Johann Wolfgang Goethe-Universität Fachbereich Informatik und Mathematik, Institut für Informatik

Dirk Metzler Von 16. Dezember 2002 bis 30. September 2008 Juniorprofessor für Bioinformatik am Institut für Informatik. Seit 1. Oktober 2008 Professor für Quantitative Genetik an der Ludwig-Maximilians-Universität in München. New homepage under construction!

Arbeitsgruppe - group

wissenschaftliche Arbeiten - publications and preprints

• 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
• 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 (to appear)
• 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
• T. Karn, D. Metzler, E. Ruckhäberle, L. Hanker, R. Gätje, C. Solbach, A. Ahr, M. Schmidt, U. Holtrich, M. Kaufmann, A. Rody (2009) 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 DOI 10.1007/s10549-009-0416-z
• 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 (to appear)
• 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
• M. Löwer, C. Weydig, D. Metzler, A. Reuter, A. Starzinski-Powitz, S. Wessler and G. Schneider (2009) 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
• 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. DOI 10.1007/s00432-008-0536-6
• 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
• 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
• A. Arribas-Gil, D. Metzler, J.-L. Plouhinec (2007) Statistical alignment with a sequence evolution model allowing rate heterogeneity along the sequence
  IEEE/ACM Transactions on Computational Biology and Bioinformatics
  29 Aug 2007. IEEE Computer Society Digital Library. IEEE Computer Society, http://doi.ieeecomputersociety.org/10.1109/TCBB.2007.70246
  
• 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
• 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

Lehre - teaching

Sommersemester 2008: Vorlesung mit Übung: Algorithmisches Lernen in der Bioinformatik
Seminar: Aktuelle Themen der Bioinformatik
Vorlesung: Evolutionsbiologie für Bioinformatiker (gemeinsam mit Dozenten der Biologie)

Sommersemester 2007: Vorlesung: Algorithmisches Lernen in der Bioinformatik
Seminar: Aktuelle Themen der Bioinformatik
Vorlesung: Evolutionsbiologie für Bioinformatiker (gemeinsam mit Dozenten der Biologie)

Wintersemester 2006/2007: Algorithmen und Modelle der Bioinformatik, Vorlesung mit Übung, 4+2 SWS

Sommersemester 2006: Vorlesung: Algorithmisches Lernen in der Bioinformatik
Seminar: Aktuelle Themen der Bioinformatik
Vorlesung: Evolutionsbiologie für Bioinformatiker (gemeinsam mit Dozenten der Biologie)

Sommersemester 2005: Vorlesung: Algorithmisches Lernen in der Bioinformatik
Seminar: Aktuelle Themen der Bioinformatik
Vorlesung: Evolutionsbiologie für Bioinformatiker (gemeinsam mit Dozenten der Biologie)

Wintersemester 2004/2005: Algorithmen und Modelle der Bioinformatik, Vorlesung mit Übung, 3+1 SWS, Einordnung ThBI und PTBI
Methoden-Seminar: Phylogenetische Analysen biologischer Sequenzdaten

Sommersemester 2004: Vorlesung: Algorithmisches Lernen in der Bioinformatik
Seminar: Aktuelle Themen der Bioinformatik

Wintersemester 2003/2004: Algorithmen und Modelle der Bioinformatik, Vorlesung mit Übung, 3+1 SWS, Einordnung ThBI und PTBI

Sommersemester 2003: Alignment und Stammbaumschätzung mit biologischen Sequenzen, Vorlesung mit Übung, 3+1 SWS, Einordnung ThBI und PTBI
Vorträge von Studierenden im Rahmen der Übung: e_wert.pdf, markov_ordnung.pdf

Wintersemester 2002/2003: Alignment und Phylogenieschätzung, ein Nachmittag in G. Schneiders Vorlesung Grundlagen der Bioinformatik

Sommersemester 2002: Theorie-Teil der Vorlesung "Einführung in die Evolutionstheorie"
(Die verwendeten OHP-Folien können bei mir zum Kopieren ausgeliehen werden)

Wintersemester 2001/2002: Mathematische Grundlagen der Informatik (Lehrauftrag am Fachbereich Biologie und Informatik)
Bericht über die Evaluation der Veranstaltung

Software

• TreeTime is an extensible C++ software package for the Bayesian sampling of phylogenetic trees.

• McQFold is a program for MCMC-sampling secondary structures with pseudoknots for a given RNA sequence.

• 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