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Vieira Mourato, B.; Haubold, B.: Fast detection of unique genomic regions. Computational and Structural Biotechnology Journal 27, pp. 843 - 850 (2025)

Vieira Mourato, B.; Haubold, B.: Detection and annotation of unique regions in mammalian genomes. G3: Genes, Genomes, Genetics 15 (1), jkae257 (2025)

Vieira Mourato, B.; Tsers, I.; Denker, S.; Klötzl, F.; Haubold, B.: Marker discovery in the large. Bioinformatics advances 4 (1), vbae113 (2024)

Haubold, B.; Klötzl, F.; Hellberg, L.; Thompson, D.; Cavalar, M.: Fur: Find unique genomic regions for diagnostic PCR. Bioinformatics 37 (15), pp. 2081 - 2087 (2021)

Dubois, J.; Rueger, J.; Haubold, B.; Far, R. K.-K.; Sczakiel, G.: Transcriptome analyses of urine RNA reveal tumor markers for human bladder cancer: validated amplicons for RT-qPCR-based detection. Oncotarget 12, pp. 1011 - 1023 (2021)

Klötzl, F.; Haubold, B.: Phylonium: fast estimation of evolutionary distances from large samples of similar genomes. Bioinformatics 36 (7), pp. 2040 - 2046 (2020)

Lynch, M.; Haubold, B.; Pfaffelhuber, P.; Maruki, T.: Inference of historical population-size changes with allele-frequency data. G3: Genes, Genomes, Genetics 10 (1), pp. 211 - 223 (2020)

Pirogov, A.; Pfaffelhuber, P.; Börsch-Haubold, A.; Haubold, B.: High-complexity regions in mammalian genomes are enriched for developmental genes. Bioinformatics 35 (11), pp. 1813 - 1819 (2019)

Odenthal-Hesse, L.; Dutheil, J. Y.; Klötzl, F.; Haubold, B.: hotspot: software to support sperm-typing for investigating recombination hotspots. Bioinformatics 32 (16), pp. 2554 - 2555 (2016)

Klötzl, F.; Haubold, B.: Support values for genome phylogenies. Life 6 (1), 11 (2016)

Krause, L.; Haubold, B.; Börsch-Haubold, A.: Social exclusion changes histone modifications H3K4me3 and H3K27ac in liver tissue of wild house mice. PLoS One 10 (8), e0133988 (2015)

Haubold, B.; Klötzl, F.; Pfaffelhuber, P.: andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics 31 (8), pp. 1169 - 1175 (2015)

Lynch, M.; Xu, S.; Maruki, T.; Jiang, X.; Pfaffelhuber, P.; Haubold, B.: Genome-wide linkage-disequilibrium profiles from single individuals. Genetics 198 (1), pp. 269 - 281 (2014)

Haubold, B.: Alignment-free phylogenetics and population genetics. Briefings in Bioinformatics 15 (3), bbt083, pp. 407 - 418 (2014)

Börsch-Haubold, A.; Montero, I.; Konrad, K.; Haubold, B.: Genome-wide quantitative analysis of histone H3 lysine 4 trimethylation in wild house mouse liver: environmental change causes epigenetic plasticity. PLoS ONE 9 (5), e97568 (2014)

Haubold, B.; Krause, L.; Horn, T.; Pfaffelhuber, P.: An alignment-free test for recombination. Bioinformatics 29 (24), pp. 3121 - 3127 (2013)

McCann, H. C.; Rikkerink, E. H. A.; Bertels, F.; Fiers, M.; Lu, A.; George, J. R.-; Andersen, M. T.; Gleave, A. P.; Haubold, B.; Wohlers, M. W. et al.; Guttman, D. S.; Wang, P. W.; Straub, C.; Vanneste, J. L.; Rainey, P. B.; Templeton, M. D.: Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actnidiae provides insight into the origins of an emergent plant disease. PLoS Pathogens 9 (7), e1003503 (2013)

Haubold, B.; Pfaffelhuber, P.: Aligment-free population genomics: an efficient estimator of sequence diversity. G3: Genes, Genomes, Genetics 2 (8), pp. 883 - 889 (2012)

Huang, W.; Haubold, B.; Hauert, C.; Traulsen, A.: Emergence of stable polymorphisms driven by evolutionary games between mutants. Nature Communications 3, 919 (2012)

Domazet-Lošo, M.; Haubold, B.: Alignment-free detection of horizontal gene transfer between closely related bacterial genomes. Mobile Genetic Elements 1 (3), pp. 230 - 235 (2011)