N. de Villiers, G.C. van Rooyen, M. Middendorf
Sewer network design: Layout optimization using ant colony algorithms
accepted (subject to minor changes) for SAICE Journal (Journal of the South African Institution of Civil Engineering)

T. Hartmann, N. Wieseke, R. Sharan, M. Middendorf, M. Bernt
Genome Rearrangement with ILP
IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear, DOI: 10.1109/TCBB.2017.2708121

T. Hartmann, A. Chu, M. Middendorf, M. Bernt
Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes
IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear, DOI 10.1109/TCBB.2016.2613522

N. de Villiers, G.C. van Rooyen, M. Middendorf
Sewer Network Design: Heuristic algorithm for hydraulic optimization
SAICE Journal (Journal of the South African Institution of Civil Engineering), 59(3): 48–56, 2017

M Al Arab, M Bernt, C Höner Zu Siederdissen, K Tout, and PF Stadler
Partially Local Three-Way Alignments and the Sequence Signatures of Mitochondrial Genome Rearrangements
Algorithms for Molecular Biology, 12:22, 2017

Y.-C. Cheng, T. Hartmann, P.-Y. Tsai, M. Middendorf
Population Based Ant Colony Optimization for Reconstructing ECG Signals
Evolutionary Intelligence, 9(3): 55-66, 2016

Y.-C. Lin, M. Clauß, M. Middendorf
Simple Probabilistic Population Based Optimization
IEEE Transactions on Evolutionary Computation, 20(2): 245 - 262, 2016.

M. Clauss, L. Lotzmann, M. Middendorf
A Population Based ACO Algorithm for the Combined Tours TSP Problem
EAI Endorsed Transactions on Self-Adaptive Systems, 16(7): e2, 2016.

A. Sahyoun, M. Hölzer, F. Jühling, C. Hoener zu Siederdissen, M. Al-Arab, K. Tout, M. Marz, M. Middendorf, P. Stadler, and M. Bernt
Towards a Comprehensive Picture of Alloacceptor tRNA Remolding in Metazoan Mitochondrial Genomes
Nucleic Acids Research, 43(16): 8044-8056, 2015.
Link

N. Wieseke, T. Hartmann, M. Bernt, M. Middendorf
Cophylogenetic Reconciliation with ILP
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(6): 1227-1235, 2015.
Link

T. Thalheim, B. Wagner, R. Kühne, M. Middendorf, G. Schüürmann
A Branch-and-Bound Approach for Tautomer Enumeration
Molecular Informatics, 34(5): 262-275, 2015.

M. Hellmuth, N. Wieseke, M. Lechner, H.-P. Lenhof, M. Middendorf, P. F. Stadler
Phylogenomics with Paralogs
Proceedings of the National Academy of Sciences (PNAS), 112(7): 2058–2063, 2015.

R. L.V. Moritz, M. Middendorf
Decentralized and Dynamic Group Formation of Reconfigurable Agents
Memetic Computing, 7:77-91, 2015.

D. Merkle, M. Middendorf, A. Scheidler
Task Allocation in Organic Computing Systems: Networks with Reconfigurable Helper Units
International Journal of Autonomous and Adaptive Communications Systems, 8(1):60-80, 2015.

R. L.V. Moritz, E. Reich, M. Schwarz, M. Bernt, and M. Middendorf
Refined Ranking Relations for Selection of Solutions in Multi Objective Metaheuristics
European Journal of Operational Research, 243: 454-464, 2015.