Niko Beerenwinkel
Orcid: 0000-0002-0573-6119
According to our database1,
Niko Beerenwinkel
authored at least 99 papers
between 2001 and 2024.
Collaborative distances:
Collaborative distances:
Timeline
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Online presence:
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on zbmath.org
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on d-nb.info
On csauthors.net:
Bibliography
2024
J. Comput. Biol., 2024
Proceedings of the Research in Computational Molecular Biology, 2024
2023
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
The Mixtures and the Neural Critics: On the Pointwise Mutual Information Profiles of Fine Distributions.
CoRR, 2023
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
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
Proceedings of the Research in Computational Molecular Biology, 2022
Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022
2021
PLoS Comput. Biol., 2021
PLoS Comput. Biol., 2021
PLoS Comput. Biol., 2021
CoRR, 2021
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data.
Bioinform., 2021
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Briefings Bioinform., 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
Bioinform., 2020
Proceedings of the Research in Computational Molecular Biology, 2020
2019
BMC Bioinform., 2019
Bioinform., 2019
2018
BMC Medical Informatics Decis. Mak., 2018
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
Bioinform., 2018
Bioinform., 2018
Proceedings of the Research in Computational Molecular Biology, 2018
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
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
2016
Bioinform., 2016
Bioinform., 2016
Bioinform., 2016
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
Proceedings of the 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2016
2015
PLoS Comput. Biol., 2015
PLoS Comput. Biol., 2015
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2015
2014
IEEE ACM Trans. Comput. Biol. Bioinform., 2014
PLoS Comput. Biol., 2014
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction.
Bioinform., 2014
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
J. Comput. Biol., 2013
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
Bioinform., 2012
2011
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
Proceedings of the Bioinformatics and Computational Biology, 2009
2008
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
J. Comput. Biol., 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
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
Nucleic Acids Res., 2003
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
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