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Andreotti, S. and Reinert, K. and Canzar, S. (2013) The duplication-loss small phylogeny problem: from cherries to trees. Journal of Computational Biology, 20 (9). pp. 643-59.

Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and Hildebrandt, A. and Hildebrandt, A. and Huber, Ch. and Reinert, K. (2008) Computational Quantification of Peptides from LC-MS data. Journal of Computational Biology, 15 (7). pp. 685-704.

Lermen, M. and Reinert, K. (2000) The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. Journal of Computational Biology . pp. 655-671.

Lenhof, H.-P. and Reinert, K. and Vingron, M. (1998) A Polyhedral Approach to RNA Sequence Structure Alignment. Journal of Computational Biology, 5 (3). pp. 517-530.