Thomas Wiehe


Tel +49-221-470-1588

Fax +49-221-470-1630


  • 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



  • 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

  • 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  doi:
  • A. Ledda, G. Achaz, T. Wiehe and L. Ferretti (2015) Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests.  arXiv:1510.06748
  • 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.  arXiv:1307.0337

  • 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.  arXiv:1210.6908

  • 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. Abstract

  • 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. Abstract

  • 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.  PDF 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