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, 20017

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.

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, 2014, DOI: 10.1016/j.ejor.2014.10.044
Link

A. H. Sahyoun, M. Bernt, P. F. Stadler, K. Tout
GC Skew and Mitochondrial Origins of Replication
Mitochondrion, 17:56-66, 2014.

R. L.V. Moritz, M. Bernt, and M. Middendorf
Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes
Biology, special issue: Developments in Bioinformatic Algorithms, 3(1), 220-242, 2014.
Link

M. Marz, N. Beerenwinkel, C. Drosten, M. Fricke, D. Frishman, I. L. Hofacker, D. Hoffmann, M. Middendorf, T. Rattei, P. F. Stadler, A. Töpfer
Challenges in RNA Virus Bioinformatics
Bioinformatics, 30 (13): 1793-1799, 2014.

N. J. R. Plowes, K. Ramsch, M. Middendorf, B. Hölldobler
An empirically based simulation of group foraging in the harvesting ant, Messor pergandei
Journal of Theoretical Biology, 340: 186–198, 2014

H. J. Osigus, M. Eitel, M. Bernt, A. Donath, B. Schierwater
Mitogenomics at the base of Metazoa
Molecular Phylogenetics and Evolution, 69(2):339-351, 2013.
link

M. Bernt, C. Bleidorn, A. Braband, J. Dambach, A. Donath, G. Fritzsch, A. Golombek, H. Hadrys, F. Jühling; K. Meusemann, M. Middendorf, B. Misof, M. Perseke, L. Podsiadlowski, B. von Reumont, B. Schierwater, M. Schlegel, M. Schrödl, S. Simon, P. F. Stadler, I. Stöger, T. H. Struck
A comprehensive analysis of bilaterian mitochondrial genomes and animal phylogeny
Molecular Phylogenetics and Evolution, 69(2):352-364, 2013.
link

S. Volke, M. Middendorf, M. Hlawitschka, J. Kasten, D. Zeckzer, G. Scheuermann
dPSO-Vis: Topological Visualization of Discrete Particle Swarm Optimization
Computer Graphics Forum, 32(3):351-360, 2013.

A. Scheidler, D. Merkle, M. Middendorf
Swarm Controlled Emergence for Ant Clustering
International Journal of Intelligent Computing and Cybernetics, 6(1):62-82, 2013.

M. Bernt, A. Braband, B. Schierwater, P. F. Stadler
Genetic aspects of mitochondrial genome evolution
Molecular Phylogenetics and Evolution, 69(2):328-338, 2013.
link

M. Bernt, A. Braband, M. Middendorf, B. Misof, O. Rota-Stabelli, P. F. Stadler
Bioinformatics Methods for the Comparative Analysis of Metazoan Mitochondrial Genome Sequences
Molecular Phylogenetics and Evolution, 69(2):320-, 2013.
link

M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Pütz, M. Middendorf, P. F. Stadler
MITOS: Improved de novo Metazoan Mitochondrial Genome Annotation
Molecular Phylogenetics and Evolution, 69(2):313-319, 2013.
link

F. Jühling, J. Pütz, M. Bernt, A. Donath, M. Middendorf, C. Florentz, P. F. Stadler
Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements.
Nucleic Acids Research, 40(7): 2833-2845, 2012,

A. Johansson, K. Ramsch, M. Middendorf, D.J. Sumpter
Tuning positive feedback for signal detection in noisy dynamic environments.
Journal of Theoretical Biology, 309: 88-95, 2012.

K. Ramsch, C. R. Reid, M. Beekman, M. Middendorf
A mathematical model of foraging in a dynamic environment by trail-laying Argentine ants
Journal of Theoretical Biology, 306:32-45, 2012.

A. Duò, R. Bruggmann, S. Zoller, M. Bernt, C. R. Gruenig
Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex
BMC Genomics, 13:166, 2012.

M. Dilcher, L. Hasib, M. Lechner, N. Wieseke, M. Middendorf, M. Marz, A. Koch, M. Spiegel, G. Dobler, F. T. Hufert, M. Weidmann
Genetic Characterisation of Tribec virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses
Virology, 423(1): 68-76, 2012.

M. Bernt, M. Middendorf
A Method for Computing an Inventory of Metazoan Mitochondrial Gene Order Rearrangements
BMC Bioinformatics, 12(Suppl 9):S6, 20122.
Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

K. Diwold, A. Aderhold, A. Scheidler, M. Middendorf
Performance Evaluation of Artificial Bee Colony Optimization and New Selection Schemes
Memetic Computing, 3(3): 149-162, 2011.

K. Diwold, T. Schaerf, M. R. Myerscough, M. Middendorf, M. Beekman
Deciding on the wing: in-flight decision making and search space sampling in the red dwarf honeybee Apis florea
Swarm Intelligence 5(2): 121-141, 2011.

A. Scheidler, M. Middendorf
Learning Classifier Systems to Evolve Classification Rules for Systems of Memory Constrained Components
Evolutionary Intelligence, 4(3): 127-143, 2011.

T. Latty, K. Ramsch, K. Ito, T. Nakagaki, D.J.T. Sumpter, M. Middendorf, and M. Beekman
Structure and formation of ant transportation networks
Journal of the Royal Society Interface, 8(62): 1298-1306, 2011.

M. Bernt, K.-Y. Chen, M.-C. Chen, A.-C. Chu, D. Merkle, H.-L. Wang, K.-M. Chao, M. Middendorf
Finding All Sorting Tandem Duplication Random Loss Operations
Journal of Discrete Algorithms, 9(1): 32-48, 2011.
link

M. Geis, M. Middendorf
Particle Swarm Optimization for Finding RNA Secondary Structures
International Journal of Intelligent Computing and Cybernetics, 4(2): 160-186, 2011.

S. Lange, M. Middendorf
Multi-level Reconfigurable Architectures in the Switch Model
Journal of Systems Architecture, 56(2-3): 103-115, 2010.

D. Merkle, M. Middendorf, N. Wieseke
A Parameter-Adaptive Dynamic Programming Approach for Inferring Cophylogenies
BMC Bioinformatics 2010, 11(Suppl 1): S60, 2010.
Paper

M. Hellmuth, D. Merkle, M. Middendorf
Extended shapes for the combinatorial design of RNA sequences
International Journal of Computational Biology and Drug Design, 2(4): 371 - 384, 2009.

K. Diwold, D. Merkle, M. Middendorf
Adapting to Dynamic Environments: Polyethism in Response Threshold Models for Social Insects
Advances in Complex Systems, 12(3): 327-346, 2009.

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.

M. Bernt, D. Merkle, K. Ramsch, G. Fritzsch, M. Perseke, D. Bernhard, M. Schlegel, P. Stadler, M. Middendorf
CREx: Inferring Genomic Rearrangements Based on Common Intervals
Bioinformatics, 23(21): 2957-2958, 2007.
link

B. Scheuermann, S. Janson, M. Middendorf
Hardware-oriented Ant Colony Optimization
Journal of Systems Architecture, 53(7): 386-402, 2007.

M. Bernt, D. Merkle, M. Middendorf
Using Median Sets for Inferring Phylogenetic Trees
Bioinformatics, 23: e129-e135, 2007.
This paper won the 3rd prize in the Best Paper Competition of the 5th European Conference on Computational Biology (ECCB), Eilat, Israel, Jan. 21-24, 2007.
link

S. Janson, M. Middendorf, M. Beekman
Searching for a new home - scouting behaviour of honeybee swarms
Behavioral Ecology, 18(2): 384-392, 2007.

S. Janson, M. Middendorf
A Hierarchical Particle Swarm Optimizer for Noisy and Dynamic Environments
Genetic Programming and Evolvable Machines, 7(4): 329-354, 2006.

M. Bernt, D. Merkle, M. Middendorf
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3): 275-288, 2006.
link

D. Merkle, M. Middendorf, A. Scheidler
Modelling Ant Brood Tending Patterns with Cellular Automata
Journal of Cellular Automata 2(2): 183-194, 2006.
Preliminary version in: Proc. of the Workshop on Modelling of Complex Systems by Cellular Automata 2005 (ICCS 2005), LNCS 3515, pp. 412-419, 2005.

E. Alba, M. Middendorf
The ‘Decent’ Project: Decentralized Metaheuristics
ERCIM News No. 64, 51-51, 2006.

S. Lange, M. Middendorf
Multi Task Hyperreconfigurable Architectures: Models and Reconfiguration Problems
International Journal of Embedded Systems, 1(3/4): 154-164, 2005.

D. Merkle, M. Middendorf
Reconstruction of the Cophylogenetic History of Related Phylogenetic Trees with Divergence Timing Information
Theory in Biosciences 4: 277-299, 2005
Paper

D. Merkle, M. Middendorf
On solving permutation scheduling problems with ant colony optimization
International Journal of Systems Science, 36(5): 255-266, 2005
Paper

S. Lange, M. Middendorf
Hyperreconfigurable Architectures and the Partition into Hypercontexts Problem
Journal of Parallel and Distributed Computing, 65(6): 743-754, 2005.
Paper

S. Janson, M. Middendorf
A Hierarchical Particle Swarm Optimizer and its Adaptive Variant
IEEE Systems, Man and Cybernetics - Part B, 32(6): 1272- 1282, 2005.
Preliminary version in Proceedings of the Congress on Evolutionary Computation (CEC 2003), IEEE Press, 770--776, (2003).
Paper

D. Merkle, M. Middendorf, A. Scheidler
Decentralized Packet Clustering in Router-based Networks
International Journal of Foundations of Computer Science, 16(2): 321-341, 2005.
Preliminary version in: Proc. International Parallel and Distributed Processing Symposium (IPDPS-2004), Sixth International Workshop on Nature Inspired Distributed Computing (NIDISC'04), IEEE-CS Press, Santa Fe, 9 pp., 2004.
Preliminary version

S. Janson, M. Middendorf, M. Beekman
Honey bee swarms: How do scouts guide a swarm of uninformed bees?
Animal Behavior, 70: 349-358, 2005.

J. Branke, M. Middendorf, G. Noeth, M. Dessouky
Waiting Strategies for Dynamic Vehicle Routing
Transportation Science, 39(3): 298–312, 2005.
Paper

D. Merkle, M. Middendorf
Dynamic Polyethism and Competition for Tasks in Threshold Reinforcement Models of Social Insects
Adaptive Behavior, 12: 251-262, 2004.
Preliminary version

M. Middendorf, D. Manlove
Combined Super-Substring and Super-/Subsequence problems
Theoretical Computer Science, 320(2-3): 247-267, 2004.
Paper

B. Scheuermann, K. So, M. Guntsch, M. Middendorf, O. Diessel, H. ElGindy, H. Schmeck
FPGA Implementation of Population-based Ant Colony Optimization
Applied Soft Computing 4(3): 303-322, 2004 (special issue on Hardware Implementations of Softcomputing Techniques)

S. Janson, D. Merkle, M. Middendorf, H. ElGindy, H. Schmeck
On Enforced Convergence of ACO and its Implementation on the Reconfigurable Mesh Architecture Using Size Reduction Tasks
Journal of Supercomputing, 26(3): 221-238, 2003.
Preliminary version in:Proceedings of the Second International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'02), Las Vegas, CSREA Press, 2002, 3-9.

D. Merkle and M. Middendorf
An Ant Algorithm with Global Pheromone Evaluation for Scheduling a Single Machine
Applied Intelligence, 18(1): 105-111, 2003.

M. Middendorf, B. Scheuermann, H. Schmeck, H. ElGindy
An Evolutionary Approach to Dynamic Task Scheduling on FPGAs
Journal of Parallel and Distributed Computing, 62(9): 1407-1420, September 2002.

D. Merkle and M. Middendorf
Modelling the Dynamics of Ant Colony Optimization Algorithms
Evolutionary Computation 10(3): 235-262, 2002.
Paper

D. Merkle and M. Middendorf
Fast Ant Colony Optimization on Runtime Reconfigurable Processor Arrays
Genetic Programming and Evolvable Machines, 3(4): 345-361, 2002.
Paper

D. Merkle, M. Middendorf, and H. Schmeck
Ant Colony Optimization for Resource-Constrained Project Scheduling
IEEE Transactions on Evolutionary Computation, 6(4): 333-346, 2002.
Paper

M. Middendorf and V. Timkovsky
On scheduling cycle shops: classification, complexity and approximation
Journal of Scheduling, 5(2): 135-169, 2002.
Paper

M. Middendorf, F. Reischle, and H. Schmeck
Multi Colony Ant Algorithms
Journal of Heuristics (special issue on Parallel Metaheuristics), 8(3): 305-320, 2002.
Paper

J. Branke, S. Leppert, M. Middendorf, and P. Eades
Width Restricted Layering of Acyclic Digraphs with Consideration of Dummy Nodes
Information Processing Letters 81(2): 59-63, 2002.
Paper

D. Merkle, Th. Worsch
Formal Language Recognition by Stochastic Cellular Automata
Fundamenta Informaticae 52(1-3): 183-201, 2002.