A. Donath, F. Jühling, M. Al-Arab,S.H. Bernhart, F. Reinhardt, P.F. Stadler, M. Middendorf, M. Bernt
Improved Annotation of Protein-Coding Genes Boundaries in Metazoan Mitochondrial Genomes
to appear in Nucleic Acids Research, https://doi.org/10.1093/nar/gkz833

T. Hartmann, M. Bannach, M. Middendorf
Sorting Signed Permutations by Inverse Tandem Duplication Random Losses
IEEE/ACM Transactions on Computational Biology and Bioinformatics, early access 10.1109/TCBB.2019.2917198

T. Hartmann, M. Bernt, M. Middendorf
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(1): 52-62, 2019.

M. Middendorf, N. Wieseke
A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
PLoS ONE 13(9): e0204907, 2018.

T. Hartmann, M. Bernt, M. Middendorf
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
BMC Bioinformatics, 19: 192, 2018.

T. Gernat, V. D. Rao, M. Middendorf, H. Dankowicz, N. Goldenfeld, G. E. Robinson
Automated monitoring of behavior reveals bursty interaction patterns and rapid spreading dynamics in honeybee social networks
Proceedings of the National Academy of Sciences (PNAS), 115 (7) 1433-1438, 2018.

N. de Villiers, G.C. van Rooyen, M. Middendorf
Sewer network design layout optimization using ant colony algorithms
SAICE Journal (Journal of the South African Institution of Civil Engineering), 60(9), pages 2-15, paper 1773, 2018

T. Hartmann, N. Wieseke, R. Sharan, M. Middendorf, M. Bernt
Genome Rearrangement with ILP
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(5):1585-1593, 2018.

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, 15(1): 83-95, 2018.

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.