Research Output per year
Research Output at NOVA
Molecular epidemiology of HIV-1 infected migrants followed up in Portugal: trends between 2001–2017
Pimentel, V., Pingarilho, M., Alves, D., Diogo, I., Fernandes, S., Miranda, M., Pineda-Peña, AC., Libin, P., Martins, MR., Vandamme, AM., Camacho, R. J., Gomes, P. & Abecasis, AB., 28 Feb 2020, In : VIRUSES-BASEL. Vol. 12, n.º 3, p. 268-283 15 p., 268.Research output: Contribution to journal › Article
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
Mavian, C., Pond, S. K., Marini, S., Brittany Rife, M., Vandamme, AM., Simon, D., Samuel V., S., Charlotte, H., Julian, V-A., Taylor K., P., Trovão, N. S., Christina, B., Yun, Z., Richard H., S., Olivier, G., Tommy Tsan-Yuk, L., Suchard, M. A., Abecasis, AB., Eduan, W., de Oliveira, T. & 16 others, , 7 May 2020, In : Proceedings of the National Academy of Sciences of the United States of America. Vol. 117, n.º 23, p. 12522-12523 2 p.Research output: Contribution to journal › Letter
A computational method for the identification of dengue, zika and chikungunya virus species and genotypes
Fonseca, V. S., Libin, P. J. K., Theys, K., Faria, N. R., Nunes, M. R. T., Restovic, M. I., Freire, M., Giovanetti, M., Cuypers, L., Nowé, A., Abecasis, AB., Deforche, K., Santiago, G. A., de Siqueira, I. C., San, E. J., Machado, K. C. B., Azevedo, V. A. D. C., de Filippis, A. M. B., da Cunha, R. V., Pybus, O. G. & 3 others, , 8 May 2019, In : PLoS Neglected Tropical Diseases. 13, 5, 15 p., e0007231.Research output: Contribution to journal › Article
Earlier initiation of antiretroviral treatment coincides with an initial control of the HIV-1 sub-subtype F1 outbreak among men-having-sex-with-men in Flanders, Belgium
Vinken, L., Katrien, F., Cuypers, L., Alexiev, I., Balotta, C., Laurent, D., Carole, S-D., Sergio Garcìa, R., Gomes, P., Incardona, F., Kaiser, R., Jean, R., Murat, S., Paraschiv, S., Paredes, R., Martine F., P., Anders B., S., Ellen, V., Vandamme, AM., Sigi, V. D. W. & 5 others, , 26 Mar 2019, In : Frontiers in Microbiology. Vol. 10, p. 613-626 13 p., 613.Research output: Contribution to journal › Article
Genome Detective: an automated system for virus identification from high-throughput sequencing data
Michael, V., Yumna, M., Sam, N., Vagner S., F., Yoika, G., Korneel, D., Raf, P., Luiz Carlos, J. A., Vanden Eynden, E., Vandamme, AM., Deforche, K. & de Oliveira, T., 1 Mar 2019, In : Bioinformatics. Vol. 35, n.º 5, p. 871-873 3 p.Research output: Contribution to journal › Article
The effect of primary drug resistance on CD4+ cell decline and the viral load set-point in HIV-positive individuals before the start of antiretroviral therapy
Anna, S., Torti, C., Alessandro, C-L., Vandamme, AM., Zazzi, M., Hellen, S., Luca, A. D., Anna Maria Aria, G., Anders B., S., Lidia, R., Laura, M., Simona, D. G., Andrea, G. & Giuseppe, L., 1 Feb 2019, In : AIDS. Vol. 33, n.º 2, p. 315-326 11 p.Research output: Contribution to journal › Article
Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology
Vasylyeva, T. I., Du Plessis, L., Pineda-Peña, AC., Kühnert, D., Lemey, P., Vandamme, AM., Gomes, P., Camacho, R. J., Pybus, O. G., Abecasis, AB. & Faria, N. R., 19 Jun 2019, In : Journal of Infectious Diseases. 220, 2, p. 233-243 10 p., jiz085.Research output: Contribution to journal › Article
Ethical considerations in global HIV phylogenetic research
Cordelia E.M., C., Anne, H., Michael, P., Liza, D., Joseph J., A., Musonda, S., Gail, G., Gail, H., Oliver B., L., Joseph D., T., Patrick Michael, E., Vladimir, N., Vandamme, AM., Janet, S., Gina A., D., Guy D., H., Mary Kate, G., Peter, G-F., Christophe, F., Myron S., C. & 10 others, , Nov 2018, In : The Lancet HIV. Vol. 5, n.º 11, p. e656-e666 10 p.Research output: Contribution to journal › Review article
Expert consensus statement on the science of HIV in the context of criminal law
F., B-S., S. S., A. K., Albert, J., L., B., C., B., P., C., A., C., B., G., Grulich, A., A., K., N., K., M. R., L., K. M., E. F., S., M., J. S. G., M., P., M., V., P., Vandamme, AM., B., Y. & P., G-F., 25 Jul 2018, In : Journal Of The International Aids Society. p. p. 1-12 12 p., e25161.Research output: Contribution to journal › Article
HIV-1 Infection in Cyprus, the Eastern Mediterranean European Frontier: A Densely Sampled Transmission Dynamics Analysis from 1986 to 2012
Pineda-Peña, A. C., Theys, K., Stylianou, D. C., Demetriades, I., Puchhammer, E., Vandamme, A. M., Aleksiev, I., Lepej, S. Z., Linka, M., Fonager, J., Liitsola, K., Kaiser, R., Hamouda, O., Paraskevis, D., Coughlan, S., Grossman, Z., Mor, O., Zazzi, M., Griskevicius, A., Lipnickiene, V. & 17 others, , 1 Dec 2018, In : Scientific Reports. 8, 1, 1702.Research output: Contribution to journal › Article
Phylogenetic analysis as a forensic tool in HIV transmission investigations
Abecasis, AB., Pingarilho, M. & Vandamme, AM., 13 Mar 2018, In : AIDS. 32, 5, p. 543-554 11 p.Research output: Contribution to journal › Review article
Predictors of non adherence to antiretroviral therapy at an urban HIV care and treatment center in Tanzania
Raphael Z., S., Mosha, F., Said, A., Appolinary R., K., Guerino E., C. G. E., Vercauteren, J., Van Wijngaerden, E., Eligius Francis, L. & Vandamme, AM., 2018, In : Drug, Healthcare and Patient Safety. Vol. 10, p. 79-88 10 p.Research output: Contribution to journal › Article
State of the antiretroviral therapy in human immunodeficiency virus drug resistance: Science and technology knowledge gap
Boucher, C. A. B., MR, B., Geretti, A. M., Chien Ching, H., Kaiser, R., Anne Geneviève, M., Anca, S-C., Jean, V. W., Patrick K., D. & Vandamme, AM., 15 Jun 2018, In : Aids Reviews. Vol. 20, n.º 1, p. p. 26-41 17 p., n.º 1.Research output: Contribution to journal › Article
State of the antiretroviral therapy in human immunodeficiency virus drug resistance: Surveillance and regional gaps
Boucher, C. A. B., MR, B., Chien Ching, H., Kaiser, R., Anne Geneviève, M., Jean, V. W., Patrick K., D. & Vandamme, AM., 15 Jun 2018, In : Aids Reviews. Vol. 20, n.º 1, p. 42-56 15 p.Research output: Contribution to journal › Article
State of the Art in HIV Drug Resistance: Science and Technology Knowledge Gap
Charles A.B., B., MR, B., Anna Maria Aria, G., Chienching, H., Kaiser, R., Anne Geneviève, M., Adrian, S-C., Jean, V. W., Patrick K., D. & Vandamme, AM., 1 Jan 2018, In : Aids Reviews. Vol. 20, n.º 1, p. 27-42 16 p.Research output: Contribution to journal › Review article
The impact of HIV-1 within-host evolution on transmission dynamics
Theys, K., Libin, P., Pineda-Peña, A. C., Nowé, A., Vandamme, A. M. & Abecasis, A. B., 1 Feb 2018, In : Current Opinion in Virology. 28, p. 92-101 10 p.Research output: Contribution to journal › Review article
Time to harmonize dengue nomenclature and classification
Cuypers, L., Pieter J.K., L., Peter, S., Nowé, A., Jorge Luis, M-J., Luiz Carlos, J. A., Vandamme, AM., Gilberto A., S. & Theys, K., 18 Oct 2018, In : VIRUSES-BASEL. Vol. 10, n.º 10, p. 569-576 7 p., 569.Research output: Contribution to journal › Article
A36 Prevalence of HIV-1 subtypes in Slovenia with an emphasis on molecular and phylogenetic investigation of subtype A
Mlakar, J., Lunar, M. M., Abecasis, A. B., Vandamme, A-M., Tomažič, J., Vovko, T. D., Pečavar, B., Volčanšek, G. & Poljak, M., Mar 2017, In : Virus evolution. 3, Suppl 1Research output: Contribution to journal › Article
A Fashi lymphoproliferative phenotype reveals non-apoptotic fas signaling in HTLV-1-associated neuroinflammation
Menezes, S. M., Leal, F. E., Dierckx, T., Khouri, R., Decanine, D., Silva-Santos, G., Schnitman, S. V., Kruschewsky, R., López, G., Alvarez, C., Talledo, M., Gotuzzo, E., Nixon, D. F., Vercauteren, J., Brassat, D., Liblau, R., Vandamme, A. M., Galvão-Castro, B. & Van Weyenbergh, J., 14 Feb 2017, In : Frontiers in Immunology. 8, FEB, 97.Research output: Contribution to journal › Article
Exploring resistance pathways for first-generation NS3/4A protease inhibitors boceprevir and telaprevir using Bayesian network learning
Cuypers, L., Libin, P., Schrooten, Y., Theys, K., Di Maio, V. C., Cento, V., Lunar, M. M., Nevens, F., Poljak, M., Ceccherini-Silberstein, F., Nowé, A., Van Laethem, K. & Vandamme, A. M., 1 Sep 2017, In : Infection, Genetics and Evolution. Vol. 53, p. p. 15-23 9 p.Research output: Contribution to journal › Article
IFN-beta induces greater antiproliferative and proapoptotic effects and increased p53 signaling compared with IFN-alpha in PBMCs of Adult T-cell Leukemia/Lymphoma patients
Dierckx, T., Khouri, R., Menezes, S. M., Decanine, D., Farre, L., Bittencourt, A., Vandamme, A. M. & Van Weyenbergh, J., 27 Jan 2017, In : BLOOD CANCER JOURNAL. Vol. 7, n.º 1, p. e519-e523 4 p., e519.Research output: Contribution to journal › Article
Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy
Cuypers, L., Vrancken, B., Fabeni, L., Marascio, N., Cento, V., Di Maio, V. C., Aragri, M., Pineda-Peña, A. C., Schrooten, Y., Van Laethem, K., Balog, D., Focà, A., Torti, C., Nevens, F., Perno, C. F., Vandamme, A. M. & Ceccherini-Silberstein, F., 7 Mar 2017, In : BMC Evolutionary Biology. Vol. 17, n.º 1, p. p. 70-80 10 p., 70.Research output: Contribution to journal › Article
Large cluster outbreaks sustain the HIV epidemic among MSM in Quebec
Brenner, B. G., Ibanescu, R. I., Hardy, I., Stephens, D., Otis, J., Moodie, E., Grossman, Z., Vandamme, A. M., Roger, M. & Wainberg, M. A., 13 Mar 2017, In : AIDS. Vol. 31, n.º 5, p. p. 707-717 11 p.Research output: Contribution to journal › Article
Phylogenetic evidence for underreporting of male-to-male sex among human immunodeficiency virus–infected donors in the Netherlands and Flanders
van de Laar, T. J., Bezemer, D., van Laethem, K., Vandewalle, G., de Smet, A., van Wijngaerden, E., Claas, E. C., van Sighem, A. I., Vandamme, A. M., Compernolle, V. & Zaaijer, H. L., 1 May 2017, In : Transfusion. 57, 5, p. 1235-1247 13 p.Research output: Contribution to journal › Article
PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context
Libin, P., Vanden Eynden, E., Incardona, F., Nowé, A., Bezenchek, A., Sönnerborg, A., Vandamme, A-M., Theys, K., Baele, G. & EucoHIV study group, 26 Aug 2017, In : Bioinformatics.Research output: Contribution to journal › Article
The epidemic emergence of HIV: What novel enabling factors were involved
Sousa, J. D., Müller, V. & Vandamme, AM., 2017, In : Future Virology.Research output: Contribution to journal › Article
Zika genomics urgently need standardized and curated reference sequences
Theys, K., Libin, P., Dallmeier, K., Pineda-Peña, A. C., Vandamme, A. M., Cuypers, L. & Abecasis, A. B., 1 Sep 2017, In : PLoS Pathogens. 13, 9, e1006528.Research output: Contribution to journal › Comment/debate
Zika virus genetic diversity and selective pressure: importance for diagnostics, vaccines and therapeutics
Cuypers, L., Libin, P., Abecasis, A., Vandamme, A. -M. & Theys, K., Oct 2017, In : Tropical medicine & international health : TM & IH. 22, Suppl 1, p. 9Research output: Contribution to journal › Article
Family aggregation of human T-lymphotropic virus 1-associated diseases: A systematic review
Alvarez, C., Gotuzzo, E., Vandamme, A. M. & Verdonck, K., 28 Oct 2016, In : Frontiers in Microbiology. 7, OCT, 1674.Research output: Contribution to journal › Review article
HCV1b genome evolution under selective pressure of the cyclophilin inhibitor alisporivir during the DEB-025-HCV-203 phase II clinical trial
Cuypers, L., Snoeck, J., Kerremans, L., Libin, P., Crabbé, R., Van Dooren, S., Vuagniaux, G. & Vandamme, A. M., 1 Oct 2016, In : Infection Genetics And Evolution. 44, p. 169-181 13 p.Research output: Contribution to journal › Article
On the contribution of Angola to the initial spread of HIV-1
Pineda-Peña, A-C., Ferreira, J. V., Sousa, J. D., Theys, K., Bártolo, I., Leitner, T., Taveira, N., Vandamme, A-M. & Abecasis, A. B., Dec 2016, In : Infection Genetics And Evolution. 46, p. 219-222 4 p.Research output: Contribution to journal › Article
Quantifying next generation sequencing sample pre-processing bias in HIV-1 complete genome sequencing
Vrancken, B., Trovão, N. S., Baele, G., Van Wijngaerden, E., Vandamme, A. M., van Laethem, K. & Lemey, P., 7 Jan 2016, In : VIRUSES-BASEL. 8, 1Research output: Contribution to journal › Article
Sub-Epidemics Explain Localized High Prevalence of Reduced Susceptibility to Rilpivirine in Treatment-Naive HIV-1-Infected Patients: Subtype and Geographic Compartmentalization of Baseline Resistance Mutations
Theys, K., van Laethem, K., Gomes, P., Baele, G., Pineda-Peña, A-C., Vandamme, A-M., Camacho, R. J. & Abecasis, A. B., May 2016, In : AIDS Research and Human Retroviruses. 32, 5, p. 427-33 7 p.Research output: Contribution to journal › Article
A new ensemble coevolution system for detecting HIV-1 protein coevolution
Li, G., Theys, K., Verheyen, J., Pineda-Peña, A. C., Khouri, R., Piampongsant, S., Eusébio, M., Ramon, J. & Vandamme, A. M., 7 Jan 2015, In : Biology Direct. 10, 1, 1.Research output: Contribution to journal › Article
An integrated map of HIV genome-wide variation from a population perspective
Li, G., Piampongsant, S., Faria, R. N., Voet, A., Pineda-Peña, A. C., Khouri, R., Lemey, P., Vandamme, A. M. & Theys, K., 15 Feb 2015, In : Retrovirology. 12, 1, 18.Research output: Contribution to journal › Article
Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals
Winand, R., Theys, K., Eusébio, M., Aerts, J., Camacho, R. J., Gomes, P., Suchard, M. A., Vandamme, A. M. & Abecasis, A. B., 24 Sep 2015, In : AIDS. 29, 15, p. 2045-2052 8 p.Research output: Contribution to journal › Article
Bridging epidemiology with population genetics in a low incidence MSM-driven HIV-1 subtype B epidemic in Central Europe
Lunar, M. M., Vandamme, A. M., Tomažič, J., Karner, P., Vovko, T. D., Pečavar, B., Volčanšek, G., Poljak, M. & Abecasis, A. B., 15 Feb 2015, In : BMC Infectious Diseases. 15, 1, 65.Research output: Contribution to journal › Article
CRF19_cpx is an evolutionary fit HIV-1 variant exclusively associated with rapid progression to AIDS in Cuba.
Kourí, V., Khouri, R., Alemán, Y., Vercauteren, J., Pineda-Peña, AC., Theys, K., Megens, S., Moutschen, M., Pfeifer, N., Weyenbergh, J. V., Pérez, A. B., Pérez, J., Pérez, L., Van Laethem, K. & Vandamme, AM., 2015, In : EBioMedicine. 2Research output: Contribution to journal › Article
Discovery and characterization of auxiliary proteins encoded by type 3 simian T-cell lymphotropic viruses
Turpin, J., Journo, C., Ko, N. L., Sinet, F., Carpentier, A., Galioot, A., Edwards, D., Vandamme, A. M., Gazzolo, L., Dodon, M. D., Gessain, A., Kashanchi, F., Balansard, I., Lacoste, R. & Mahieux, R., 2015, In : Journal of Virology. 89, 2, p. 931-951 21 p.Research output: Contribution to journal › Article
Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis
Rhee, S. Y., Blanco, J. L., Jordan, M. R., Taylor, J., Lemey, P., Varghese, V., Hamers, R. L., Bertagnolio, S., de Wit, T. F. R., Aghokeng, A. F., Albert, J., Avi, R., Avila-Rios, S., Bessong, P. O., Brooks, J. I., Boucher, C. A. B., Brumme, Z. L., Busch, M. P., Bussmann, H., Chaix, M. L. & 53 others, , 1 Apr 2015, In : PLoS Medicine. 12, 4, e1001810.Research output: Contribution to journal › Article
Global dispersal pattern of HIV type 1 subtype CRF01-AE: A genetic trace of human mobility related to heterosexual sexual activities centralized in southeast Asia
Angelis, K., Albert, J., Mamais, I., Magiorkinis, G., Hatzakis, A., Hamouda, O., Struck, D., Vercauteren, J., Wensing, A. M. J., Alexiev, I., Åsjö, B., Balotta, C., Camacho, R. J., Coughlan, S., Griskevicius, A., Grossman, Z., Horban, A., Kostrikis, L. G., Lepej, S., Liitsola, K. & 14 others, , 1 Jun 2015, In : Journal of Infectious Diseases. 211, 11, p. 1735-1744 10 p.Research output: Contribution to journal › Article
Origin and distribution of HIV-1 subtypes
Abecasis, AB. & Vandamme, AM., 29 Jul 2015, Encyclopedia of AIDS. Hope, T. J., Stevensen, M. & Richman, D. (eds.). 2015 ed. Berlin: Springer-Verlag, p. 1-16 15 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba
Alemán, Y., Vinken, L., Kourí, V., Pérez, L., Álvarez, A., Abrahantes, Y., Fonseca, C., Pérez, J., Correa, C., Soto, Y., Schrooten, Y., Vandamme, A. M. & Van Laethem, K., 11 Feb 2015, In : PlosOne. 10, 2, e0117176.Research output: Contribution to journal › Article
Predicted residual activity of rilpivirine in HIV-1 infected patients failing therapy including NNRTIs efavirenz or nevirapine
Theys, K., Camacho, R. J., Gomes, P., Vandamme, A. M. & Rhee, S. Y., 1 Jun 2015, In : Clinical Microbiology And Infection. 21, 6, p. 607.e1-607.e8Research output: Contribution to journal › Article
A near-full length genotypic assay for HCV1b
Cuypers, L., Snoeck, J., Vrancken, B., Kerremans, L., Vuagniaux, G., Verbeeck, J., Nevens, F., Camacho, R. J., Vandamme, A. M. & Van Dooren, S., 1 Dec 2014, In : Journal Of Virological Methods. 209, p. 126-135 10 p.Research output: Contribution to journal › Article
Bioinformatics tools for the investigation of viral evolution and molecular epidemiology
Salemi, M. & Vandamme, A. M., 1 Dec 2014, In : Infection Genetics And Evolution. 28, p. 349-350 2 p.Research output: Contribution to journal › Editorial
CD80+ and CD86+ B cells as biomarkers and possible therapeutic targets in HTLV-1 associated myelopathy/tropical spastic paraparesis and multiple sclerosis
Menezes, S. M., Decanine, D., Brassat, D., Khouri, R., Schnitman, S. V., Kruschewsky, R., López, G., Alvarez, C., Talledo, M., Gotuzzo, E., Vandamme, A. M., Galvão-Castro, B., Liblau, R. & Weyenbergh, J. V., 29 Jan 2014, In : Journal of Neuroinflammation. 11, 18.Research output: Contribution to journal › Article
Characterization of amino acids Arg, Ser and Thr at position 70 within HIV-1 reverse transcriptase
Megens, S., De Wit, S., Bernatchez, J., Dekeersmaeker, N., Vinken, L., Covens, K., Theys, K., Camacho, R. J., Vandamme, A. M., Götte, M. & Van Laethem, K., 1 Oct 2014, In : Acta Clinica Belgica. 69, 5, p. 348-357 10 p.Research output: Contribution to journal › Article
Clinical and virological response to antiretroviral drugs among HIV patients on first-line treatment in Dar-es-Salaam, Tanzania
Mosha, F., Ledwaba, J., Ndugulile, F., Ng'ang'a, Z., Nsubuga, P., Morris, L., Kasubi, M., Swai, A., Vercauteren, J. & Vandamme, A. M., 2014, In : Journal Of Infection In Developing Countries. 8, 7, p. 845-852 8 p.Research output: Contribution to journal › Article
HIV-1 Gag C-terminal amino acid substitutions emerging under selective pressure of protease inhibitors in patient populations infected with different HIV-1 subtypes
Li, G., Verheyen, J., Theys, K., Piampongsant, S., Van Laethem, K. & Vandamme, A. M., 25 Sep 2014, In : Retrovirology. 11, 1, 79.Research output: Contribution to journal › Article