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Author Details

Niko Beerenwinkel
ETH Zurich
2002
210
50
PMIDPaper TitleJournal TitlePublished Year
36346321Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data.Sci Transl Med2023
37719146Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues.Cell Genom2023
38012143Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer.Nat Commun2023
37582954COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data.Nat Commun2023
37610338Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression.Bioinformatics2023
37986825Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity.Res Sq2023
37777714Predicting tumour content of liquid biopsies from cell-free DNA.BMC Bioinformatics2023
37564129Because I'm happy - positive affect and its predictive value for future disease activity in patients with inflammatory bowel diseases: a retrospective cohort study.Therap Adv Gastroenterol2023
37088333Biallelic ELOC-Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity.Mod Pathol2023
37344522Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees.Nat Commun2023
37245006Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers.Clin Epigenetics2023
37305441Expanding epidemic of recently acquired HCV in HIV-coinfected patients over a period of 10 years.JHEP Rep2023
36680285Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland.Viruses2023
35260685Discovery of antimicrobials by massively parallelized growth assays (Me<sup>x</sup>).Sci Rep2022
35679575Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks.Brief Bioinform2022
35605437Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example.Epidemics2022
35396471Unlocking capacities of genomics for the COVID-19 response and future pandemics.Nat Methods2022
35822578Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study.Swiss Med Wkly2022
35724832dCas9-mediated dysregulation of gene expression in human induced pluripotent stem cells during primitive streak differentiation.Metab Eng2022
35787660Author Correction: GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers.Commun Biol2022
35851854Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC.Nat Microbiol2022
35658001scAmpi-A versatile pipeline for single-cell RNA-seq analysis from basics to clinics.PLoS Comput Biol2022
36517508Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens.Nat Commun2022
36451239SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data.Genome Biol2022
36000873Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence.Bioinformatics2022
36067230Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model.PLoS Comput Biol2022
36265464What are the keys to succeeding as a computational biologist in today's research climate?Cell Syst2022
35215999Detecting Selection in the HIV-1 Genome during Sexual Transmission Events.Viruses2022
35272748Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021.Euro Surveill2022
34903604Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk.Cancer Res2022
34927666Identifying cancer pathway dysregulations using differential causal effects.Bioinformatics2022
31266731Tracing Clonal Dynamics Reveals that Two- and Three-dimensional Patient-derived Cell Models Capture Tumor Heterogeneity of Clear Cell Renal Cell Carcinoma.Eur Urol Focus2021
33600806Evaluating key characteristics of ideal colorectal cancer screening modalities: the microsimulation approach.Gastrointest Endosc2021
33617647Inferring perturbation profiles of cancer samples.Bioinformatics2021
33925452ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics.Viruses2021
34885114Multiparametric Circulating Tumor Cell Analysis to Select Targeted Therapies for Breast Cancer Patients.Cancers (Basel)2021
34910733Statistical tests for intra-tumour clonal co-occurrence and exclusivity.PLoS Comput Biol2021
34555024Drug-induced resistance evolution necessitates less aggressive treatment.PLoS Comput Biol2021
34819356Hierarchy of TGFβ/SMAD, Hippo/YAP/TAZ, and Wnt/β-catenin signaling in melanoma phenotype switching.Life Sci Alliance2021
34491984Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C.PLoS Comput Biol2021
34488035Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland.Epidemics2021
34348664Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma.BMC Genomics2021
34153841Quantitative measures of within-host viral genetic diversity.Curr Opin Virol2021
34313788Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens.Nucleic Acids Res2021
34112201The Bourque distances for mutation trees of cancers.Algorithms Mol Biol2021
33972555Author Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics.Nat Commun2021
33946379Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma.Cancers (Basel)2021
33471068V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data.Bioinformatics2021
33482122The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support.Cancer Cell2021
33147627Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.Brief Bioinform2021
  • 1 - 50 of 210

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Collaborators

Holger Moch
University Hospital Zurich
Co-authored papers 10
Pejman Mohammadi
Co-authored papers 9
J??rg Rahnenf??hrer
TU Dortmund University
Co-authored papers 9
Moritz Gerstung
German Cancer Research Centre DKFZ
Co-authored papers 9
Simona Cristea
Dana-Farber Cancer Institute
Co-authored papers 8
Alejandro A Sch??ffer
National Cancer Institute, National Institutes of Health
Co-authored papers 7
Charlotte K Y Ng
University of Bern
Co-authored papers 6
Mitchell P Levesque
University Hospital Zurich
Co-authored papers 6
Matthias Cavassini
Lausanne University Hospital, University of Lausanne
Co-authored papers 5
Roger D Kouyos
Institute of Medical Virology, University of Zurich
Co-authored papers 5
Amalio Telenti
Vir Biotechnology Inc.
Co-authored papers 5
Salvatore Piscuoglio
University of Basel
Co-authored papers 5
Reinhard Dummer
University Hospital Zurich
Co-authored papers 4
Florian Markowetz
CRUK Cambridge Institute, University of Cambridge
Co-authored papers 4
Bernd Wollscheid
ETH Zurich
Co-authored papers 4
Rainer Spang
University of Regensburg
Co-authored papers 3
Robert W Shafer
Co-authored papers 3
Bert Vogelstein
Co-authored papers 3
Peter J Wild
Co-authored papers 3
Christian von Mering
Co-authored papers 3
Holger Fr??hlich
Bonn-Aachen International Center for IT (B-IT), University of Bonn
Co-authored papers 3
Jacques Fellay
Ecole Polytechnique Federale de Lausanne
Co-authored papers 3
Phillip A Futreal
The University of Texas MD Anderson Cancer Center
Co-authored papers 3
Thomas Rattei
Co-authored papers 2
Guillermo Garcia-Manero
MD Anderson Cancer Center
Co-authored papers 2
Xingzhi Song
The University of Texas MD Anderson Cancer Center
Co-authored papers 2
Yves Moreau
KU Leuven - University of Leuven
Co-authored papers 2
Lucas Pelkmans
University of Zurich
Co-authored papers 2
Markus G Manz
Co-authored papers 2
Victor E Velculescu
Co-authored papers 2
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