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Niko Beerenwinkel

Department of Biosystems Science and Engineering

70H-index
497Paper Count
2.4WCitation Count
Published Papers 136
Publication Date
A tumor profiling resource for ovarian cancer: insights into chemotherapy-driven heterogeneity and personalized treatment strategy
err2026-07-13
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errFrancis Jacob; Rebekka Wegmann; Joanna Ficek-Pascual; Ulrike Lischetti; Jack Kuipers; Stéphane Chevrier; Michael Prummer; Nora C. Toussaint; Ilaria Alborelli; Ricardo Coelho; Ruben Casanova; Sandra Goetze; Gabriele Gut; Monica-Andreea Baciu-Drăgan; Anne Bertolini; Ximena Bonilla; Jon Brugger; Magdalena M. Brune; Byron Calgua; Stefanie Engler; Cinzia Esposito; Pedro F. Ferreira; Andrea Jacobs; Flavio C. Lombardo; Paola Malsot; Julien Mena; Nicola Miglino; Emanuela S. Milani; Jacobo Sarabia Del Castillo; Sujana Sivapatham; Bettina A. Sobottka-Brillout; Tanmay Tanna; Tibor A. Zwimpfer; Rudolf Aebersold; Marina Bacac; Niko Beerenwinkel; Christian Beisel; Bernd Bodenmiller; Viktor H. Koelzer; Kjong-Van Lehmann; Mitchell P. Levesque; Holger Moch; Simone Muenst; Lucas Pelkmans; Markus G. Manz; Gunnar Rätsch; Franziska Singer; Berend Snijder; Alexandre P. A. Theocharides; Markus Tolnay; Andreas Wicki; Bernd Wollscheid; Viola Heinzelmann-Schwarz
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Wastewater-based sequencing of respiratory syncytial virus to investigate lineage dynamics and antigenic site mutations: a retrospective genomic epidemiology study
err2026-06-11
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errJolinda de Korne-Elenbaas; Auguste Rimaite; Ivan Topolsky; David Dreifuss; Charlyne Bürki; Lara Fuhrmann; Louis du Plessis; William J Fitzsimmons; Emily E Bendall; Tanja Stadler; Niko Beerenwinkel; Timothy R Julian
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Unifying non-Markovian dynamics and agent heterogeneity in scalable stochastic networks
err2026-03-02
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errAurélien Pélissier; Miroslav Phan; Didier Le Bail; Niko Beerenwinkel; María Rodríguez Martínez
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Generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings
err2026-01-19
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errDiane Duroux; Paul P Meyer; Giovanni Visoná; Niko Beerenwinkel
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SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities
err2026-01-12
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errViorel Munteanu; Michael A. Saldana; David Dreifuss; Wenhao O. Ouyang; Jannatul Ferdous; Fatemeh Mohebbi; Jessica Schlueter Roseberry; Dumitru Ciorba; Viorel Bostan; Victor Gordeev; Nicolae Drabcinski; Justin Maine Su; Nadiia Kasianchuk; Nitesh Kumar Sharma; Sergey Knyazev; Eva Aßmann; Andrei Lobiuc; Mihai Covasa; Keith A. Crandall; Nicholas C. Wu; Christopher E. Mason; Braden T. Tierney; Alexander G. Lucaci; Roel A. Ophoff; Cynthia Gibas; Piotr Rzymski; Pavel Skums; Helena Solo-Gabriele; Beerenwinkel Niko; Alex Zelikovsky; Martin Hölzer; Adam Smith; Serghei Mangul
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mhn : a Python package for analyzing cancer progression with Mutual Hazard Networks
err2026-01-01
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errVocht, Stefan; Hu, Yanren Linda; Losch, Andreas; Rupp, Kevin; Wettig, Tilo; Grasedyck, Lars; Beerenwinkel, Niko; Spang, Rainer; Schill, Rudolf
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Ovarian cancer metastasis to the human omentum disrupts organ homeostasis and induces fundamental tissue reprogramming
err2025-12-16
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errUlrike Lischetti; Ching-Yeu Liang; Matteo Carrara; Ricardo Coelho; Antoine Hanns; Flavio Lombardo; Arthur Dondi; Sandra Goetze; Michal Hensler; Christian Kurzeder; Céline Montavon; Jitka Fucikova; Franziska Singer; Niko Beerenwinkel; Christian Beisel; Viola Heinzelmann-Schwarz; Francis Jacob
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A recurrent adaptive mutation in the transmembrane 2B protein of an insect picorna-like virus in a nonnative host
err2025-12-01
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PREAI
errLezcano, Oscar M.; Fuhrmann, Lara; Bos, Reinder T.; Wang, Haitao; Stevens, Milou; Beerenwinkel, Niko; Huynen, Martijn A.; van Rij, Ronald P.
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DelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data
err2025-08-29
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errSenbai Kang; Nico Borgsmüller; Monica Valecha; Magda Markowska; Jack Kuipers; Niko Beerenwinkel; David Posada; Ewa Szczurek
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Characterizing influenza A virus lineages and clinically relevant mutations through high-coverage wastewater sequencing
err2025-08-21
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PREAI
errAnika John; Seju Kang; Lara Fuhrmann; Ivan Topolsky; Christopher Kent; Joshua Quick; Tanja Stadler; Timothy R. Julian; Niko Beerenwinkel
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Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding
err2025-08-12
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errDavid Dreifuss; Jana S. Huisman; Johannes C. Rusch; Lea Caduff; Pravin Ganesanandamoorthy; Alexander J. Devaux; Charles Gan; Tanja Stadler; Tamar Kohn; Christoph Ort; Niko Beerenwinkel; Timothy R. Julian
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Publisher Correction: Feasibility of multiomics tumor profiling for guiding treatment of melanoma
err2025-08-01
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errNicola Miglino; Nora C. Toussaint; Alexander Ring; Ximena Bonilla; Marina Tusup; Benedict Gosztonyi; Tarun Mehra; Gabriele Gut; Francis Jacob; Stephane Chevrier; Kjong-Van Lehmann; Ruben Casanova; Andrea Jacobs; Sujana Sivapatham; Laura Boos; Parisa Rahimzadeh; Manuel Schuerch; Bettina Sobottka; Natalia Chicherova; Shuqing Yu; Rebekka Wegmann; Julien Mena; Emanuela S. Milani; Sandra Goetze; Cinzia Esposito; Jacobo Sarabia del Castillo; Anja L. Frei; Marta Nowak; Anja Irmisch; Jack Kuipers; Monica-Andreea Baciu-Drăgan; Pedro F. Ferreira; Franziska Singer; Anne Bertolini; Michael Prummer; Ulrike Lischetti; Rudolf Aebersold; Marina Bacac; Gerd Maass; Holger Moch; Michael Weller; Alexandre P. A. Theocharides; Markus G. Manz; Niko Beerenwinkel; Christian Beisel; Lucas Pelkmans; Berend Snijder; Bernd Wollscheid; Viola Heinzelmann; Bernd Bodenmiller; Mitchell P. Levesque; Viktor H. Koelzer; Gunnar Rätsch; Reinhard Dummer; Andreas Wicki
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Bayesian inference of fitness landscapes via tree-structured branching processes
err2025-07-01
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errLuo, Xiang Ge; Kuipers, Jack; Rupp, Kevin; Takahashi, Koichi; Beerenwinkel, Niko
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Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies
err2025-04-30
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errBayer, Fritz; Roncador, Marco; Moffa, Giusi; Morita, Kiyomi; Takahashi, Koichi; Beerenwinkel, Niko; Kuipers, Jack
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Assessing different next-generation sequencing technologies for wastewater-based epidemiology
err2024-12-01
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errJohn, Anika; Dreifuss, David; Kang, Seju; Bratus-Neuenschwander, Anna; Zajac, Natalia; Topolsky, Ivan; Dondi, Arthur; Aquino, Catharine; Julian, Timothy R.; Beerenwinkel, Niko
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MDS-AML Aggregative Risk Classification System ( MARCS ): A Novel, Enhanced Risk Stratification System Derived from the Combined Unsupervised Analysis of 7,480 MDS and AML Patients
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IF23.1
err2024-11-05
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PREAI
errRoncador, Marco; Bayer, Fritz; Deuel, Jeremy W.; Kuipers, Jack; Manz, Markus G.; Boettcher, Steffen; Beerenwinkel, Niko; Balabanov, Stefan
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V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation
err2024-09-30
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errFuhrmann, Lara; Jablonski, Kim Philipp; Topolsky, Ivan; Batavia, Aashil A.; Borgsmueller, Nico; Baykal, Pelin Icer; Carrara, Matteo; Chen, Chaoran; Dondi, Arthur; Dragan, Monica; Dreifuss, David; John, Anika; Langer, Benjamin; Okoniewski, Michal; du Plessis, Louis; Schmitt, Uwe; Singer, Franziska; Stadler, Tanja; Beerenwinkel, Niko
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Genomic reproducibility in the bioinformatics era
err2024-08-09
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errOAAI
errBaykal, Pelin Icer; Labaj, Pawel Piotr; Markowetz, Florian; Schriml, Lynn M.; Stekhoven, Daniel J.; Mangul, Serghei; Beerenwinkel, Niko
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