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
- Schäfer Y, Palitzsch K, Leptin M, Whiteley AR, Wiehe T, Suurväli J (2024)
Copy number variation and population-specific immune genes in the model vertebrate zebrafish
eLife 13:e98058 - Bechir Ferchichi K, Böhnert T, Ritter B, Harpke D, Stoll A, Morales P, Fiedler S, Mu F, Bechteler J, Münker c, Koch MA, Wiehe T, Quandt D (2024)
Genetic diversity of the Atacama Desert shrub Huidobria chilensis in the context of geography and climate
Global and Planetary Change 234:104385 - Villegas L, Ferretti L, Wiehe T, Waldvogel A, Schiffer P (2024)
Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes
Ecology and Evolution 14:e10831 - Otto M, Grablowitz P, Zheng Y, Wiehe T (2024)
Detecting adaptive changes in gene copy number distribution accompanying the human out-of-Africa expansion
Human Genome Variation 11:37 - Otto M, Wiehe T (2023)
The structured coalescent in the context of gene copy number variation
Theoretical Population Biology 154:67-78 - Otto M, Zheng Y, Wiehe T (2022)
Recombination, selection and the evolution of tandem gene arrays
Genetics 221:iyac052 - Wiehe T (2021)
Counting, grafting and evolving binary trees
In: Probabilistic Structures in Evolution (E.Baake & A. Wakolbinger, eds.), EMS Publishing House, Berlin, pp. 427-450. arXiv:2010.06409 - Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T (2020)
The genetic factors of bilaterian evolution
eLife 9:e45530 - Disanto F, Wiehe T (2020)
Measuring the external branches of a Kingman tree: a discrete approach
Theoretical Population Biology 134:92-105 - Suurväli J, Whiteley AR, Zheng Y, Gharbi K, Leptin M, Wiehe T (2019)
The laboratory domestication of zebrafish: from diverse populations to inbred substrains
Molecular Biology and Evolution 37:1056-1069 - Merklinger FF, Zheng Y, Luebert F, Harpke D, Böhnert T, Stoll A, Koch MA, Weigend M, Blattner FR, Wiehe T, Quandt D (2019)
Population genomics of Tillandsia landbeckii reveals unbalanced genetic diversity and founder effects in the Atacama Desert
Global and Planetary Change 184:103076 - Schiffer PH, Danchin EGJ, Burnell AM, Schiffer AM, Creevey CJ, Wong S, Dix I, O’Mahony G, Culleton BA, Rancurel C, Stier G, Martínez-Salazar EA, Marconi A, Trivedi U, Kroiher M, Thorne MAS, Schierenberg E, Wiehe T, Blaxter M (2019)
Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes
iScience 21:587-602 - Zheng Y, Wiehe T (2019)
Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps
PLoS Computational Biology 15:e1007426 - Jabbari K, Chakraborty M, Wiehe T (2019)
DNA sequence-dependent chromatin architecture and nuclear hub formation
Scientific Reports 9:14646 - Wirtz J, Wiehe T (2019)
The Evolving Moran Genealogy
Theoretical Population Biology 130:94-105 - Jabbari K, Wirtz J, Rauscher M, Wiehe T (2019)
A common genomic code for chromatin architecture and recombination landscape
PloS One 14:e0213278 - Wirtz J, Rauscher M, Wiehe T (2018)
Topological linkage disequilibrium calculated from coalescent genealogies
Theoretical Population Biology 124:41-50 - Ferretti L, Klassmann A, Raineri E, Ramos-Onsins SE, Wiehe T, Achaz G (2018)
The neutral frequency spectrum of linked sites
Theoretical Population Biology 123:70-79 - Yang Y, Li J, Wiehe T, Li H (2018)
Detecting recent positive selection with a single locus test bi-partitioning the coalescent tree
Genetics 208:791-805 - Jabbari K, Heger P, Sharma R, Wiehe T (2018)
The diverging routes of BORIS and CTCF: An interactomic and phylogenomic analysis
Life 8:4-18 - Ferretti L, Ledda A, Wiehe T, Achaz G, Ramos-Onsins SE (2017)
Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests
Genetics 207:229-240 - Pauli T, Vedder L, Dowling D, Petersen M, Meusemann K, Donath A, Peters RS, Podsiadlowski Mayer LC, Liu S, X. Zhou, Heger P, Wiehe T, Hering L, Mayer G, Misof B, Niehuis O (2016)
Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects
BMC Genomics 17:861-870 - Schiffer P, Gravemeyer J, Rauscher M, Wiehe T (2016)
Ultra large gene families: a matter of adaptation or genomic parasites?
Life 6:32-40 - Kraemer-Eis A, Ferretti L, Schiffer P, Heger P, Wiehe T (2016)
A catalogue of Bilaterian-specific genes - their function and expression profiles in early development
doi:10.1101/041806 - Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni J, Soylemez O, Kondrashov F, Leptin M (2016)
Structure and evolutionary history of a large family of NLR proteins in the zebrafish
Open Biology 6:160009-160023 - Disanto F, Wiehe T (2014)
On the sub-permutations of pattern avoiding permutations
Discrete Mathematics 337:127-141 - Rafajlovic M, Klassmann A, Eriksson A, Wiehe T, Mehlig B (2014)
Demography-adjusted tests of neutrality based on genome-wide SNP data
Theoretical Population Biology 95:1-12 - Heger P, Wiehe T (2014)
New tools in the box: an evolutionary synopsis of chromatin insulators.
Trends in Genetics 30:161-171 - Disanto F, Schlizio A, Wiehe T (2013)
Yule-generated trees constrained by node imbalance
Mathematical Biosciences 246:139–147 - Heger P, George R, Wiehe T (2013)
Successive gain of insulator proteins in arthropod evolution
Evolution 67:2945–2956 - Li H, Wiehe T (2013)
Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation
Plos Computational Biology 9:e1003060 - Ferretti L, Disanto F, Wiehe T (2013)
The effect of single recombination events on coalescent tree height and shape
PloS One 8:e60123 - Disanto F, Wiehe T (2013)
Exact enumeration of cherries and pitchforks in ranked trees under the coalescent model
Mathematical Biosciences 242:195-200 - Heger P, Marin B, Bartkuhn M, Schierenberg E, Wiehe T (2012)
The chromatin insulator CTCF and the emergence of metazoan diversity
PNAS 109:17507-17512 - Disanto F, Wiehe T (2012)
Some instances of a sub-permutation problem on pattern avoiding permutations
arXiv:1210.6908 - Uhrig S, Coutelle O, Wiehe T, Perabo L, Hallek M, Büning H (2011)
Successful target cell transduction of capsid-engineered rAAV vectord requires clathrin-dependent endocytosis
Gene Therapy 19:210-218 - Richardson D, Wiehe T (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, Springer Berlin. Abstract - Haubold B, Pfaffelhuber P, Domazet-Loso D, Wiehe T (2009)
Estimating mutation distances from unaligned genomes
Journal of Computational Biology 16:1487-1500 - Kim Y, Wiehe T (2008)
Simulation of DNA sequence evolution under models of recent directional selection
Briefings in Bioinformatics 10:84-96 - Haubold B, Domazet-Loso M, Wiehe T (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 - Teschke M, Mukabayire O, Wiehe T, Tautz D (2008)
Identification of selective sweeps in closely related populations of the house mouse based on microsatellite scans
Genetics 180:1537-1545 - Živkovic D, Wiehe T (2008)
Second order moments of segregating sites under variable population size
Genetics 180:341-357 - Stephan M, Möller F, Wiehe T, Kleffe J (2007)
Self-alignments to detect mutually exclusive exon usage
In Silico Biology 7:613-621 - Vukusic I, Nagaraja Grellscheid S, Wiehe T (2007)
Applying genetic programming to the prediction of alternative mRNA splice variants
Genomics 89:471-479 - Thomas M, Möller F, Wiehe T, Tautz D (2007)
A pooling approach to detect signatures of selective sweeps in genome scans using microsatellites
Molecular Ecology Notes 7:400-403 - Wiehe T, Nolte V, Živkovic D, Schlötterer C (2007)
Identification of selective sweeps using a dynamically adjusted number of linked microsatellites
Genetics 175:207-218 - Haubold B, Wiehe T (2006)
How repetitive are genomes?
BMC Bioinformatics 7:541-550 - Pierstorff N, Bergman C, Wiehe T (2006)
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA
Bioinformatics 22:2858-2864 - Haubold B, Wiehe T (2006)
Introduction to Computational Biology. An Evolutionary Approach.
Textbook, 328p. Birkhauser, Basel. Link - Haubold B, Pierstorff N, Möller F, Wiehe T (2005)
Genome comparison without alignment using shortest unique substrings
BMC Bioinformatics. 6:123-133 - Thomas M, Ihle S, Ravaoarimanana I, Krächter S, Wiehe T, Tautz D (2005)
Microsatellite variability in wild populations of the house mouse is not influenced by differences in chromosomal recombination rates
Biological Journal of the Linnean Society 84:629-635 - Wiehe T, Schmid K, Stephan W (2005)
Selective sweeps in structured populations
In: D. Nurminsky, editor, Selective Sweep. Landes Biosciences, Georgetown, pp. 104-117 - Haubold B, Wiehe T (2004)
Comparative Genomics: methods and applications
Naturwissenschaften 91:405-421
Abril J, Guigó R, Wiehe T (2003)
gff2aplot: Plotting sequence comparisons
Bioinformatics 19:2477-2479 - Parrá G, Agarwal P, Abril J, Wiehe T, Fickett J, Guigó R (2003)
Comparative gene prediction in human and mouse
Genome Research 13:108-117 - Guigó R, Wiehe T (2003)
Gene prediction accuracy in large DNA sequences
In: M. Galperin and E. Koonin, editors, Frontiers in Computational Genomics. Caister Academic Press, Norfolk, pp.1-33