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Cerutti, B. and Bader, J. and Ehmer, J. and Pfeiffer, K. and Klimkait, T. and Labhardt, N. D.. (2016) Performance of risk-charts to guide targeted HIV viral load monitoring of ART : applying the method on the data from a multi-centre-study in rural Lesotho. Journal of acquired immune deficiency syndromes and human retrovirology, 72 (1). e22-e25.

Masimba, P. and Kituma, E. and Klimkait, T. and Horvath, E. and Stoeckle, M. and Hatz, C. and Mossdorf, E. and Mwaigomole, E. and Khamis, S. and Jullu, B. and Abdulla, S. and Tanner, M. and Felger, I.. (2013) Prevalence of drug resistance mutations and HIV type 1 subtypes in an HIV type 1-infected cohort in rural Tanzania. AIDS research and human retroviruses, Vol. 29, H. 9. pp. 1229-1236.

Cusini, A. and Vernazza, P. L. and Yerly, S. and Decosterd, L. A. and Ledergerber, B. and Fux, C. A. and Rohrbach, J. and Widmer, N. and Hirschel, B. and Gaudenz, R. and Cavassini, M. and Klimkait, T. and Zenger, F. and Gutmann, C. and Opravil, M. and Gunthard, H. F. and Swiss HIV Cohort Study, . (2013) Higher CNS Penetration-Effectiveness of Long-term Combination Antiretroviral Therapy Is Associated With Better HIV-1 Viral Suppression in Cerebrospinal Fluid. JAIDS: journal of acquired immune deficiency syndromes, Vol. 62, H. 1. pp. 28-35.

Louvel, S. and Moodley, N. and Seibert, I. and Steenkamp, P. and Nthambeleni, R. and Vidal, V. and Maharaj, V. and Klimkait, T.. (2013) Identification of compounds from the plant species Alepidea amatymbica active against HIV. South African journal of botany, Vol. 86. pp. 9-14.

Schupbach, J. and Gebhardt, M. D. and Scherrer, A. U. and Bisset, L. R. and Niederhauser, C. and Regenass, S. and Yerly, S. and Aubert, V. and Suter, F. and Pfister, S. and Martinetti, G. and Andreutti, C. and Klimkait, T. and Brandenberger, M. and Gunthard, H. F. and Swiss HIV Cohort Study, . (2013) Simple Estimation of Incident HIV Infection Rates in Notification Cohorts Based on Window Periods of Algorithms for Evaluation of Line-Immunoassay Result Patterns. PLoS one, Vol. 8, H. 8 , e71662.

Beerenwinkel, N. and Montazeri, H. and Schuhmacher, H. and Knupfer, P. and von Wyl, V. and Furrer, H. and Battegay, M. and Hirschel, B. and Cavassini, M. and Vernazza, P. and Bernasconi, E. and Yerly, S. and Boni, J. and Klimkait, T. and Cellerai, C. and Gunthard, H. F. and Swiss HIV Cohort Study, . (2013) The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients. PLoS Computational Biology, Vol. 9, H. 8 , e1003203.

Mehling, M. and Fritz, S. and Hafner, P. and Eichin, D. and Yonekawa, T. and Klimkait, T. and Lindberg, R. L. and Kappos, L. and Hess, C.. (2013) Preserved Antigen-Specific Immune Response in Patients with Multiple Sclerosis Responding to IFNbeta-Therapy. PLoS one, Vol. 8, H. 11 , e78532.

Vidal, V. and Potterat, O. and Louvel, S. and Hamy, F. and Mojarrab, M. and Sanglier, J. J. and Klimkait, T. and Hamburger, M.. (2012) Library-based discovery and characterization of Daphnane diterpenes as potent and selective HIV inhibitors in Daphne gnidium. Journal of natural products, Vol. 75, H. 3. pp. 414-419.

von Wyl, Viktor and Yerly, Sabine and Böni, Jürg and Shah, Cyril and Cellerai, Cristina and Klimkait, Thomas and Battegay, Manuel and Bernasconi, Enos and Cavassini, Matthias and Furrer, Hansjakob and Hirschel, Bernard and Vernazza, Pietro L. and Ledergerber, Bruno and Günthard, Huldrych F. and Swiss HIV Cohort Study, . (2012) Incidence of HIV-1 drug resistance among antiretroviral treatment-naive individuals starting modern therapy combinations. Clinical Infectious Diseases, Vol. 54, H. 1. pp. 131-140.

Klimkait, Thomas. (2012) The XTrack system: application and advantage. Intervirology, 55 (2). pp. 118-122.

Leventhal, G. E. and Kouyos, R. and Stadler, T. and von Wyl, V. and Yerly, S. and Boni, J. and Cellerai, C. and Klimkait, T. and Gunthard, H. F. and Bonhoeffer, S.. (2012) Inferring epidemic contact structure from phylogenetic trees. PLoS Computational Biology, Vol. 8, H. 3 , e1002413.

Kemal, K. S. and Ramirez, C. M. and Burger, H. and Foley, B. and Mayers, D. and Klimkait, T. and Hamy, F. and Anastos, K. and Petrovic, K. and Minin, V. N. and Suchard, M. A. and Weiser, B.. (2012) Recombination between variants from genital tract and plasma : evolution of multidrug-resistant HIV type 1. Aids research and human retroviruses, Vol. 28, H. 12. pp. 1766-1774.

Stadler, T. and Kouyos, R. and von Wyl, V. and Yerly, S. and Boni, J. and Burgisser, P. and Klimkait, T. and Joos, B. and Rieder, P. and Xie, D. and Gunthard, H. F. and Drummond, A. J. and Bonhoeffer, S. and Swiss HIV Cohort Study, . (2012) Estimating the basic reproductive number from viral sequence data. Molecular biology and evolution, Vol. 29, no 1. pp. 347-357.

Schupbach, J. and Bisset, L. R. and Gebhardt, M. D. and Regenass, S. and Burgisser, P. and Gorgievski, M. and Klimkait, T. and Andreutti, C. and Martinetti, G. and Niederhauser, C. and Yerly, S. and Pfister, S. and Schultze, D. and Brandenberger, M. and Schoni-Affolter, F. and Scherrer, A. U. and Gunthard, H. F. and Swiss HIV Cohort Study, . (2012) Diagnostic performance of line-immunoassay based algorithms for incident HIV-1 infection. BMC infectious diseases, Vol. 12 , 88.

Scherrer, A. U. and von Wyl, V. and Gotte, M. and Klimkait, T. and Cellerai, C. and Yerly, S. and Boni, J. and Held, L. and Ledergerber, B. and Gunthard, H. F. and Swiss HIV Cohort Study, . (2012) Polymorphic mutations associated with the emergence of the multinucleoside/tide resistance mutations 69 insertion and Q151M. Journal of acquired immune deficiency syndromes and human retrovirology, Vol. 59, H. 2. pp. 105-112.

Scherrer, A. U. and Ledergerber, B. and von Wyl, V. and Boni, J. and Yerly, S. and Klimkait, T. and Cellerai, C. and Furrer, H. and Calmy, A. and Cavassini, M. and Elzi, L. and Vernazza, P. L. and Bernasconi, E. and Gunthard, H. F. and Swiss HIV Cohort Study Shcs, . (2012) Minor protease inhibitor mutations at baseline do not increase the risk for a virological failure in HIV-1 subtype B infected patients. PLoS one, Vol. 7, H. 6 , e37983.

Scherrer, A. U. and Boni, J. and Yerly, S. and Klimkait, T. and Aubert, V. and Furrer, H. and Calmy, A. and Cavassini, M. and Elzi, L. and Vernazza, P. L. and Bernasconi, E. and Ledergerber, B. and Gunthard, H. F. and Swiss HIV Cohort Study Shcs, . (2012) Long-lasting protection of activity of nucleoside reverse transcriptase inhibitors and protease inhibitors (PIs) by boosted PI containing regimens. PLoS one, Vol. 7, H. 11 , e50307.

Lubbe, A. and Seibert, I. and Klimkait, T. and van der Kooy, F.. (2012) Ethnopharmacology in overdrive : the remarkable anti-HIV activity of Artemisia annua. Journal of ethnopharmacology, Vol. 141, H. 3. pp. 854-859.

Omolo, J. J. and Maharaj, V. and Naidoo, D. and Klimkait, T. and Malebo, H. M. and Mtullu, S. and Lyaruu, H. V. M. and de Koning, C. B.. (2012) Bioassay-guided investigation of the Tanzanian plant Pyrenacantha kaurabassana for potential anti-HIV-active compounds. Journal of natural products, Vol. 75, H. 10. pp. 1712-1716.

Vandekerckhove, L. P. R. and Wensing, A. M. J. and Kaiser, R. and Brun-Vezinet, F. and Clotet, B. and De Luca, A. and Dressler, S. and Garcia, F. and Geretti, A. M. and Klimkait, T. and Korn, K. and Masquelier, B. and Perno, C. F. and Schapiro, J. M. and Soriano, V. and Sonnerborg, A. and Vandamme, A. M. and Verhofstede, C. and Walter, H. and Zazzi, M. and Boucher, C. A. B. and European Consensus Grp Clinical, . (2011) European guidelines on the clinical management of HIV-1 tropism testing. The Lancet infectious diseases, Vol. 11, H. 5. pp. 394-407.

von Wyl, Viktor and Kouyos, Roger D. and Yerly, Sabine and Böni, Jürg and Shah, Cyril and Bürgisser, Philippe and Klimkait, Thomas and Weber, Rainer and Hirschel, Bernard and Cavassini, Matthias and Staehelin, Cornelia and Battegay, Manuel and Vernazza, Pietro L. and Bernasconi, Enos and Ledergerber, Bruno and Bonhoeffer, Sebastian and Günthard, Huldrych F. and Swiss HIV Cohort Study, . (2011) The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland. Journal of Infectious Diseases, Vol. 204, no. 7. pp. 1095-1103.

Scherrer, A. U. and von Wyl, V. and Boni, J. and Yerly, S. and Klimkait, T. and Burgisser, P. and Garzoni, C. and Hirschel, B. and Cavassini, M. and Battegay, M. and Vernazza, P. L. and Bernasconi, E. and Ledergerber, B. and Gunthard, H. F. and Swiss HIV Cohort Study Shcs, . (2011) Viral suppression rates in salvage treatment with raltegravir improved with the administration of genotypic partially active or inactive nucleoside/tide reverse transcriptase inhibitors. JAIDS, Vol. 57, H. 1. pp. 24-31.

Kouyos, R. D. and von Wyl, V. and Yerly, S. and Boni, J. and Rieder, P. and Joos, B. and Taffe, P. and Shah, C. and Burgisser, P. and Klimkait, T. and Weber, R. and Hirschel, B. and Cavassini, M. and Rauch, A. and Battegay, M. and Vernazza, P. L. and Bernasconi, E. and Ledergerber, B. and Bonhoeffer, S. and Gunthard, H. F. and Swiss HIV Cohort Study, . (2011) Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clinical Infectious Diseases, Vol. 52, H. 4. pp. 532-539.

Daikeler, Thomas and Hoenger, Gideon and Oehri, Ineke and Tyndall, Alan and Gratwohl, Alois and Brander, Christian and Klimkait, Thomas and Gasser, Olivier and Hess, Christoph. (2011) Dominant Epstein-Barr virus-specific T-cell responses are maintained during moderate and intense immunosuppressive treatment. Annals of the rheumatic diseases, Vol. 70, H. 2. pp. 395-396.

Scherrer, Alexandra U. and Ledergerber, Bruno and von Wyl, Viktor and Böni, Jürg and Yerly, Sabine and Klimkait, Thomas and Bürgisser, Philippe and Rauch, Andri and Hirschel, Bernard and Cavassini, Matthias and Elzi, Luigia and Vernazza, Pietro L. and Bernasconi, Enos and Held, Leonhard and Günthard, Huldrych F. and Swiss HIV Cohort Study, . (2011) Improved virological outcome in White patients infected with HIV-1 non-B subtypes compared to subtype B. Clinical Infectious Diseases, Vol. 53, H. 11. pp. 1143-1152.

Mehling, M. and Hilbert, P. and Fritz, S. and Durovic, B. and Eichin, D. and Gasser, O. and Kuhle, J. and Klimkait, T. and Lindberg, R. L. P. and Kappos, L. and Hess, C.. (2011) Antigen-specific adaptive immune responses in fingolimod-treated multiple sclerosis patients. Annals of neurology, Vol. 69, H. 2. pp. 408-413.

Scherrer, A. U. and von Wyl, V. and Joos, B. and Klimkait, T. and Burgisser, P. and Yerly, S. and Boni, J. and Ledergerber, B. and Gunthard, H. F. and Swiss HIV Cohort Study, . (2011) Predictors for the emergence of the 2 multi-nucleoside/nucleotide resistance mutations 69 insertion and Q151M and their impact on clinical outcome in the Swiss HIV cohort study. Journal of Infectious Diseases, Vol. 203, no. 6. pp. 791-797.

Miazga, Agnieszka and Hamy, François and Louvel, Séverine and Klimkait, Thomas and Pietrusiewicz, Zofia and Kurzy?ska-Kokorniak, Anna and Figlerowicz, Marek and Wi?ska, Patrycja and Kulikowski, Tadeusz. (2011) Thiated derivatives of 2',3'-dideoxy-3'-fluorothymidine : synthesis, in vitro anti-HIV-1 activity and interaction with recombinant drug resistant HIV-1 reverse transcriptase forms. Antiviral research, Vol. 92, H. 1. pp. 57-63.

Schüpbach, Jörg and Bisset, Leslie R. and Regenass, Stephan and Bürgisser, Philippe and Gorgievski, Meri and Steffen, Ingrid and Andreutti, Corinne and Martinetti, Gladys and Shah, Cyril and Yerly, Sabine and Klimkait, Thomas and Gebhardt, Martin and Schöni-Affolter, Franziska and Rickenbach, Martin and Swiss HIV Cohort Study, and Barth, J. and Battegay, M. and Bernascon, E. and Böni, J. and Bucher, H. C. and Bürgisser, P. and Burton-Jeangros, C. and Calmy, A. and Cavassini, M. and Dubs, R. and Egger, M. and Elzi, L. and Fehr, J. and Fischer, M. and Flepp, M. and Francioli, P. and Furrer, H. and Fux, C. A. and Gorgievski, M. and Günthard, H. and Hasse, B. and Hirsch, H. H. and Hirschel, B. and Hösli, I. and Kahlert, C. and Kaiser, L. and Keiser, O. and Kind, C. and Klimkait, T. and Kovari, H. and Ledergerber, B. and Martinetti, G. and Martinez de Tejada, B. and Müller, N. and Nadal, D. and Pantaleo, G. and Rauch, A. and Regenass, S. and Rickenbach, M. and Rudin, C. and Schmid, P. and Schultze, D. and Schöni-Affolter, F. and Schüpbach, J. and Speck, R. and Taffé, P. and Telenti, A. and Trkola, A. and Vernazza, P. and von Wyl, V. and Weber, R. and Yerly, S.. (2011) High specificity of line-immunoassay based algorithms for recent HIV-1 infection independent of viral subtype and stage of disease. BMC infectious diseases, Vol. 11 , 254. p. 254.

Kouyos, R. D. and von Wyl, V. and Hinkley, T. and Petropoulos, C. J. and Haddad, M. and Whitcomb, J. M. and Boni, J. and Yerly, S. and Cellerai, C. and Klimkait, T. and Gunthard, H. F. and Bonhoeffer, S. and Swiss HIV Cohort Study, . (2011) Assessing predicted HIV-1 replicative capacity in a clinical setting. PLoS Pathogens, Vol. 7, H. 11 , e1002321.

Fehr, J. and Glass, T. R. and Louvel, S. and Hamy, F. and Hirsch, H. H. and von Wyl, V. and Boni, J. and Yerly, S. and Burgisser, P. and Cavassini, M. and Fux, C. A. and Hirschel, B. and Vernazza, P. and Martinetti, G. and Bernasconi, E. and Gunthard, H. F. and Battegay, M. and Bucher, H. C. and Klimkait, T.. (2011) Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals - the Swiss HIV Cohort Study. Journal of translational medicine, Vol. 9 , 14. p. 14.

Opravil, Milos and Klimkait, Thomas and Louvel, Severine and Wolf, Eva and Battegay, Manuel and Fux, Christoph A. and Bernasconi, Enos and Vogel, Martin and Speck, Roberto and Weber, Rainer and Swiss HIV Cohort Study, . (2010) Prior therapy influences the efficacy of lamivudine monotherapy in patients with lamivudine-resistant HIV-1 infection. JAIDS: journal of acquired immune deficiency syndromes, Vol. 54, H. 1. pp. 51-58.

Kouyos, Roger D. and von Wyl, Viktor and Yerly, Sabine and Böni, Jürg and Taffé, Patrick and Shah, Cyril and Bürgisser, Philippe and Klimkait, Thomas and Weber, Rainer and Hirschel, Bernard and Cavassini, Matthias and Furrer, Hansjakob and Battegay, Manuel and Vernazza, Pietro L. and Bernasconi, Enos and Rickenbach, Martin and Ledergerber, Bruno and Bonhoeffer, Sebastian and Günthard, Huldrych F.. (2010) Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. The Journal of Infectious Diseases, Vol. 201, no. 10. pp. 1488-1497.

von Wyl, Viktor and Ehteshami, Maryam and Demeter, Lisa M. and Bürgisser, Philippe and Nijhuis, Monique and Symons, Jori and Yerly, Sabine and Böni, Jürg and Klimkait, Thomas and Schuurman, Rob and Ledergerber, Bruno and Götte, Matthias and Günthard Huldrych, F. and Swiss HIV Cohort Study, . (2010) HIV-1 reverse transcriptase connection domain mutations : dynamics of emergence and implications for success of combination antiretroviral therapy. Clinical Infectious Diseases, Vol. 51, H. 5. pp. 620-628.

Rieder, Philip and Joos, Beda and von Wyl, Viktor and Kuster, Herbert and Grube, Christina and Leemann, Christine and Böni, Jürg and Yerly, Sabine and Klimkait, Thomas and Bürgisser, Philipp and Weber, Rainer and Fischer, Marek and Günthard Huldrych, F. and Swiss HIV Cohort Study, . (2010) HIV-1 transmission after cessation of early antiretroviral therapy among men having sex with men. AIDS, Vol. 24, H. 8. pp. 1177-1183.

von Wyl, Viktor and Ehteshami, Maryam and Symons, Jori and Bürgisser, Philippe and Nijhuis, Monique and Demeter, Lisa M. and Yerly, Sabine and Böni, Jürg and Klimkait, Thomas and Schuurman, Rob and Ledergerber, Bruno and Götte, Matthias and Günthard Huldrych, F. and Swiss HIV Cohort Study, . (2010) Epidemiological and biological evidence for a compensatory effect of connection domain mutation N348I on M184V in HIV-1 reverse transcriptase. The Journal of Infectious Diseases, Vol. 201, no. 7. pp. 1054-1062.

Scherrer, Alexandra U. and von Wyl, Viktor and Fux, Christof A. and Opravil, Milos and Bucher, Heiner C. and Fayet, Aurélie and Decosterd, Laurent A. and Hirschel, Bernhard and Khanlari, Bettina and Yerly, Sabine and Klimkait, Thomas and Furrer, Hansjakob and Ledergerber, Bruno and Günthard, Huldrych F.. (2010) Implementation of raltegravir in routine clinical practice : selection criteria for choosing this drug, virologic response rates, and characteristics of failures. JAIDS: journal of acquired immune deficiency syndromes, Vol. 53, H. 4. pp. 464-471.

Kouyos, R. D. and von Wyl, V. and Yerly, S. and Boni, J. and Rieder, P. and Joos, B. and Taffe, P. and Shah, C. and Burgisser, P. and Klimkait, T. and Weber, R. and Hirschel, B. and Cavassini, M. and Rauch, A. and Battegay, M. and Vernazza, P. L. and Bernasconi, E. and Ledergerber, B. and Bonhoeffer, S. and Gunthard, H. F. and Swiss HIV Cohort Study, . (2010) Ambiguity in population-based sequencing of HIV-1 as a marker for the age of HIV infection. Antiviral therapy, Vol. 15 , A158-A158.

von Wyl, Viktor and Yerly, Sabine and Bürgisser, Philippe and Klimkait, Thomas and Battegay, Manuel and Bernasconi, Enos and Cavassini, Matthias and Furrer, Hansjakob and Hirschel, Bernard and Vernazza, Pietro L. and Francioli, Patrick and Bonhoeffer, Sebastian and Ledergerber, Bruno and Günthard Huldrych, F. and Swiss HIV Cohort Study, . (2009) Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland. Clinical Infectious Diseases, Vol. 48. pp. 979-987.

Scherrer, A. U. and Hasse, B. and von Wyl, V. and Yerly, S. and Böni, J. and Bürgisser, P. and Klimkait, T. and Bucher, H. C. and Ledergerber, B. and Günthard, H. F.. (2009) Prevalence of etravirine mutations and impact on response to treatment in routine clinical care : the Swiss HIV Cohort Study (SHCS). HIV medicine : the official journal of the British HIV Association (BHIVA) and the European AIDS Clinical Society (EACS), Vol. 10. pp. 647-656.

Müller, Viktor and von Wyl, Viktor and Yerly, Sabine and Böni, Jürg and Klimkait, Thomas and Bürgisser, Philippe and Ledergerber, Bruno and Günthard, Huldrych F. and Bonhoeffer, Sebastian. (2009) African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study. AIDS : official journal of the International AIDS Society, Vol. 23. pp. 1269-1276.

von Wyl, V. and Yerly, S. and Böni, J. and Bürgisser, P. and Klimkait, T. and Battegay, M. and Bernasconi, E. and Cavassini, M. and Furrer, H. and Hirschel, B. and Vernazza, P. L. and Rickenbach, M. and Ledergerber, B. and Günthard, H. F. and Swiss, HIV Cohort Study. (2008) Factors associated with the emergence of K65R in patients with HIV-1 infection treated with combination antiretroviral therapy containing tenofovir. Clinical Infectious Diseases, Vol. 46. pp. 1299-1309.

Weiser, B. and Philpott, S. and Klimkait, T. and Burger, H. and Kitchen, C. and Bürgisser, P. and Gorgievski, M. and Perrin, L. and Piffaretti, J. C. and Ledergerber, B. and Swiss, HIV Cohort Study. (2008) HIV-1 coreceptor usage and CXCR4-specific viral load predict clinical disease progression during combination antiretroviral therapy. AIDS, Vol. 22. pp. 469-479.

Louvel, S. and Battegay, M. and Vernazza, P. and Bregenzer, T. and Klimkait, T. and Hamy, F. and Swiss, HIV Cohort Study. (2008) Detection of drug-resistant HIV minorities in clinical specimens and therapy failure. HIV medicine, Vol. 9. pp. 133-141.

Tschudin, S. and Steimann, S. and Bitzer, J. and Hösli, I. and Holzgreve, W. and Elzi, L. and Klimkait, T. and Rudin, C. and Battegay, M. and De Geyter, C.. (2008) Round-table multidisciplinary counselling of couples with HIV prior to assisted reproduction. Reproductive biomedicine online, Vol. 17, H. 2. pp. 167-174.