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Prof. Dr. Thomas Wiehe

  • since 2003 Professor for Bioinformatics and Population Genetics at University of Cologne
  • 2001 - 2002 Leader of an independent young investigators group at FU Berlin and Berlin Center for Genome-based Bioinformatics
  • 1999 -2001 Group leader in Bioinforamtics at MPI for Chemical Ecology in Jena
  • 1997 - 1999 Postdoc with A. Rosenthal at IMB-Jena, Deputy group leader in Comparative Genomics
  • 1995 - 1997 Postdoc with M. Slatkin at University of California, Berkeley, USA
  • 1990 - 1994 Ph.D. thesis in Theoretical Biology with W. Stephan at University of Maryland, College Park, USA and P. Schuster at IMB-Jena and University of Vienna, Austria
  • 1989 Diplom (M.S.) in Mathematics and Philosophy at University of Erlangen


  • K. Jabbari, P. Heger, R. Sharma, T. Wiehe (2018)
    The diverging routes of BORIS and CTCF: An interactomic and phylogenomic analysis

  • L. Ferretti, A. Klassmann, E. Raineri, T. Wiehe, S.E. Ramos-Onsins, G. Achaz (2018)
    The expected neutral frequency spectrum of linked sites

  • The third moments of the site frequency spectrum

  • Z. Yang, J. Li, T. Wiehe, H. Li (2017)
    Detecting recent positive selection with a single locus test bi-partitioning the coalescent tree
    In press in Genetics
  • L. Ferretti, A. Ledda, T. Wiehe, G. Achaz and S.E. Ramos-Onsins (2017)
    Decomposing the Site Frequency Spectrum: The Impact ofr Tree Topology on Neutrality Tests
  • T. Pauli, L. Vedder, D. Dowling, M. Petersen, K. Meusemann, A. Donath, R.S. Peters, L. Podsiadlowski, C. Mayer, S. Liu, X. Zhou, P. Heger, T. Wiehe, L. Hering, G. Mayer, B. Misof, O. Niehuis (2016)
    Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects
    BMC Genomics, 17:861
  • P. Schiffer, J. Gravemeyer, M. Rauscher, T. Wiehe (2016)
    Ultra large gene families: a matter of adaptation or genomic parasites?
    Life 2016, 6(3),32
  • L. Ferretti, A. Klassmann, T. Wiehe, S.E. Ramos-Onsins, G. Achaz (2016)
    The expected neutal frequency spectrum of two linked sites
  • A. Kraemer-Eis, L. Ferretti, P. Schiffer, P. Heger, T. Wiehe (2016)
    The developmental genetic toolkit shared by bilaterian crown clades after a billion years of divergence
  • A. Ledda, G. Achaz, T. Wiehe and L. Ferretti (2015)
    Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests.
  • K. Howe, P.H. Schiffer, J. Zielinski, T. Wiehe, G.K. Laird, J. Marioni, O. Soylemez, F. Kondrashov and M. Leptin (2015)
    Structure and evolutionary history of a large family o NLR proteins in the zebrafish.
  • M. Rafajlovic, A. Klassmann, A. Eriksson, T. Wiehe, B. Mehlig (2013)
    Demography-adjusted tests of neutrality based on genome-wide SNP data.

  • F. Disanto, A. Schlizio, T. Wiehe (2013)
    Yule-generated trees constrained by node imbalance. Math Biosci
    (online access)

  • P. Heger, R. George and T. Wiehe (2013)
    Successive gain of insulator proteins in arthropod evolution. Evolution
    (online access)

  • H. Li, T. Wiehe (2013)
    Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation.
    Plos Comput Biol. 9(5):e1003060

  • L. Ferretti, F. Disanto, T. Wiehe (2013)
    The effect of single recombination events on coalescent tree height and shape.
    PloS One 8(4):e60123

  • F. Disanto, T. Wiehe (2013)
    Exact enumeration of cherries and pitchforks in ranked trees under the coalescent model.
    Math Biosci. 242:195-200

  • P. Heger, B. Marin, M. Bartkuhn, E. Schierenberg, T. Wiehe (2012)
    The chromatin insulator CTCF and the emergence of metazoan diversity.
    PNAS 109:17507

  • F. Disanto, T. Wiehe (2012)
    Some instances of a sub-permutation problem on pattern avoiding permutations.

  • S. Uhrig, O. Coutelle, T. Wiehe, L. Perabo, M. Hallek, H. Büning (2011)
    Successful target cell transduction of capsid-engineered rAAV vectord requires clathrin-dependent endocytosis.
    Gene Ther. 19(2):210-8

  • D. Richardson and T. Wiehe (2009)
    Properties of sequence conservation in upstream regulatory and protein coding regions among paralogs in Arabidopsis thaliana.Lecture Notes
    in: Computer Science: Lecture Notes in Bioinformatics, Vol. 5817, Ciccarelli, F.; Miklos, I. (Eds.) 2009, pp 217-218, Springer Berlin.

  • B. Haubold, P. Pfaffelhuber, D. Domazet-Loso and T. Wiehe (2009)
    Estimating mutation distances from unaligned genomes.
    J Comput Biol. 16(10):1487-1500

  • Y. Kim and T. Wiehe (2008)
    Simulation of DNA sequence evolution under models of recent directional selection.
    Brief Bioinform. 10(1):84-96

  • B. Haubold, M. Domazet-Loso and T. Wiehe (2008)
    An alignment-free distance measure for closely related genomes. Lecture Notes
    in: Computer Science: Lecture Notes in Bioinformatics, Vol. 5267, Nelson, C.; Vialette, S. (Eds.) 2008, X, 265 p., Springer Berlin.

  • M. Teschke, O. Mukabayire, T. Wiehe and D. Tautz (2008)
    Identification of selective sweeps in closely related populations of the house mouse based on microsatellite scans.
    Genetics. 180:1537-1545

  • D. Živkovi? and T. Wiehe (2008)
    Second order moments of segregating sites under variable population size.
    Genetics. 180:341-357

  • M. Stephan, F. Möller, T. Wiehe, J. Kleffe (2007)
    Self-alignments to detect mutually exclusive exon usage.
    In Silico Biol. 7(6):613-621

  • I. Vukusic, S. Nagaraja Grellscheid, T. Wiehe (2007)
    Applying genetic programming to the prediction of alternative mRNA splice variants.
    Genomics. 89(4):471-479

  • M. Thomas, F. Möller, T. Wiehe and D. Tautz (2007)
    A pooling approach to detect signatures of selective sweeps in genome scans using microsatellites.
    Mol Ecol Notes. 7(3):400-403

  • T. Wiehe, V. Nolte, D. Živkovi? and C. Schlötterer (2007)
    Identification of selective sweeps using a dynamically adjusted number of linked microsatellites.
    Genetics. 175(1):207-218

  • B. Haubold, T. Wiehe (2006)
    How repetitive are genomes?
    BMC Bioinformatics. 7:541

  • N. Pierstorff, C. Bergman and T. Wiehe (2006)
    Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.
    Bioinformatics. 22(23):2858-2864

  • B. Haubold and T. Wiehe (2006)
    Introduction to Computational Biology. An Evolutionary Approach. Textbook, 328p. Birkhauser, Basel. Link

  • B. Haubold, N. Piersdorff, F. Möller and T. Wiehe (2005)
    Genome comparison without alignment using shortest unique substrings.
    BMC Bioinformatics. 6:123

  • M. Thomas, S. Ihle, I. Ravaoarimanana, S. Krächter, T. Wiehe and D. Tautz (2005)
    Microsatellite variability in wild populations of the house mouse is not influenced by differences in chromosomal recombination rates.
    Biol J Linn Soc Lond. 84(3):629-635

  • T. Wiehe, K. Schmid and W. Stephan (2005)
    Selective sweeps in structured populations.
    In: D. Nurminsky, editor, Selective Sweep. Landes Biosciences, Georgetown, pp. 104-117

  • B. Haubold, N. Pierstorff, F. Möller, T. Wiehe (2004)
    Comparative Genomics: methods and applications.
    Naturwissenschaften 91(9):405-421

  • J. Abril, R. Guigó and T. Wiehe (2003)
    gff2aplot: Plotting sequence comparisons.
    Bioinformatics 19(18):2477-2479

  • G. Parrá, P. Agarwal, J. Abril, T. Wiehe, J. Fickett and R. Guigó (2003)
    Comparative gene prediction in human and mouse.
    Genome Res. 13(1):108-117

  • R. Guigó and T. Wiehe (2003)
    Gene prediction accurancy in large DNA sequences.
    In: M. Galperin and E. Koonin, editors, Frontiers in Computational Genomics. Caister Academic Press, Norfolk

  • B. Haubold, J. Kroymann, A. Ratzka, T. Mitchell-Olds and T. Wiehe (2002)
    Recombination and gene conversion in a 170kb genomic region of Arabidopsis thaliana.
    Genetics 161(3):1269-1278

  • B. Haubold and T. Wiehe (2002)
    Calculating the SNP-effective sample size from an alignment.
    Bioinformatics 18(1):36-38

  • T. Wiehe, S. Gebauer-Jung, T. Mitchell-Olds and R. Guigó (2001)
    SGP-1: prediction and validation of homologous genes based on sequence alignments.
    Genome Res. 11(9):1574-1583

  • B. Haubold and T. Wiehe (2001)
    Statistics of divergence times.
    Mol Biol Evol. 18:1157-1160

  • T. Wiehe, R. Giogó and W. Miller (2000)
    Genome sequence comparisons: hurdles in the fast lane to functional genomics.
    Brief Bioinform. 1(4):381-388

  • K. Reichwald, J. Thiessen, T. Wiehe, J. Weitzel, W.H. Sträteling, et. al. (2000)
    Comparative sequence analysis of the MECP2-locus in human and mouse reveals new transcribed regions.
    Mamm Genome 11(3):182-190

  • T. Wiehe, J. Mountain, P. Parham and M. Slatkin (2000)
    Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns. Genet Res. 75(1):61-73

  • Z. Zhang, P. Berman, T. Wiehe, W. Miller (1999)
    Post-processing long pairwise alignments. Bioinformatics 15(12):1012-1019

  • C. Schlötterer and T. Wiehe (1999)
    Microsatellites, a neutral marker to infer selective sweeps.
    In D. B. Goldstein and C. Schlötterer, editors, Microsatellites - Evolution and Apllications, pp. 238-248, Oxford University Press, Oxford

  • P. Kioschis, S. Wiemann, N. Heiss, F. Francis, C. Götz, A. Poustka, S. Taudien, M. Platzer, T. Wiehe, G. Beckmann, J. Weber, G. Nordsiek and A. Rosenthal (1998)
    Genomic organization of a 225-kb region in Xq28 containing the gene for X-linked myotubular myopathy (MTM1) and a related gene (MTMR1).
    Genomics 54(2):256-266

  • M. Platzer, T. Wiehe, K. Reichwald, G. Nordsiek, W. Zhao, G. Hermann and A. Rosenthal (1998)
    Comparative analysis of 1.15Mb of genomic DNA from mouse X chromosome and the corresponding regions of human Xq28.
    In 12th International Mouse Genome Conference, Garmisch Partenkirchen, Germany, p. A4

  • M. Slatkin and T. Wiehe (1998)
    Genetic hitchhiking in a subdivided population.
    Genet Res. 71(2):155-160

  • T. Wiehe (1998)
    The effect of selective sweeps on the variance of the allele distribution of a linked multiallele locus: hitchhiking of microsatellites.
    Theor Popul Biol. 53(3):272-283

  • T. Wiehe, M. Slatkin (1998)
    Epistatic selection in a multi-locus Levene model and implications for linkage disequilibrium.
    Theor Popul Biol. 53(1):75-84

  • T. Wiehe (1997)
    Model dependency of error thresholds: The role of fitness functions and contrasts of the finite and infinite sites models.
    Genet Res (Camp). 71:155-160

  • E. Baake and T. Wiehe (1997)
    Bifurcations in haploid and diploid sequence space models.
    J Math Biol. 35(3):321-343

  • T. Wiehe, E. Baake and P. Schuster (1995)
    Error propagation in reproduction of diploid organisms. A case study on single peaked landscapes.
    J Theor Biol. 177(1):1-15

  • T. Wiehe and W. Stephan (1993)
    Analysis of a genetic hitchhiking model, and its application to DNA polymorphism data from Drosophila melanogaster.
    Mol Biol Evol. 10(4):842-854

  • W. Stephan, T. Wiehe and M. Lenz (1992)
    The effect of strongly selected substitutions on neutral polymorphism: Analytical results based on diffusion theory.
    Theor Popul Biol. 41(2):237-254