Publications

2013

• Shiho Kawamura, Moritz Gerstung, Alexandro T. Colozo, Jonne Helenius, Akiko Maeda, Niko Beerenwinkel, Paul S.-H. Park, and Daniel J. Müller.
  Kinetic, energetic, and mechanical differences between dark-state rhodopsin and opsin.
  Structure, 21(3):426-437, 2013.
  DOI: 10.1016/j.str.2013.01.011

• Armin Töpfer, Dirk Höper, Sandra Blome, Martin Beer, Niko Beerenwinkel, Nicolas Ruggli, and Immanuel Leifer.
  Sequencing approach to analyse the role of quasispecies for classical swine fever.
  Virology, 438(1):14-19, 2013.
  DOI: 10.1016/j.virol.2012.11.020

• Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, and Renato Paro.
  The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila.
  Genome Biology, 14:R18, 2013.
  DOI: 10.1186/gb-2013-14-2-r18

• Armin Töpfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Roth, Eran Halperin, and Niko Beerenwinkel.
  Probabilistic inference of viral quasispecies subject to recombination.
  Journal of Computational Biology, 20(2):113-123, 2013.
  DOI: 10.1089/cmb.2012.0232 | Software: QuasiRecomb
   
  Extended abstract appeared in B. Chor, editor, RECOMB 2012 – Research in Computational Molecular Biology, volume 7262 of Lecture Notes in Bioinformatics, pages 342–354. Springer, 2012.

• Pejman Mohammadi, Sebastien Desfarges, Istvan Bartha, Beda Joos, Nadine Zangger, Miguel Muñoz, Huldrych F. Günthard, Niko Beerenwinkel, Amalio Telenti, Angela Ciuffi.
  24 hours in the life of HIV-1 in a T cell line.
  PLOS Pathogens, 9(1):e1003161, 2013.
  DOI: 10.1371/journal.ppat.1003161 | Web server

2012

• Thomas Sakoparnig and Niko Beerenwinkel.
  Efficient sampling for Bayesian inference of Conjunctive Bayesian Networks.
  Sixth International Workshop on Machine Learning in Systems Biology, 2012.
  Bioinformatics, 28(18):2318–2324, 2012.
  DOI: 10.1093/bioinformatics/bts433 | Software: bayes-cbn

• Osvaldo Zagordi, Martin Däumer, Christian Beisel, and Niko Beerenwinkel.
  Read length versus depth of coverage for viral quasispecies reconstruction.
  PLoS ONE, 7(10):e47046, 2012.
  DOI: 10.1371/journal.pone.0047046

• Niko Beerenwinkel, Huldrych F. Günthard, Volker Roth, and Karin J. Metzner.
  Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.
  Frontiers in Microbiology, 3:329, 2012.
  DOI: 10.3389/fmicb.2012.00329

• Samuel Ojosnegros, Edgar Delgado-Eckert, and Niko Beerenwinkel.
  Competition-colonization trade-off promotes coexistence of low-virulence viral strains.
  Journal of the Royal Society Interface, 9:2244–2254, 2012.
  DOI: 10.1098/​rsif.2012.0160

• Juliane Siebourg, Gunter Merdes, Benjamin Misselwitz, Wolf-Dietrich Hardt, and Niko Beerenwinkel.
  Stability of gene rankings from RNAi screens.
  Bioinformatics, 28(12):1612-1618, 2012.
  DOI: 10.1093/bioinformatics/bts192 | Software: staRank

• Moritz Gerstung, Christian Beisel, Markus Rechsteiner, Peter Wild, Peter Schraml, Holger Moch, and Niko Beerenwinkel.
  Reliable detection of subclonal single-nucleotide variants in tumor cell populations.
  Nature Communications, 3:811, 2012.
  DOI: 10.1038/ncomms1814 | Software: deepSNV

• Niko Beerenwinkel and Juliane Siebourg.
  Statistics, probability, and computational science.
  In Maria Anisimova, editor, Evolutionary Genomics: Statistical and Computational Methods, Volume 1, chapter 3, pages 77–110. Springer, New York, 2012.
  DOI: 10.1007/978-1-61779-582-4_3

• Thomas Sakoparnig, Tobias Kockmann, Renato Paro, Christian Beisel, and Niko Beerenwinkel.
  Binding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing.
  8th Annual RECOMB Satellite on Regulatory Genomics, 2011.
  Journal of Computational Biology, 19(2):126-138, 2012.
  DOI:10.1089/cmb.2011.0258 | PubMed

• Srikant Ambatipudi, Moritz Gerstung, Manishkumar Pandey, Tanuja Samant, Asawari Patil, Shubhada Kane, Rajiv S. Desai, Alejandro A. Schäffer, Niko Beerenwinkel, and Manoj B. Mahimkar.
  Genome-wide expression and copy number analysis identifies driver genes in gingivobuccal cancers.
  Genes, Chromosomes and Cancer, 51(2):161-73, 2012.

2011

• Moritz Gerstung, Nicholas Eriksson, Jimmy Lin, Bert Vogelstein, and Niko Beerenwinkel.
  The temporal order of genetic and pathway alterations in tumorigenesis.
  PLoS ONE, 6(11):e27136, 2011.
  DOI:10.1371/journal.pone.0027136

• Moritz Gerstung, Hani Nakhoul, and Niko Beerenwinkel.
  Evolutionary games with affine fitness functions: applications to cancer.
  Dynamic Games and Applications, 1:370–385, 2011.
  DOI:10.1007/s13235-011-0029-0 | arXiv

• Niko Beerenwinkel and Osvaldo Zagordi.
  Ultra-deep sequencing for the analysis of viral populations.
  Current Opinion in Virology, 1:413–418, 2011.
  DOI:10.1016/j.coviro.2011.07.008 | PDF

• Edgar Delgado-Eckert, Samuel Ojosnegros, and Niko Beerenwinkel.
  The evolution of virulence in RNA viruses under a competition-colonization trade-off.
  Bulletin of Mathematical Biology, 73(8):1881-908, 2011.
  PubMed

• Osvaldo Zagordi, Arnab Bhattacharya, Nicholas Eriksson, and Niko Beerenwinkel.
  ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
  BMC Bioinformatics, 12:119, 2011.
  BMC | Software: ShoRAH

• Gregory Lefebvre, Sébastien Desfarges, Frédéric Uyttebroeck, Miguel Muñoz, Niko Beerenwinkel, Jacques Rougemont, Amalio Telenti, and Angela Ciuffi.
  Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell.
  Journal of Virology, 85(13):6205-11, 2011.
  PubMed

• Swapnali M. Pathare, Moritz Gerstung, Niko Beerenwinkel, Alejandro A. Schäffer, Sadhana Kannan, Prathamesh Pai, K. Alok Pathak, Anita M. Borges, and Manoj B. Mahimkar.
  Clinicopathological and prognostic implications of genetic alterations in oral cancers.
  Oncology Letters, 2:445-451, 2011.
  PubMed

• Srikant Ambatipudi, Moritz Gerstung, Ravindra Gowda, Prathamesh Pai, Anita M Borges, Alejandro A. Schäffer, Niko Beerenwinkel, and Manoj B. Mahimkar.
  Genomic profiling of advanced-stage oral cancers reveals chromosome 11q alterations as markers of poor clinical outcome.
  PLoS ONE, 6(2):e17250, 2011.
  PubMed | PLoS

• Niko Beerenwinkel, Patrick Knupfer, and Achim Tresch.
  Learning monotonic genotype-phenotype maps.
  Statistical Applications in Genetics and Molecular Biology, Vol. 10, Iss. 1, Art. 3, 2011.
  bepress | Software: icbn

2010

• Osvaldo Zagordi, Rolf Klein, Martin Däumer, and Niko Beerenwinkel.
  Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.
  Nucleic Acids Research, 38(21):7400-7409, 2010.
  OUP | Data

• Samuel Ojosnegros and Niko Beerenwinkel.
  Models of RNA virus evolution and their roles in vaccine design.
  Immunome Research, 6(Suppl 2):S6, 2010.
  Full text

• Helmut Schöllnberger, Niko Beerenwinkel, Rudolf Hoogenveen, and Paolo Vineis.
  Cell selection as driving force in lung and colon carcinogenesis.
  Cancer Research, 70(17):6797-6803, 2010.
  AACR

• Moritz Gerstung and Niko Beerenwinkel.
  Waiting time models of cancer progression.
  Mathematical Population Studies, 17(3):115-135, 2010.
  arXiv:0807.3638 | Taylor & Francis

• Samuel Ojosnegros, Niko Beerenwinkel, Tibor Antal, Martin A. Nowak, Cristina Escarmís, and Esteban Domingo.
  Competition-colonization dynamics in an RNA virus.
  Proceedings of the National Academy of Sciences U. S. A., 107(5):2108–2112, 2010.
  PubMed
   
  Addendum article:
  Samuel Ojosnegros, Niko Beerenwinkel, and Esteban Domingo.
  Competition-colonization dynamics: An ecology approach to quasispecies dynamics and virulence evolution in RNA viruses.
  Communicative & Integrative Biology, 3(4), 2010.
  Landes Bioscience

• Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, and Niko Beerenwinkel.
  Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction.
  Journal of Computational Biology, 17:417-428, 2010.
  PubMed | Software: ShoRAH
   
  Exteneded abstract appeared in S. Batzoglou, editor, RECOMB 2009 - Research in Computational Molecular Biology, Lecture Notes in Bioinformatics 5541, pages 271-284, Springer 2009.
  PDF | Springer

2009

• Moritz Gerstung, Michael Baudis, Holger Moch, and Niko Beerenwinkel.
  Quantifying cancer progression with conjunctive Bayesian networks.
  Bioinformatics, 25(21):2809-2815, 2009.
  OUP | Software: CT-CBN

• Niko Beerenwinkel and Seth Sullivant.
  Markov models for accumulating mutations.
  Biometrika, 96(3):645-861, 2009.
  OUP | arXiv:0709.2646 | Software: CT-CBN

• Fahad Saeed, Ashfaq Khokhar, Osvaldo Zagordi, and Niko Beerenwinkel.
  Multiple sequence alignment system for pyrosequencing reads.
  In S. Rajasekaran, editor, BICoB 2009 -- Bioinformatics and Computational Biology, Lecture Notes in Bioinformatics 5462, pages 362-375, Springer 2009.
  Springer

• Swapnali Pathare, Alejandro A. Schäffer, Niko Beerenwinkel, and Manoj Mahimkar.
  Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression.
  International Journal of Cancer, 124:2864-2871, 2009.
  PubMed

• Andre Altmann, Martin Däumer, Niko Beerenwinkel, Yardena Peres, Eugen Schülter, Joachim Büch, Soo-Yon Rhee, Anders Sönnerborg, W Jeffrey Fessel, Robert W Shafer, Maurizio Zazzi, Rolf Kaiser, and Thomas Lengauer.
  Predicting response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database.
  Journal of Infectious Diseases, 199(7):999-1006, 2009.
  PubMed

2008

• Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, and Niko Beerenwinkel.
  Viral population estimation using pyrosequencing.
  PLoS Computational Biology, 4(5):e1000074, 2008.
  PLoS | arXiv:0707.0114 | Software: ShoRAH

• Siân Jones, Wei-dong Chen, Giovanni Parmigiani, Frank Diehl, Niko Beerenwinkel, Tibor Antal, Arne Traulsen, Martin A. Nowak, Christopher Siegel, Victor E. Velculescu, Kenneth W. Kinzler, Bert Vogelstein, Joseph Willis, and Sanford D. Markowitz.
  Comparative lesion sequencing provides insights into tumor evolution.
  Proceedings of the National Academy of Sciences U. S. A., 105(11):4283-8, 2008.
  PubMed

2007

• Niko Beerenwinkel, Tibor Antal, David Dingli, Arne Traulsen, Kenneth W. Kinzler, Victor E. Velculescu, Bert Vogelstein, and Martin A. Nowak.
  Genetic progression and the waiting time to cancer.
  PLoS Computational Biology, 3(11):e225, 2007.
  PLoS | arXiv:0707.3770

• Tobias Sing, Andrew J. Low, Niko Beerenwinkel, Oliver Sander, Peter K. Cheung, Francisco S. Domingues, Joachim Büch, Martin Däumer, Rolf Kaiser, Thomas Lengauer, and P. Richard Harrigan.
  Predicting HIV co-receptor usage based on genetic and clinical covariates.
  Antiviral Therapy, 12(7):1097-1106, 2007.
  PubMed

• Niko Beerenwinkel, Nicholas Eriksson, and Bernd Sturmfels.
  Conjunctive Bayesian networks.
  Bernoulli, 13(4):893–909, 2007.
  arXiv:math/0608417 | Software: CBN

• Niko Beerenwinkel, Lior Pachter, and Bernd Sturmfels.
  Epistasis and shapes of fitness landscapes.
  Statistica Sinica, 17:1317-1342, 2007.
  arXiv:q-bio/0603034 | Stat Sinica

• Niko Beerenwinkel, Lior Pachter, Bernd Sturmfels, Santiago F. Elena, and Richard E. Lenski.
  Analysis of epistatic interactions and fitness landscapes using a new geometric approach.
  BMC Evolutionary Biology, 7:60, 2007.
  PubMed

• Golo Ahlenstiel, Kirsten Roomp, Martin Däumer, Jacob Nattermann, Martin Vogel, Jürgen K. Rockstroh, Niko Beerenwinkel, Rolf Kaiser, Hans-Dieter Nischalke, Tilman Sauerbruch, Thomas Lengauer, and Ulrich Spengler.
  Selective pressures of HLA genotypes and antiviral therapy on HIV-1 sequence mutation at a population level.
  Clinical and Vaccine Immunology, 14(10):1266-1273, 2007.
  PubMed

• Andre Altmann, Niko Beerenwinkel, Tobias Sing, Igor Savenkov, Martin Däumer, Rolf Kaiser, Soo-Yon Rhee, W. Jeffrey Fessel, Robert W. Shafer, and Thomas Lengauer.
  Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance.
  Antiviral Therapy, 12(2):169-178, 2007.
  PubMed

• Ralf Ketter, Steffi Urbschat, Wolfram Henn, Wolfgang Feiden, Niko Beerenwinkel, Thomas Lengauer, Wolf-Ingo Steudel, Klaus D. Zang, and Jörg Rahnenführer.
  Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas.
  International Journal of Cancer, 121(7):1473-80, 2007.
  PubMed

• Tobias Sing and Niko Beerenwinkel.
  Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype.
  In B. Schölkopf, J. Platt, and T. Hoffman, editors, Advances in Neural Information Processing Systems 19, pages 1297-1304, MIT Press, Cambridge, MA, 2007.
  NIPS Proceedings

• Niko Beerenwinkel and Mathias Drton.
  A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data.
  Biostatistics, 8(1):53-71, 2007.
  arXiv:q-bio/0603031 | PubMed | Software: MtreeHMM

• Oette M, Kaiser R, Däumer M, Fätkenheuer G, Rockstroh JK, Knechten H, Mitrenga D, Beerenwinkel N, Sagir A, Pfister H, Häussinger D.
  Epidemiology of primary drug resistance in chronically HIV-infected patients in Nordrhein-Westfalen, Germany, 2001-2005.
  Dtsch Med Wochenschr 132(18):977-82, 2007.
  PubMed

• Niko Beerenwinkel, Kirsten Roomp, and Martin Däumer.
  Evolution of drug resistance in HIV.
  In Thomas Lengauer, editor, Bioinformatics - From Genomes to Therapies, chapter 40, pages 1457-1495. Wiley-VCH, Weinheim, Germany, 2007.
  Wiley-VCH

2006

• Clara J. F. Lehmann, Martin Däumer, Ibrahim Boussaad, Tobias Sing, Niko Beerenwinkel, Thomas Lengauer, Norbert Schmeisser, Christoph Wyen, Gerd Fätkenheuer, and Rolf Kaiser.
  Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART: Implications for therapy with coreceptor inhibitors.
  Journal of Clinical Virology, 80(14):7186-98, 2006.
  PubMed

• Niko Beerenwinkel, Nicholas Eriksson, and Bernd Sturmfels.
  Evolution on distributive lattices.
  Journal of Theoretical Biology, 242(2):409-420, 2006.
  arXiv:q-bio/0511039 | PubMed | Software: riskPoly

• Junming Yin, Niko Beerenwinkel, Jörg Rahnenführer, and Thomas Lengauer.
  Model selection for mixtures of mutagenetic trees.
  Statistical Applications in Genetics and Molecular Biology, Vol. 5, Iss. 1, Article 17, 2006.
  PubMed | Software: Mtreemix

• 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.
  In Ulf Leser, Felix Naumann, and Barbara Eckman, editors, Data Integration in the Life Sciences: Third International Workshop, DILS 2006, Hinxton, UK, July 20-22, 2006, volume 4075 of Lecture Notes in Computer Science, pages 185-194. Springer, 2006.
  Springer

• Valentina Svicher, Tobias Sing, Maria Mercedes Santoro, Federica Forbici, Fatima Rodrmguez-Barrios, Ada Bertoli, Niko Beerenwinkel, Maria Concetta Bellocchi, Federigo Gago, Antonella d'Arminio Monforte, Andrea Antinori, Thomas Lengauer, Francesca Ceccherini-Silberstein, and Carlo Federico Perno.
  Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors.
  Journal of Virology, 80(14):7186-7198, 2006.
  PubMed

• Niko Beerenwinkel, Colin N. Dewey, and Kevin M. Woods.
  Parametric inference of recombination in HIV genomes.
  arXiv:q-bio/0512019

2005

• Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kisten Roomp, Igor Savenkov, Roman Fischer, Daniel Hoffmann, Joachim Selbig, Klaus Korn, Hauke Walter, Thomas Berg, Patrick Braun, Gerd Fätkenheuer, Mark Oette, Jürgen Rockstroh, Bernd Kupfer, Rolf Kaiser, Martin Däumer.
  Computational methods for the design of effective therapies against drug resistant HIV strains.
  Bioinformatics, 21(21):3943-3950, 2005.
  PubMed

• Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, and Thomas Lengauer.
  Learning multiple evolutionary pathways from cross-sectional data.
  Journal of Computational Biology, 12(6):584-598, 2005. (RECOMB 2004 paper)
  PubMed

• Tobias Sing, Valentina Svicher, Niko Beerenwinkel, Francesca Ceccherini-Silberstein, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, Mark Oette, Jürgen K. Rockstroh, Gert Fädtkenheuer, Carlo-Federico Perno, and Thomas Lengauer.
  Characterization of novel HIV drug resistance mutations using clustering, multidimensional scaling and SVM-based feature ranking.
  In Alipio Jorge, Luis Torgo, Pavel Brazdil, Rui Camacho, and Joao Gama, editors, Knowledge Discovery in Databases: PKDD 2005, 9th European Conference on Principles and Practice of Knowledge Discovery in Databases, Porto, Portugal, October 3-7, 2005, volume 3721 of Lecture Notes in Computer Science, pages 285-296. Springer, 2005.
  PDF

• Melanie Balduin, Saleta Sierra Aragon, Martin Däumer, Jürgen K. Rockstroh, Mark Oette, Gert Fätkenheuer, Bernd Kupfer, Niko Beerenwinkel, Daniel Hoffmann, Joachim Selbig, Herbert J. Pfister, Rolf Kaiser.
  Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy.
  Journal of Clinical Virology, 34(4):277-287, 2005.
  PubMed

• Silke Wemmert, Ralf Ketter, Jörg Rahnenführer, Niko Beerenwinkel, Martin Strowitzki, Wolfgang Feiden, Christian Hartmann, Thomas Lengauer, Florian Stockhammer, Klaus D. Zang, Eckart Meese, Wolf-Ingo Steudel, Andreas von Deimling, and Steffi Urbschat.
  Patients with high grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment.
  Neoplasia, 7(10):883-893, 2005.
  PubMed

• Tobias Sing, Oliver Sander, Niko Beerenwinkel, and Thomas Lengauer.
  ROCR: Visualizing classifier performance.
  Bioinformatics, 21(20):3940-3941, 2005.
  PubMed | Software: ROCR

• Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig, and Thomas Lengauer.
  Mtreemix: a software package for learning and using mixture models of mutagenetic trees.
  Bioinformatics, 21(9):2106-2107, 2005.
  PubMed | Software: Mtreemix

• Niko Beerenwinkel, Martin Däumer, Tobias Sing, Jörg Rahnenführer, Thomas Lengauer, Joachim Selbig, Daniel Hoffmann, and Rolf Kaiser.
  Estimating HIV evolutionary pathways and the genetic barrier to drug resistance.
  Journal of Infectious Diseases, 191(11):1953-1960, 2005.
  PubMed

• Jörg Rahnenführer, Niko Beerenwinkel, Wolfgang A. Schulz, Christian Hartmann, Andreas von Deimling, Bernd Wullich, and Thomas Lengauer.
  Estimating cancer survival and clinical outcome based on genetic tumor progression scores.
  Bioinformatics, 21:2438-2446, 2005.
  PubMed

• Niko Beerenwinkel and Mathias Drton.
  Mutagenetic tree models.
  In Lior Pachter and Bernd Sturmfels, editors, Algebraic Statistics for Computational Biology, chapter 14, pages 278-290. Cambridge University Press, Cambridge, UK, 2005.
  book

2004

• Tobias Sing, Niko Beerenwinkel, and Thomas Lengauer.
  Learning mixtures of localized rules by maximizing the area under the ROC curve.
  In Jose Hernandez-Orallo, Cesar Ferri, Nicolas Lachiche, and Peter A. Flach, editors, ROC Analysis in Artificial Intelligence, 1st International Workshop, ROCAI-2004, Valencia, Spain, August 22, 2004, pages 89-96, 2004.
  PDF

• Niko Beerenwinkel.
  Computational Analysis of HIV Drug Resistance Data.
  Shaker, Aachen, Germany, 2004.
  PhD Thesis, Naturwissenschaftlich-Technische Fakultät I der Universität des Saarlandes.
  Shaker | PDF

2003

• Niko Beerenwinkel, Thomas Lengauer, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, and Joachim Selbig.
  Methods for optimizing antiviral combination therapies.
  Bioinformatics, 19(suppl. 1):i16-i25, 2003. (ISMB 2003 paper)
  PubMed

• Katharina Wolf, Hauke Walter, Niko Beerenwinkel, Wilco Keulen, Rolf Kaiser, Daniel Hoffmann, Thomas Lengauer, Joachim Selbig, Anne-Mieke Vandamme, Klaus Korn, and Barbara Schmidt.
  Tenofovir resistance and resensitization.
  Antimicrobial Agents and Chemotherapy, 47(11):3478-3484, 2003.
  PubMed

• Niko Beerenwinkel, Martin Däumer, Mark Oette, Klaus Korn, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig, and Hauke Walter.
  Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes.
  Nucleic Acids Research, 31(13):3850-3855, 2003.
  PubMed | Web server: geno2pheno

2002

• Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, and Joachim Selbig.
  Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype.
  Proceedings of the National Acadamy of Sciences U. S. A., 99(12):8271-8276, 2002.
  PubMed

2001

• Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, and Joachim Selbig.
  Identifying drug resistance-associated patterns in HIV genotypes.
  In Edgar Wingender, editor, Computer Science and Biology: Proceedings of the German Conference on Bioinformatics, GCB 2001, October 7-10, 2001, Braunschweig, Germany, pages 126-130. German Research Center for Biotechnology, 2001.
  GCB

• Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, and Joachim Selbig.
  Geno2pheno: Interpreting genotypic HIV drug resistance tests.
  IEEE Intelligent Systems, 16:35-41, 2001.
  IEEE

1999

• Niko Beerenwinkel.
  Hochheben von Kurven in positiver Charakteristik nach Charakteristik Null.
  Master’s thesis, Mathematisches Institut, Mathematisch-Naturwissenschaftliche Fakultät der Universität Bonn, 1999.
  PDF