Papers

2025

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

2024

• Vieira Mourato, B., Tsers, I., Denker, S., Klötzl, F., and Haubold, B. (2024). Marker discovery in the large. Advances in Bioinformatics, 4:vbae113.
• Vieira Mourato, B. and Haubold, B. (2024). Detection and Annotation of Unique Regions in Mammalian Genomes. G3, 15:jkae257.

2021

• Haubold, B., Klötzl, F., Hellberg, L., Thompson, D., and Cavalar, M. (2021). Fur: Find unique genomic regions for diagnostic PCR. Bioinformatics. Software.
• Haubold, B. and Klötzl, F. (2021). Fast phylogeny reconstruction from genomes of closely related microbes. In Bacterial Pangenomics, 2nd Ed.: Methods and Protocols. Springer, p. 77–89.

2020

• Klötzl, F. and Haubold, B. (2020). Phylonium: Fast estimation of evolutionary distances from large samples of similar genomes. Bioinformatics, 36:2040–2046. Software.
• Lynch, M., Haubold, B., Pfaffelhuber, P., and Maruki, T. (2020). Inference of historical population-size changes with allele frequency data. G3, 10:211–223. Software.

2019

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

2016

• Klötzl, F. and Haubold, B. (2016). Support values for genome phylogenies. Life, 6:11. Software and data sets.
• Odenthal-Hesse, L., Dutheil, J. Y., Klötzl, F., and Haubold, B. (2016). hotspot: Software to support sperm-typing for investigating recombination hotspots. Bioinformatics, 32:2554–2555. Software.

2015

• Haubold, B., Klötzl, F., and Pfaffelhuber, P. (2015). andi: Fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics, 31:1169–1175. Software.
• Krause, L., Haubold, B., and Börsch-Haubold, A. G. (2015). Social exclusion changes histone modifications H3K4me3 and H3K27ac in liver tissue of wild house mice. PLOSone, DOI: 10.1371/journal.pone.0133988.

2014

• Börsch-Haubold, A. G., Montero, I., Konrad, K., and Haubold, B. (2014). Genome-wide quantitative analysis of histone H3 lysine 4 trimethylation in wild house mouse liver: Environmental change causes epigenetic plasticity. PLOSone, DOI: 10.1371/journal.pone.0097568. Press Release.
• Lynch, M., Xu, S., Maruki, T., Jiang, X., Pfaffelhuber, P., and Haubold, B. (2014). Genome-wide linkage-disequilibrium profiles from single individuals. Genetics, 198:269–281.

2013

• McCann, H. C., Rikkerink, E. H. A., Bertels, F., Fiers, M., Lu, A., Rees-George, J., Andersen, M. T., Gleave, A. P., Haubold, B., Wohlers, M. W., Guttman, D. S., Wang, P. W., Straub, C., Vanneste, J. L., Rainey, P. B., and Templeton, M. D. (2013). Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease. PLOS-Pathogens, 9:e1003503.
• Thota, A., Haubold, B., Michael, S, Doak,T., Xu, S., and Henschel, R. (2013). Making campus bridging work for researchers: a case study with mlRho. In: Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 17:1–17:8. ACM, New York.
• Haubold, B., Krause, L., Horn, T., and Pfaffelhuber, P. (2013). An Alignment-free Test for Recombination. Bioinformatics, 24:3121–3127.

2012

• Huang, W., Haubold, B., Hauert, C. and Traulsen, A. (2012). Emergence of stable polymorphisms driven by evolutionary games between mutants. Nature Communications, 3:919.
• Haubold, B. and Pfaffelhuber, P. (2012). Alignment-Free Population Genomics: An Efficient Estimator of Sequence Diversity. Genes, Genomes, Genetics, 2:883–889. Software.

2011

• Haubold, B., Reed, F. and Pfaffelhuber, P. (2011). Alignment-free estimation of nucleotide diversity. Bioinformatics, 27:449–455. Software.
• Domazet-Lošo, M. and Haubold, B. (2011). Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics, 27:1466–1472. Software.
• Tellier, A., Pfaffelhuber, P., Haubold, B., Naduvilezhath, L., Rose, L. E., Städler, T., Stephan, W. and Metzler, D. (2011). Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. PLoSone, 6:18155.
• Domazet-Lošo, M. and Haubold, B. (2011). Alignment-free detection of horizontal gene transfer between closely related bacterial genomes. Mobile Genetic Elements, 1:230–235.

2010

• Wolf, J., Bayer, T., Haubold, B., Schilhabel, M., Rosenstiel, P. and Tautz, D. (2010). Nucleotide divergence versus gene expression differentiation: 454 transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology, 19:162–175.
• Haubold, B., Pfaffelhuber, P. and Lynch, M. (2010). mlRho—A program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Molecular Ecology, 19:277–284. Software.

2009

• Städler, T., Haubold, B., Merino, C., Stephan, W., Pfaffelhuber, P. (2009). The impact of sampling schemes on the site frequency spectrum in non-equilibrium subdivided populations. Genetics, 182:205–216.
• Haubold, B., Pfaffelhuber, P., Domazet-Lošo, M. and Wiehe, T. (2009). Estimating mutation distances from unaligned genomes. Journal of Computational Biology, 16: 1487–1500. Software.
• Domazet-Lošo, M. and Haubold, B. (2009). Efficient estimation of pairwise distances between genomes. Bioinformatics, 25: 3221–3227. Software.

2008

• Haubold, B., Domazet-Lošo, M. and Wiehe, T. (2008). An alignment-free distance measure for closely related genomes. In C. R. Nelson and S. Vialette, editors, RECOMB-CG 2008, volume 5267 of Lecture Notes in Bioinformatics, 87–99. Springer.