Primary Research

  1. Haubold, B. and Rainey, P. B. (1996). Genetic and ecotypic structure of a fluorescent Pseudomonas population. Molecular Ecology, 5:747-761.
  2. Haubold, B. and Rainey, P. B. (1997). Towards an understanding of the population genetics of plant-colonizing bacteria. Advances in Botanical Research incorporating Plant Pathology, 24:335-351.
  3. Preston, G. H., Haubold, B. and Rainey, P. B. (1998). Bacterial Genomics and adaptation to life on plants: Implications for the evolution of pathogenicity and symbiosis. Current Opinion in Microbiology, 1:589-597. Abstract.
  4. Haubold, B., Travisano, M., Rainey, P. B. and Hudson, R. R. (1998). Detecting linkage disequilibrium in bacterial populations. Genetics, 150:1341-1348. Abstract.
  5. Anderson, T.J.C., Haubold, B., Richardson, L., Estrada-Franco, J. G., Mollinedo, R., Bockarie, M., Mokili, J., Mharakurwa, S., French, N., Whitworth, J., Velez, I. D., Brockmann, A., Nosten, F., Ferriera, M. U. and Day, K. P. (2000). Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Molecular Biology and Evolution, 17:1467-1482. Abstract.
  6. Koch, M., Haubold, B. and Mitchell-Olds, T. (2000). Comparative evolutionary analysis of the chalcone synthase and alcohol dehydrogenase loci among different lineages of Arabidopsis, Arabis and related genera. Molecular Biology and Evolution, 17:1483-1498. Abstract.
  7. Haubold, B. and Hudson, R. R. (2000). LIAN 3.0: detecting linkage disequilibrium in multilocus data. Bioinformatics, 16:847-848. Abstract, software.
  8. Sharbel, T. F., Haubold, B. and Mitchell-Olds, T. (2000). Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Molecular Ecology, 9:2109-2118. Abstract.
  9. Koch, M., Haubold, B. and Mitchell-Olds, T. (2001). Molecular systematics of the Cruciferae: evidence from coding plastidic matK and nuclear chs sequences. Americal Journal of Botany, 88:534-544. Abstract.
  10. Haubold, B. and Wiehe, T. (2001). Statistics of divergence times. Molecular Biology and Evolution, 18:1157-1160. Abstract, software.
  11. Koch, M., Weisshaar, B., Kroymann, J., Haubold, B. and Mitchell-Olds, T. (2001). Comparative genomics and regulatory evolution: conservation and function of the CHS and APETALA3 promoters. Molecular Biology and Evolution, 18:1882-1891. Abstract.
  12. Haubold, B. and Wiehe, T. (2002). Calculating the SNP-effective sampling size from an alignment. Bioinformatics, 18:36-38. Abstract.
  13. Eriksson, A., Haubold, B. and Mehlig, B. (2002). Statistics of genetic variation. Physical Review Letters, E (Rapid Communications), 65:040901. Abstract.
  14. Haubold, B., Kroymann, J., Ratzka, A., Mitchell-Olds, T. and Wiehe, T. (2002). Recombination and gene conversion in a 170 kb genomic region of Arabidopsis thaliana.Genetics, 161:1269-1278. Abstract.
  15. Otte, K., Kranz, H., Kober, I., Thompson, P., Hoefer, M., Haubold, B., Remmel, B., Voss, H., Kaiser, C., Albers, M., Cheruvallath, Z., Jackson, D., Casari, G., Koegl, M., Pääbo, S., Mous, J., Kremoser, C., and Deuschle, U. (2003). Identification of farnesoid x receptor beta as a novel mammalian nuclear receptor sensing lanosterol. Mololecular and Cellular Biology. 23:864-72. Abstract.
  16. Haubold, B., Pierstorff, N, Möller, F. and Wiehe, T. (2005). Genome comparison without alignment using shortest unique substrings. BMC Bioinformatics, 6:123. Abstract, software.
  17. Pfaffelhuber, P., Haubold, B., and Wakolbinger, A. (2006). Approximate genealogies under genetic hitchhiking. Genetics, 174:1995-2008. Abstract.
  18. Haubold, B. and Wiehe, T. (2006). How repetitive are genomes? BMC Bioinformatics, 7:541. Abstract, software.
  19. 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 Verlag, Heidelberg. Proofs.
  20. 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. doi:10.1534/genetics.108.094904. Software.
  21. 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.
  22. Domazet-Lošo, M. and Haubold, B. (2009). Efficient estimation of pairwise distances between genomes. Bioinformatics, 25: 3221-3227. Software.
  23. 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.
  24. 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.
  25. Haubold, B., Reed, F. and Pfaffelhuber, P. (2011). Alignment-free estimation of nucleotide diversity. Bioinformatics, 27:449-455. Software.
  26. Domazet-Lošo, M. and Haubold, B. (2011). Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics, 27:1466-1472. Software.
  27. 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.
  28. 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.
  29. Huang, W., Haubold, B., Hauert, C. and Traulsen, A. (2012). Emergence of stable polymorphisms driven by evolutionary games between mutants. Nature Communications, 3:919.
  30. Haubold, B. and Pfaffelhuber, P. (2012). Alignment-Free Population Genomics: An Efficient Estimator of Sequence Diversity. Genes, Genomes, Genetics, 2:883-889. Software.
  31. 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.
  32. 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.
  33. Haubold, B., Krause, L., Horn, T., and Pfaffelhuber, P. (2013). An Alignment-free Test for Recombination . Bioinformatics, 24:3121-3127.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. Klötzl, F. and Haubold, B. (2016). Support values for genome phylogenies. Life, 6:11. Software and data sets.
  39. 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.
  40. 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.
  41. Klötzl, F. and Haubold, B. (2019). Phylonium: Fast estimation of evolutionary distances from large samples of similar genomes.. Bioinformatics, in press.