tuttle, D.L., C.B. Anders, M.J. Acquino-de Jesus, P.P. Poole, S.L. Lamers, D.R. Briggs, S.M. Pomeroy, L. Alexander, K.W.C.Peden, W.A. Andiman, J.W. Sleasman, and M.M. Goodenow. Increased replication by nonsyncytium-inducing HIV-1 isolates in monocyte-derived macrophages is linked to clinical decline in patients. AIDS Res Hum Retroviruses. 2002 Mar 20;18(5):353-62.
24.    M. Salemi and A-M. Vandamme. Evolutionary patterns of Hepatitis C virus studied through analysis of full genome sequences (2002). J. Mol. Evol.: 54, 62-70.
25.    N. Shindo, L. C. J. Alcantara, S. Van Dooren, M. Salemi, M. C. R. Costa, S. Kashima, D. T. Covas, A. Teva, M. Pellegrini, I. Brito, A-M. Vandamme and B. Galvao-Castro. Human retroviruses (HIV and HTLV) in Brazilian Indians: seroepidemiological study and molecular epidemiology of HTLV type 2 isolates. (2002). AIDS Res. Hum. Retrovir. 18:71-77
26.    P. Lemey, M. Salemi, L. Bassit, H. Heuverswyn, and Anne-Mieke Vandamme. Phylogenetic classification of TT virus groups based on the N22 region is unreliable (2002). Virus Res.: 85:47-59.
27.    M. J. Lewis, N. Sheehy, M. Salemi, A-M. Vandamme, and W. W. Hall. Comparison of CREB- and NF-kappaB-mediated transactivation by human T lymphotropic virus type II (HTLV-II) and type I (HTLV-I) tax proteins (2002). Virology: 295:182-189.
28.    V. Courgnaud, M. Salemi, X. Pourrut, E. Mpoudi-Ngole, B. Abela, P. Auzel, F. Bibollet-Ruche, B. Hahn, A.-M. Vandamme, E. Delaporte, M. Peeters Characterization of a novel simian immunodeficiency virus with a vpu gene from greater spot-nosed monkeys (Cercopithecus nictitans) provides new insights into simian/human immunodeficiency virus phylogeny (2002). J. Virol. 76:8298-309.
29.    M. Duffy, M. Salemi, N. Sheehy, A-M. Vandamme, J. Hegarty, M. Curry, N. Nolan, D. Kelleher, S. McKiernan, W.W. Hall.   Comparative Rates of Nucleotide Sequence Variation in the Hypervariable Region of E1/E2 and the NS5b Region of Hepatitis C Virus in Patients with a Spectrum of Liver Disease Resulting from a Common Source of Infection (2002). Virology 301:354-364.
30.    X. Xia, Z. Xie, M. Salemi, L. Chen, Y. Wang. An index of substitution saturation and its application (2003). Mol. Phylogenet. Evol. 26:1-7.
31.    P. Lemey, O. G. Pybus, B. Wang, N. K. Saksena, M. Salemi, A-M. Vandamme. Tracing the origin and history of HIV-2 epidemics (2003). Proc. Natl. Acad. Sci U.S.A.: 100:6588-6592.
32.    K. E. Robbins, P. Lemey, O. G. Pybus, H. W. Jaffe, A. M. Saekhou, T. M. Brown, M. Salemi, A-M. Vandamme, M. L. Kalish. Characterization of Early U.S. HIV-1 Strains, Dating of the Introduction of HIV-1 into the U.S. and Estimation of Population History of the U.S. Epidemic (2003). J. Virol.: 77:6359-6366.
33.    M. Salemi, T. De Oliveira, V. Courgnaud, V. Moulton, B. Holland, S. Cassol, W. M. Switzer, A-M. Vandamme. Mosaic genomes of the six major Primate lentivirus lineages revealed by phylogenetic analyses (2003). J. Virol. 77:7202-7213.
34.    L. C. Alcantara, N. Shindo, S. Van Dooren, M. Salemi, M. C. Costa, S. Kashima, D. T. Covas, A-M. Vandamme, B. Galvao-Castro. Brazilian HTLV type 2a strains from intravenous drug users (IDUs) appear to have originated from two sources: Brazilian Amerindians and European/North American IDUs (2003). AIDS. Res. Hum. Retrovir. 6:519-23.
35.    D. Paraskevis, P. Lemey, M. Salemi, M. Suchard, Y. Van der Peer, A.-M. Vandamme. Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using Bayesian inference: Implications for the origin of HIV-1 (2003). Mol. Biol. Evol. 20:1986-96.
36.    P. Lemey, M. Salemi, B. Wang, M. Duffy, W.W. Hall, N. Saksena, A-M. Vandamme. Site stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non-clock-like behavior on viral phylogenetic reconstructions (2003). FEMS Immunol. Med. Microbiol. 39:125-32.
37.    de Oliveira T., Susan Engelbrecht, Estrelita Janse van Rensburg, Michelle Gordon, Karen Bishop, Jan zur Megede, Susan W. Barnett, Sharon Cassol. Variability at HIV-1 Subtype C Protease Cleavage Sites: An Indication of Viral Fitness ? Journal of Virology, 2003, 77(17): 9422-30
38.    de Oliveira T, Miller R, Tarin M, Cassol S. An Integrated Genetic Data Environment (GDE)-Based LINUX Interface for Analysis of HIV-1 and Other Microbial Sequences.  Bioinformatics , 2003, 19(1): 153-4.   
39.    Gordon M, de Oliveira T, Bishop K, Coovadia HM, Madurai L, Engelbrecht S, Janse van Rensburg E, Mosam A, Smith A, Cassol S.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.
40.    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. A Specific subtype C of human immunodeficiency virus type 1 circulates in Brazil.  AIDS, 2003, 17: 11-22.
41.    S.L. Lamers, S. Beason, R. Compton, L. Dunlap, M. Salemi. HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental, and clinical data (2004). Bioinformatics 20:436-38.
42.    M. Salemi, W. M. Fitch, M. Ciccozzi, , M. J. Ruiz-Alvarez, G. Rezza, M. J. Lewis. SARS-CoV sequence characteristics and evolutionary rate estimate from maximum likelihood analysis (2004). J. Virol. 78:1602-03.
43.    T. De Oliveira, M. Salemi, M. Gordon, A-M. Vandamme, E. J. van Rensburg, S. Engelbrecht, A. Smith, S. Cassol. Codon-Substitutions Models as Indicators of Positive Selection and Amino Acid Diversification: An Alternative Approach to HIV-1 Vaccine Development (2004). Genetics 167:1047-58.
44.    S. Van Dooren, O. G. Pybus, M. Salemi, H.-F. Liu, P. Goubau, C. Remondegui, A. Talarmin, E. Gotuzzo, L. C. J. Alcantara, B. Galvao-Castro, A-M. Vandamme. The low evolutionary rate of Human T-Cell Lymphotropic Virus type-1 confirmed by  analysis of vertical transmission chains (2004). Mol. Biol. Evol.: 21:603-611.
45.    M. Salemi, T. de Oliveira, M. A. Soares, O. G. Pybus, A. T. Dumans, A-M. Vandamme, A. Tanuri, S. Cassol, W. M. Fitch. Different epidemic potentials of HIV-1 B and C subtypes (2005). J. Mol. Evol. 60:598-605.
46.    W. M. Switzer, M. Salemi, V. Shanmugam, F. Gao, M. Cong, C. Kuiken, V. Bhullar, B. Beer, D. Vallet, A. Gautier-Hion, Z. Tooze, F. Villinger, E.C. Holmes, and W. Heneine. Ancient Co-speciation of simian foamy viruses and primates (2005). Nature: 434:376-380.
47.    M Salemi, S. L. Lamers, S. Yu, T. De Oliveira, W. M. Fitch, M. S. McGrath. Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS (2005). J. Virol. 79:11343-52.
48.    L. Cali, B. Wang, M. Mikhail, M. J. Gill, B. Beckthold, M. Salemi, D. A. Jans, S.C. Piller, N. K. Saksena. Evidence for host-driven selection of the HIV type 1 vpr gene in vivo during HIV disease progression in a transfusion-acquired cohort (2005). AIDS Res. Hum. Retrovir. 8:728-233.
49.    de Oliveira T and Cassol S. (developers). Scourge of a Continent: The BioAfrica Website. Science, 2005, 310: 1872.
50.    de Oliveira T., K. Deforche, S. Cassol, M. Salminen, R. Camacho, D. Pavareskevis, C. Seebregts, J. Snoeck, A.M. VanDamme. The HIV-1 Automated Subtyping Tool. Bioinformatics, 2005 ,21: 3797-3800
51.    Doherty RS, de Oliveira T, Seebregts C, Danaviah S, Gordon M, Cassol S. BioAfrica's HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools. Retrovirology. 2005, 9;2(1):18
52.    L. Campitelli, M. Ciccozzi, M. Salemi, F. Taglia, S. Boros, I. Donatelli, G. Rezza (2006). H5N1 influenza virus evolution: a comparison of different epidemics in birds and humans (2006). J. Gen. Virol. 87:955-960.
53.    S. L. Lamers, M. Salemi, M. S. McGrath, G. B. Fogel. Predicting HIV R5, X4 and Dual tropic phenotype using evolved neural networks (2006). IEEE/ACM Trans. Comp. Biol. Bioinf.
54.    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. Molecular Epidemiology of New HIV-1 and HCV Sequences From Benghazi, Libya. Nature, 2006, in press.
55.    de Oliveira T. Out of Africa: The BioAfrica Website. BioTechniques, 2006, 41(2): 129.
56.    Gifford R, de Oliveira, T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme A, Kellam P, and D. Pillay. Assessment of Automated Genotyping Protocols as Tools for Surveillance of HIV-1 Genetic Diversity.  AIDS, 2006, 20(11):1521-9.
57.    Alcantara LC, de Oliveira T, Gordon M, Pybus O, Mascarenhas RE, Seixas MO, Goncalves M, Hlela C, Cassol S, Galvao-Castro B.Tracing the origin of Brazilian HTLV-1 as determined by analysis of host and viral genes.AIDS. 2006, 20(5):780-782.