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, Evolutionary Biology, Genetics and Genomics

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
Elsevier, Science Direct, Global and Planetary Change

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

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, Hum Genome Var 11, 37 (2024)

Otto M, Wiehe T (2023)
The structured coalescent in the context of gene copy number variation
Theoretical Population Biology, Volume 154, December 2023, Pages 67-78

Otto M, Zheng Y, Wiehe T (2022)
Recombination, selection and the evolution of tandem gene arrays
Genetics, Volume 221, Issue 3, July 2022

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

Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T (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
Theor Popul Biol 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
Mol Biol Evol 37:1056-1069

Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser J, Wilson JY, Rosenblad MA, Burguera D, Gutnik S, Michiels N, Tölpel M, Pankov K, Schloissnig S, Winkler S (2020)
The round goby genome provides insights into mechanisms that may facilitate biological invasions
BMC Biol 18:11

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

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 Comput Biol. 15:e1007426

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

Panfilio KA, Vargas Jentzsch IM, ..., Heger P, ..., Gibbs RA, Richards S (2019)
Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome
Genome Biol 20:64

Wirtz J, Wiehe T (2019)
The Evolving Moran Genealogy
Theor Popul Biol 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
Theor Popul Biol 124:41-50

Jabbari K et al. (2018)
Rare gene deletions in genetic generalized and rolandic epilepsies
PloS One 13:e0202022

Zheng Y, Graur D, Azevedo RBR (2018)
Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences
J Mol Evol 86:365-378

Ferretti L, Klassmann A, Raineri E, Ramos-Onsins SE, Wiehe T, Achaz G (2018)
The neutral frequency spectrum of linked sites
Theor Popul Biol 123:70-79

Thier K, Möckel M, Palitzsch K, Döhner K, Sodeik B, Knebel-Mörsdorf D (2018)
Entry of Herpes Simplex Virus 1 into Epidermis and Dermal Fibroblasts is Independent of the Scavenger Receptor MARCO
J Virol 92:e00490-18

Klassmann A, Ferretti L (2018)
The third moments of the site frequency spectrum
Theor Popul Biol 120:16-28

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

Bobbili D, Lal D, May P, Reinthaler E, Jabbari K, Thiele H, Nothnagel M, Jurkowski W, Feucht M, Nürnberg P, Lerche H, Zimprich F, Krause R,  Neubauer B, Reinthaler E, Zimprich F, Feucht M , Steinböck H, Neophytou B, Geldner J, Gruber-Sedlmayr U, Haberlandt E, Ronen G, Altmüller J, Sander T, Thiele H, Krause R, May P, Balling R,  Neubauer B (2018)
Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy
Eur J Hum Genet 26:258-264

Zheng Y, Janke A. (2018)
Gene flow analysis method, the D-statistic, is robust in a wide parameter space
BMC Bioinformatics 19:10-28

Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janka A. (2018)
Speciation Generates Mosaic Genomes in Kangaroos
Genome Biol Evol 10:33-44

Suurväli J, Boudinot P, Kanellopoulos J, Boudinot SR (2017)
P2X4: A fast and sensitive purinergic receptor
Biomed J 40:245-256

Venter PC, Nitsche F, Domonell A, Heger P, Arndt H (2017)
The Protistan Microbiome of Grassland Soil: Diversity in the Mesoscale
Protist 168:546-564

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 Biol 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
Theor Pop Biol 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

Schiffer PH, Kroiher M, Kraus C, Koutsovoulos GD, Kumar S, Camps JI, Nsah NA, Stappert D, Morris K, Heger P, Altmüller J, Frommolt P, Nürnberg P, Thomas WK, laxter ML, Schierenberg E (2013)
The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda
BMC Genomics 14:923-938

Disanto F, Schlizio A, Wiehe T (2013)
Yule-generated trees constrained by node imbalance
Math Biosci 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 Comput Biol. 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
Math Biosci 242:195-200

Disanto F (2013)
Unbalanced subtrees in binary rooted ordered and un-ordered trees
Séminaire Lotharingien de Combinatoire 68, Article B68b

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 Ther. 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
J Comput Biol 16:1487-1500

Kim Y, Wiehe T (2008)
Simulation of DNA sequence evolution under models of recent directional selection
Brief Bioinform 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 Biol 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
Mol Ecol 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
Biol J Linn Soc Lond 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(9):405-421

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

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

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