Niko Beerenwinkel

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Evolution on distributive lattices
    Niko Beerenwinkel
    Department of Mathematics, University of California, Berkeley, CA 94720, USA
    J Theor Biol 242:409-20. 2006
  2. ncbi request reprint Computational methods for the design of effective therapies against drug resistant HIV strains
    Niko Beerenwinkel
    Department of Mathematics, University of California, Berkeley, CA, USA
    Bioinformatics 21:3943-50. 2005
  3. ncbi request reprint Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Saarbrucken, Germany
    J Infect Dis 191:1953-60. 2005
  4. ncbi request reprint Mtreemix: a software package for learning and using mixture models of mutagenetic trees
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:2106-7. 2005
  5. ncbi request reprint A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data
    Niko Beerenwinkel
    Department of Mathematics, University of California, 1073 Evans Hall, Berkeley, CA 94720 USA
    Biostatistics 8:53-71. 2007
  6. ncbi request reprint Methods for optimizing antiviral combination therapies
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Bioinformatics 19:i16-25. 2003
  7. ncbi request reprint Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
    Andre Altmann
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:169-78. 2007
  8. doi request reprint Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database
    Andre Altmann
    Max Planck Institute for Informatics, Saarbrucken, University of Cologne, Cologne, Germany
    J Infect Dis 199:999-1006. 2009
  9. pmc Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, D 66115 Saarbrücken, Germany
    Nucleic Acids Res 31:3850-5. 2003
  10. ncbi request reprint Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
    Tobias Sing
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:1097-106. 2007

Collaborators

Detail Information

Publications26

  1. ncbi request reprint Evolution on distributive lattices
    Niko Beerenwinkel
    Department of Mathematics, University of California, Berkeley, CA 94720, USA
    J Theor Biol 242:409-20. 2006
    ..In an application to the development of drug resistance in HIV, we study the risk of viral escape from treatment with the protease inhibitors ritonavir and indinavir...
  2. ncbi request reprint Computational methods for the design of effective therapies against drug resistant HIV strains
    Niko Beerenwinkel
    Department of Mathematics, University of California, Berkeley, CA, USA
    Bioinformatics 21:3943-50. 2005
    ..We have developed several computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genomic data...
  3. ncbi request reprint Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Saarbrucken, Germany
    J Infect Dis 191:1953-60. 2005
    ..The evolution of drug-resistant viruses challenges the management of human immunodeficiency virus (HIV) infections. Understanding this evolutionary process is important for the design of effective therapeutic strategies...
  4. ncbi request reprint Mtreemix: a software package for learning and using mixture models of mutagenetic trees
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:2106-7. 2005
    ..We provide programs for model fitting, model selection, simulation, likelihood computation and waiting time estimation...
  5. ncbi request reprint A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data
    Niko Beerenwinkel
    Department of Mathematics, University of California, 1073 Evans Hall, Berkeley, CA 94720 USA
    Biostatistics 8:53-71. 2007
    ..Using HIV mutation data from clinical trials, we estimate the order and rate of occurrence of seven amino acid changes that are associated with resistance to the reverse transcriptase inhibitor efavirenz...
  6. ncbi request reprint Methods for optimizing antiviral combination therapies
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Bioinformatics 19:i16-25. 2003
    ..The evolution of drug-resistant genetic variants in response to therapy plays a key role in treatment failure and finding a new potent drug combination after therapy failure is considered challenging...
  7. ncbi request reprint Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
    Andre Altmann
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:169-78. 2007
    ..The virus's evolutionary potential for escaping from drug pressure is explored as an additional predictor...
  8. doi request reprint Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database
    Andre Altmann
    Max Planck Institute for Informatics, Saarbrucken, University of Cologne, Cologne, Germany
    J Infect Dis 199:999-1006. 2009
    ....
  9. pmc Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, D 66115 Saarbrücken, Germany
    Nucleic Acids Res 31:3850-5. 2003
    ..The geno2pheno system makes these genotype interpretations available via the Internet (http://www.genafor.org/)...
  10. ncbi request reprint Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
    Tobias Sing
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:1097-106. 2007
    ..We compared several statistical learning methods for the prediction of HIV coreceptor use from clonal HIV third hypervariable (V3) loop sequences, and evaluated and improved their effectiveness on clinical samples...
  11. ncbi request reprint Model selection for mixtures of mutagenetic trees
    Junming Yin
    Department of EECS, University of California, Berkeley, CA, USA
    Stat Appl Genet Mol Biol 5:Article17. 2006
    ..Thus, this model selection criterion can also be used for large data sets for which cross-validation becomes computationally infeasible...
  12. ncbi request reprint ROCR: visualizing classifier performance in R
    Tobias Sing
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:3940-1. 2005
    ..Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage...
  13. ncbi request reprint Estimating cancer survival and clinical outcome based on genetic tumor progression scores
    Jörg Rahnenführer
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
    Bioinformatics 21:2438-46. 2005
    ..The accumulation of genetic alterations during tumor progression can be used for the assessment of the genetic status of the tumor. For modeling dependences between the genetic events, evolutionary tree models have been applied...
  14. doi request reprint Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction
    Sebastian Dümcke
    Institute for Genetics, University of Cologne, 50674 Cologne, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Gene Center, Department of Biochemistry, Ludwig Maximilians University, 81379 Munich, Germany, Insitute for Functional Genomics, 93053 Regensburg, Germany, Department of Radiology, Center for Cancer Systems Biology, Stanford University, Stanford, CA 94305 5488, USA and ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26 4058 Basel, Switzerland
    Bioinformatics 30:414-9. 2014
    ..Even with this kind of data it is still a major and largely unsolved challenge to infer the topology and interaction logic of the underlying regulatory network...
  15. pmc Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
    Valentina Svicher
    Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
    J Virol 80:7186-98. 2006
    ....
  16. pmc Tenofovir resistance and resensitization
    Katharina Wolf
    Institute of Clinical and Molecular Virology, German National Reference Centre for Retroviruses, University of Erlangen Nuremberg, Erlangen, Germany
    Antimicrob Agents Chemother 47:3478-84. 2003
    ..5- and 4.0-fold reduced susceptibilities, respectively. Thus, clinically relevant resistance may be conferred by the accumulation of TAMs, and the resensitizing effect of M184V should be considered only minor...
  17. pmc Viral population estimation using pyrosequencing
    Nicholas Eriksson
    Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Comput Biol 4:e1000074. 2008
    ..Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies...
  18. ncbi request reprint Learning multiple evolutionary pathways from cross-sectional data
    Niko Beerenwinkel
    Max Planck Institut für Informatik, Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
    J Comput Biol 12:584-98. 2005
    ..We obtain a generative probabilistic model for the development of drug resistance in HIV that agrees with biological knowledge. Further applications and extensions of the model are discussed...
  19. pmc Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level
    Golo Ahlenstiel
    Department of Internal Medicine I, University of Bonn, 53105 Bonn, Germany
    Clin Vaccine Immunol 14:1266-73. 2007
    ..As several of the HLA-associated mutations lie at positions associated with drug resistance, our results indicate possible negative effects of HLA genotypes on the development of HIV-1 drug resistance...
  20. ncbi request reprint Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy
    Melanie Balduin
    Institute of Virology, University of Cologne, Fuerst Pueckler Str 56, D 50935 Cologne, Germany
    J Clin Virol 34:277-87. 2005
    ..To analyse the evolution of resistance patterns in patients undergoing treatment interruption (TI) and re-initiating highly active anti-retroviral therapy (HAART)...
  21. pmc Analysis of epistatic interactions and fitness landscapes using a new geometric approach
    Niko Beerenwinkel
    Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
    BMC Evol Biol 7:60. 2007
    ..In this paper, we propose and employ a new mathematical approach that allows a more complete description of multi-way interactions and provides new insights into the structure of fitness landscapes...
  22. pmc Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype
    Niko Beerenwinkel
    GMD German National Research Center for Information Technology, Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, D 53754 Sankt Augustin, Germany
    Proc Natl Acad Sci U S A 99:8271-6. 2002
    ..We found prediction errors of 9.6-15.5% for all drugs except for zalcitabine, didanosine, and stavudine, with prediction errors between 25.4% and 32.0%. A prediction service is freely available at http://cartan.gmd.de/geno2pheno.html...
  23. ncbi request reprint Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas
    Ralf Ketter
    Department of Neurosurgery, Saarland University, Homburg Saar, Germany
    Int J Cancer 121:1473-80. 2007
    ..As a quantitative measure the GPS allows a more precise assessment of the prognosis of meningiomas than categorical cytogenetic markers based on single chromosomal aberrations...
  24. pmc Genetic progression and the waiting time to cancer
    Niko Beerenwinkel
    Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 3:e225. 2007
    ..The complexity of cancer progression can be understood as the result of multiple sequential mutations, each of which has a relatively small but positive effect on net cell growth...
  25. pmc Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment
    Silke Wemmert
    Institute of Human Genetics, Saarland University, Homburg Saar D 66421, Germany
    Neoplasia 7:883-93. 2005
    ..This study demonstrates that molecular genetic and cytogenetic analyses potentially predict responses to chemotherapy in patients with newly diagnosed glioblastomas...
  26. ncbi request reprint Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART
    Clara Lehmann
    Department of Internal Medicine, University of Cologne, Germany
    J Clin Virol 37:300-4. 2006
    ..Disease progression in HIV infection has been associated with switch of viral coreceptor usage from CCR5 to CXCR4...