M. Bernt, D. Merkle, M. Middendorf
Solving the Preserving Reversal Median Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(3): 332-347, 2008.
link

D. Merkle, M. Middendorf
Swarm Intelligence and Signal Processing
IEEE Signal Processing Magazine, 25(6): 152-158, 2008.

T. Thalheim, D. Merkle, M. Middendorf
Protein Folding in the HP-Model Solved With a Hybrid Population Based ACO Algorithm
IAENG International Journal of Computer Science, 35(3): 291-300, 2008.

A. Scheidler, D. Merkle, M. Middendorf
Stability and Performance of Ant Queue Inspired Task Partitioning Methods
Theory in Biosciences, 127(2): 149-161, 2008.

M. Geis, C. Flamm, M. T. Wolfinger, I. L. Hofacker, M. Middendorf, C. Mandl, P. F. Stadler, C. Thurner
Folding Kinetics of Large RNAs
Journal of Molecular Biology, 379(1): 160-173, 2008.

D. Merkle, M. Middendorf, A. Scheidler
Self-Organized Task Allocation for Service Tasks in Computing Systems with Reconfigurable Components
Journal of Mathematical Modelling and Algorithms, 7(2): 237-254, 2008.

M. Geis, M. Middendorf
Creating Melodies and Baroque Harmonies with Ant Colony Optimization
International Journal of Intelligent Computing and Cybernetics, 1(2): 213-238, 2008.

S. Janson, D. Merkle, M. Middendorf
A Decentralization Approach for Swarm Intelligence Algorithms in Networks Applied to Multi Swarm PSO
International Journal of Intelligent Computing and Cybernetics, 1(1): 25-45, 2008.
This paper has won the Highly Commended Award of IJICC.

M. Perseke, G. Fritzsch, K. Ramsch, M. Bernt, D. Merkle, M. Middendorf, D. Bernhard, P. F. Stadler, M. Schlegel
Evolution of Mitochondrial Gene Orders in Echinoderms
Molecular Phylogenetics and Evolution, 47: 855–864, 2008.
link

S. Lange, M. Middendorf
Design Aspects of Multi-level Reconfigurable Architectures
Journal of Signal Processing Systems for Signal, Image, and Video Technology, 51(1): 23-37, 2008.

S. Janson, D. Merkle, M. Middendorf
Molecular Docking with Multi-Objective Particle Swarm Optimization
Applied Soft Computing, 8(1): 666-675, 2008.