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)

Domazet-Lošo, M.; Haubold, B.: Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics 27 (11), pp. 1466 - 1472 (2011)

Tellier, A.; Pfaffelhuber, P.; Haubold, B.; Naduvilezhath, L.; Rose, L. E.; Städler, T.; Stephan, W.; Metzler, D.: Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. PLoS ONE 6 (5), e18155 (2011)

Haubold, B.; Reed, F. A.; Pfaffelhuber, P.: Alignment-free estimation of nucleotide diversity. Bioinformatics 27 (4), pp. 449 - 455 (2011)

Wolf, J. B. W.; Bayer, T.; Haubold, B.; Schilhabel, M.; Rosenstiel, P.; Tautz, D.: Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology 19 (1), pp. 162 - 175 (2010)

Haubold, B.; Pfaffelhuber, P.; Lynch, M.: mlRho – a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Molecular Ecology 19 (1), pp. 277 - 284 (2010)

Domazet-Lošo, M.; Haubold, B.: Efficient estimation of pairwise distances between genomes. Bioinformatics 25 (24), pp. 3221 - 3227 (2009)

Städler, T.; Haubold, B.; Merino, C.; Stephan, W.; Pfaffelhuber, P.: The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 182 (1), pp. 205 - 216 (2009)

Haubold, B.; Pfaffelhuber, P.; Domazet-Lošo, M.; Wiehe, T.: Estimating mutation distances from unaligned genomes. Journal of Computational Biology 16 (10), pp. 1487 - 1500 (2009)

Haubold, B.; Börsch-Haubold, A.: Bioinformatics for Evolutionary Biologists: a problems approach. Springer, Cham (2023), IX, 411 pp.

Haubold, B.; Börsch-Haubold, A.: Bioinformatics for evolutionary biologists: a problems approach. Springer International Publishing, Cham (2017), X, 318 pp.

Haubold, B.; Klötzl, F.: Fast phylogeny reconstruction from genomes of closely related microbes. In: Bacterial Pangenomics: Methods in Molecular Biology, Vol. 2242, (Chapter 6), pp. 77 - 89 (Eds. Mengoni, A.; Bacci, G.; Fondi, M.). Springer US, New York, NY (2021)

Thota, A.; Haubold, B.; Michael, S.; Doak, T.; Xu, S.; Henschel, R.: 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. XSEDE '13 (Ed. Wilkins-Diehr, N.). Extreme Science and Engineering Discovery Environment: Gateway to Discovery, San Diego, CA, USA, July 22, 2013 - July 25, 2013. Association for Computing Machinery, New York, NY, USA (2013)

Haubold, B.; Domazet-Lošo, M.; Wiehe, T.: An alignment-free distance measure for closely related genomes. In: Comparative genomics: international workshop, RECOMB-CG 2008, Paris, France, October 13-15, 2008 ; Proceedings, pp. 87 - 99 (Eds. Nelson, C. E.; Vialette, S.). RECOMB Workshop on Comparative Genomics, Paris, October 13, 2008 - October 15, 2008. Springer, Berlin, Heidelberg (2008)

Klötzl, F.: Fast computation of genome distances. Dissertation, xv, 95 pp., Universität zu Lübeck. Institut für Neuro- und Bioinformatik., Lübeck (2020)

Domazet-Lošo, M.: Algorithms for efficient alignment-free sequence comparison. Dissertation, University of Zagreb, Zagreb (2010)

Kryjewska, M.: The role of the duplicated NinaB genes in moonlight insensitivity in Clunio marinus. Master, 71 pp., Universität zu Lübeck, Lübeck (2023)

Gmelin, D.: Fast multiple sequence alignment. Master, ix, 45 pp., Universität zu Lübeck, Institut für Neuro- und Bioinformatik, Lübeck (2022)

Denker, S.: Marker development using taxonomic information. Master, 42 pp., Universität zu Lübeck, Lübeck (2022)