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, 36:2040–2046. Software.
  42. 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.
  43. Haubold, B., Klötzl, F., Hellberg, L., Thompson, D., and Cavalar, M. (2021). Fur: Find unique genomic regions for diagnostic PCR. Bioinformatics. Software.