Niko Beerenwinkel

ORCID

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 64

Top Venues

Publications

Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel
Overcoming Observation Bias for Cancer Progression Modeling. RECOMB (2024)
Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers
Fair Clustering: A Causal Perspective. CoRR (2023)
Kim Philipp Jablonski, Niko Beerenwinkel
Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression. Bioinform. 39 (8) (2023)
Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx
Beyond Normal: On the Evaluation of Mutual Information Estimators. CoRR (2023)
Polina Suter, Jack Kuipers, Giusi Moffa, Niko Beerenwinkel
Package BiDAG. J. Stat. Softw. 105 (9) (2023)
Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx
Beyond Normal: On the Evaluation of Mutual Information Estimators. NeurIPS (2023)
Mathias Cardner, Francesco Marass, Erika Gedvilaite, Julie L. Yang, Dana W. Y. Tsui, Niko Beerenwinkel
Predicting tumour content of liquid biopsies from cell-free DNA. BMC Bioinform. 24 (1) (2023)
Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx
The Mixtures and the Neural Critics: On the Pointwise Mutual Information Profiles of Fine Distributions. CoRR (2023)
Pelin Icer Baykal, Niko Beerenwinkel, Serghei Mangul
Reproducibility of Bioinformatics Tools. IPDPS Workshops (2022)
Polina Suter, Eva Dazert, Jack Kuipers, Charlotte K. Y. Ng, Tuyana Boldanova, Michael N. Hall, Markus H. Heim, Niko Beerenwinkel
Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS Comput. Biol. 18 (9) (2022)
Kim Philipp Jablonski, Martin Pirkl, Domagoj Cevid, Peter Bühlmann, Niko Beerenwinkel
Identifying cancer pathway dysregulations using differential causal effects. Bioinform. 38 (6) (2022)
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
scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. PLoS Comput. Biol. 18 (6) (2022)
Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel
Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees. RECOMB (2022)
Jack Kuipers, Jochen Singer, Niko Beerenwinkel
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. Bioinform. 38 (20) (2022)
Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel
Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. RECOMB (2022)
Polina Suter, Jack Kuipers, Niko Beerenwinkel
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. Briefings Bioinform. 23 (4) (2022)
Fritz M. Bayer, Giusi Moffa, Niko Beerenwinkel, Jack Kuipers
Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference. CoRR (2021)
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
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22 (2) (2021)
Martin Pirkl, Niko Beerenwinkel
Inferring perturbation profiles of cancer samples. Bioinform. 37 (16) (2021)
Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel
Statistical tests for intra-tumour clonal co-occurrence and exclusivity. PLoS Comput. Biol. 17 (12) (2021)
Teemu Kuosmanen, Johannes Cairns, Robert Noble, Niko Beerenwinkel, Tommi Mononen, Ville Mustonen
Drug-induced resistance evolution necessitates less aggressive treatment. PLoS Comput. Biol. 17 (9) (2021)
Susana Posada-Céspedes, Gert van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger D. Kouyos, Huldrych F. Günthard, Niko Beerenwinkel
Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Comput. Biol. 17 (9) (2021)
Katharina Jahn, Niko Beerenwinkel, Louxin Zhang
The Bourque distances for mutation trees of cancers. Algorithms Mol. Biol. 16 (1) (2021)
Susana Posada-Céspedes, David Seifert, Ivan Topolsky, Kim Philipp Jablonski, Karin J. Metzner, Niko Beerenwinkel
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. Bioinform. 37 (12) (2021)
Katharina Jahn, Niko Beerenwinkel, Louxin Zhang
The Bourque Distances for Mutation Trees of Cancers. WABI (2020)
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
Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. PLoS Comput. Biol. 16 (2) (2020)
Ewa Szczurek, Tyll Krüger, Barbara Klink, Niko Beerenwinkel
A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment. PLoS Comput. Biol. 16 (10) (2020)
Brian Lang, Jack Kuipers, Benjamin Misselwitz, Niko Beerenwinkel
Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. PLoS Comput. Biol. 16 (2) (2020)
Nico Borgsmüller, José Bonet, Francesco Marass, Abel Gonzalez-Perez, Núria López-Bigas, Niko Beerenwinkel
Bayesian Non-parametric Clustering of Single-Cell Mutation Profiles. RECOMB (2020)
Nico Borgsmüller, José Bonet, Francesco Marass, Abel Gonzalez-Perez, Núria López-Bigas, Niko Beerenwinkel
BnpC: Bayesian non-parametric clustering of single-cell mutation profiles. Bioinform. 36 (19) (2020)
Jochen Singer, Anja Irmisch, Hans-Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Bioinformatics for precision oncology. Briefings Bioinform. 20 (3) (2019)
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
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7 (2019)
Mathias Cardner, Nathalie Meyer-Schaller, Gerhard Christofori, Niko Beerenwinkel
Inferring signalling dynamics by integrating interventional with observational data. Bioinform. 35 (14) (2019)
Simon Dirmeier, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel
PyBDA: a command line tool for automated analysis of big biological data sets. BMC Bioinform. 20 (1) (2019)
Sayed-Rzgar Hosseini, Ramón Díaz-Uriarte, Florian Markowetz, Niko Beerenwinkel
Estimating the predictability of cancer evolution. Bioinform. 35 (14) (2019)
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
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. Bioinform. 34 (1) (2018)
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
SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics. BMC Medical Informatics Decis. Mak. 18 (1) (2018)
Martin Pirkl, Niko Beerenwinkel
Single cell network analysis with a mixture of Nested Effects Models. Bioinform. 34 (17) (2018)
Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan
ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. RECOMB (2018)
Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Luca Häfliger, Jonas Behr, Hesam Montazeri, Michael N. Hall, Niko Beerenwinkel
Network-based integration of multi-omics data for prioritizing cancer genes. Bioinform. 34 (14) (2018)
Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
Ensemble outlier detection and gene selection in triple-negative breast cancer data. BMC Bioinform. 19 (1) (2018)
Sumana Srivatsa, Jack Kuipers, Fabian Schmich, Simone Eicher, Mario Emmenlauer, Christoph Dehio, Niko Beerenwinkel
Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. Bioinform. 34 (13) (2018)
Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. RECOMB (2018)
Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel
Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. RECOMB (2018)
Meher K. Prakash, Brian Lang, Henriette Heinrich, Piero V. Valli, Peter Bauerfeind, Amnon Sonnenberg, Niko Beerenwinkel, Benjamin Misselwitz
CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies. BMC Medical Informatics Decis. Mak. 17 (1) (2017)
Simona Cristea, Jack Kuipers, Niko Beerenwinkel
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. J. Comput. Biol. 24 (6) (2017)
Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinform. 18 (1) (2017)
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
Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS Comput. Biol. 13 (8) (2017)
Niko Beerenwinkel, Yana Bromberg
ISMB/ECCB 2017 proceedings. Bioinform. 33 (14) (2017)
Niko Beerenwinkel, Holger Fröhlich, Susan A. Murphy
Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472). Dagstuhl Reports 7 (11) (2017)
Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz
Inferring modulators of genetic interactions with epistatic nested effects models. PLoS Comput. Biol. 13 (4) (2017)
Katharina Jahn, Jack Kuipers, Niko Beerenwinkel
Tree Inference for Single-Cell Data. RECOMB (2016)
Simona Constantinescu, Ewa Szczurek, Pejman Mohammadi, Jörg Rahnenführer, Niko Beerenwinkel
TiMEx: a waiting time model for mutually exclusive cancer alterations. Bioinform. 32 (7) (2016)
Simona Cristea, Jack Kuipers, Niko Beerenwinkel
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. RECOMB (2016)
Monica Golumbeanu, Pejman Mohammadi, Niko Beerenwinkel
BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. Bioinform. 32 (7) (2016)
Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren
Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput. Biol. 12 (2) (2016)
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
Large-scale inference of conjunctive Bayesian networks. Bioinform. 32 (17) (2016)
Susana Posada-Céspedes, David Seifert, Niko Beerenwinkel
Detecting patterns of co-variation in deep-sequenced virus populations. ICCABS (2016)
Ewa Szczurek, Niko Beerenwinkel
Linear effects models of signaling pathways from combinatorial perturbation data. Bioinform. 32 (12) (2016)
Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs Greber, Holger Fröhlich, Niko Beerenwinkel
NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation. PLoS Comput. Biol. 11 (4) (2015)
Vinay Jethava, Niko Beerenwinkel
Finding Dense Subgraphs in Relational Graphs. ECML/PKDD (2) (2015)
Thomas Sakoparnig, Patrick Fried, Niko Beerenwinkel
Identification of Constrained Cancer Driver Genes Based on Mutation Timing. PLoS Comput. Biol. 11 (1) (2015)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. Comput. J. 58 (7) (2015)
Yves Moreau, Niko Beerenwinkel
ISMB/ECCB 2015. Bioinform. 31 (12) (2015)
Sathej Gopalakrishnan, Hesam Montazeri, Stephan Menz, Niko Beerenwinkel, Wilhelm Huisinga
Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data. PLoS Comput. Biol. 10 (11) (2014)
Ewa Szczurek, Niko Beerenwinkel
Modeling Mutual Exclusivity of Cancer Mutations. RECOMB (2014)
Ewa Szczurek, Niko Beerenwinkel
Modeling Mutual Exclusivity of Cancer Mutations. PLoS Comput. Biol. 10 (3) (2014)
Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang, Niko Beerenwinkel, Achim Tresch
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. Bioinform. 30 (3) (2014)
Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel
Viral Quasispecies Assembly via Maximal Clique Enumeration. PLoS Comput. Biol. 10 (3) (2014)
Sandhya Prabhakaran, Mélanie Rey, Osvaldo Zagordi, Niko Beerenwinkel, Volker Roth
HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (1) (2014)
Armin Töpfer, Niko Beerenwinkel
Viral quasispecies assembly from paired-end reads. ICCABS (2014)
Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel
Viral Quasispecies Assembly via Maximal Clique Enumeration. RECOMB (2014)
Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer
Challenges in RNA virus bioinformatics. Bioinform. 30 (13) (2014)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. LATA (2014)
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
The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients. PLoS Comput. Biol. 9 (8) (2013)
Armin Töpfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel
Probabilistic Inference of Viral Quasispecies Subject to Recombination. J. Comput. Biol. 20 (2) (2013)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. CoRR (2013)
Armin Töpfer, Francesca Di Giallonardo, Karin J. Metzner, Huldrych F. Günthard, Niko Beerenwinkel
Probing of viral diversity by global haplotype prediction. ICCABS (2013)
Osvaldo Zagordi, Armin Töpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel
Probabilistic Inference of Viral Quasispecies Subject to Recombination. RECOMB (2012)
Thomas Sakoparnig, Niko Beerenwinkel
Efficient sampling for Bayesian inference of conjunctive Bayesian networks. Bioinform. 28 (18) (2012)
Thomas Sakoparnig, Tobias Kockmann, Renato Paro, Christian Beisel, Niko Beerenwinkel
Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing. J. Comput. Biol. 19 (2) (2012)
Juliane Siebourg, Gunter Merdes, Benjamin Misselwitz, Wolf-Dietrich Hardt, Niko Beerenwinkel
Stability of gene rankings from RNAi screens. Bioinform. 28 (12) (2012)
Osvaldo Zagordi, Arnab Bhattacharya, Nicholas Eriksson, Niko Beerenwinkel
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinform. 12 (2011)
Moritz Gerstung, Hani Nakhoul, Niko Beerenwinkel
Evolutionary Games with Affine Fitness Functions: Applications to Cancer. Dyn. Games Appl. 1 (3) (2011)
Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. J. Comput. Biol. 17 (3) (2010)
Moritz Gerstung, Michael Baudis, Holger Moch, Niko Beerenwinkel
Quantifying cancer progression with conjunctive Bayesian networks. Bioinform. 25 (21) (2009)
Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. RECOMB (2009)
Fahad Saeed, Ashfaq A. Khokhar, Osvaldo Zagordi, Niko Beerenwinkel
Multiple Sequence Alignment System for Pyrosequencing Reads. BICoB (2009)
Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel
Viral Population Estimation Using Pyrosequencing. PLoS Comput. Biol. 4 (5) (2008)
Niko Beerenwinkel, Tibor Antal, David Dingli, Arne Traulsen, Kenneth W. Kinzler, Victor E. Velculescu, Bert Vogelstein, Martin A. Nowak
Genetic Progression and the Waiting Time to Cancer. PLoS Comput. Biol. 3 (11) (2007)
Tobias Sing, Niko Beerenwinkel
Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype. NIPS (2006)
Kirsten Roomp, Niko Beerenwinkel, Tobias Sing, Eugen Schülter, Joachim Büch, Saleta Sierra-Aragon, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig
Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV. DILS (2006)
Jörg Rahnenführer, Niko Beerenwinkel, Wolfgang A. Schulz, Christian Hartmann, Andreas von Deimling, Bernd Wullich, Thomas Lengauer
Estimating cancer survival and clinical outcome based on genetic tumor progression scores. Bioinform. 21 (10) (2005)
Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig, Thomas Lengauer
Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinform. 21 (9) (2005)
Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
ROCR: visualizing classifier performance in R. Bioinform. 21 (20) (2005)
Tobias Sing, Niko Beerenwinkel, Thomas Lengauer, Valentina Svicher, Francesca Ceccherini-Silberstein, Carlo-Federico Perno
Supervised and Unsupervised Approaches for Analyzing Covariation and Phenotypic Impact of HIV Drug Resistance Mutations. LWA (2005)
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
Characterization of Novel HIV Drug Resistance Mutations Using Clustering, Multidimensional Scaling and SVM-Based Feature Ranking. PKDD (2005)
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
Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinform. 21 (21) (2005)
Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer
Learning Multiple Evolutionary Pathways from Cross-Sectional Data. J. Comput. Biol. 12 (6) (2005)
Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer
Learning multiple evolutionary pathways from cross-sectional data. RECOMB (2004)

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Publication Activity (10 Years)

Top Topics

Top Venues

Niko Beerenwinkel