Search filters

List of works by Niko Beerenwinkel

24 hours in the life of HIV-1 in a T cell line

scientific article

A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations

scientific article published on 19 December 2015

A Genome-Wide siRNA Screen Implicates Spire1/2 in SipA-Driven Salmonella Typhimurium Host Cell Invasion

scientific article

A Hierarchical Regulatory Landscape during the Multiple Stages of EMT

scientific article published on 31 January 2019

A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory

scientific article

A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment

scientific article published on 02 October 2020

A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data

scientific article

A stochastic model of metastatic bottleneck predicts patient outcome and therapy response

A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila

scientific article published on 21 March 2018

Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias

scientific article

Advances in understanding tumour evolution through single-cell sequencing

scientific article published on 10 February 2017

Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example

scientific article published on 14 May 2022

Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell

scientific article

Analysis of epistatic interactions and fitness landscapes using a new geometric approach

scientific article

Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas.

scientific article

Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy

scientific article published on 6 February 2017

BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data

scientific article

Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times

scientific article published on 21 October 2020

Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing ⬇️

scientific article published on February 1, 2012

Bioinformatics for precision oncology

scientific article published on 18 December 2017

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

scientific article published on 13 February 2015

BnpC: Bayesian non-parametric clustering of single-cell mutation profiles

scientific article published on 27 June 2020

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies

scientific article

Cell selection as driving force in lung and colon carcinogenesis

scientific article

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

scientific article (publication date: 2012)

Challenges in RNA virus bioinformatics

scientific article published on 03 March 2014

Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer.

scientific article

Clinicopathological and prognostic implications of genetic alterations in oral cancers

scientific article

Clonal evolution driven by superdriver mutations

scientific article published on 20 July 2020

Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics

scientific article published on 21 October 2020

Clonal hematopoiesis in donors and long-term survivors of related allogeneic hematopoietic stem cell transplantation

scientific article published on 16 March 2020

Comparative lesion sequencing provides insights into tumor evolution

scholarly article

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C

scientific article published on 07 September 2021

Competition-colonization dynamics in an RNA virus

scientific article

Competition-colonization dynamics: An ecology approach to quasispecies dynamics and virulence evolution in RNA viruses

scientific article published on July 2010

Competition–colonization trade-off promotes coexistence of low-virulence viral strains ⬇️

scientific article published on April 18, 2012

Computational Analysis of DNA and RNA Sequencing Data Obtained from Liquid Biopsies

scientific article published on 01 January 2020

Computational Cancer Biology: An Evolutionary Perspective

scientific article

Computational Data Integration in Toxicogenomics

Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts

scientific article published on 10 June 2020

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

scientific article published on 23 May 2020

Computational approaches for the identification of cancer genes and pathways

scientific article published on 11 November 2016

Computational methods for the design of effective therapies against drug resistant HIV strains

scientific article

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

scientific article published on 04 November 2020

Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression

scientific article published on June 2009

Context-dependent deposition and regulation of mRNAs in P-bodies

Context-dependent deposition and regulation of mRNAs in P-bodies.

scientific article published on 3 January 2018

Correction: 24 Hours in the Life of HIV-1 in a T Cell Line

scientific article published on 15 June 2015

Correction: Context-dependent deposition and regulation of mRNAs in P-bodies

Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction

scientific article published on 01 March 2010

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers

scientific article

Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART

scientific article published on 19 July 2019

Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype

scientific article

Drug-induced resistance evolution necessitates less aggressive treatment

scientific article published on 24 September 2021

Dynamic models of viral replication and latency

scientific article

Dynamics of HIV latency and reactivation in a primary CD4+ T cell model

scientific article

Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation

scientific article published on 30 September 2015

Editorial: the influence of genetic factors in mediating the effects of tobacco smoke in IBD-Authors' reply.

scientific article published in January 2018

Efficient sampling for Bayesian inference of conjunctive Bayesian networks ⬇️

scientific article published on July 10, 2012

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

Ensemble outlier detection and gene selection in triple-negative breast cancer data.

scientific article

Erratum to: gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens

scientific article published on 21 October 2015

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

scientific article

Estimating Fitness of Viral Quasispecies from Next-Generation Sequencing Data

scientific article

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance

scientific article published on 28 April 2005

Estimating HIV-1 fitness characteristics from cross-sectional genotype data

scientific article (publication date: November 2014)

Estimating cancer survival and clinical outcome based on genetic tumor progression scores

scientific article published on 10 February 2005

Estimating the dynamics and dependencies of accumulating mutations with applications to HIV drug resistance

scientific article published on 14 May 2015

Estimating the predictability of cancer evolution

scientific article published on 01 July 2019

Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy

scientific article

Evolution on distributive lattices

scientific article published on 2 May 2006

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction

scientific article published on 30 November 2013

Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD

Expression and Mutation Patterns of PBRM1, BAP1 and SETD2 Mirror Specific Evolutionary Subtypes in Clear Cell Renal Cell Carcinoma

From hype to reality: data science enabling personalized medicine

scientific article published on 27 August 2018

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

scientific article

Genetic polymorphisms associated with smoking behaviour predict the risk of surgery in patients with Crohn's disease.

scientific article published on 20 October 2017

Genetic progression and the waiting time to cancer

scientific article

Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes

scientific article

Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance

scientific article published on 01 March 2020

Genome-wide expression and copy number analysis identifies driver genes in gingivobuccal cancers

scientific article published on 10 November 2011

Genomic profiling of advanced-stage oral cancers reveals chromosome 11q alterations as markers of poor clinical outcome

scientific article

Genomic variant annotation workflow for clinical applications

scientific article published on 12 August 2016

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

scientific article published on January 2014

HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages

scientific article published on 30 July 2015

Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART

scientific article published on 02 November 2020

High-dimensional microbiome interactions shape host fitness

Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation

scientific article published on 10 February 2020

Host genomics of the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment

scientific article published on 18 August 2020

ISMB/ECCB 2015.

scientific article published on June 2015

ISMB/ECCB 2017 proceedings

scientific article published in July 2017

Identification and Validation of a Biomarker Signature in Patients With Resectable Pancreatic Cancer via Genome-Wide Screening for Functional Genetic Variants

scientific article published on 19 June 2019

Identification of constrained cancer driver genes based on mutation timing

scientific article published on 8 January 2015

Improved pathway reconstruction from RNA interference screens by exploiting off-target effects.

scientific article published in July 2018

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance

scientific article published in January 2007

Inferring Genetic Interactions From Comparative Fitness Data

Inferring genetic interactions from comparative fitness data.

scientific article published on 20 December 2017

Inferring modulators of genetic interactions with epistatic nested effects models

scientific article

Inferring signalling dynamics by integrating interventional with observational data

scientific article published on 01 July 2019

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data

article published in 2017

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data.

scientific article

Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors

scientific article

Kinetic, energetic, and mechanical differences between dark-state rhodopsin and opsin

scientific article published on 21 February 2013

Large-scale inference of conjunctive Bayesian networks

scientific article

Learning Monotonic Genotype-Phenotype Maps ⬇️

scientific article published on January 6, 2011

Learning epistatic gene interactions from perturbation screens

scientific article published on 13 July 2021

Learning multiple evolutionary pathways from cross-sectional data

scientific article

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.

scientific article published on 21 August 2017

Linear effects models of signaling pathways from combinatorial perturbation data

scientific article

Methods for optimizing antiviral combination therapies

scientific article

Microbiome interactions shape host fitness

article published in the Proceedings of the National Academy of Sciences of the United States of America

Microbiome interactions shape host fitness

scientific article published on 11 December 2018

Model selection for mixtures of mutagenetic trees

scientific article published on 23 June 2006

Modeling mutual exclusivity of cancer mutations

scientific article

Models of RNA virus evolution and their roles in vaccine design ⬇️

scientific article published on November 3, 2010

Mtreemix: a software package for learning and using mixture models of mutagenetic trees

scientific article published on 18 January 2005

Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma

scientific article published on 04 August 2021

Mutagenetic Tree Models

Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype ⬇️

scientific article published in January 2007

Mutational interactions define novel cancer subgroups

scientific article published in Nature Communications

Myeloid differentiation primary response gene (MyD) 88 signalling is not essential for intestinal fibrosis development.

scientific article published on 15 December 2017

NEMix: single-cell nested effects models for probabilistic pathway stimulation

scientific article

NGS-pipe: a flexible, easily extendable, and highly configurable framework for NGS analysis.

scientific article published on 28 August 2017

Network-based integration of multi-omics data for prioritizing cancer genes

scientific article published on 14 March 2018

Neutrophils escort circulating tumour cells to enable cell cycle progression

scientific article published on 06 February 2019

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination

scientific article

Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment

scientific article

Perturbing resistance: a network perspective.

scientific article

Predicting HIV coreceptor usage on the basis of genetic and clinical covariates.

scientific article published in January 2007

Predicting cancer type from tumour DNA signatures.

scientific article published on 28 November 2017

Predicting colorectal cancer risk from adenoma detection via a two-type branching process model

scientific article published on 05 February 2020

Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database

scientific article published in April 2009

Principles of Systems Biology, No. 31

scientific article published on 01 August 2018

Probabilistic inference of viral quasispecies subject to recombination

scientific article published on February 2013

Probability, Statistics, and Computational Science

scientific article published on 01 January 2019

Probability, statistics, and computational science

scientific article published on January 2012

Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection

scientific article published in Scientific Reports

Publisher Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics

scientific article published on 19 November 2020

PyBDA: a command line tool for automated analysis of big biological data sets

scientific article published on 12 November 2019

Quantifying cancer progression with conjunctive Bayesian networks

scientific article published on 19 August 2009

ROCR: visualizing classifier performance in R

scientific article (publication date: 15 October 2005)

Read length versus depth of coverage for viral quasispecies reconstruction

scientific article

Recent advances in inferring viral diversity from high-throughput sequencing data

scientific article

Recurring Amplification at 11q22.1-q22.2 Locus Plays an Important Role in Lymph Node Metastasis and Radioresistance in OSCC.

scientific article published on 22 November 2017

Reliable detection of subclonal single-nucleotide variants in tumour cell populations

scientific article published in May 2012

Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level

scientific article

Sequencing approach to analyze the role of quasispecies for classical swine fever

scientific article published on 13 February 2013

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data ⬇️

scientific article (publication date: 26 April 2011)

Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer Driver Modules

scientific article published on 15 May 2019

Simultaneous analysis of large-scale RNAi screens for pathogen entry

scientific article

Single cell network analysis with a mixture of Nested Effects Models

scholarly article by Martin Pirkl published in September 2018

Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.

scientific article

Single-cell mutation identification via phylogenetic inference

scientific article published in Nature Communications

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

scientific article

Stability of gene rankings from RNAi screens

scientific article published on 17 April 2012

Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART

scientific article published on 26 September 2006

Statistical tests for intra-tumour clonal co-occurrence and exclusivity

scientific article published on 15 December 2021

Structure-function relationships of HDL in diabetes and coronary heart disease

scientific article published on 16 January 2020

Sulforaphane Preconditioning Sensitizes Human Colon Cancer Cells towards the Bioreductive Anticancer Prodrug PR-104A

scientific article

SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics

article

Tenofovir resistance and resensitization

scientific article published on November 2003

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila

scientific article

The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation

scientific article published on 19 May 2016

The International Virus Bioinformatics Meeting 2020

scientific article published on 06 December 2020

The evolution of virulence in RNA viruses under a competition-colonization trade-off.

scientific article published on 17 November 2010

The geometry of partial fitness orders and an efficient method for detecting genetic interactions

The geometry of partial fitness orders and an efficient method for detecting genetic interactions

scientific article published on 07 May 2018

The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients

scientific article (publication date: 2013)

The temporal order of genetic and pathway alterations in tumorigenesis

scientific article

TiMEx: a waiting time model for mutually exclusive cancer alterations

scientific article published on 9 July 2015

Tracing Clonal Dynamics Reveals that Two- and Three-dimensional Patient-derived Cell Models Capture Tumor Heterogeneity of Clear Cell Renal Cell Carcinoma

scientific article published on 29 June 2019

Transcriptomic responses of cancerous and noncancerous human colon cells to sulforaphane and selenium

scientific article published on 13 January 2014

Tree inference for single-cell data

scientific article

Trophic Interactions of Infant Bifidobacteria and Eubacterium hallii during L-Fucose and Fucosyllactose Degradation ⬇️

scientific article published on 30 January 2017

Ultra-deep sequencing for the analysis of viral populations

scientific article published on 17 August 2011

Unlocking capacities of genomics for the COVID-19 response and future pandemics

scientific article published on 08 April 2022

Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection

scientific article published on 01 June 2019

Viral population estimation using pyrosequencing

scientific article

Viral quasispecies assembly via maximal clique enumeration

scientific article (publication date: March 2014)

gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens

scientific article published on 7 October 2015

netprioR: a probabilistic model for integrative hit prioritisation of genetic screens

scientific article published on 06 March 2019

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics

scientific article published on 12 December 2016

scAmpi-A versatile pipeline for single-cell RNA-seq analysis from basics to clinics

scientific article published on 03 June 2022

αV-class integrins exert dual roles on α5β1 integrins to strengthen adhesion to fibronectin.

scientific article published on 27 January 2017

Paulina is supported by:

About Paulina

Help