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Publications by Dirk Metzler

  • V.M. Link, C.E. Romanoski, D. Metzler, C.K. Glass (2018) MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements Nucleic Acids Research gky491
  • V.M. Link, S. Duttke, H. Chun, I. Holtman, E. Westin, M. Hoeksema, Y. Abe,D. Skola, C. Romanoski, J. Tao, G. Fonseca, T. Troutman, N. Spann, T. Strid, M. Sakai, M. Yu, R. Hu, F. Fang, D. Metzler, B. Ren, C.K. Glass (2018) Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell 173:1796-1809
  • M.J. Wittmann, H. Stuis, D. Metzler (2018) Genetic Allee effects and their interaction with ecological Allee effects
    Journal of Animal Ecology 87:11--23
  • K.C. Wollenberg Valero, J. Garcia-Porta, A. Rodriguez, M. Arias, A. Shah, R.D. Randrianiaina, J.L. Brown, F. Glaw, F. Amat, S. Künzel, D. Metzler, R.D. Isokpehi, M. Vences (2017) Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases.
    Nature Communications 8:15213
  • F. Grandke, S. Ranganathan, N. van Bers, J.R. de Haan, D. Metzler (2017) PERGOLA: Fast and deterministic linkage mapping of polyploids
    BMC Bioinformatics 18:12
  • X. Gong, L. Bräcker, N. Bölke, C. Plata, S. Zeitlmayr, D. Metzler, K. Olbricht, N. Gompel, M. Parniske (2016) Identification of strawberry accessions with reduced emergence rates of the pest Drosophila suzukii
    Front. Plant Sci. 7:1880. doi: 10.3389/fpls.2016.01880
  • D. Metzler, F. Jordan, T. Pamminger, S. Foitzik (2016) The influence of space and time on the evolution of altruistic defense: the case of ant slave rebellion
    Journal of Evolutionary Biology 29: 874–886
  • P. Staab, D. Metzler (2016) coala: An R framework for coalescent simulation
    Bioinformatics 32(12): 1903-1904
  • F. Grandke, P. Singh, H.C.M. Heuven, J.R. de Haan, D. Metzler (2016) Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids: a comparative study in hexaploid chrysanthemum
    BMC Genomics 17:672
  • W. von Thienen, D. Metzler, V. Witte (2016) How memory and motivation modulate the responses to trail pheromones in three ant species
    Behavioral Ecology and Sociobiology 70(3): 393-407
  • P. Staab, S. Zhu, D. Metzler, and G. Lunter (2015) scrm: efficiently simulating long sequences using the approximated coalescent with recombination
    Bioinformatics 31(10): 1680-1682
  • W. von Thienen, D. Metzler, V. Witte (2015) Modeling shortest path selection of the ant Linepithema humile using psychophysical theory and realistic parameter values
    Journal of Theoretical Biology 372: 168-178
  • F. Gatzmann, D. Metzler, S. Krebs, H. Blum, A. Sing, A. Takano, H. Kawabata, V. Fingerle, G. Margos, N.S. Becker (2015) NGS population genetics analyses reveal divergent evolution of a Lyme Borreliosis agent in Europe and Asia
    Ticks and Tick-Borne Diseases 6(3): 344-351
  • M.J. Wittmann, W. Gabriel, D. Metzler (2014) Genetic diversity in introduced populations with Allee effect
    Genetics 198: 299-310
  • M.J. Wittmann, W. Gabriel, D. Metzler (2014) Population genetic consequences of the Allee effect and the role of offspring-number variation
    Genetics 198: 311-320
  • T. Pamminger, S. Foitzik, D. Metzler, P.S. Pennings (2014) Oh sister, where art thou? Spatial population structure and the evolution of an altruistic defence trait
    Journal of Evolutionary Biology 27: 2443-56
  • W. von Thienen, D. Metzler, D.-H. Choe, V. Witte (2014) Pheromone Communication in ants: A Detailed Analysis of Concentration Dependent Decisions in Three Species
    Behavioral Ecology and Sociobiology 68: 1611-1627
  • D.P. Lyras, D. Metzler (2014) ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach
    BMC Bioinformatics 15: 265
  • M.J. Wittmann, D. Metzler, W. Gabriel, J.M. Jeschke (2014) Decomposing propagule pressure: the effects of propagule size and propagule frequency on invasion success
    Oikos 123: 441-450.
  • F. Grandke , S. Ranganathan, A. Czech, J.R. de Haan, D. Metzler (2014) Bioinformatic Tools for Polyploid Crops
    Journal of Agricultural Science and Technology B 4: 593-601
  • L. Mathew, L. Rose, P. Staab, D. Metzler (2013) Why to account for finite-sites in population genetic studies and how to do this with Jaatha 2.0.
    Ecology and Evolution 3: 3647–3662.
    DOI: 10.1002/ece3.722
  • M.J. Wittmann, M. Hutzenthaler, W. Gabriel, D. Metzler (2013) Ecological and genetic effects of introduced species on their native competitors.
    Theoretical Population Biology 84: 25-35 http://dx.doi.org/10.1016/j.tpb.2012.11.003, preprint version available via arXiv:1208.1294
  • C. Pokalyuk, L. Mathew, D. Metzler, P. Pfaffelhuber (2013) Competing islands limit the rate of adaptation in structured populations
    Theoretical Population Biology 90: 1-11.
  • M. Linnenbrink, J. Wang, E. Hardouin, S. Künzel, D. Metzler, J. Baines (2013) The role of biogeography in shaping diversity of the intestinal microbiota in house mice.
    Molecular Ecology 22(7):1904-1916
  • G. Doose, D. Metzler (2012) Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots. Bioinformatics 28(17): 2242-2248
  • D. Hoffmann, M. Hutzenthaler, J. Seebach, M. Panning, A. Umgelter, H. Menzel, U. Protzer, D. Metzler (2012) Norovirus GII.4 and GII.7 Capsid Sequences Undergo Positive Selection in Chronically Infected Patients
    Infection, Genetics and Evolution. 12: 461-466
  • P. Pavlidis, D. Metzler, W. Stephan (2012) Selective Sweeps in Multilocus Models of Quantitative Traits Genetics 192(1) 225-239
  • L. Nauheimer, D. Metzler, S.S. Renner (2012) Global history of the ancient monocot family Araceae inferred with models accounting for past continental positions and previous ranges based on fossils. New Phytologist 195(4): 938–950
  • T. Karn, L. Pusztai, E. Ruckhäberle, C. Liedtke, V. Müller, M. Schmidt, D. Metzler, J. Wang, K.R. Coombes, R. Gätje, L. Hanker, C. Solbach, A. Ahr, U. Holtrich, A. Rody, M. Kaufmann (2012) Melanoma antigen family A identified by the bimodality index defines a subset of triple negative breast cancers as candidates for immune response augmentation
    European Journal of Cancer 48(1):12-23
  • S. Foitzik, M.H. Rüger, I.M. Kureck, D. Metzler (2011) Macro- and microgeographic genetic structure in an ant species with alternative reproductive tactics in sexuals
    Journal of Evolutionary Biology 24(12): 2721–30
  • L. Naduvilezhath, L.E. Rose, D. Metzler (2011) Jaatha: a fast composite-likelihood approach to estimate demographic parameters
    Molecular Ecology 20(13):2709-23
  • A. Tellier, P. Pfaffelhuber, B. Haubold, L. Naduvilezhath, L. E. Rose, T. Städler, W. Stephan, and D. Metzler (2011) Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum
    PLoS One 6(5): e18155
  • N. Svetec, A. Werzner, R. Wilches, P. Pavlidis, J.M. Alvarez-Castro, K.W. Broman, D. Metzler, W. Stephan (2011) Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis
    Molecular Ecology 20(3):530-544
  • A. Rody, T. Karn, C. Liedtke, L. Pusztai, E. Ruckhaeberle, L. Hanker, R. Gaetje, C. Solbach, A. Ahr, D. Metzler, M. Schmidt, V. Müller, U. Holtrich, M. Kaufmann (2011) A clinically relevant gene signature in triple negative and basal-like breast cancer
    Breast Cancer Research 2011 13(5):R97
  • S. Foitzik, I. Kureck, M. Rüger, D. Metzler (2010) Alternative reproductive tactics and the influence of local competition on sex allocation in the ant Hypoponera opacior.
    Behavioral Ecology and Sociobiology 64:1641-1654
  • T. Karn, D. Metzler, E. Ruckhäberle, L. Hanker, R. Gätje, C. Solbach, A. Ahr, M. Schmidt, U. Holtrich, M. Kaufmann, A. Rody (2010) Data driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer
    Breast Cancer Res Treat 120(3):567-579
  • D. Metzler (2010) Book Review: Biostatistics and Microbiology - A Survival Manual. by D. S. Paulson (Springer, 2008).
    Biometrical Journal DOI: 10.1002/bimj.201000033
  • L. Himmelmann, D. Metzler (2009) TreeTime: An extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
    Bioinformatics 25(18):2440-2441 doi:10.1093/bioinformatics/btp417, TreeTime homepage
  • C. A. Hipsley, L. Himmelmann, D. Metzler, J. Mueller (2009) Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards
    BMC Evolutionary Biology 9:151, doi:10.1186/1471-2148-9-151
  • D. Metzler, R. Fleißner (2009) Sequence Evolution Models for Simultaneous Alignment and Phylogeny Reconstruction.
    In: M.S. Rosenberg (Ed.) Sequence Alignment: Methods, Models, Concepts, and Strategies. University of California Press
  • A. Arribas-Gil, D. Metzler, J.-L. Plouhinec (2009) Statistical alignment with a sequence evolution model allowing rate heterogeneity along the sequence
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(2): 281-295
  • O. Jurjut, D. Nikolic, G. Pipa, W. Singer, D. Metzler, and R. Muresan (2009) A color-based visualization technique for multi-electrode spike trains
    Journal of Neurophysiology 102: 3766-3778
  • S. Eckerle, V. Brune, C. Döring, E. Tiacci, V. Bohle, C. Sundström, R. Kodet, M. Paulli, B. Falini, W. Klapper, A. Baur Chaubert, K. Willenbrock, D. Metzler, Andreas Bräuninger, R. Küppers, M.-L. Hansmann (2009) Gene expression profiling of isolated tumor cells from anaplastic large cell lymphomas: insights into its cellular origin, pathogenesis and relation to Hodgkin lymphoma
    Leukemia 23: 2129-2138
  • E. Ruckhäberle, T. Karn, L. Hanker, R. Gätje, D. Metzler, U. Holtrich, M. Kaufmann, A. Rody (2009) Prognostic relevance of glucosylceramide synthase (GCS) expression in breast cancer
    Journal of Cancer Research and Clinical Oncology 135(1), 81-90
  • E. Ruckhäberle, T. Karn, A. Rody, L. Hanker, R. Gätje, D. Metzler, U. Holtrich, M. Kaufmann (2009) Gene expression of ceramide kinase, galactosyl ceramide synthase and ganglioside GD3 synthase is associated with prognosis in breast cancer J. Cancer. Res. Clin. Oncol. 135(8): 1005-1013
  • E. Ruckhäberle, U. Holtrich, K. Engels, L. Hanker, R. Gaetje, D. Metzler, T. Karn, A. Rody, M.Kaufmann (2009) Prognostic value of gene expression of ASAH1, LASS4 and LASS6 in breast cancer. Breast 18 Suppl. 1 S29
  • A. Rody, T. Karn, E. Ruckhäberle, L. Hanker, D. Metzler, V. Müller, C. Solbach, A. Ahr, R. Gätje, U. Holtrich, M. Kaufmann (2009) Loss of Plexin B1 is highly prognostic in low proliferating ER positive breast cancers - results of a large scale microarray analysis
    European Journal of Cancer 45 (3), 405-413, http://www.ncbi.nlm.nih.gov/pubmed/19054665
  • A. Rody, U. Holtrich, L. Pusztai, C. Liedtke, R. Gätje, E. Ruckhäberle, C. Solbach, L. Hanker, A. Ahr, D. Metzler, K. Engels, T. Karn, M. Kaufmann (2009) T-cell metagene predicts a favourable prognosis in estrogen receptor negative and HER2 positive breast cancers
    Breast Cancer Research 11:R15 doi:10.1186/bcr2234
  • A. Kovács, B. Turowski, U. Stefenelli, D. Metzler (2009) Primary Tumor Volume as Predicitive Parameter for Remission after Intraarterial High-dose Cisplatin in Oral and Oropharyngeal Cancer: a Mathematical Model Analysis.
    Cranio Maxillofacial Surgery and Orthodontics 3, 174-186
  • E. Ruckhäberle, U. Holtrich, K. Engels, L. Hanker, R. Gatje, D. Metzler, T. Karn, M. Kaufmann, A. Rody (2009) Acid ceramidase 1 expression correlates with a better prognosis in ER-positive breast cancer. Climacteric 12(6), 502-513
  • M. Löwer, C. Weydig, D. Metzler, A. Reuter, A. Starzinski-Powitz, S. Wessler and G. Schneider (2008) Prediction of extracellular proteases of the human pathogen Helicobacter pylori reveals proteolytic activity of the Hp1018/19 protein HtrA
    PLoS ONE 3(10): e3510. doi:10.1371/journal.pone.0003510
  • V. Brune, E. Tiacci, I. Pfeil, C. Döring, S. Eckerle, C.J.M. van Noesel, W. Klapper, B. Falini, A. von Heydebreck, D. Metzler, A. Bräuninger, Martin-Leo Hansmann, Ralf Küppers (2008) Origin and pathogenesis of nodular lymphocyte-predominant Hodgkin lymphoma as revealed by global gene expression analysis
    The Journal of Experimental Medicine 205(10), 2251-2268
  • D. Metzler, M. Nebel (2008) Predicting RNA Secondary Structures with Pseudoknots by MCMC Sampling
    Journal of Mathematical Biology 56, 161-181
    Supplementary Material, see also http://www.informatik.uni-frankfurt.de/~metzler/McQFold
  • O.F. Jurjut, D. Nikolić, W. Singer, D. Metzler, RC Mureşan (2008) Multidimensional patterns of neuronal activity: how do we see them? BMC Neuroscience 9(1), 1
  • A. Rody, U. Holtrich, R. Gatje, V. Müller, M. Gehrmann, K. Engels, S. Loibl, G. von Minckwitz, R. Diallo, D. Metzler, E. Ruckäberle, A. Ahr, C. Solbach, T. Karn, M. Kaufmann (2008) Relevance of stem cell like breast cancers for adjuvant endocrine treatment decision. Onkologie 31 supp. 1, 27
  • L.M. Himmelmann, D. Metzler (2007) A Study on the Empirical Support for Prior Distributions on Phylogenetic Tree Topologies
    in: C. Falter, A. Schliep, J. Selbig, M. Vingron, D. Walther (Eds.) Proceedings of the German Conference on Bioinformatics, September 26-28, 2007, Potsdam, Germany, Lecture Notes in Informatics - Series of the Gesellschaft für Informatik (GI) 115, 101-110
  • M. Frank, C. Döring, D. Metzler, S. Eckerle, M.-L. Hansmann (2007) Global Gene Expression Profiling of Formalin-Fixed Paraffin-Embedded Tumor Samples: A Comparison to Snap-Frozen Material Using Oligonucleotide Microarrays
    Virchows Archiv 450(6), 699-711
  • K. Engels, S. K. Knauer, D. Metzler, C. Simf, O. Struschka, C. Bier, W. Mann, A. F. Kovacs, R. H. Stauber (2007) Dynamic intracellular survivin as an early prognostic marker in oral squamous cell carcinomas: underlying molecular mechanism and potential
    Journal of Pathology 211(5), 532-540
  • A. Rody, U. Holtrich, R. Gaetje, M. Gehrmann, K. Engels, G. von Minckwitz, S. Loibl, E. Ruckhäberle, D. Metzler, A. Ahr, C. Solbach, T. Karn, M. Kaufmann (2007) Poor outcome in estrogen receptor positive breast cancers predicted by loss of Plexin B1 the receptor for growth repelling semaphorin 4D
    Clinical Cancer Research 13(4), 1115-1122
  • K. Engels, S.K. Knauer, D. Metzler, W. Mann, A.F. Kovacs, R.H. Stauber (2007) The distribution of nuclear and cytoplasmic survivin is a predictive marker of survival and sensitivity to chemo- and radiation induced apoptosis in oral squamous cell carcinoma.
    Pathology Research and Practice 203(5), 270-271
  • V. Brune, I. Pfeil, C. Doering, E. Tiacci, S. Eckerle, C.J.M. Van Noesel, W. Klapper, G. Mechtersheimer, B. Falini, D. Metzler, A. Bräuninger, M.L. Hansmann, R. K¨ppers (2007) Insights into the pathogenesis of primary nodular lymphocyte-predominant Hodgkin lymphoma (NLPH) by global gene expression analysis of isolated L&H cells.
    Haematologica – The Haematology Journal 92 Suppl. 5, 40
  • S. Eckerle, V. Brune, C. Doering, E. Tiacci, C. Sundstrom, R. Kodet, M. Paulli, B. Falini, W. Klapper, A.B. Chaubert, D. Metzler, A. Bräuninger, R. Küppers, M.L. Hansmann (2007) Differences and similarities between classical Hodgkin lymphoma and subtypes of anaplastic large cell lymphomas as revealed by global gene expression profiling of microdissected lymphoma cells
    Haematologica – The Haematology Journal 92 Suppl. 5, 41
  • A.F. Kovacs, B. Turowski, D. Metzler, R. Sader (2007) Tumor volume is a prognostic parameter for remission in oral and oropharyngeal cancer. Oral Oncology 1 Suppl. S, 103
  • D. Metzler (2006) Robust E-Values for Gapped Local Alignments
    Journal of Computational Biology 13, 882-896
  • D. Metzler, M.E. Nebel (2006) An MCMC-Method for Sampling RNA Secondary Structures with Pseudoknots.
    Proceedings of the IASTED International Conference Computational and Systems Biology, November 13-14, 2006, Dallas, TX, USA.
  • R. Fleißner, D. Metzler, A. von Haeseler (2005) Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction.
    Syst. Biol. 54, 548-561
  • D. Metzler (2005) A Poisson Model Heuristic for Judging the Significance of Gapped Local Alignments
    Oberwolfach Reports 40 (Proceedings of the Workshop Mathematical Population Genetics, organized by E. Baake, W. Ewens, and A. Wakolbinger), 2277-2279
  • D. Metzler, R. Fleißner, A. Wakolinger, A. v. Haeseler (2005) Stochastic insertion-deletion processes and statistical sequence alignment. MFWvH04.pdf
    In: J.D. Deuschel, A. Greven (Eds.) Interacting Stochastic Systems, Springer
  • D. Metzler (2003) Statistical Alignment based on fragment insertion and deletion models.
    Bioinformatics19.4 490-499,
    see also http://www.math.uni-frankfurt.de/~stoch/software/mcmcsalut/index.html
  • D. Metzler, S. Grossmann, A. Wakolbinger (2002) A Poisson model for gapped local alignments.
    Stat. Prob. Letters. 60, 91-100
    preprint version: localign.pdf (165 kb), localign.ps (230 kb), localign.ps.gz (62 kb)
  • I. Ebersberger, D. Metzler, C. Schwarz, S. Pääbo (2002) Genome-wide comparison of DNA sequences between humans and chimpanzees.
    Am. J. Hum. Genet. 70 , 1490-1497
  • D. Metzler, R. Fleißner, A. Wakolbinger, A. von Haeseler (2001) Assessing variability by joint sampling of alignments and mutation rates.
    J. Mol. Evol. 53.6 , 660-669; see also http://www.math.uni-frankfurt.de/~stoch/software/mcmcalgn/)
  • R. Fleißner, D. Metzler, A. von Haeseler (2000) Can one estimate distances from pairwise sequence alignments?
    In: E. Bornberg-Bauer, U. Rost, J. Stoye, M.Vingron (eds.) GCB 2000, Proceedings of the German Conference on Bioinformatics, October 5-7, 2000, Heidelberg, Logos Verlag, Berlin, 89-95
  • D. Metzler (1999) Poisson-Approxmationen für genetische Fingerabdrücke
    Dissertation, FB Mathematik der J.W.Goethe-Universität Frankfurt. diss.ps  (1529KB), diss.ps.gz  (401 KB)
  • S. Anulova, J. Bennies, J. Lenhard, D. Metzler, Y. Sung, A. Weber (1999) Six Ways of Looking at Burtins Lemma.
    Amer. Math. Monthly,
    106.4, 345-351
  • B. Schierwater, D. Metzler, K. Krüger, B. Streit (1996) The Effects of Nested Primer Binding Sites on the Reproducibility of PCR: Mathematical Modeling and Computer Simulation Studies.
    J. Comp. Biol. 3.2, 235-251


for analyzing population genetic data:
  • Jaatha is an R package for estimating demographic parameters from population genetic data.
for Bayesian phylogeny estimation:
  • TreeTime is an extensible C++ software package for the Bayesian sampling of phylogenetic trees.
for RNA structure prediction:
  • PhyloQFold is a program for MCMC-sampling conserved secondary structures with pseudoknots for given RNA sequence alignments.
  • McQFold is a program for MCMC-sampling secondary structures with pseudoknots for given RNA sequences.
for alignment sampling:
  • MCMCSALUT is a program for joint sampling alignments an mutation parameter estimates for a given pair of DNA sequences.
    It is based on a model allowing insertions and deletions of more than one site at a time in combination several options for the subtitution process.
  • MCMCALGN is a program for joint sampling alignments an mutation parameter estimates for a given pair of DNA sequences.
    It is based on a model for the process of insertions and deletions of single nucleotides that was proposed by
    J. Thorne, H. Kishino and J. Felsenstein (1991, J. Mol. Evol. 33).

for geo-referenced clustering: http://www.math.uni-frankfurt.de/~stoch/software/ivhg/index.html