Motif depletion in bacteriophages infecting hosts with CRISPR systems
A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).

Complete genome sequence of the novel phage MG- infecting bacillus weihenstephanensis
R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).

Probabilistic models for CRISPR spacer content evolution 
A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.

A consistent phylogenetic backbone for the fungi
I. Ebersberger, R. De Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, A. Von Haeseler, Molecular Biology and Evolution 29 (2012) 1319–1334.

Consequences of different null models on the tree shape bias of supertree methods
A. Kupczok, Systematic Biology 60 (2011) 218–225.

Split based computation of majority rule supertrees
A. Kupczok, BMC Evolutionary Biology 11 (2011).

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets 
A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology 5 (2010).

Comment on 'A congruence index for testing topological similarity between trees'.
A. Kupczok, A. Von Haeseler, Bioinformatics 25 (2009) 147–149.

An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.
A. Kupczok, A. Von Haeseler, S. Klaere, Journal of Computational Biology 15 (2008) 577–591.

Determinants of simulated RNA evolution.
A. Kupczok, P. Dittrich, Journal of Theoretical Biology 238 (2006) 726–35.