Niko Beerenwinkel
Niko Beerenwinkel
Professor of Computational Biology, ETH Zurich
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ROCR: visualizing classifier performance in R
T Sing, O Sander, N Beerenwinkel, T Lengauer
Bioinformatics 21 (20), 3940-3941, 2005
Comparative lesion sequencing provides insights into tumor evolution
S Jones, W Chen, G Parmigiani, F Diehl, N Beerenwinkel, T Antal, ...
Proceedings of the National Academy of Sciences 105 (11), 4283-4288, 2008
Genetic progression and the waiting time to cancer
N Beerenwinkel, T Antal, D Dingli, A Traulsen, KW Kinzler, VE Velculescu, ...
PLoS Computational Biology 3 (11), e225, 2007
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes
N Beerenwinkel, M Däumer, M Oette, K Korn, D Hoffmann, R Kaiser, ...
Nucleic Acids Research 31 (13), 3850-3855, 2003
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype
N Beerenwinkel, B Schmidt, H Walter, R Kaiser, T Lengauer, D Hoffmann, ...
Proceedings of the National Academy of Sciences 99 (12), 8271-8276, 2002
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data
O Zagordi, A Bhattacharya, N Eriksson, N Beerenwinkel
BMC Bioinformatics 12 (1), 119, 2011
Viral population estimation using pyrosequencing
N Eriksson, L Pachter, Y Mitsuya, SY Rhee, C Wang, B Gharizadeh, ...
PLoS Comput Biol 4 (5), e1000074, 2008
Cancer evolution: mathematical models and computational inference
N Beerenwinkel, RF Schwarz, M Gerstung, F Markowetz
Systematic Biology 64 (1), e1-e25, 2015
Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
O Zagordi, R Klein, M Däumer, N Beerenwinkel
Nucleic Acids Research 38 (21), 7400-7409, 2010
Neutrophils escort circulating tumour cells to enable cell cycle progression
BM Szczerba, F Castro-Giner, M Vetter, I Krol, S Gkountela, J Landin, ...
Nature 566 (7745), 553-557, 2019
Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data
N Beerenwinkel, HF Günthard, V Roth, KJ Metzner
Frontiers in Microbiology 3, 329, 2012
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
T Sing, AJ Low, N Beerenwinkel, O Sander, PK Cheung, FS Domingues, ...
Antiviral Therapy 12 (7), 1097, 2007
Reliable detection of subclonal single-nucleotide variants in tumour cell populations
M Gerstung, C Beisel, M Rechsteiner, P Wild, P Schraml, H Moch, ...
Nature Communications 3, 811, 2012
Ultra-deep sequencing for the analysis of viral populations
N Beerenwinkel, O Zagordi
Current Opinion in Virology 1 (5), 413-418, 2011
Learning multiple evolutionary pathways from cross-sectional data
N Beerenwinkel, J Rahnenführer, M Däumer, D Hoffmann, R Kaiser, ...
Journal of Computational Biology 12 (6), 584-598, 2005
Tree inference for single-cell data
K Jahn, J Kuipers, N Beerenwinkel
Genome Biology 17 (1), 86, 2016
Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction
O Zagordi, L Geyrhofer, V Roth, N Beerenwinkel
Journal of Computational Biology 17 (3), 417-428, 2010
Computational methods for the design of effective therapies against drug resistant HIV strains
N Beerenwinkel, T Sing, T Lengauer, J Rahnenführer, K Roomp, ...
Bioinformatics 21 (21), 3943-3950, 2005
24 hours in the life of HIV-1 in a T cell line
P Mohammadi, S Desfarges, I Bartha, B Joos, N Zangger, M Munoz, ...
PLoS Pathog 9 (1), e1003161, 2013
Probabilistic inference of viral quasispecies subject to recombination
A Töpfer, O Zagordi, S Prabhakaran, V Roth, E Halperin, N Beerenwinkel
Journal of Computational Biology 20 (2), 113-123, 2013
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