Affiliation: Frankfurt am Main
- Assessing variability by joint sampling of alignments and mutation ratesD 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...
- Statistical alignment based on fragment insertion and deletion modelsDirk 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...
- Data-driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancerThomas 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...
- T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancersAchim 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...
- Gene expression of ceramide kinase, galactosyl ceramide synthase and ganglioside GD3 synthase is associated with prognosis in breast cancerEugen 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...
- Predicting RNA secondary structures with pseudoknots by MCMC samplingDirk 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...
- Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarraysMatthias 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...
- Robust E-values for gapped local alignmentsDirk 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...
- TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibrationLin 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...
- Prediction of extracellular proteases of the human pathogen Helicobacter pylori reveals proteolytic activity of the Hp1018/19 protein HtrAMartin 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...
- Simultaneous statistical multiple alignment and phylogeny reconstructionRoland 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...
- Origin and pathogenesis of nodular lymphocyte-predominant Hodgkin lymphoma as revealed by global gene expression analysisVerena 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...
- Genomewide comparison of DNA sequences between humans and chimpanzeesIngo 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...