Beerenwinkel, Niko

Egger, Matthias; Sauermann, Mamatha; Loosli, Tom; Hossmann, Stefanie; Riedo, Selma; Beerenwinkel, Niko; Jaquet, Antoine; Minga, Albert; Ross, Jeremy; Giandhari, Jennifer; Kouyos, Roger D; Lessells, Richard (2024). HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre study (DTG RESIST). BMJ open, 14(8) BMJ Publishing Group 10.1136/bmjopen-2024-085819

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

Zaika, Viktor; Prakash, Meher K; Cheng, Chih-Yuan; Schlander, Michael; Lang, Brian M; Beerenwinkel, Niko; Sonnenberg, Amnon; Krupka, Niklas; Misselwitz, Benjamin; Poleszczuk, Jan (2024). Optimal timing of a colonoscopy screening schedule depends on adenoma detection, adenoma risk, adherence to screening and the screening objective: A microsimulation study. PLoS ONE, 19(e0304374) Public Library of Science 10.1371/journal.pone.0304374

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

Lang, Brian M; Ledergerber, Martina; Jordi, Sebastian Bruno Ulrich; Krupka, Niklas; Biedermann, Luc; Schreiner, Philipp; Juillerat, Pascal; Wyss, Jacqueline; Vavricka, Stephan R; Zeitz, Jonas; von Känel, Roland; Rogler, Gerhard; Beerenwinkel, Niko; Misselwitz, Benjamin (2023). Because I'm happy - positive affect and its predictive value for future disease activity in patients with inflammatory bowel diseases: a retrospective cohort study. Therapeutic advances in gastroenterology, 16(17562848231179335), p. 17562848231179335. Sage 10.1177/17562848231179335

Srivatsa, Sumana; Montazeri, Hesam; Bianco, Gaia; Coto-Llerena, Mairene; Marinucci, Mattia; Ng, Charlotte K Y; Piscuoglio, Salvatore; Beerenwinkel, Niko (2022). Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nature communications, 13(1), p. 7748. Nature Publishing Group 10.1038/s41467-022-35378-z

Suter, Polina; Dazert, Eva; Kuipers, Jack; Ng, Charlotte K Y; Boldanova, Tuyana; Hall, Michael N; Heim, Markus H; Beerenwinkel, Niko (2022). Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS computational biology, 18(9), e1009767. Public Library of Science 10.1371/journal.pcbi.1009767

Bianco, Gaia; Coto-Llerena, Mairene; Gallon, John; Kancherla, Venkatesh; Taha-Mehlitz, Stephanie; Marinucci, Mattia; Konantz, Martina; Srivatsa, Sumana; Montazeri, Hesam; Panebianco, Federica; Tirunagaru, Vijaya G; De Menna, Marta; Paradiso, Viola; Ercan, Caner; Dahmani, Ahmed; Montaudon, Elodie; Beerenwinkel, Niko; Kruithof-de Julio, Marianna; Terracciano, Luigi M; Lengerke, Claudia; ... (2022). Author Correction: GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Communications biology, 5(1), p. 658. Springer Nature 10.1038/s42003-022-03612-5

Bianco, Gaia; Coto-Llerena, Mairene; Gallon, John; Kancherla, Venkatesh; Taha-Mehlitz, Stephanie; Marinucci, Mattia; Konantz, Martina; Srivatsa, Sumana; Montazeri, Hesam; Panebianco, Federica; Tirunagaru, Vijaya G; De Menna, Marta; Paradiso, Viola; Ercan, Caner; Dahmani, Ahmed; Montaudon, Elodie; Beerenwinkel, Niko; Kruithof-de Julio, Marianna; Terracciano, Luigi M; Lengerke, Claudia; ... (2022). GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Communications biology, 5(1), p. 373. Springer Nature 10.1038/s42003-022-03296-x

Chen, Chaoran; Nadeau, Sarah Ann; Topolsky, Ivan; Manceau, Marc; Huisman, Jana S; Jablonski, Kim Philipp; Fuhrmann, Lara; Dreifuss, David; Jahn, Katharina; Beckmann, Christiane; Redondo, Maurice; Noppen, Christoph; Risch, Lorenz; Risch, Martin; Wohlwend, Nadia; Kas, Sinem; Bodmer, Thomas; Roloff, Tim; Stange, Madlen; Egli, Adrian; ... (2021). Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland. Epidemics, 37, p. 100480. Elsevier 10.1016/j.epidem.2021.100480

Montazeri, Hesam; Coto-Llerena, Mairene; Bianco, Gaia; Zangene, Ehsan; Taha-Mehlitz, Stephanie; Paradiso, Viola; Srivatsa, Sumana; de Weck, Antoine; Roma, Guglielmo; Lanzafame, Manuela; Bolli, Martin; Beerenwinkel, Niko; von Flüe, Markus; Terracciano, Luigi M; Piscuoglio, Salvatore; Ng, Charlotte K Y (2021). Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens. Nucleic acids research, 49(15), pp. 8488-8504. Oxford University Press 10.1093/nar/gkab627

Dimitrakopoulos, Christos; Hindupur, Sravanth Kumar; Colombi, Marco; Liko, Dritan; Ng, Charlotte K Y; Piscuoglio, Salvatore; Behr, Jonas; Moore, Ariane L; Singer, Jochen; Ruscheweyh, Hans-Joachim; Matter, Matthias S; Mossmann, Dirk; Terracciano, Luigi M; Hall, Michael N; Beerenwinkel, Niko (2021). Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma. BMC Genomics, 22(1), p. 592. BioMed Central 10.1186/s12864-021-07876-9

Deibel, Ansgar; Deng, Lu; Cheng, Chih-Yuan; Schlander, Michael; Ran, Tao; Lang, Brian; Krupka, Niklas; Beerenwinkel, Niko; Rogler, Gerhard; Wiest, Reiner; Sonnenberg, Amnon; Poleszczuk, Jan; Misselwitz, Benjamin (2021). Evaluating key characteristics of ideal colorectal cancer screening modalities: the microsimulation approach. Gastrointestinal endoscopy, 94(2), 379-390.e7. Elsevier 10.1016/j.gie.2021.02.013

Irmisch, Anja; Bonilla, Ximena; Chevrier, Stéphane; Lehmann, Kjong-Van; Singer, Franziska; Toussaint, Nora C; Esposito, Cinzia; Mena, Julien; Milani, Emanuela S; Casanova, Ruben; Stekhoven, Daniel J; Wegmann, Rebekka; Jacob, Francis; Sobottka, Bettina; Goetze, Sandra; Kuipers, Jack; Sarabia Del Castillo, Jacobo; Prummer, Michael; Tuncel, Mustafa A; Menzel, Ulrike; ... (2021). The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer cell, 39(3), pp. 288-293. Cell Press 10.1016/j.ccell.2021.01.004

Ledergerber, Martina; Lang, Brian M; Heinrich, Henriette; Biedermann, Luc; Begré, Stefan; Zeitz, Jonas; Krupka, Niklas; Rickenbacher, Andreas; Turina, Matthias; Greuter, Thomas; Schreiner, Philipp; Roth, René; Siebenhüner, Alexander; Vavricka, Stephan R; Rogler, Gerhard; Beerenwinkel, Niko; Misselwitz, Benjamin (2021). Abdominal pain in patients with inflammatory bowel disease: association with single-nucleotide polymorphisms prevalent in irritable bowel syndrome and clinical management. BMC gastroenterology, 21(1), p. 53. BioMed Central 10.1186/s12876-021-01622-x

Hufsky, Franziska; Beerenwinkel, Niko; Meyer, Irmtraud M; Roux, Simon; Cook, Georgia May; Kinsella, Cormac M; Lamkiewicz, Kevin; Marquet, Mike; Nieuwenhuijse, David F; Olendraite, Ingrida; Paraskevopoulou, Sofia; Young, Francesca; Dijkman, Ronald; Ibrahim, Bashar; Kelly, Jenna; Le Mercier, Philippe; Marz, Manja; Ramette, Alban; Thiel, Volker (2020). The International Virus Bioinformatics Meeting 2020. Viruses, 12(12) MDPI 10.3390/v12121398

Wan, Chenjie; Bachmann, Nadine; Mitov, Venelin; Blanquart, François; Céspedes, Susana Posada; Turk, Teja; Neumann, Kathrin; Beerenwinkel, Niko; Bogojeska, Jasmina; Fellay, Jacques; Roth, Volker; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Battegay, Manuel; Walti, Laura; Calmy, Alexandra; Vernazza, Pietro; Bernasconi, Enos; ... (2020). Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART. Nature communications, 11(1), p. 5542. Nature Publishing Group 10.1038/s41467-020-19198-7

Thorball, Christian W; Borghesi, Alessandro; Bachmann, Nadine; Von Siebenthal, Chantal; Vongrad, Valentina; Turk, Teja; Neumann, Kathrin; Beerenwinkel, Niko; Bogojeska, Jasmina; Roth, Volker; Kok, Yik Lim; Parbhoo, Sonali; Wieser, Mario; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Battegay, Manuel; Rauch, Andri; Schmid, Patrick; ... (2020). Host genomics of the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. Journal of acquired immune deficiency syndromes, 85(4), pp. 517-524. Wolters Kluwer Health 10.1097/QAI.0000000000002473

Lang, Brian M.; Kuipers, Jack; Misselwitz, Benjamin; Beerenwinkel, Niko (2020). Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. PLoS computational biology, 16(2), e1007552. Public Library of Science 10.1371/journal.pcbi.1007552

Bachmann, Nadine; von Siebenthal, Chantal; Vongrad, Valentina; Turk, Teja; Neumann, Kathrin; Beerenwinkel, Niko; Bogojeska, Jasmina; Fellay, Jaques; Roth, Volker; Kok, Yik Lim; Thorball, Christian W; Borghesi, Alessandro; Parbhoo, Sonali; Wieser, Mario; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Battegay, Manuel; Rauch, Andri; ... (2019). Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nature communications, 10(1), pp. 1-11. Nature Publishing Group 10.1038/s41467-019-10884-9

Carlisle, Louisa A; Turk, Teja; Kusejko, Katharina; Metzner, Karin J; Leemann, Christine; Schenkel, Corinne; Bachmann, Nadine; Posada, Susana; Beerenwinkel, Niko; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Braun, Dominique L; Rauch, Andri; Calmy, Alexandra; Cavassini, Matthias; Battegay, Manuel; Vernazza, Pietro; Bernasconi, Enos; ... (2019). Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection. The journal of infectious diseases, 220(2), pp. 254-265. Oxford University Press 10.1093/infdis/jiz094

Di Giallonardo, Francesca; Zagordi, Osvaldo; Duport, Yannick; Leemann, Christine; Joos, Beda; Künzli-Gontarczyk, Marzanna; Bruggmann, Rémy; Beerenwinkel, Niko; Günthard, Huldrych F.; Metzner, Karin J. (2013). Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination. PLoS ONE, 8(9), e74249. Public Library of Science 10.1371/journal.pone.0074249

Beerenwinkel, Niko; Montazeri, Hesam; Schuhmacher, Heike; Knupfer, Patrick; von Wyl, Viktor; Furrer, Hansjakob; Battegay, Manuel; Hirschel, Bernard; Cavassini, Matthias; Vernazza, Pietro; Bernasconi, Enos; Yerly, Sabine; Böni, Jürg; Klimkait, Thomas; Cellerai, Cristina; Günthard, Huldrych F.; Vandamme, Anne-Mieke (2013). The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients. PLoS computational biology, 9(8), e1003203. Public Library of Science 10.1371/journal.pcbi.1003203