Niko Beerenwinkel
Swiss Institute of Bioinformatics
382 Papers
1K Citations
Niko Beerenwinkel is an academic researcher from Swiss Institute of Bioinformatics. The author has contributed to research in topics: Biology & Population. The author has an hindex of 56, co-authored 294 publications. Previous affiliations of Niko Beerenwinkel include ETH Zurich & Max Planck Society.
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Papers
Beyond Normal: On the Evaluation of Mutual Information Estimators
TL;DR: In this article , the authors show how to construct a diverse family of distributions with known ground-truth mutual information and propose a language-independent benchmarking platform for mutual information estimators, and discuss the general applicability and limitations of classical and neural estimators in settings involving high dimensions, sparse interactions, long-tailed distributions, and high mutual information.
ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma.
Ossia M. Eichhoff,Corinne Isabelle Stoffel,Jan Käsler,L. Briker,Patrick Turko,Gergely Karsai,Nina Zila,Verena Paulitschke,Phil F. Cheng,Alexander Leitner,Andrea Bileck,Nicola Zamboni,Anja Irmisch,Zsolt Balázs,Aizhan Tastanova,Susana Pascoal,Pål Johansen,Julien Mena,Alaa Othman,Vasanthi S. Viswanathan,Judith Wenzina,A. Aloia,Annalisa Saltari,Andreas Dzung,Rudolf Aebersold,Melike Ak,Faisal S. Al-Quaddoomi,Silvana Iuliana Albert,Jonas B Albinus,Ilaria Alborelli,Sonali Andani,Per-Olof Attinger,Marina Bacac,Daniel Baumhoer,Beatrice Beck-Schimmer,Niko Beerenwinkel,Christian Beisel,Lara Bernasconi,Annette Bertolini,Bernd Bodenmiller,Ximena Bonilla,Lars Bosshard,Byron Calgua,Ruben Casanova,Stéphane Chevrier,Natalia Chicherova,Ricardo Coelho,Maya D’Costa,Esther Danenberg,Natalie R. Davidson,Monica-Andreea Dragan,Stefanie Engler,Martin Erkens,Katja Eschbach,Cinzia Esposito,André Fedier,Pedro Ferreira,Joanna Ficek,Anja Frei,Bruno S. Frey,Sandra Goetze,Linda Grob,Gabriele Gut,Detlef Günther,Martina Haberecker,Pirmin Haeuptle,Viola Heinzelmann-Schwarz,Sylvia Herter,René Holtackers,Tamara Huesser,Alexander Immer,Francis Jacob,Andrea Jacobs,Tim Jaeger,Katharina Jahn,Alva Rani James,Philip Jermann,André Kahles,Abdullah Kahraman,Viktor H. Koelzer,Werner Kuebler,Jack Kuipers,Christian P. Kunze,Christian Kurzeder,Kjong-Van Lehmann,Mitchell P. Levesque,Ulrike Lischetti,Sebastian Lugert,Gerd Maass,Markus G. Manz,Philipp Markolin,Martin Mehnert,Julian Metzler,Nicola Miglino,Emanuela S. Milani,Holger Moch,Simone Muenst,Riccardo Murri,Charlotte K.Y. Ng,Stefan Nicolet,Marta Nowak,Mónica Núñez López,Patrick Ga Pedrioli,Lucas Pelkmans,Salvatore Piscuoglio,Michael Prummer,Natalie Rimmer,Mathilde Ritter,Christian Rommel,M. L. Rosano-González,Gunnar Rätsch,Natascha Santacroce,Jacobo Sarabia del Castillo,Ramona Schlenker,Petra C. Schwalie,Severin Schwan,Tobias Schär,Gabriela Senti,Wen-Chuan Shao,Franziska Singer,Sujana Sivapatham,Bettina Sobottka,Vipin T. Sreedharan,Stefan G. Stark,Daniel J. Stekhoven,Tanmay Tanna,Alexandre Theocharides,Tinu Thomas,Markus Tolnay,Vinko Tosevski,Nora C. Toussaint,Mustafa Anil Tuncel,Marina Tusup,Audrey van Drogen,Marcus Vetter,Tatjana Vlajnic,Sandra Weber,Walter P. Weber,Rebekka Wegmann,Michael Weller,Fabian Wendt,Norbert Wey,Andreas Wicki,Mattheus H.E. Wildschut,Bernd Wollscheid,Shuqing Yu,Johanna S Ziegler,Marc Zimmermann,Martin Zoche,Gregor Zuend,Michael Krauthammer,Stuart L. Schreiber,Thorsten Hornemann,Martin Distel,Berend Snijder,Reinhard Dummer +155 more
TL;DR: In this article , the authors used multi-omics analyses to reveal that NRAS-mutated melanoma cells adopt a mesenchymal phenotype with a quiescent metabolic program to resist cellular stress induced by MEK inhibition.
Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection.
Louisa A Carlisle,Teja Turk,Katharina Kusejko,Karin J. Metzner,Christine Leemann,Corinne D. Schenkel,Nadine Bachmann,Susana Posada,Niko Beerenwinkel,Niko Beerenwinkel,Jürg Böni,Sabine Yerly,Thomas Klimkait,Matthieu Perreau,Dominique L Braun,Andri Rauch,Alexandra Calmy,Matthias Cavassini,Manuel Battegay,Pietro Vernazza,Enos Bernasconi,Huldrych F. Günthard,Roger D. Kouyos +22 more
TL;DR: In this article, the average pairwise diversity calculated using NGS sequences provided a more exact prediction of the time since infection and classification of infection recency (<1 year after infection, compared with the fraction of ambiguous nucleotides.
Markov models for accumulating mutations
Niko Beerenwinkel,Seth Sullivant +1 more
TL;DR: In this article, the authors introduce and analyze a waiting time model for the accumulation of genetic changes, defined by a partially ordered set of mutations and by the rate of fixation of each mutation.
COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
TL;DR: Comparing the joint phylogeny of SNVs and CNAs from targeted scDNAseq data detected clonal CNAs that could be orthogonally validated with bulk data, in addition to subclonal ones that require single-cell resolution, some of which point toward convergent evolution.