Niko Beerenwinkel

发表

Probing of viral diversity by global haplotype prediction

Armin Töpfer, Francesca Di Giallonardo, Karin J. Metzner, 2013, 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

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

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472)

Holger Fröhlich, Susan A. Murphy, Niko Beerenwinkel, 2017, Dagstuhl Reports.

Single cell network analysis with a mixture of Nested Effects Models

Niko Beerenwinkel, Martin Pirkl, 2018 .

Computational Cancer Biology: An Evolutionary Perspective

Niko Beerenwinkel, Jens Lagergren, Chris D. Greenman, 2016, PLoS Comput. Biol..

Challenges in RNA virus bioinformatics

Christian Drosten, Dmitrij Frishman, Martin Middendorf, 2014, Bioinform..

The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients

Huldrych F. Günthard, Niko Beerenwinkel, Matthias Cavassini, 2013, PLoS Comput. Biol..

Models of RNA virus evolution and their roles in vaccine design

Niko Beerenwinkel, Samuel Ojosnegros, N. Beerenwinkel, 2010, Immunome research.

Methods for optimizing antiviral combination therapies

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2003, ISMB.

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

Jack Kuipers, Niko Beerenwinkel, Simona Cristea, 2017, J. Comput. Biol..

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

Niko Beerenwinkel, Thomas Sakoparnig, Tobias Kockmann, 2012, J. Comput. Biol..

Covering Pairs in Directed Acyclic Graphs

Paola Bonizzoni, Riccardo Dondi, Yuri Pirola, 2015, Comput. J..

Viral Quasispecies Assembly via Maximal Clique Enumeration

Alexander Schönhuth, Armin Töpfer, Niko Beerenwinkel, 2014, PLoS Comput. Biol..

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

Simon Dirmeier, Niko Beerenwinkel, Mario Emmenlauer, 2019, BMC Bioinformatics.

Visualizing the Performance of Scoring Classifiers [R package ROCR version 1.0-11]

Thomas Lengauer, Oliver Sander, Niko Beerenwinkel, 2020 .

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

Bernd Rinn, Niko Beerenwinkel, Thomas Wüst, 2017, Bioinform..

ROCR: visualizing classifier performance in R

Thomas Lengauer, Niko Beerenwinkel, Oliver Sander, 2005, Bioinform..

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

Jack Kuipers, Niko Beerenwinkel, Jochen Singer, 2017, BMC Bioinformatics.

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

Niko Beerenwinkel, Jaume Bonet, N. Borgsmueller, 2020, bioRxiv.

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

Jack Kuipers, Niko Beerenwinkel, Mario Emmenlauer, 2018 .

Viral Population Estimation Using Pyrosequencing

Lior Pachter, Nicholas Eriksson, Niko Beerenwinkel, 2007, PLoS Comput. Biol..

Data and text mining Computational methods for the design of effective therapies against drug resistant HIV strains

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2005 .

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

Niko Beerenwinkel, Hesam Montazeri, Victor DeGruttola, 2020, Statistical applications in genetics and molecular biology.

Identification of Constrained Cancer Driver Genes Based on Mutation Timing

Niko Beerenwinkel, Patrick Fried, Thomas Sakoparnig, 2015, PLoS Comput. Biol..

Inferring modulators of genetic interactions with epistatic nested effects models

Holger Fröhlich, Niko Beerenwinkel, Martin Pirkl, 2017, PLoS Comput. Biol..

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

Niko Beerenwinkel, Susana Vinga, André Veríssimo, 2018, BMC Bioinformatics.

Finding Dense Subgraphs in Relational Graphs

Niko Beerenwinkel, Vinay Jethava, N. Beerenwinkel, 2015, ECML/PKDD.

Identifying drug resistance-associated patterns in HIV genotypes

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2001, German Conference on Bioinformatics.

Large-scale inference of conjunctive Bayesian networks

Jack Kuipers, Huldrych F. Günthard, Niko Beerenwinkel, 2016, Bioinform..

Estimating the predictability of cancer evolution

Niko Beerenwinkel, Ramón Díaz-Uriarte, Florian Markowetz, 2019, Bioinform..

TiMEx: a waiting time model for mutually exclusive cancer alterations

Niko Beerenwinkel, Ewa Szczurek, Simona Constantinescu, 2015, Bioinform..

Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data

Niko Beerenwinkel, Wilhelm Huisinga, Hesam Montazeri, 2014, PLoS Comput. Biol..

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

Niko Beerenwinkel, Yaakov Benenson, Pejman Mohammadi, 2017, Cell systems.

Genetic Progression and the Waiting Time to Cancer

Martin A. Nowak, Arne Traulsen, Niko Beerenwinkel, 2007, PLoS Comput. Biol..

TiMEx: a waiting time model for mutually exclusive cancer alterations

Niko Beerenwinkel, Ewa Szczurek, Jörg Rahnenführer, 2015, Bioinform..

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

Volker Roth, Niko Beerenwinkel, Lukas Geyrhofer, 2009, RECOMB.

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

Niko Beerenwinkel, Nuria Lopez-Bigas, Nico Borgsmüller, 2020, Bioinform..

V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data

Karin J. Metzner, Niko Beerenwinkel, David Seifert, 2020, bioRxiv.

Single cell network analysis with a mixture of Nested Effects Models

Niko Beerenwinkel, Martin Pirkl, N. Beerenwinkel, 2018, bioRxiv.

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

Nicholas Eriksson, Niko Beerenwinkel, Arnab Bhattacharya, 2011, BMC Bioinformatics.

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

Niko Beerenwinkel, Pejman Mohammadi, Monica Golumbeanu, 2015, Bioinform..

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

Jack Kuipers, Niko Beerenwinkel, Benjamin Misselwitz, 2020, PLoS Comput. Biol..

Supervised and Unsupervised Approaches for Analyzing Covariation and Phenotypic Impact of HIV Drug Resistance Mutations

Thomas Lengauer, Niko Beerenwinkel, Tobias Sing, 2005, LWA.

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

Thomas Lengauer, Niko Beerenwinkel, Christian Hartmann, 2005, Bioinform..

PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You

Matthias Bethge, Gunnar Blohm, Kevin Bretonnel Cohen, 2017, PLoS Comput. Biol..

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

Roded Sharan, Niko Beerenwinkel, Dana Silverbush, 2019, Cell systems.

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

Volker Roth, Niko Beerenwinkel, Lukas Geyrhofer, 2009, RECOMB.

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

Jack Kuipers, Niko Beerenwinkel, Salem Malikic, 2017, Nature Communications.

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

Niko Beerenwinkel, Meher K. Prakash, Brian Lang, 2017, BMC Medical Informatics and Decision Making.

Markov models for accumulating mutations

Seth Sullivant, Niko Beerenwinkel, S. Sullivant, 2007, 0709.2646.

Viral quasispecies assembly from paired-end reads

Armin Töpfer, Niko Beerenwinkel, 2014, 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

Efficient sampling for Bayesian inference of conjunctive Bayesian networks

Niko Beerenwinkel, Thomas Sakoparnig, N. Beerenwinkel, 2012, Bioinform..

Linear effects models of signaling pathways from combinatorial perturbation data

Niko Beerenwinkel, Ewa Szczurek, 2016, Bioinform..

Viral Quasispecies Assembly via Maximal Clique Enumeration

Alexander Schönhuth, Armin Töpfer, Niko Beerenwinkel, 2014, RECOMB.

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

Niko Beerenwinkel, Tobias Sing, N. Beerenwinkel, 2006, NIPS.

Covering Pairs in Directed Acyclic Graphs

Paola Bonizzoni, Riccardo Dondi, Yuri Pirola, 2013, Comput. J..

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

Jack Kuipers, Niko Beerenwinkel, Mario Emmenlauer, 2018, bioRxiv.

Inferring signalling dynamics by integrating interventional with observational data

Niko Beerenwinkel, Gerhard Christofori, Mathias Cardner, 2019, Bioinform..

Learning Multiple Evolutionary Pathways from Cross-Sectional Data

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2005, J. Comput. Biol..

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

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2005, Bioinform..

Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2001, IEEE Intell. Syst..

SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics

Niko Beerenwinkel, Andreas Wicki, Jochen Singer, 2018, BMC Medical Informatics and Decision Making.

Detecting patterns of co-variation in deep-sequenced virus populations

Niko Beerenwinkel, David Seifert, Susana Posada-Cespedes, 2016, ICCABS.

Probabilistic Inference of Viral Quasispecies Subject to Recombination

Volker Roth, Eran Halperin, Armin Töpfer, 2012, RECOMB.

Learning Mixtures of Localized Rules by Maximizing the Area Under the ROC Curve

Thomas Lengauer, Niko Beerenwinkel, Tobias Sing, 2004, ROCAI.

Single-cell mutation identification via phylogenetic inference

Jack Kuipers, Niko Beerenwinkel, Jochen Singer, 2018, Nature Communications.

Quantifying cancer progression with conjunctive Bayesian networks

Niko Beerenwinkel, Michael Baudis, Moritz Gerstung, 2009, Bioinform..

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

Niko Beerenwinkel, Axel Visel, Len A. Pennacchio, 2017, PLoS Comput. Biol..

Modeling Mutual Exclusivity of Cancer Mutations

Niko Beerenwinkel, Ewa Szczurek, 2014, RECOMB.

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2003, Nucleic Acids Res..

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

Niko Beerenwinkel, Michael N. Hall, Hesam Montazeri, 2018, Bioinform..

Multiple Sequence Alignment System for Pyrosequencing Reads

Niko Beerenwinkel, Ashfaq A. Khokhar, Fahad Saeed, 2009, BICoB.

Tree inference for single-cell data

Jack Kuipers, Niko Beerenwinkel, Katharina Jahn, 2016 .

Evolutionary Games with Affine Fitness Functions: Applications to Cancer

Niko Beerenwinkel, Moritz Gerstung, Hani Nakhoul, 2011, Dyn. Games Appl..

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

Achim Tresch, Niko Beerenwinkel, Rainer Spang, 2014, Bioinform..

Bayesian Non-parametric Clustering of Single-Cell Mutation Profiles

Niko Beerenwinkel, Francesco Marass, Núria López-Bigas, 2020, RECOMB.

ISMB/ECCB 2017 proceedings

Niko Beerenwinkel, Yana Bromberg, N. Beerenwinkel, 2017, Bioinform..

Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV

Joachim Büch, Thomas Lengauer, Joachim Selbig, 2006, DILS.

Learning epistatic gene interactions from perturbation screens

Niko Beerenwinkel, Ewa Szczurek, Alex Gavryushkin, 2020, bioRxiv.

NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation

Holger Fröhlich, Niko Beerenwinkel, Pauli Rämö, 2015, PLoS Comput. Biol..

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression

Jack Kuipers, Niko Beerenwinkel, Simona Cristea, 2016, RECOMB.

Stability of gene rankings from RNAi screens

Niko Beerenwinkel, Wolf-Dietrich Hardt, Juliane Siebourg-Polster, 2012, Bioinform..

ISMB/ECCB 2015

Yves Moreau, Niko Beerenwinkel, Y. Moreau, 2015, Bioinform..

Characterization of Novel HIV Drug Resistance Mutations Using Clustering, Multidimensional Scaling and SVM-Based Feature Ranking

Thomas Lengauer, Niko Beerenwinkel, Hauke Walter, 2005, PKDD.

Probabilistic Inference of Viral Quasispecies Subject to Recombination

Volker Roth, Eran Halperin, Armin Töpfer, 2013, J. Comput. Biol..

Learning multiple evolutionary pathways from cross-sectional data

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2004, J. Comput. Biol..

Single-cell copy number calling and event history reconstruction

Jack Kuipers, Niko Beerenwinkel, Katharina Jahn, 2020, bioRxiv.

Modeling Mutual Exclusivity of Cancer Mutations

Niko Beerenwinkel, Ewa Szczurek, N. Beerenwinkel, 2014, RECOMB.

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

Volker Roth, Niko Beerenwinkel, Sandhya Prabhakaran, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

Simon Dirmeier, Niko Beerenwinkel, Lars Kaderali, 2020, PLoS Comput. Biol..

The Bourque distances for mutation trees of cancers

Niko Beerenwinkel, Katharina Jahn, Louxin Zhang, 2021, Algorithms Mol. Biol..

Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference pdf

Giusi Moffa, Jack Kuipers, Niko Beerenwinkel, 2021, ArXiv.

V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data

Karin J. Metzner, Niko Beerenwinkel, Susana Posada-Céspedes, 2021, Bioinform..

Bayesian Structure Learning and Sampling of Bayesian Networks with the R Package BiDAG

Giusi Moffa, Jack Kuipers, Niko Beerenwinkel, 2021, J. Stat. Softw..

Inferring perturbation profiles of cancer samples

Niko Beerenwinkel, Martin Pirkl, 2021, Bioinform..

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

Jack Kuipers, Niko Beerenwinkel, Benjamin J. Raphael, 2017, Genome research.

Ultra-deep sequencing for the analysis of viral populations.

Niko Beerenwinkel, Osvaldo Zagordi, N. Beerenwinkel, 2011, Current opinion in virology.

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

Niko Beerenwinkel, Mathias Drton, M. Drton, 2006, Biostatistics.

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

Martin Beer, Armin Töpfer, Niko Beerenwinkel, 2013, Virology.

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

Volker Roth, Beda Joos, Armin Töpfer, 2014, Nucleic acids research.

Learning Monotonic Genotype-Phenotype Maps

Achim Tresch, Niko Beerenwinkel, Patrick Knupfer, 2011, Statistical applications in genetics and molecular biology.

A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory

Karin J. Metzner, Huldrych F. Günthard, Niko Beerenwinkel, 2014, Genetics.

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

Niko Beerenwinkel, Thomas Sakoparnig, Florian Markowetz, 2015, Genome Biology.

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

Thomas Lengauer, Niko Beerenwinkel, Jörg Rahnenführer, 2007, International journal of cancer.

Geno2pheno is predictive of short-term virological response

Thomas Lengauer, Joachim Selbig, Niko Beerenwinkel, 2002 .

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

Niko Beerenwinkel, Osvaldo Zagordi, Martin Däumer, 2010, Nucleic acids research.

Algebraic Statistics for Computational Biology: Mutagenetic Tree Models

Niko Beerenwinkel, Mathias Drton, 2005 .

Comparative lesion sequencing provides insights into tumor evolution

Martin A. Nowak, Arne Traulsen, Niko Beerenwinkel, 2008, Proceedings of the National Academy of Sciences.

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

Niko Beerenwinkel, Tobias Kockmann, Renato Paro, 2013, Genome Biology.

Inferring genetic interactions from comparative fitness data

Niko Beerenwinkel, Alex Gavryushkin, Devin Greene, 2017, bioRxiv.

The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support.

Jack Kuipers, Niko Beerenwinkel, Bernd Wollscheid, 2020, Cancer cell.

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

Robert D. Finn, Alex Bateman, Niko Beerenwinkel, 2020, Briefings Bioinform..

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

Thomas Lengauer, Niko Beerenwinkel, Rolf Kaiser, 2006, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

Statistical Applications in Genetics and Molecular Biology

Achim Tresch, Niko Beerenwinkel, Patrick Knupfer, 2010 .

Predicting cancer type from tumour DNA signatures

Niko Beerenwinkel, Ewa Szczurek, Thomas Sakoparnig, 2017, Genome Medicine.

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

Niko Beerenwinkel, Christian Beisel, Osvaldo Zagordi, 2012, PloS one.

12 Grand Challenges in Single-Cell Data Science

Alexander Zelikovsky, Fabian J. Theis, Marcel J. T. Reinders, 2019, PeerJ Prepr..

Spatial structure governs the mode of tumour evolution

Niko Beerenwinkel, Jakob Nikolas Kather, Robert Noble, 2019, bioRxiv.

Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance

Niko Beerenwinkel, Federico Gago, Tobias Sing, 2005 .

HIV-Haplotype Inference using a Constraint-based Dirichlet Process Mixture Model

Volker Roth, Niko Beerenwinkel, Sandhya Prabhakaran, 2010 .

The Bourque distances for mutation trees of cancers

Niko Beerenwinkel, Katharina Jahn, Louxin Zhang, 2020, Algorithms for Molecular Biology.

Inferring Genetic Interactions From Comparative Fitness Data

Niko Beerenwinkel, Alex Gavryushkin, Devin Greene, 2017 .

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

Niko Beerenwinkel, Thomas Elbert, Torsten Schwede, 2017, Nature Human Behaviour.

Genomic variant annotation workflow for clinical applications.

Niko Beerenwinkel, Thomas Thurnherr, Franziska Singer, 2016, F1000Research.

Conjunctive Bayesian networks

Nicholas Eriksson, Bernd Sturmfels, Niko Beerenwinkel, 2006, math/0608417.

The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis

Nicholas Eriksson, Niko Beerenwinkel, Bert Vogelstein, 2011, PloS one.

Simultaneous analysis of large-scale RNAi screens for pathogen entry

Bernd Rinn, Pascale Cossart, Niko Beerenwinkel, 2014, BMC Genomics.

Cell selection as driving force in lung and colon carcinogenesis.

Paolo Vineis, Niko Beerenwinkel, P. Vineis, 2010, Cancer research.

From hype to reality: data science enabling personalized medicine

Holger Fröhlich, Thomas Lengauer, Blaz Zupan, 2018, BMC Medicine.

Geno2pheno[coreceptor]: a Tool for Predicting Coreceptor Usage from Genotype and for Monitoring Coreceptor-associated Sequence Alterations

Thomas Lengauer, Niko Beerenwinkel, Rolf Kaiser, 2005 .

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model.

Volker Roth, Niko Beerenwinkel, Sandhya Prabhakaran, 2013, IEEE/ACM transactions on computational biology and bioinformatics.

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

Niko Beerenwinkel, Susana Posada-Cespedes, David Seifert, 2017, Virus research.

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

Niko Beerenwinkel, Alejandro A Schäffer, Manoj Mahimkar, 2009, International journal of cancer.

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

Jack Kuipers, Niko Beerenwinkel, Salem Malikic, 2019, Nature Communications.

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

Lior Pachter, Bernd Sturmfels, Niko Beerenwinkel, 2007, BMC Evolutionary Biology.

Model Selection for Mixtures of Mutagenetic Trees

Thomas Lengauer, Niko Beerenwinkel, Junming Yin, 2006, Statistical applications in genetics and molecular biology.

Structured hierarchical models for probabilistic inference from perturbation screening data

Simon Dirmeier, Niko Beerenwinkel, N. Beerenwinkel, 2019, bioRxiv.

Evolution on distributive lattices.

Nicholas Eriksson, Bernd Sturmfels, Niko Beerenwinkel, 2005, Journal of theoretical biology.