Niko Beerenwinkel

117 papers A* 1B 14C 2Journal 85Unranked 14

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop. PLoS Comput. Biol. David Dreifuss, Ivan Topolsky, Pelin Icer Baykal, Niko Beerenwinkel
2025	J	`jnl`	Bayesian inference of fitness landscapes via tree-structured branching processes. Bioinform. Xiang Ge Luo, Jack Kuipers, Kevin Rupp, Koichi Takahashi, Niko Beerenwinkel
2025	J	`jnl`	ELLIPSIS: robust quantification of splicing in scRNA-seq. Bioinform. Marie Van Hecke, Niko Beerenwinkel, Thibault Lootens, Jan Fostier, Robrecht Raedt, Kathleen Marchal
2025	—	`conf`	Fair Clustering: A Causal Perspective. CLeaR Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers
2025	J	`jnl`	HIVMedQA: Benchmarking large language models for HIV medical decision support. CoRR Gonzalo Cardenal-Antolin, Jacques Fellay, Bashkim Jaha, Roger D. Kouyos, Niko Beerenwinkel, Diane Duroux
2025	J	`jnl`	On the Properties and Estimation of Pointwise Mutual Information Profiles. Trans. Mach. Learn. Res. Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx
2025	J	`jnl`	Single-cell copy number calling and event history reconstruction. Bioinform. Jack Kuipers, Mustafa Anil Tuncel, Pedro F. Ferreira, Katharina Jahn, Niko Beerenwinkel
2024	J	`jnl`	Correcting for Observation Bias in Cancer Progression Modeling. J. Comput. Biol. Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel
2024	J	`jnl`	Modeling metastatic progression from cross-sectional cancer genomics data. Bioinform. Kevin Rupp, Andreas Lösch, Y. Linda Hu, Chenxi Nie, Rudolf Schill, Maren Klever, Simon Pfahler, Lars Grasedyck, Tilo Wettig, Niko Beerenwinkel, Rainer Spang
2024	J	`jnl`	Oncotree2vec - a method for embedding and clustering of tumor mutation trees. Bioinform. Monica-Andreea Baciu-Dragan, Niko Beerenwinkel
2024	B	`conf`	Overcoming Observation Bias for Cancer Progression Modeling. RECOMB Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel
2023	J	`jnl`	Bayesian Structure Learning and Sampling of Bayesian Networks with the J. Stat. Softw. Polina Suter, Jack Kuipers, Giusi Moffa, Niko Beerenwinkel
2023	A*	`conf`	Beyond Normal: On the Evaluation of Mutual Information Estimators. NeurIPS Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx
2023	J	`jnl`	Beyond Normal: On the Evaluation of Mutual Information Estimators. CoRR Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx
2023	J	`jnl`	Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression. Bioinform. Kim Philipp Jablonski, Niko Beerenwinkel
2023	J	`jnl`	Fair Clustering: A Causal Perspective. CoRR Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers
2023	J	`jnl`	Predicting tumour content of liquid biopsies from cell-free DNA. BMC Bioinform. Mathias Cardner, Francesco Marass, Erika Gedvilaite, Julie L. Yang, Dana W. Y. Tsui, Niko Beerenwinkel
2023	J	`jnl`	The Mixtures and the Neural Critics: On the Pointwise Mutual Information Profiles of Fine Distributions. CoRR Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx
2022	J	`jnl`	Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. Briefings Bioinform. Polina Suter, Jack Kuipers, Niko Beerenwinkel
2022	J	`jnl`	Identifying cancer pathway dysregulations using differential causal effects. Bioinform. Kim Philipp Jablonski, Martin Pirkl, Domagoj Cevid, Peter Bühlmann, Niko Beerenwinkel
2022	B	`conf`	Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees. RECOMB Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel
2022	B	`conf`	Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. RECOMB Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel
2022	J	`jnl`	Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS Comput. Biol. Polina Suter, Eva Dazert, Jack Kuipers, Charlotte K. Y. Ng, Tuyana Boldanova, Michael N. Hall, Markus H. Heim, Niko Beerenwinkel
2022	—	`conf`	Reproducibility of Bioinformatics Tools. IPDPS Workshops Pelin Icer Baykal, Niko Beerenwinkel, Serghei Mangul
2022	J	`jnl`	Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. Bioinform. Jack Kuipers, Jochen Singer, Niko Beerenwinkel
2022	J	`jnl`	scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. PLoS Comput. Biol. Anne Bertolini, Michael Prummer, Mustafa Anil Tuncel, Ulrike Menzel, María Lourdes Rosano-González, Jack Kuipers, Daniel J. Stekhoven, Tumor Profiler Consortium, Niko Beerenwinkel, Franziska Singer
2021	J	`jnl`	Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Comput. Biol. Susana Posada-Céspedes, Gert van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger D. Kouyos, Huldrych F. Günthard, Niko Beerenwinkel
2021	J	`jnl`	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria Jesus Martin, Roman Martin, Julian O. Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Pineros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna J. Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz
2021	J	`jnl`	Drug-induced resistance evolution necessitates less aggressive treatment. PLoS Comput. Biol. Teemu Kuosmanen, Johannes Cairns, Robert Noble, Niko Beerenwinkel, Tommi Mononen, Ville Mustonen
2021	J	`jnl`	Inferring perturbation profiles of cancer samples. Bioinform. Martin Pirkl, Niko Beerenwinkel
2021	J	`jnl`	Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference. CoRR Fritz M. Bayer, Giusi Moffa, Niko Beerenwinkel, Jack Kuipers
2021	J	`jnl`	Statistical tests for intra-tumour clonal co-occurrence and exclusivity. PLoS Comput. Biol. Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel
2021	J	`jnl`	The Bourque distances for mutation trees of cancers. Algorithms Mol. Biol. Katharina Jahn, Niko Beerenwinkel, Louxin Zhang
2021	J	`jnl`	V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. Bioinform. Susana Posada-Céspedes, David Seifert, Ivan Topolsky, Kim Philipp Jablonski, Karin J. Metzner, Niko Beerenwinkel
2020	J	`jnl`	A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment. PLoS Comput. Biol. Ewa Szczurek, Tyll Krüger, Barbara Klink, Niko Beerenwinkel
2020	B	`conf`	Bayesian Non-parametric Clustering of Single-Cell Mutation Profiles. RECOMB Nico Borgsmüller, José Bonet, Francesco Marass, Abel González-Pérez, Núria López-Bigas, Niko Beerenwinkel
2020	J	`jnl`	BnpC: Bayesian non-parametric clustering of single-cell mutation profiles. Bioinform. Nico Borgsmüller, José Bonet, Francesco Marass, Abel González-Pérez, Núria López-Bigas, Niko Beerenwinkel
2020	J	`jnl`	Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. PLoS Comput. Biol. Simon Dirmeier, Christopher Dächert, Martijn van Hemert, Ali Tas, Natacha S. Ogando, Frank J. M. van Kuppeveld, Ralf Bartenschlager, Lars Kaderali, Marco Binder, Niko Beerenwinkel
2020	J	`jnl`	Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. PLoS Comput. Biol. Brian Lang, Jack Kuipers, Benjamin Misselwitz, Niko Beerenwinkel
2020	C	`conf`	The Bourque Distances for Mutation Trees of Cancers. WABI Katharina Jahn, Niko Beerenwinkel, Louxin Zhang
2019	J	`jnl`	12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
2019	J	`jnl`	Bioinformatics for precision oncology. Briefings Bioinform. Jochen Singer, Anja Irmisch, Hans-Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
2019	J	`jnl`	Estimating the predictability of cancer evolution. Bioinform. Sayed-Rzgar Hosseini, Ramón Díaz-Uriarte, Florian Markowetz, Niko Beerenwinkel
2019	J	`jnl`	Inferring signalling dynamics by integrating interventional with observational data. Bioinform. Mathias Cardner, Nathalie Meyer-Schaller, Gerhard Christofori, Niko Beerenwinkel
2019	J	`jnl`	PyBDA: a command line tool for automated analysis of big biological data sets. BMC Bioinform. Simon Dirmeier, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel
2018	J	`jnl`	Ensemble outlier detection and gene selection in triple-negative breast cancer data. BMC Bioinform. Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
2018	J	`jnl`	Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. Bioinform. Sumana Srivatsa, Jack Kuipers, Fabian Schmich, Simone Eicher, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel
2018	B	`conf`	Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. RECOMB Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel
2018	B	`conf`	ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. RECOMB Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan
2018	J	`jnl`	NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. Bioinform. Jochen Singer, Hans-Joachim Ruscheweyh, Ariane L. Hofmann, Thomas Thurnherr, Franziska Singer, Nora C. Toussaint, Charlotte K. Y. Ng, Salvatore Piscuoglio, Christian Beisel, Gerhard Christofori, Reinhard Dummer, Michael N. Hall, Wilhelm Krek, Mitchell P. Levesque, Markus G. Manz, Holger Moch, Andreas Papassotiropoulos, Daniel J. Stekhoven, Peter Wild, Thomas Wüst, Bernd Rinn, Niko Beerenwinkel
2018	J	`jnl`	Network-based integration of multi-omics data for prioritizing cancer genes. Bioinform. Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Luca Häfliger, Jonas Behr, Hesam Montazeri, Michael N. Hall, Niko Beerenwinkel
2018	B	`conf`	SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. RECOMB Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
2018	J	`jnl`	Single cell network analysis with a mixture of Nested Effects Models. Bioinform. Martin Pirkl, Niko Beerenwinkel
2018	J	`jnl`	SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics. BMC Medical Informatics Decis. Mak. Franziska Singer, Anja Irmisch, Nora C. Toussaint, Linda Grob, Jochen Singer, Thomas Thurnherr, Niko Beerenwinkel, Mitchell P. Levesque, Reinhard Dummer, Luca Quagliata, Sacha I. Rothschild, Andreas Wicki, Christian Beisel, Daniel J. Stekhoven
2017	J	`jnl`	Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472). Dagstuhl Reports Niko Beerenwinkel, Holger Fröhlich, Susan A. Murphy
2017	J	`jnl`	CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies. BMC Medical Informatics Decis. Mak. Meher K. Prakash, Brian Lang, Henriette Heinrich, Piero V. Valli, Peter Bauerfeind, Amnon Sonnenberg, Niko Beerenwinkel, Benjamin Misselwitz
2017	J	`jnl`	Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinform. Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
2017	J	`jnl`	ISMB/ECCB 2017 proceedings. Bioinform. Niko Beerenwinkel, Yana Bromberg
2017	J	`jnl`	Inferring modulators of genetic interactions with epistatic nested effects models. PLoS Comput. Biol. Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz
2017	J	`jnl`	Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS Comput. Biol. Remo Monti, Iros Barozzi, Marco Osterwalder, Elizabeth Lee, Momoe Kato, Tyler H. Garvin, Ingrid Plajzer-Frick, Catherine S. Pickle, Jennifer A. Akiyama, Veena Afzal, Niko Beerenwinkel, Diane E. Dickel, Axel Visel, Len A. Pennacchio
2017	J	`jnl`	pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. J. Comput. Biol. Simona Cristea, Jack Kuipers, Niko Beerenwinkel
2016	J	`jnl`	BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. Bioinform. Monica Golumbeanu, Pejman Mohammadi, Niko Beerenwinkel
2016	J	`jnl`	Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput. Biol. Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren
2016	—	`conf`	Detecting patterns of co-variation in deep-sequenced virus populations. ICCABS Susana Posada-Céspedes, David Seifert, Niko Beerenwinkel
2016	J	`jnl`	Large-scale inference of conjunctive Bayesian networks. Bioinform. Hesam Montazeri, Jack Kuipers, Roger D. Kouyos, Jürg Böni, Sabine Yerly, Thomas Klimkait, Vincent Aubert, Huldrych F. Günthard, Niko Beerenwinkel, The Swiss Hiv Cohort Study
2016	J	`jnl`	Linear effects models of signaling pathways from combinatorial perturbation data. Bioinform. Ewa Szczurek, Niko Beerenwinkel
2016	J	`jnl`	TiMEx: a waiting time model for mutually exclusive cancer alterations. Bioinform. Simona Constantinescu, Ewa Szczurek, Pejman Mohammadi, Jörg Rahnenführer, Niko Beerenwinkel
2016	B	`conf`	Tree Inference for Single-Cell Data. RECOMB Katharina Jahn, Jack Kuipers, Niko Beerenwinkel
2016	B	`conf`	pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. RECOMB Simona Cristea, Jack Kuipers, Niko Beerenwinkel
2015	J	`jnl`	Covering Pairs in Directed Acyclic Graphs. Comput. J. Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2015	—	`conf`	Finding Dense Subgraphs in Relational Graphs. ECML/PKDD (2) Vinay Jethava, Niko Beerenwinkel
2015	J	`jnl`	ISMB/ECCB 2015. Bioinform. Yves Moreau, Niko Beerenwinkel
2015	J	`jnl`	Identification of Constrained Cancer Driver Genes Based on Mutation Timing. PLoS Comput. Biol. Thomas Sakoparnig, Patrick Fried, Niko Beerenwinkel
2015	J	`jnl`	NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation. PLoS Comput. Biol. Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs F. Greber, Holger Fröhlich, Niko Beerenwinkel
2014	J	`jnl`	Challenges in RNA virus bioinformatics. Bioinform. Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer
2014	C	`conf`	Covering Pairs in Directed Acyclic Graphs. LATA Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2014	J	`jnl`	Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data. PLoS Comput. Biol. Sathej Gopalakrishnan, Hesam Montazeri, Stephan Menz, Niko Beerenwinkel, Wilhelm Huisinga
2014	J	`jnl`	Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. Bioinform. Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang, Niko Beerenwinkel, Achim Tresch
2014	J	`jnl`	HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. IEEE ACM Trans. Comput. Biol. Bioinform. Sandhya Prabhakaran, Mélanie Rey, Osvaldo Zagordi, Niko Beerenwinkel, Volker Roth
2014	B	`conf`	Modeling Mutual Exclusivity of Cancer Mutations. RECOMB Ewa Szczurek, Niko Beerenwinkel
2014	J	`jnl`	Modeling Mutual Exclusivity of Cancer Mutations. PLoS Comput. Biol. Ewa Szczurek, Niko Beerenwinkel
2014	B	`conf`	Viral Quasispecies Assembly via Maximal Clique Enumeration. RECOMB Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel
2014	J	`jnl`	Viral Quasispecies Assembly via Maximal Clique Enumeration. PLoS Comput. Biol. Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel
2014	—	`conf`	Viral quasispecies assembly from paired-end reads. ICCABS Armin Töpfer, Niko Beerenwinkel
2013	J	`jnl`	Covering Pairs in Directed Acyclic Graphs. CoRR Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2013	J	`jnl`	Probabilistic Inference of Viral Quasispecies Subject to Recombination. J. Comput. Biol. Armin Töpfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel
2013	—	`conf`	Probing of viral diversity by global haplotype prediction. ICCABS Armin Töpfer, Francesca Di Giallonardo, Karin J. Metzner, Huldrych F. Günthard, Niko Beerenwinkel
2013	J	`jnl`	The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients. PLoS Comput. Biol. Niko Beerenwinkel, Hesam Montazeri, Heike Schuhmacher, Patrick Knupfer, Viktor von Wyl, Hansjakob Furrer, Manuel Battegay, Bernard Hirschel, Matthias Cavassini, Pietro Vernazza, Enos Bernasconi, Sabine Yerly, Jürg Böni, Thomas Klimkait, Cristina Cellerai, Huldrych F. Günthard
2012	J	`jnl`	Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing. J. Comput. Biol. Thomas Sakoparnig, Tobias Kockmann, Renato Paro, Christian Beisel, Niko Beerenwinkel
2012	J	`jnl`	Efficient sampling for Bayesian inference of conjunctive Bayesian networks. Bioinform. Thomas Sakoparnig, Niko Beerenwinkel
2012	B	`conf`	Probabilistic Inference of Viral Quasispecies Subject to Recombination. RECOMB Osvaldo Zagordi, Armin Töpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel
2012	J	`jnl`	Stability of gene rankings from RNAi screens. Bioinform. Juliane Siebourg, Gunter Merdes, Benjamin Misselwitz, Wolf-Dietrich Hardt, Niko Beerenwinkel
2011	J	`jnl`	Evolutionary Games with Affine Fitness Functions: Applications to Cancer. Dyn. Games Appl. Moritz Gerstung, Hani Nakhoul, Niko Beerenwinkel
2011	J	`jnl`	ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinform. Osvaldo Zagordi, Arnab Bhattacharya, Nicholas Eriksson, Niko Beerenwinkel
2010	J	`jnl`	Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. J. Comput. Biol. Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel
2009	B	`conf`	Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. RECOMB Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel
2009	—	`conf`	Multiple Sequence Alignment System for Pyrosequencing Reads. BICoB Fahad Saeed, Ashfaq A. Khokhar, Osvaldo Zagordi, Niko Beerenwinkel
2009	J	`jnl`	Quantifying cancer progression with conjunctive Bayesian networks. Bioinform. Moritz Gerstung, Michael Baudis, Holger Moch, Niko Beerenwinkel
2008	J	`jnl`	Viral Population Estimation Using Pyrosequencing. PLoS Comput. Biol. Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel
2007	J	`jnl`	Genetic Progression and the Waiting Time to Cancer. PLoS Comput. Biol. Niko Beerenwinkel, Tibor Antal, David Dingli, Arne Traulsen, Kenneth W. Kinzler, Victor E. Velculescu, Bert Vogelstein, Martin A. Nowak
2006	—	`conf`	Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV. DILS Kirsten Roomp, Niko Beerenwinkel, Tobias Sing, Eugen Schülter, Joachim Büch, Saleta Sierra-Aragon, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig
2006	—	`conf`	Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype. NIPS Tobias Sing, Niko Beerenwinkel
2005	—	`conf`	Characterization of Novel HIV Drug Resistance Mutations Using Clustering, Multidimensional Scaling and SVM-Based Feature Ranking. PKDD Tobias Sing, Valentina Svicher, Niko Beerenwinkel, Francesca Ceccherini-Silberstein, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, Mark Oette, Jürgen K. Rockstroh, Gerd Fätkenheuer, Carlo-Federico Perno, Thomas Lengauer
2005	J	`jnl`	Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinform. Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kirsten Roomp, Igor Savenkov, Roman Fischer, Daniel Hoffmann, Joachim Selbig, Klaus Korn, Hauke Walter, Thomas Berg, Patrick Braun, Gerd Fätkenheuer, Mark Oette, Jürgen K. Rockstroh, Bernd Kupfer, Rolf Kaiser, Martin Däumer
2005	J	`jnl`	Estimating cancer survival and clinical outcome based on genetic tumor progression scores. Bioinform. Jörg Rahnenführer, Niko Beerenwinkel, Wolfgang A. Schulz, Christian Hartmann, Andreas von Deimling, Bernd Wullich, Thomas Lengauer
2005	J	`jnl`	Learning Multiple Evolutionary Pathways from Cross-Sectional Data. J. Comput. Biol. Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer
2005	J	`jnl`	Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinform. Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig, Thomas Lengauer
2005	J	`jnl`	ROCR: visualizing classifier performance in R. Bioinform. Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
2005	—	`conf`	Supervised and Unsupervised Approaches for Analyzing Covariation and Phenotypic Impact of HIV Drug Resistance Mutations. LWA Tobias Sing, Niko Beerenwinkel, Thomas Lengauer, Valentina Svicher, Francesca Ceccherini-Silberstein, Carlo-Federico Perno
2004	—	`—`	Computational analysis of HIV drug resistance data. Niko Beerenwinkel
2004	—	`conf`	Learning Mixtures of Localized Rules by Maximizing the Area Under the ROC Curve. ROCAI Tobias Sing, Niko Beerenwinkel, Thomas Lengauer
2004	B	`conf`	Learning multiple evolutionary pathways from cross-sectional data. RECOMB Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer
2003	J	`jnl`	Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res. Niko Beerenwinkel, Martin Däumer, Mark Oette, Klaus Korn, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig, Hauke Walter
2003	—	`conf`	Methods for optimizing antiviral combination therapies. ISMB (Supplement of Bioinformatics) Niko Beerenwinkel, Thomas Lengauer, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, Joachim Selbig
2002	J	`jnl`	Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype. Proc. Natl. Acad. Sci. USA Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, Joachim Selbig
2001	J	`jnl`	Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests. IEEE Intell. Syst. Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, Joachim Selbig
2001	—	`conf`	Identifying drug resistance-associated patterns in HIV genotypes. German Conference on Bioinformatics Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, Joachim Selbig