T. Hartmann, M. Middendorf, M. Bernt
Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches
accepted for "Comparative Genomics" in the Springer Series "Methods in Molecular Biology"

M. Bernt, D. Merkle, M. Middendorf, B. Schierwater, M. Schlegel, and P. F. Stadler
Computational methods for the analysis of mitochondrial genome rearrangements
In: Deep Metazoan Phylogeny: The backbone of the Tree of Life. Wägele J.W.; Bartholomäus T.; Misof B.; Vogt L. (Hrsg.). De Gruyter. pp. 515-529, 2014
Link

D. Merkle, M. Middendorf
Swarm Intelligence
In E. Burke, G. Kendall (eds.), Search Methodologies - Introductory Tutorials in Optimisation and Decision Support Methodology, Springer, 213-242, 2nd ed. 2014

S. Volke, S. Bin, D. Zeckzer, M. Middendorf, G. Scheuermann
Visual Analysis of Discrete Particle Swarm Optimization using Fitness Landscapes
In H. Richter, A. Engelbrecht (Eds.), Recent Advances in the Theory and Application of Fitness Landscapes, Springer, Series Emergence, Complexity and Computation, Volume 6, pages 487-507, 2014

M. Bernt, R. Machne, A. H. Sahyoun, M. Middendorf, P. F. Stadler
Mitochondrial genome evolution
eLS (formerly Encyclopedia of Life Sciences), Advanced Article, Wiley, 2013
Link

A. Scheidler, A. Brutschy, K. Diwold, M. Merkle, M.Middendorf
Ant Inspired Methods for Organic Computing
Organic Computing: A Paradigm Shift for Complex Systems, Springer, 95-110, 2011.

K. Diwold, M. Beekman, M.Middendorf
Honeybee Optimisation – An Overview and a new Bee Inspired Optimisation Scheme
Handbook of Swarm Intelligence – Concepts, Principles and Application, Springer, 295 - 328, 2011.

S.Lange, M.Middendorf
Models and Algorithms for Hyperreconfigurable Hardware
In M. Platzner, J. Teich, N. Wehn (Eds.), Dynamically Reconfigurable Systems, Springer, 75-94, 2010.

D. Merkle, M. Middendorf, A. Scheidler
Organic Computing and Swarm Intelligence
In C. Blum, M. Merkle (Eds.), Swarm Intelligence, Springer, 253-281, 2008.

D. Merkle, M. Middendorf, A. Scheidler
Self-Adaptive Worker-Helper Systems with Self-Organized Task Allocation
In Rolf P. Würtz (Ed.), Organic Computing. Springer, 221-240, 2008

E. Petzold, A. von Haeseler, D. Merkle, M. Middendorf, and H.A. Schmidt
Phylogenetic Parameter Estimation on COWs
In A. Zomaya (Ed.), Parallel Computing in Bioinformatics and Computational Biology, Wiley, 347-368, 2006.
Paper

D. Merkle, M. Middendorf
Swarm Intelligence
In E. Burke, G. Kendall (eds.), Search Methodologies - Introductory Tutorials in Optimisation and Decision Support Methodology, Springer, 401-435, 2006.

S. Janson, D. Merkle, M. Middendorf
Parallel Ant Algorithms
In E. Alba (Ed.), Parallel Metaheuristics, Wiley Book Series on Parallel and Distributed Computing, ISBN: 0-471-67806-6, 171-201, 2005.

D. Merkle, M. Middendorf
Ant Colony Optimization: Biological Motivation, Phase Structure, and Modelling
Proc. 4th International Symposium on Mathematical and Computational Biology (BIOMAT 2004), Vol. 2, 67-88, 2005.

D. Merkle, M. Middendorf
On the behavior of ACO algorithms: Studies on simple problems
In: M. G. C. Resende and J. Pinho de Sousa (Eds.) Metaheuristics: Computer Decision-Making, Kluwer, 465-480, 2003.