Niko Beerenwinkel

According to our database1, Niko Beerenwinkel authored at least 97 papers between 2001 and 2023.

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Bibliography

2023
Predicting tumour content of liquid biopsies from cell-free DNA.
BMC Bioinform., December, 2023

Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression.
Bioinform., August, 2023

Bayesian Structure Learning and Sampling of Bayesian Networks with the <i>R</i> Package BiDAG.
J. Stat. Softw., 2023

Fair Clustering: A Causal Perspective.
CoRR, 2023

The Mixtures and the Neural Critics: On the Pointwise Mutual Information Profiles of Fine Distributions.
CoRR, 2023

Beyond Normal: On the Evaluation of Mutual Information Estimators.
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2022
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence.
Bioinform., October, 2022

Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model.
PLoS Comput. Biol., September, 2022

scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics.
PLoS Comput. Biol., 2022

Identifying cancer pathway dysregulations using differential causal effects.
Bioinform., 2022

Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks.
Briefings Bioinform., 2022

Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees.
Proceedings of the Research in Computational Molecular Biology, 2022

Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees.
Proceedings of the Research in Computational Molecular Biology, 2022

Reproducibility of Bioinformatics Tools.
Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

2021
Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C.
PLoS Comput. Biol., 2021

Drug-induced resistance evolution necessitates less aggressive treatment.
PLoS Comput. Biol., 2021

Statistical tests for intra-tumour clonal co-occurrence and exclusivity.
PLoS Comput. Biol., 2021

Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference.
CoRR, 2021

V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data.
Bioinform., 2021

Inferring perturbation profiles of cancer samples.
Bioinform., 2021

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Briefings Bioinform., 2021

The Bourque distances for mutation trees of cancers.
Algorithms Mol. Biol., 2021

2020
A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment.
PLoS Comput. Biol., 2020

Predicting colorectal cancer risk from adenoma detection via a two-type branching process model.
PLoS Comput. Biol., 2020

Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation.
PLoS Comput. Biol., 2020

BnpC: Bayesian non-parametric clustering of single-cell mutation profiles.
Bioinform., 2020

Bayesian Non-parametric Clustering of Single-Cell Mutation Profiles.
Proceedings of the Research in Computational Molecular Biology, 2020

2019
12 Grand Challenges in Single-Cell Data Science.
PeerJ Prepr., 2019

PyBDA: a command line tool for automated analysis of big biological data sets.
BMC Bioinform., 2019

Estimating the predictability of cancer evolution.
Bioinform., 2019

Inferring signalling dynamics by integrating interventional with observational data.
Bioinform., 2019

Bioinformatics for precision oncology.
Briefings Bioinform., 2019

2018
SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics.
BMC Medical Informatics Decis. Mak., 2018

Ensemble outlier detection and gene selection in triple-negative breast cancer data.
BMC Bioinform., 2018

Improved pathway reconstruction from RNA interference screens by exploiting off-target effects.
Bioinform., 2018

NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis.
Bioinform., 2018

Single cell network analysis with a mixture of Nested Effects Models.
Bioinform., 2018

Network-based integration of multi-omics data for prioritizing cancer genes.
Bioinform., 2018

SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference.
Proceedings of the Research in Computational Molecular Biology, 2018

ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules.
Proceedings of the Research in Computational Molecular Biology, 2018

Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data.
Proceedings of the Research in Computational Molecular Biology, 2018

2017
Inferring modulators of genetic interactions with epistatic nested effects models.
PLoS Comput. Biol., 2017

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.
PLoS Comput. Biol., 2017

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies.
BMC Medical Informatics Decis. Mak., 2017

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics.
J. Comput. Biol., 2017

Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472).
Dagstuhl Reports, 2017

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers.
BMC Bioinform., 2017

ISMB/ECCB 2017 proceedings.
Bioinform., 2017

2016
Computational Cancer Biology: An Evolutionary Perspective.
PLoS Comput. Biol., 2016

Linear effects models of signaling pathways from combinatorial perturbation data.
Bioinform., 2016

Large-scale inference of conjunctive Bayesian networks.
Bioinform., 2016

BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data.
Bioinform., 2016

TiMEx: a waiting time model for mutually exclusive cancer alterations.
Bioinform., 2016

Tree Inference for Single-Cell Data.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Detecting patterns of co-variation in deep-sequenced virus populations.
Proceedings of the 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2016

2015
NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation.
PLoS Comput. Biol., 2015

Identification of Constrained Cancer Driver Genes Based on Mutation Timing.
PLoS Comput. Biol., 2015

Covering Pairs in Directed Acyclic Graphs.
Comput. J., 2015

ISMB/ECCB 2015.
Bioinform., 2015

Finding Dense Subgraphs in Relational Graphs.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2015

2014
HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Viral Quasispecies Assembly via Maximal Clique Enumeration.
PLoS Comput. Biol., 2014

Modeling Mutual Exclusivity of Cancer Mutations.
PLoS Comput. Biol., 2014

Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data.
PLoS Comput. Biol., 2014

Challenges in RNA virus bioinformatics.
Bioinform., 2014

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction.
Bioinform., 2014

Viral quasispecies assembly from paired-end reads.
Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

2013
The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients.
PLoS Comput. Biol., 2013

Probabilistic Inference of Viral Quasispecies Subject to Recombination.
J. Comput. Biol., 2013

Probing of viral diversity by global haplotype prediction.
Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013

2012
Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing.
J. Comput. Biol., 2012

Stability of gene rankings from RNAi screens.
Bioinform., 2012

Efficient sampling for Bayesian inference of conjunctive Bayesian networks.
Bioinform., 2012

2011
Evolutionary Games with Affine Fitness Functions: Applications to Cancer.
Dyn. Games Appl., 2011

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
BMC Bioinform., 2011

2010
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction.
J. Comput. Biol., 2010

2009
Quantifying cancer progression with conjunctive Bayesian networks.
Bioinform., 2009

Multiple Sequence Alignment System for Pyrosequencing Reads.
Proceedings of the Bioinformatics and Computational Biology, 2009

2008
Viral Population Estimation Using Pyrosequencing.
PLoS Comput. Biol., 2008

2007
Genetic Progression and the Waiting Time to Cancer.
PLoS Comput. Biol., 2007

2006
Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype.
Proceedings of the Advances in Neural Information Processing Systems 19, 2006

Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV.
Proceedings of the Data Integration in the Life Sciences, Third International Workshop, 2006

2005
Learning Multiple Evolutionary Pathways from Cross-Sectional Data.
J. Comput. Biol., 2005

ROCR: visualizing classifier performance in R.
Bioinform., 2005

Estimating cancer survival and clinical outcome based on genetic tumor progression scores.
Bioinform., 2005

Computational methods for the design of effective therapies against drug resistant HIV strains.
Bioinform., 2005

Mtreemix: a software package for learning and using mixture models of mutagenetic trees.
Bioinform., 2005

Characterization of Novel HIV Drug Resistance Mutations Using Clustering, Multidimensional Scaling and SVM-Based Feature Ranking.
Proceedings of the Knowledge Discovery in Databases: PKDD 2005, 2005

Supervised and Unsupervised Approaches for Analyzing Covariation and Phenotypic Impact of HIV Drug Resistance Mutations.
Proceedings of the Lernen, 2005

2004
Computational analysis of HIV drug resistance data.
PhD thesis, 2004

Learning Mixtures of Localized Rules by Maximizing the Area Under the ROC Curve.
Proceedings of the ROC Analysis in Artificial Intelligence, 1st International Workshop, 2004

2003
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes.
Nucleic Acids Res., 2003

Methods for optimizing antiviral combination therapies.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002
Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype.
Proc. Natl. Acad. Sci. USA, 2002

2001
Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests.
IEEE Intell. Syst., 2001

Identifying drug resistance-associated patterns in HIV genotypes.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001


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