Huber, Michael

Zeeb, Marius; Frischknecht, Paul; Huber, Michael; Schenkel, Corinne D; Neumann, Kathrin; Leeman, Christine; Notter, Julia; Rauch, Andri; Stöckle, Marcel; Cavassini, Matthias; Bernasconi, Enos; Braun, Dominique L; Günthard, Huldrych F; Metzner, Karin J; Kouyos, Roger D (2024). Genetic diversity from proviral DNA as a proxy for time since HIV-1 infection. The journal of infectious diseases, 230(3), e631-e636. Oxford University Press 10.1093/infdis/jiae149

Fernbach, Sonja; Mair, Nina K; Abela, Irene A; Groen, Kevin; Kuratli, Roger; Lork, Marie; Thorball, Christian W; Bernasconi, Enos; Filippidis, Paraskevas; Leuzinger, Karoline; Notter, Julia; Rauch, Andri; Hirsch, Hans H; Huber, Michael; Günthard, Huldrych F; Fellay, Jacques; Kouyos, Roger D; Hale, Benjamin G (2024). Loss of tolerance precedes triggering and lifelong persistence of pathogenic type I interferon autoantibodies. Journal of experimental medicine, 221(9) Rockefeller University Press 10.1084/jem.20240365

Abela, Irene A; Hauser, Anthony; Schwarzmüller, Magdalena; Pasin, Chloé; Kusejko, Katharina; Epp, Selina; Cavassini, Matthias; Battegay, Manuel; Rauch, Andri; Calmy, Alexandra; Notter, Julia; Bernasconi, Enos; Fux, Christoph A; Leuzinger, Karoline; Perreau, Matthieu; Ramette, Alban; Gottschalk, Jochen; Schindler, Eméry; Wepf, Alexander; Marconato, Maddalena; ... (2024). Deciphering factors linked with reduced SARS-CoV-2 susceptibility in the Swiss HIV Cohort Study. The journal of infectious diseases, 230(2), e292-e304. Oxford University Press 10.1093/infdis/jiae002

Lopez-Labrador, F Xavier; Huber, Michael; Sidorov, Igor A; Brown, Julianne R; Cuypers, Lize; Laenen, Lies; Vanmechelen, Bert; Maes, Piet; Fischer, Nicole; Pichler, Ian; Storey, Nathaniel; Atkinson, Laura; Schmutz, Stefan; Kufner, Verena; van Boheemen, Sander; Mulders, Claudia E; Grundhoff, Adam; Blümke, Patrick; Robitaille, Alexis; Cinek, Ondrej; ... (2024). Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics. Journal of clinical virology, 173(105695), p. 105695. Elsevier 10.1016/j.jcv.2024.105695

Neuner-Jehle, Nadia; Zeeb, Marius; Thorball, Christian W; Fellay, Jacques; Metzner, Karin J; Frischknecht, Paul; Neumann, Kathrin; Leeman, Christine; Rauch, Andri; Stöckle, Marcel; Huber, Michael; Perreau, Matthieu; Bernasconi, Enos; Notter, Julia; Hoffmann, Matthias; Leuzinger, Karoline; Günthard, Huldrych F; Pasin, Chloé; Kouyos, Roger D (2024). Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen. PLoS pathogens, 20(8), e1012385. Public Library of Science 10.1371/journal.ppat.1012385

Wegner, Fanny; Cabrera-Gil, Blanca; Tanguy, Araud; Beckmann, Christiane; Beerenwinkel, Niko; Bertelli, Claire; Carrara, Matteo; Cerutti, Lorenzo; Chen, Chaoran; Cordey, Samuel; Dumoulin, Alexis; du Plessis, Louis; Friedli, Marc; Gerth, Yannick; Greub, Gilbert; Härri, Adrian; Hirsch, Hans; Howald, Cedric; Huber, Michael; Imhof, Alexander; ... (2024). How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort. Microbiology spectrum, 12(5), e0362823. American Society for Microbiology 10.1128/spectrum.03628-23

Zeeb, Marius; Pasin, Chloé; Cavassini, Matthias; Bieler-Aeschlimann, Mélanie; Frischknecht, Paul; Kusejko, Katharina; Fellay, Jacques; Blanquart, François; Metzner, Karin J; Neumann, Kathrin; Jörimann, Lisa; Tschumi, Jasmin; Bernasconi, Enos; Huber, Michael; Kovari, Helen; Leuzinger, Karoline; Notter, Julia; Perreau, Matthieu; Rauch, Andri; Ramette, Alban; ... (2024). Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study. Brain Communications, 6(4) Oxford University Press 10.1093/braincomms/fcae188

Kristen-Burmann, Claudia; Rogger, Peter; Berenguer Veiga, Inês; Riebesehl, Stefanie; Rappe, Julie; Ebert, Nadine; Sautter, Carmen A; Kelly, Jenna N; Stalder, Hanspeter; Ehmann, Rosina; Huber, Michael; Posthaus, Horst; Ruggli, Nicolas; Thiel, Volker; Tekes, Gergely (2023). Reverse Genetic Assessment of the Roles Played by the Spike Protein and ORF3 in Porcine Epidemic Diarrhea Virus Pathogenicity. Journal of virology, 97(7), e0196422. American Society for Microbiology 10.1128/jvi.01964-22

Neves, Aitana; Walther, Daniel; Martin-Campos, Trinidad; Barbie, Valerie; Bertelli, Claire; Blanc, Dominique; Bouchet, Gérard; Erard, Frédéric; Greub, Gilbert; Hirsch, Hans H; Huber, Michael; Kaiser, Laurent; Leib, Stephen L; Leuzinger, Karoline; Lazarevic, Vladimir; Mäusezahl, Mirjam; Molina, Jorge; Neher, Richard A; Perreten, Vincent; Ramette, Alban; ... (2023). The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata. Microbial genomics, 9(5) Microbiology Society 10.1099/mgen.0.001001

Balakrishna, Suraj; Loosli, Tom; Zaheri, Maryam; Frischknecht, Paul; Huber, Michael; Kusejko, Katharina; Yerly, Sabine; Leuzinger, Karoline; Perreau, Matthieu; Ramette, Alban; Wymant, Chris; Fraser, Christophe; Kellam, Paul; Gall, Astrid; Hirsch, Hans H; Stoeckle, Marcel; Rauch, Andri; Cavassini, Matthias; Bernasconi, Enos; Notter, Julia; ... (2023). Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1. The journal of antimicrobial chemotherapy, 78(3), pp. 656-664. Oxford University Press 10.1093/jac/dkac430

Labarile, Marco; Loosli, Tom; Zeeb, Marius; Kusejko, Katharina; Huber, Michael; Hirsch, Hans H; Perreau, Matthieu; Ramette, Alban; Yerly, Sabine; Cavassini, Matthias; Battegay, Manuel; Rauch, Andri; Calmy, Alexandra; Notter, Julia; Bernasconi, Enos; Fux, Christoph; Günthard, Huldrych F; Pasin, Chloé; Kouyos, Roger D (2023). Quantifying and predicting ongoing Human Immunodeficiency Virus Type 1 (HIV-1) transmission dynamics in Switzerland using a distance-based clustering approach. The journal of infectious diseases, 227(4), pp. 554-564. Oxford University Press 10.1093/infdis/jiac457

Nadeau, Sarah A; Vaughan, Timothy G; Beckmann, Christiane; Topolsky, Ivan; Chen, Chaoran; Hodcroft, Emma; Schär, Tobias; Nissen, Ina; Santacroce, Natascha; Burcklen, Elodie; Ferreira, Pedro; Jablonski, Kim Philipp; Posada-Céspedes, Susana; Capece, Vincenzo; Seidel, Sophie; Santamaria de Souza, Noemi; Martinez-Gomez, Julia M; Cheng, Phil; Bosshard, Philipp P; Levesque, Mitchell P; ... (2023). Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Science translational medicine, 15(680), eabn7979. American Association for the Advancement of Science 10.1126/scitranslmed.abn7979

Chaudron, Sandra E; Leemann, Christine; Kusejko, Katharina; Nguyen, Huyen; Tschumi, Nadine; Marzel, Alex; Huber, Michael; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Ramette, Alban; Hirsch, Hans H; Rauch, Andri; Calmy, Alexandra; Vernazza, Pietro; Bernasconi, Enos; Cavassini, Matthias; Metzner, Karin J; Kouyos, Roger D; ... (2022). A systematic molecular epidemiology screen reveals numerous HIV-1 superinfections in the Swiss HIV Cohort Study. The journal of infectious diseases, 226(7), pp. 1256-1266. Oxford University Press 10.1093/infdis/jiac166

Kusejko, Katharina; Tschumi, Nadine; Chaudron, Sandra E; Nguyen, Huyen; Battegay, Manuel; Bernasconi, Enos; Böni, Jürg; Huber, Michael; Calmy, Alexandra; Cavassini, Matthias; Egle, Alexander; Grabmeier-Pfistershammer, Katharina; Haas, Bernhard; Hirsch, Hans; Klimkait, Thomas; Öllinger, Angela; Perreau, Matthieu; Ramette, Alban; Flury, Baharak Babouee; Sarcletti, Mario; ... (2022). Similar but different: Integrated phylogenetic analysis of Austrian and Swiss HIV-1 sequences reveal differences in transmission patterns of the local HIV-1 epidemics. Journal of acquired immune deficiency syndromes, 90(4), e4-e12. Wolters Kluwer Health 10.1097/QAI.0000000000002949

Nguyen, Huyen; Hampel, Benjamin; Nuñez, David Garcia; Battegay, Manuel; Hachfeld, Anna; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Vernazza, Pietro; Fellay, Jacques; Rudolph, Hannes; Huber, Michael; Leuzinger, Karoline; Perreau, Matthieu; Scherrer, Alexandra; Ramette, Alban Nicolas; Yerly, Sabine; Günthard, Huldrych F; Kouyos, Roger D and Kusejko, Katharina (2022). Correction to: Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group. Clinical infectious diseases, 74(12), p. 2266. Oxford University Press 10.1093/cid/ciac242

Nguyen, Huyen; Hampel, Benjamin; Nuñez, David Garcia; Battegay, Manuel; Hachfeld, Anna; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Vernazza, Pietro; Fellay, Jacques; Rudolph, Hannes; Huber, Michael; Leuzinger, Karoline; Perreau, Matthieu; Scherrer, Alexandra; Ramette, Alban Nicolas; Yerly, Sabine; Günthard, Huldrych F; Kouyos, Roger D and Kusejko, Katharina (2022). Identifying and Characterizing Trans women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group. Clinical infectious diseases, 74(8), pp. 1468-1475. Oxford University Press 10.1093/cid/ciab628

Scherrer, Alexandra U; Traytel, Anna; Braun, Dominique L; Calmy, Alexandra; Battegay, Manuel; Cavassini, Matthias; Furrer, Hansjakob; Schmid, Patrick; Bernasconi, Enos; Stoeckle, Marcel; Kahlert, Christian; Trkola, Alexandra; Kouyos, Roger D; Tarr, Philip; Marzolini, Catia; Wandeler, Gilles; Fellay, Jacques; Bucher, Heiner; Yerly, Sabine; Suter, Franziska; ... (2022). Cohort Profile Update: The Swiss HIV Cohort Study (SHCS). International journal of epidemiology, 51(1), 33-34j. Oxford University Press 10.1093/ije/dyab141

Wegner, Fanny; Roloff, Tim; Huber, Michael; Cordey, Samuel; Ramette, Alban; Gerth, Yannick; Bertelli, Claire; Stange, Madlen; Seth-Smith, Helena M B; Mari, Alfredo; Leuzinger, Karoline; Cerutti, Lorenzo; Harshman, Keith; Xenarios, Ioannis; Le Mercier, Philippe; Bittel, Pascal; Neuenschwander, Stefan; Opota, Onya; Fuchs, Jonas; Panning, Marcus; ... (2022). External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories. Journal of clinical microbiology, 60(1), e0169821. American Society for Microbiology 10.1128/JCM.01698-21

Duran Ramirez, Jessy J; Ballouz, Tala; Nguyen, Huyen; Kusejko, Katharina; Chaudron, Sandra E; Huber, Michael; Hirsch, Hans H; Perreau, Matthieu; Ramette, Alban; Yerly, Sabine; Cavassini, Matthias; Stöckle, Marcel; Furrer, Hansjakob; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D (2022). Increasing Frequency and Transmission of HIV-1 Non-B Subtypes among Men Who Have Sex with Men in the Swiss HIV Cohort Study. The journal of infectious diseases, 225(2), pp. 306-316. Oxford University Press 10.1093/infdis/jiab360

Pyngottu, Ashima; Scherrer, Alexandra U; Kouyos, Roger; Huber, Michael; Hirsch, Hans; Perreau, Matthieu; Yerly, Sabine; Calmy, Alexandra; Cavassini, Matthias; Stöckle, Marcel; Furrer, Hansjakob; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F (2021). Predictors of virological failure and time to viral suppression of first line integrase inhibitor based antiretroviral treatment. Clinical infectious diseases, 73(7), e2134-e2141. Oxford University Press 10.1093/cid/ciaa1614

Vavassori, Stefano; Chou, Janet; Faletti, Laura Eva; Haunerdinger, Veronika; Opitz, Lennart; Joset, Pascal; Fraser, Christopher J; Prader, Seraina; Gao, Xianfei; Schuch, Luise A; Wagner, Matias; Hoefele, Julia; Maccari, Maria Elena; Zhu, Ying; Elakis, George; Gabbett, Michael T; Forstner, Maria; Omran, Heymut; Kaiser, Thomas; Kessler, Christina; ... (2021). Multisystem inflammation and susceptibility to viral infections in human ZNFX1 deficiency. Journal of allergy and clinical immunology, 148(2), pp. 381-393. Elsevier 10.1016/j.jaci.2021.03.045

Goncalves Cabecinhas, Ana Rita; Roloff, Tim; Stange, Madlen; Bertelli, Claire; Huber, Michael; Ramette, Alban; Chen, Chaoran; Nadeau, Sarah; Gerth, Yannick; Yerly, Sabine; Opota, Onya; Pillonel, Trestan; Schuster, Tobias; Metzger, Cesar M J A; Sieber, Jonas; Bel, Michael; Wohlwend, Nadia; Baumann, Christian; Koch, Michel C.; Bittel, Pascal; ... (2021). SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms, 9(4), p. 677. MDPI 10.3390/microorganisms9040677

Carlisle, Louisa A; Turk, Teja; Metzner, Karin J; Mbunkah, Herbert A; Shah, Cyril; Böni, Jürg; Huber, Michael; Braun, Dominique L; Fehr, Jan; Salazar-Vizcaya, Luisa; Rauch, Andri; Yerly, Sabine; Nguyen, Aude; Cavassini, Matthias; Stoeckle, Marcel; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D (2020). HCV Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection. Viruses, 12(11) MDPI 10.3390/v12111241

Junier, Thomas; Huber, Michael; Schmutz, Stefan; Kufner, Verena; Zagordi, Osvaldo; Neuenschwander, Stefan; Ramette, Alban; Kubacki, Jakub; Bachofen, Claudia; Qi, Weihong; Laubscher, Florian; Cordey, Samuel; Kaiser, Laurent; Beuret, Christian; Barbié, Valérie; Fellay, Jacques; Lebrand, Aitana (2019). Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial. Genes, 10(9) MDPI 10.3390/genes10090655

Kouyos, Roger D; Rusert, Peter; Kadelka, Claus; Huber, Michael; Marzel, Alex; Ebner, Hanna; Schanz, Merle; Liechti, Thomas; Friedrich, Nikolas; Braun, Dominique L; Scherrer, Alexandra U; Weber, Jacqueline; Uhr, Therese; Baumann, Nicolas S; Leemann, Christine; Kuster, Herbert; Chave, Jean-Philippe; Cavassini, Matthias; Bernasconi, Enos; Hoffmann, Matthias; ... (2018). Tracing HIV-1 strains that imprint broadly neutralizing antibody responses. Nature, 561(7723), pp. 406-410. Macmillan Journals Ltd. 10.1038/s41586-018-0517-0

Kadelka, Claus; Liechti, Thomas; Ebner, Hanna; Schanz, Merle; Rusert, Peter; Friedrich, Nikolas; Stiegeler, Emanuel; Braun, Dominique L; Huber, Michael; Scherrer, Alexandra U; Weber, Jacqueline; Uhr, Therese; Kuster, Herbert; Misselwitz, Benjamin; Cavassini, Matthias; Bernasconi, Enos; Hoffmann, Matthias; Calmy, Alexandra; Battegay, Manuel; Rauch, Andri; ... (2018). Distinct, IgG1-driven antibody response landscapes demarcate individuals with broadly HIV-1 neutralizing activity. Journal of experimental medicine, 215(6), pp. 1589-1608. Rockefeller University Press 10.1084/jem.20180246

Rusert, Peter; Kouyos, Roger D; Kadelka, Claus; Ebner, Hanna; Schanz, Merle; Huber, Michael; Braun, Dominique L; Hozé, Nathanael; Scherrer, Alexandra; Magnus, Carsten; Weber, Jacqueline; Uhr, Therese; Cippa, Valentina; Thorball, Christian W; Kuster, Herbert; Cavassini, Matthias; Bernasconi, Enos; Hoffmann, Matthias; Calmy, Alexandra; Battegay, Manuel; ... (2016). Determinants of HIV-1 broadly neutralizing antibody induction. Nature medicine, 22(11), pp. 1260-1267. Nature Publishing Group 10.1038/nm.4187

Weigelt-Schlesinger, Yvonne; Huber, Michael (2009). Der Ball, mein Freund. Ausgewählte Übungen und Spielformen. Bewegungserziehung, 63(4), pp. 18-22. Purkersdorf: Hollinek