D Metzler

Summary

Affiliation: Frankfurt am Main
Country: Germany

Publications

  1. ncbi request reprint Assessing variability by joint sampling of alignments and mutation rates
    D Metzler
    Johann Wolfgang Goethe Universitat, Fachbereich Mathematik, D 60054 Frankfurt am Main, Germany
    J Mol Evol 53:660-9. 2001
  2. ncbi request reprint Statistical alignment based on fragment insertion and deletion models
    Dirk Metzler
    Johann Wolfgang Goethe Universitat, Fachbereich Mathematik, Frankfurt am Main, Germany
    Bioinformatics 19:490-9. 2003
  3. doi request reprint Data-driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer
    Thomas Karn
    Department of Obstetrics and Gynecology, J W Goethe University, Theodor Stern Kai 7, 60590, Frankfurt, Germany
    Breast Cancer Res Treat 120:567-79. 2010
  4. pmc T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers
    Achim Rody
    Department of Obstetrics and Gynecology, JW Goethe University, Theodor Stern Kai 7, Frankfurt, Germany
    Breast Cancer Res 11:R15. 2009
  5. doi request reprint Gene expression of ceramide kinase, galactosyl ceramide synthase and ganglioside GD3 synthase is associated with prognosis in breast cancer
    Eugen Ruckhäberle
    Department of Obstetrics and Gynecology, J W Goethe University, Theodor Stern Kai 7, 60590 Frankfurt, Germany
    J Cancer Res Clin Oncol 135:1005-13. 2009
  6. ncbi request reprint Predicting RNA secondary structures with pseudoknots by MCMC sampling
    Dirk Metzler
    Institut fur Informatik, J W Goethe Universitat, Robert Mayer Str 11 15, 60325 Frankfurt am Main, Germany
    J Math Biol 56:161-81. 2008
  7. ncbi request reprint Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays
    Matthias Frank
    Senckenbergisches Institut für Pathologie, Klinikum der Johann Wolfgang Goethe Universitat Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
    Virchows Arch 450:699-711. 2007
  8. ncbi request reprint Robust E-values for gapped local alignments
    Dirk Metzler
    Institut fur Informatik, Johann Wolfgang Goethe Universitat, Frankfurt am Main, Germany
    J Comput Biol 13:882-96. 2006
  9. doi request reprint TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
    Lin Himmelmann
    Department for Computer Science and Mathematics, Goethe University, Frankfurt am Main, Germany
    Bioinformatics 25:2440-1. 2009
  10. pmc Prediction of extracellular proteases of the human pathogen Helicobacter pylori reveals proteolytic activity of the Hp1018/19 protein HtrA
    Martin Löwer
    Goethe University, Institute of Cell Biology and Neuroscience CMP, Frankfurt am Main, Germany
    PLoS ONE 3:e3510. 2008

Collaborators

Detail Information

Publications13

  1. ncbi request reprint Assessing variability by joint sampling of alignments and mutation rates
    D Metzler
    Johann Wolfgang Goethe Universitat, Fachbereich Mathematik, D 60054 Frankfurt am Main, Germany
    J Mol Evol 53:660-9. 2001
    ..We illustrate our method with human and orangutan sequences from the hyper variable region I and with gene-pseudogene pairs...
  2. ncbi request reprint Statistical alignment based on fragment insertion and deletion models
    Dirk Metzler
    Johann Wolfgang Goethe Universitat, Fachbereich Mathematik, Frankfurt am Main, Germany
    Bioinformatics 19:490-9. 2003
    ..J. Mol. Evol., 34, 3-16, 1992). The computational tractability of the model depends on certain restrictions in the insertion/deletion process; possible effects we discuss...
  3. doi request reprint Data-driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer
    Thomas Karn
    Department of Obstetrics and Gynecology, J W Goethe University, Theodor Stern Kai 7, 60590, Frankfurt, Germany
    Breast Cancer Res Treat 120:567-79. 2010
    ..In contrast, markers displaying a continuous distribution like proliferation markers as Ki67 rather describe the composition of the mixture of cells in the tumor...
  4. pmc T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers
    Achim Rody
    Department of Obstetrics and Gynecology, JW Goethe University, Theodor Stern Kai 7, Frankfurt, Germany
    Breast Cancer Res 11:R15. 2009
    ..However, specific lymphocytes might also promote tumor progression by shifting the cytokine milieu in the tumor...
  5. doi request reprint Gene expression of ceramide kinase, galactosyl ceramide synthase and ganglioside GD3 synthase is associated with prognosis in breast cancer
    Eugen Ruckhäberle
    Department of Obstetrics and Gynecology, J W Goethe University, Theodor Stern Kai 7, 60590 Frankfurt, Germany
    J Cancer Res Clin Oncol 135:1005-13. 2009
    ..Sphingolipids are bioactive lipids implicated in apoptosis, cell survival and proliferation. We analyzed the prognostic value of enzymes from sphingolipid metabolism in breast cancer...
  6. ncbi request reprint Predicting RNA secondary structures with pseudoknots by MCMC sampling
    Dirk Metzler
    Institut fur Informatik, J W Goethe Universitat, Robert Mayer Str 11 15, 60325 Frankfurt am Main, Germany
    J Math Biol 56:161-81. 2008
    ..We demonstrate the benefit of our method in examples with tmRNA and also with simulated data. McQFold, an implementation of our method, is freely available from http://www.cs.uni-frankfurt.de/~metzler/McQFold...
  7. ncbi request reprint Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays
    Matthias Frank
    Senckenbergisches Institut für Pathologie, Klinikum der Johann Wolfgang Goethe Universitat Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
    Virchows Arch 450:699-711. 2007
    ..Thus, global gene expression analyses using solely FFPE material seem to be feasible with nearly comparable results to frozen tissue studies...
  8. ncbi request reprint Robust E-values for gapped local alignments
    Dirk Metzler
    Institut fur Informatik, Johann Wolfgang Goethe Universitat, Frankfurt am Main, Germany
    J Comput Biol 13:882-96. 2006
    ..Simulation studies give evidence that this method gives reasonable results even when the usual assumptions like the independence of sequence positions are violated...
  9. doi request reprint TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
    Lin Himmelmann
    Department for Computer Science and Mathematics, Goethe University, Frankfurt am Main, Germany
    Bioinformatics 25:2440-1. 2009
    ..To calibrate the branch lengths of the tree with times assigned to geo-historical events or fossils, it is necessary to select a relaxed molecular clock model to specify how mutation rates can change along the phylogeny...
  10. pmc Prediction of extracellular proteases of the human pathogen Helicobacter pylori reveals proteolytic activity of the Hp1018/19 protein HtrA
    Martin Löwer
    Goethe University, Institute of Cell Biology and Neuroscience CMP, Frankfurt am Main, Germany
    PLoS ONE 3:e3510. 2008
    ..These data demonstrate that H. pylori secretes HtrA as an active protease, which might represent a novel candidate target for therapeutic intervention strategies...
  11. ncbi request reprint Simultaneous statistical multiple alignment and phylogeny reconstruction
    Roland Fleissner
    Initiative for Bioinformatics and Evolutionary Studies IBEST, University of Idaho Moscow, Idaho 83844 1103, USA
    Syst Biol 54:548-61. 2005
    ..Our method is also the first application of the TKF2 model in the context of multiple sequence alignment. We validate the method via simulations and illustrate it using a data set of primate mtDNA...
  12. pmc Origin and pathogenesis of nodular lymphocyte-predominant Hodgkin lymphoma as revealed by global gene expression analysis
    Verena Brune
    Institute for Cell Biology Tumor Research, University of Duisburg Essen Medical School, 45122 Essen, Germany
    J Exp Med 205:2251-68. 2008
    ..Thus, these findings shed new light on the nature of L&H cells, reveal several novel pathogenetic mechanisms in NLPHL, and may help in differential diagnosis and lead to novel therapeutic strategies...
  13. pmc Genomewide comparison of DNA sequences between humans and chimpanzees
    Ingo Ebersberger
    Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D 04103 Leipzig, Germany
    Am J Hum Genet 70:1490-7. 2002
    ..However, since the extent of divergence differs significantly among autosomes, additional unknown factors must also influence the accumulation of substitutions in the human genome...