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2020 – today
- 2024
[j70]Rudolf Schill
, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel:
Correcting for Observation Bias in Cancer Progression Modeling. J. Comput. Biol. 31(10): 927-945 (2024)- [c30]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: 217-234 - 2023
- [j69]Kim Philipp Jablonski, Niko Beerenwinkel:
Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression. Bioinform. 39(8) (2023) - [j68]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): 368 (2023) - [j67]Polina Suter, Jack Kuipers, Giusi Moffa, Niko Beerenwinkel:
Bayesian Structure Learning and Sampling of Bayesian Networks with the R Package BiDAG. J. Stat. Softw. 105(9) (2023) - [c29]Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx:
Beyond Normal: On the Evaluation of Mutual Information Estimators. NeurIPS 2023 - [i7]Pawel Czyz, Frederic Grabowski, Julia E. Vogt, Niko Beerenwinkel, Alexander Marx:
Beyond Normal: On the Evaluation of Mutual Information Estimators. CoRR abs/2306.11078 (2023) - [i6]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 abs/2310.10240 (2023) - [i5]Fritz M. Bayer, Drago Plecko, Niko Beerenwinkel, Jack Kuipers:
Fair Clustering: A Causal Perspective. CoRR abs/2312.09061 (2023) - 2022
- [j66]Polina Suter, Jack Kuipers, Niko Beerenwinkel:
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. Briefings Bioinform. 23(4) (2022) - [j65]Kim Philipp Jablonski, Martin Pirkl, Domagoj Cevid, Peter Bühlmann, Niko Beerenwinkel:
Identifying cancer pathway dysregulations using differential causal effects. Bioinform. 38(6): 1550-1559 (2022) - [j64]Jack Kuipers, Jochen Singer, Niko Beerenwinkel:
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. Bioinform. 38(20): 4713-4719 (2022) - [j63]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) - [j62]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): 1009767 (2022) - [c28]Pelin Icer Baykal, Niko Beerenwinkel, Serghei Mangul:
Reproducibility of Bioinformatics Tools. IPDPS Workshops 2022: 216 - [c27]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: 304-305 - [c26]Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel:
Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. RECOMB 2022: 380-381 - 2021
- [j61]Katharina Jahn, Niko Beerenwinkel, Louxin Zhang:
The Bourque distances for mutation trees of cancers. Algorithms Mol. Biol. 16(1): 9 (2021) - [j60]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): 642-663 (2021) - [j59]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): 1673-1680 (2021) - [j58]Martin Pirkl, Niko Beerenwinkel:
Inferring perturbation profiles of cancer samples. Bioinform. 37(16): 2441-2449 (2021) - [j57]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) - [j56]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) - [j55]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) - [i4]Fritz M. Bayer, Giusi Moffa, Niko Beerenwinkel, Jack Kuipers:
Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference. CoRR abs/2112.09217 (2021) - 2020
- [j54]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): 4854-4859 (2020) - [j53]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) - [j52]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) - [j51]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) - [c25]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: 229-230 - [c24]Katharina Jahn, Niko Beerenwinkel, Louxin Zhang:
The Bourque Distances for Mutation Trees of Cancers. WABI 2020: 14:1-14:22
2010 – 2019
- 2019
- [j50]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): 778-788 (2019) - [j49]Sayed-Rzgar Hosseini, Ramón Díaz-Uriarte, Florian Markowetz, Niko Beerenwinkel:
Estimating the predictability of cancer evolution. Bioinform. 35(14): i389-i397 (2019) - [j48]Mathias Cardner, Nathalie Meyer-Schaller, Gerhard Christofori, Niko Beerenwinkel:
Inferring signalling dynamics by integrating interventional with observational data. Bioinform. 35(14): i577-i585 (2019) - [j47]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): 564:1-564:6 (2019) - [i3]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: e27885 (2019) - 2018
- [j46]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): 107-108 (2018) - [j45]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): i519-i527 (2018) - [j44]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): 2441-2448 (2018) - [j43]Martin Pirkl, Niko Beerenwinkel:
Single cell network analysis with a mixture of Nested Effects Models. Bioinform. 34(17): i964-i971 (2018) - [j42]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): 168:1-168:15 (2018) - [j41]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): 89:1-89:18 (2018) - [c23]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: 269-270 - [c22]Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan:
ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. RECOMB 2018: 283-284 - [c21]Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel:
SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. RECOMB 2018: 285-286 - 2017
- [j40]Niko Beerenwinkel, Yana Bromberg:
ISMB/ECCB 2017 proceedings. Bioinform. 33(14): i1-i2 (2017) - [j39]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): 8:1-8:15 (2017) - [j38]Simona Cristea, Jack Kuipers, Niko Beerenwinkel:
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. J. Comput. Biol. 24(6): 603-615 (2017) - [j37]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): 80:1-80:16 (2017) - [j36]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) - [j35]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) - [i2]Niko Beerenwinkel, Holger Fröhlich, Susan A. Murphy:
Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472). Dagstuhl Reports 7(11): 130-141 (2017) - 2016
- [j34]Simona Constantinescu, Ewa Szczurek, Pejman Mohammadi, Jörg Rahnenführer, Niko Beerenwinkel:
TiMEx: a waiting time model for mutually exclusive cancer alterations. Bioinform. 32(7): 968-975 (2016) - [j33]Monica Golumbeanu, Pejman Mohammadi, Niko Beerenwinkel:
BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. Bioinform. 32(7): 976-983 (2016) - [j32]Ewa Szczurek, Niko Beerenwinkel:
Linear effects models of signaling pathways from combinatorial perturbation data. Bioinform. 32(12): 297-305 (2016) - [j31]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): 727-735 (2016) - [j30]Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren:
Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput. Biol. 12(2) (2016) - [c20]Susana Posada-Céspedes, David Seifert, Niko Beerenwinkel:
Detecting patterns of co-variation in deep-sequenced virus populations. ICCABS 2016: 1 - [c19]Simona Cristea, Jack Kuipers, Niko Beerenwinkel:
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. RECOMB 2016: 65-82 - [c18]Katharina Jahn, Jack Kuipers, Niko Beerenwinkel:
Tree Inference for Single-Cell Data. RECOMB 2016: 252 - 2015
- [j29]Yves Moreau, Niko Beerenwinkel:
ISMB/ECCB 2015. Bioinform. 31(12): 1-2 (2015) - [j28]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. Comput. J. 58(7): 1673-1686 (2015) - [j27]Thomas Sakoparnig, Patrick Fried, Niko Beerenwinkel:
Identification of Constrained Cancer Driver Genes Based on Mutation Timing. PLoS Comput. Biol. 11(1) (2015) - [j26]Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs F. Greber, Holger Fröhlich, Niko Beerenwinkel:
NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation. PLoS Comput. Biol. 11(4) (2015) - [c17]Vinay Jethava, Niko Beerenwinkel:
Finding Dense Subgraphs in Relational Graphs. ECML/PKDD (2) 2015: 641-654 - 2014
- [j25]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): 414-419 (2014) - [j24]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): 1793-1799 (2014) - [j23]Ewa Szczurek, Niko Beerenwinkel:
Modeling Mutual Exclusivity of Cancer Mutations. PLoS Comput. Biol. 10(3) (2014) - [j22]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) - [j21]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) - [j20]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): 182-191 (2014) - [c16]Armin Töpfer, Niko Beerenwinkel:
Viral quasispecies assembly from paired-end reads. ICCABS 2014: 1 - [c15]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. LATA 2014: 126-137 - [c14]Ewa Szczurek, Niko Beerenwinkel:
Modeling Mutual Exclusivity of Cancer Mutations. RECOMB 2014: 307-308 - [c13]Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel:
Viral Quasispecies Assembly via Maximal Clique Enumeration. RECOMB 2014: 309-310 - 2013
- [j19]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): 113-123 (2013) - [j18]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) - [c12]Armin Töpfer, Francesca Di Giallonardo, Karin J. Metzner, Huldrych F. Günthard, Niko Beerenwinkel:
Probing of viral diversity by global haplotype prediction. ICCABS 2013: 1 - [i1]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. CoRR abs/1310.5037 (2013) - 2012
- [j17]Juliane Siebourg, Gunter Merdes, Benjamin Misselwitz, Wolf-Dietrich Hardt, Niko Beerenwinkel:
Stability of gene rankings from RNAi screens. Bioinform. 28(12): 1612-1618 (2012) - [j16]Thomas Sakoparnig, Niko Beerenwinkel:
Efficient sampling for Bayesian inference of conjunctive Bayesian networks. Bioinform. 28(18): 2318-2324 (2012) - [j15]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): 126-138 (2012) - [c11]Osvaldo Zagordi, Armin Töpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel:
Probabilistic Inference of Viral Quasispecies Subject to Recombination. RECOMB 2012: 342-354 - 2011
- [j14]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: 119 (2011) - [j13]Moritz Gerstung, Hani Nakhoul, Niko Beerenwinkel:
Evolutionary Games with Affine Fitness Functions: Applications to Cancer. Dyn. Games Appl. 1(3): 370 (2011) - 2010
- [j12]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): 417-428 (2010)
2000 – 2009
- 2009
- [j11]Moritz Gerstung, Michael Baudis, Holger Moch, Niko Beerenwinkel:
Quantifying cancer progression with conjunctive Bayesian networks. Bioinform. 25(21): 2809-2815 (2009) - [c10]Fahad Saeed, Ashfaq A. Khokhar, Osvaldo Zagordi, Niko Beerenwinkel:
Multiple Sequence Alignment System for Pyrosequencing Reads. BICoB 2009: 362-375 - [c9]Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel:
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. RECOMB 2009: 271-284 - 2008
- [j10]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) - 2007
- [j9]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) - 2006
- [c8]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: 185-194 - [c7]Tobias Sing, Niko Beerenwinkel:
Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype. NIPS 2006: 1297-1304 - 2005
- [j8]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): 2106-2107 (2005) - [j7]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): 2438-2446 (2005) - [j6]Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer:
ROCR: visualizing classifier performance in R. Bioinform. 21(20): 3940-3941 (2005) - [j5]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): 3943-3950 (2005) - [j4]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): 584-598 (2005) - [c6]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: 234-239 - [c5]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: 285-296 - 2004
- [b1]Niko Beerenwinkel:
Computational analysis of HIV drug resistance data. Saarland University, Germany, 2004 - [c4]Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer:
Learning multiple evolutionary pathways from cross-sectional data. RECOMB 2004: 36-44 - [c3]Tobias Sing, Niko Beerenwinkel, Thomas Lengauer:
Learning Mixtures of Localized Rules by Maximizing the Area Under the ROC Curve. ROCAI 2004: 89-96 - 2003
- [j3]Niko Beerenwinkel, Martin Däumer, Mark Oette, Klaus Korn, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig, Hauke Walter:
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res. 31(13): 3850-3855 (2003) - [c2]Niko Beerenwinkel, Thomas Lengauer, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, Joachim Selbig:
Methods for optimizing antiviral combination therapies. ISMB (Supplement of Bioinformatics) 2003: 16-25 - 2002
- [j2]Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, Joachim Selbig:
Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype. Proc. Natl. Acad. Sci. USA 99(12): 8271-8276 (2002) - 2001
- [j1]Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, Joachim Selbig:
Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests. IEEE Intell. Syst. 16(6): 35-41 (2001) - [c1]Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, Joachim Selbig:
Identifying drug resistance-associated patterns in HIV genotypes. German Conference on Bioinformatics 2001: 126-130
Coauthor Index
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