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Faculty of Mathematics and Natural SciencesAG Wiehe

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 Bioinformatics 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

Publications

  • T. Wiehe (2020) Counting, grafting and evolving binary trees arXiv

  • P. Heger, W. Zheng, A. Rottmann, K.A. Panfilio, T. Wiehe (2020) The genetic factors of bilaterian evolution eLife 9

  • Disanto F, Wiehe T (2020) Measuring the external branches of a Kingman tree: a discrete approach Theo Pop Biol 134:92-105

  • F.F. Merklinger, Y. Zheng, F. Luebert, D. Harpke, T. Böhnert, A. Stoll, M.A. Koch, M. Weigend, F.R. Blattner, T. Wiehe, D. Quandt  (2019) Population genomics of Tillandsia landbeckii reveals unbalanced genetic diversity and founder effects in the Atacama Desert Global and Planetary Change 184

  • J. Suurväli, A. R. Whiteley, Y. Zheng, K. Gharbi, M. Leptin, T. Wiehe (2019) The laboratory domestication of zebrafish: from diverse populations to inbred substrains Mol Biol Evol (in press), doi:/10.1093/molbev/msz289 

  • P.H. Schiffer, E.G.J. Danchin, A.M. Burnell, A.M. Schiffer, C.J. Creevey, S. Wong, I. Dix, G. O’Mahony, B.A. Culleton, C. Rancurel, G. Stier, E.A. Martínez-Salazar, A. Marconi, U. Trivedi, M. Kroiher, M.A.S. Thorne, E. Schierenberg, T. Wiehe, Blaxter M (2019) Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes iScience 21:587-602

  • Y. Zheng, T. Wiehe (2019) Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps PLoS Comput Biol. 15:e1007426

  • K. Jabbari, M. Chakraborty, T. Wiehe (2019) DNA sequence-dependent chromatin architecture and nuclear hub formation Sci Rep 9(1):14646

  • J. Wirtz, T. Wiehe (2019) The Evolving Moran Genealogy Theor Popul Biol 130:94-105
  • K. Jabbari, J. Wirtz, M. Rauscher, T. Wiehe (2019) A common genomic code for chromatin architecture and recombination landscape PloS One 14:e0213278
  • J. Wirtz, M. Rauscher, T. Wiehe (2018) Topological linkage disequilibrium calculated from coalescent genealogies Theor Popul Biol 124:41-50
  • K. Jabbari, P. Heger, R. Sharma, T. Wiehe (2018) The diverging routes of BORIS and CTCF: An interactomic and phylogenomic analysis doi:10.3390/life8010004
  • L. Ferretti, A. Klassmann, E. Raineri, T. Wiehe, S.E. Ramos-Onsins, G. Achaz (2018) The expected neutral frequency spectrum of linked sites doi:https://doi.org/10.1101/100123
  • Z. Yang, J. Li, T. Wiehe, H. Li (2017) Detecting recent positive selection with a single locus test bi-partitioning the coalescent tree Genetics 208(2):791-805
  • 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 Genetics, q-bio.GN
  • 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 17:861-870
  • P. Schiffer, J. Gravemeyer, M. Rauscher, T. Wiehe (2016) Ultra large gene families: a matter of adaptation or genomic parasites? Life 6:32-40
  • L. Ferretti, A. Klassmann, T. Wiehe, S.E. Ramos-Onsins, G. Achaz (2016) The expected neutal frequency spectrum of two linked sites http://arxiv.org/abs/1604.06713
  • 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: http://dx.doi.org/10.1101/041806
  • 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 Open Biol. 2016 6
  • P. Heger and T. Wiehe (2014) New tools in the box: an evolutionary synopsis of chromatin insulators Trends Genet 30(5):161-71
  • M. Rafajlovic, A. Klassmann, A. Eriksson, T. Wiehe, B. Mehlig (2013) Demography-adjusted tests of neutrality based on genome-wide SNP data Theor Popul Biol 95:1-12
  • F. Disanto, A. Schlizio, T. Wiehe (2013) Yule-generated trees constrained by node imbalance Math Biosci 246(1):139-47
  • P. Heger, R. George and T. Wiehe (2013) Successive gain of insulator proteins in arthropod evolution Evolution 67(10):2945-56
  • 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) On the sub-permutations of 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. Živkovic 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. Pierstorff, 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, 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