Journals


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
to appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 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, 2016

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

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.

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.

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, 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.

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.

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.

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.

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):320-327, 2013.

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.

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

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.

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.

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.

M. Bernt, M. Middendorf
A Method for Computing an Inventory of Metazoan Mitochondrial Gene Order Rearrangements
BMC Bioinformatics, 12(Suppl 9):S6 , 2011.
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.

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.

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.
Paper

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): 24-45, 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.

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. Perserke, D. Bernhard, M. Schlegel, P. Stadler, M. Middendorf
CREx: Inferring Genomic Rearrangements Based on Common Intervals
Bioinformatics, 23(21): 2957-2958, 2007.

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, January 21-24, 2007.

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.

D. Merkle, M. Middendorf, A. Scheidler
Modelling Ant Brood Tending Behaviour 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, 123(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.

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.

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.

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.
Prelininary 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
Ant Colony Optimization with Global Pheromone Evaluation for Scheduling a Single Machine.
Applied Intelligence, 18(1): 105-111, 2003.
Preliminary version in: S. Cagnoni et al. (Eds.), Real-World Applications of Evolutionary Computing, Proceedings of EvoWorkshops 2000, Edinburgh, 17. April 2000, Springer Verlag, LNCS 1803 (2000) 287-296.

D. Merkle and M. Middendorf
Modelling the Dynamics of Ant Colony Optimization Algorithms
Evolutionary Computation 10(3): 235-262, 2002.
Preliminary version in: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2002), New York, 2002, 105-112.
Paper

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, 2002.
Preliminary version in: R.W. Hartenstein, H. Grünbacher (Eds.), Field Programmable Logic and Applications, 10th International Conference FPL 2000, Villach, Austria, August 28-30, 2000, Springer Verlag, LNCS 1896, 379-388, 2000.

D. Merkle and M. Middendorf
Fast Ant Colony Optimization on Runtime Reconfigurable Processor Arrays
Genetic Programming and Evolvable Machines, 3(4): 345-361, 2002.
Preliminary version in: Proceedings of the 8th Reconfigurable Architectures Workshop 2001 (RAW 2001), San Francisco, 2001.
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.
Preliminary version in: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2000), Las Vegas, Nevada, July 8-12 2000, Morgan Kaufmann, 893-900, 2000.
Paper

M. Middendorf and V. Timkovsky
On scheduling cycle shops: classification, complexity and approximation
Journal of Scheduling, 5(2): 135-169, 2002.
Preliminary version: Technical Report 394, Institute AIFB, University of Karlsruhe, Germany, Oktober 1999.
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.
Preliminary version in: J. Rolim (Ed.) Parallel and Distributed Computing, Proceedings of the 15 IPDPS 2000 Workshops, Third Workshop on Biologically Inspired Solutions to Parallel Processing Problems (BioSP3), Mai 1-5 2000, Cancun, Mexico, Springer-Verlag, LNCS 1800, 645-652, 2000.
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.

O. Diessel, H. ElGindy, M. Middendorf, B. Schmidt, and H. Schmeck
Dynamic scheduling of tasks on partially reconfigurable FPGAs
IEE - Proceedings - Computer and Digital Techniques (Special Issue on Reconfigurable Systems), 147(3): 181-188, 2000.

M. Middendorf and V. Timkovsky
Transversal graphs for partially ordered sets: sequencing, merging and scheduling problems
Journal of Combinatorial Optimization 3(4): 417-435, 1999.

M. Middendorf, H. Schmeck, H. Schröder, and G. Turner
Multiplication of matrices with different sparseness properties on dynamically reconfigurable meshes
VLSI Design 9: 69-81, 1999.

M. Middendorf, W. Löwe, and W. Zimmermann
Scheduling inverse trees under the communication model of the LogP-machine
Theoretical Computer Science 215: 137-168, 1999.
Preliminary version: Technical Report 336, Institute AIFB, University of Karlsruhe, Germany, Mai 1996.

M. Middendorf and H. ElGindy
Matrix Multiplication on processor arrays with optical buses
Informatica (Special Issue on Computing on Bus-Based Architectures) 22: 255-262, 1998.
Preliminary version: Technical Report 371, Institute AIFB, University of Karlsruhe, Germany, November 1997.

J. Branke, M. Middendorf, and F. Schneider
Improved heuristics and a genetic algorithm for finding short supersequences
OR-Spektrum 20: 39-46, 1998.
Preliminary versions: J. Branke, M. Middendorf: Searching for Shortest Common Supersequences by Means of a Heuristic Based Genetic Algorithm, Proceedings of the Second Nordic Workshop on Genetic Algorithms and their Applications, Finnish Artificial Intelligence Society, 1996, pp. 105-114. TR 370, Institute AIFB, University of Karlsruhe, 1997.

M. Middendorf
Shortest common superstrings and scheduling with coordinated starting times
Theoretical Computer Science, 191: 205-214, 1998.
Preliminary version: Technical Report 339, Institute AIFB, University of Karlsruhe, Germany, August 1996.

M. Middendorf
Manhattan Channel Routing is NP-complete under truly restricted settings
Chicago Jounal of Theoretical Computer Science 2: 1-19, 1996.

J.E. Atkins and M. Middendorf
On physical mapping and the consecutive ones property for sparse matrices
Discrete Applied Mathematics (First Special Issue on Computational Molecular Biology) 71: 5-22, 1996.

M. Middendorf
2-Dimensional partitioning problems
Theoretical Computer Science, 164: 73-106, 1996.

C. Fraser, R. Irving, and M. Middendorf
Maximal common subsequences and minimal common supersequences
Information and Computation 124: 145-153, 1996.

M. Middendorf, H. Schmeck, and G. Turner
Sparse matrix multiplication on a reconfigurable mesh
The Australian Computer Journal 27: 37-40, 1995.

M. Middendorf
On finding various minimal, maximal, and consistent sequences over a binary alphabet
Theoretical Computer Science 145: 317-327, 1995.
Preliminary version in: Proc. 5th International Symposium on Algorithms and Computation (ISAAC), LNCS 843, 306--314, 1994.

M. Middendorf
More on the complexity of common superstring and supersequence problems
Theoretical Computer Science 125: 205-228, 1994.

H. Schmeck, H. Schröder, J. Straunstrup, and M. Middendorf
Problem Heaps and their Evaluation
Parallel Processing Letters 3: 147-155, 1993.

M. Middendorf
Minimum Broadcast Time is NP-complete for 3-regular planar graphs and deadline 2
Information Processing Letters 46: 281-287, 1993.

M. Middendorf
The shortest common nonsupersequence problem is NP-complete
Theoretical Computer Science 108: 365-369, 1993.

J. Duske, M. Middendorf, and R. Parchmann
Indexed counter languages
R.A.I.R.O. Inform. Theor. Appl. 26: 93-113, 1992.

Guest Editor Journal


Guest editors: Engelbrecht, A.; Li, X.; Middendorf, M.; Gambardella, L. M.
IEEE Transactions on Evolutionary Computation, Special Issue: Swarm Intelligence
Guest Editorial: 13(4): 677-680, 2009

Guest Editors: J. Jost, D. Helbing, A. Lorincz, M. Middendorf
Theory in Biosciences, Special Issue "European Conference on Complex Systems 2007"
Guest Editorial: 127(2): 67-68, 2008.
To the journal

Guest Editors: Jens Gottlieb, Emma Hart, Martin Middendorf, Günther Raidl, Colin Reeves
Journal of Mathematical Modelling and Algorithms: Special Issue on Evolutionary Computation in Combinatorial Optimization
Guest Editorial 3(4): 311-312, 2004.
To the journal

Guest Editors: M. Dorigo, L.M. Gambardella, M. Middendorf, and T. Stützle
IEEE Transactions on Evolutionary Computation: Special Issue on "Ant Algorithms and Swarm Intelligence"
Guest Editorial 6(4): 317-320, 2002.
Link

Books (Editor)


Y. Shi, K.C. Tan, M. Zhang, K. Tang, X. Li, Q. Zhang, Y. Tan, M. Middendorf, Y. Jin (Eds.)
Simulated Evolution and Learning - 11th International Conference, SEAL 2017, Shenzhen, China, November 10–13, 2017, Proceedings
Springer Verlag, LNCS 10593, 2017.

M. Middendorf, C. Blum
Evolutionary Computation in Combinatorial Optimization - 13th European Conference, EvoCOP 2013, Proceedings
Springer Verlag, LNCS 7832, 2013.

Jin-Kao Hao, Martin Middendorf (Eds.)
Evolutionary Computation in Combinatorial Optimization - 12th European Conference, EvoCOP 2012, Proceedings
Springer Verlag, LNCS 7245, 2012.

S. Cagnoni, J.J. Romero Cardalda, D. Corne, J. Gottlieb, A. Guillot, E. Hart, C.G. Johnson, E. Marchiori, J.-A. Meyer, M. Middendorf, G.R. Raidl (Eds.)
Applications of Evolutionary Computing - EvoWorkshops 2003: EvoBIO, EvoCOP, EvoIASP, EvoMUSART, EvoSTIM, EvoROB
Springer Verlag, LNCS 2611, 2003.
Link

S. Cagnoni, J. Gottlieb, E. Hart, M. Middendorf, G.R. Raidl (Eds.)
Applications of Evolutionary Computing - EvoWorkshops 2002: EvoCOP, EvoIASP, EvoSTIM/EvoPLAN Kinsale, Ireland, April 3-4
Springer Verlag, LNCS 2279, 2002.
Link

Book Chapters


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.

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, DOI: 10.1002/9780470015902.a0025142

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.

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. Updated version in 2nd ed. 2013.

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

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

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

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.
Preliminary version in: Proceedings of the 4th Metaheuristics International Conference (MIC`2001), Porto, 573-577, 2001.

R. Michels, M. Middendorf
An Ant System for the Shortest Common Supersequence Problem
in: D. Corne, M. Dorigo, F. Glover (Eds.), New Ideas in Optimization, McGraw-Hill, 51-61, 1999.
Preliminary versions in: Proc. Fifth International Conference On Parallel Problem Solving From Nature (PPSN'98), Amsterdam, Netherlands, Springer Verlag, LNCS 1498, 692-701, 1998. Technical Report 378, Institute AIFB, University of Karlsruhe, Germany, June 1998.

Publications in Conference Proceedings


T. Hartmann, M. Bernt, M. Middendorf
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements
accepted for the Sixtheenth Asia Pacific Bioinformatics Conference (APBC2018)

T. Hartmann, N. Wieseke, R. Sharan, M. Middendorf, M. Bernt
Genome Rearrangement with ILP
accepted for the Fifteenth Asia Pacific Bioinformatics Conference (APBC2017)

S. Volke, G. Scheuermann, M. Middendorf
Coarse-Graining Large Search Landscapes using Massive Edge Collapse
accepted for TopoInVis 2017

Y.-C. Cheng, T. Hartmann, P.-Y. Tsai, M. Middendorf
Population Based Ant Colony Optimization for Reconstructing ECG Signals
Proc. 19th European Conference on Applications of Evolutionary Computation (EvoApplications 2016), LNCS 9597, 770-785, 2016.

R. L. V. Moritz, E. Reich, M. Bernt, M. Middendorf
A Property Preserving Method for Extending a Single-objective Problem Instance to Multiple Objectives with Specific Correlations
Proc. 16th European Conference on Evolutionary Computation in Combinatorial Optimization (EvoCOP 2016), LNCS 9595, 18-33, 2016.

Martin Clauß, Lydia Lotzmann, Martin Middendorf
A Population Based ACO Algorithm for the Combined Tours TSP Problem
accepted for BICT 2015

Martin Clauß, Lydia Lotzmann, Martin Middendorf
A Population Based ACO Algorithm for the Combined Tours TSP Problem
accepted for BICT 2015

T. Gernat, W. Deng, V. Rao, M. Middendorf, N.D. Goldenfeld, H. Dankowicz, G.E. Robinson
Automated tracking of individuals reveals temporal structure and resiliency of honey bee social networks
accepted for Conference on Complex systems (CCS 2015), Tempe Arizona, 2015

S. Volke, D. Zeckzer, G. Scheuermann, M. Middendorf
A Visual Method for Analysis and Comparison of Search Landscapes
Proc. Genetic and Evolutionary Computation Conference (GECCO 2015), 497-504, 2015.

R. L. V. Moritz, M. Middendorf
Evolutionary Mechanisms in Multi-Objective Multi-Agent Systems Solving Multi-Agent Tasks
Proc. Genetic and Evolutionary Computation Conference (GECCO 2015), 65-72, 2015.

S. Volke, D. Zeckzer, M. Middendorf, G. Scheuermann
Visualizing Topological Properties of the Search Landscape of Combinatorial Optimization Problems
accpeted for TopoInVis 2015 workshop

N. Wieseke, T. Hartmann, M. Bernt, M. Middendorf
Cophylogenetic Reconciliation with ILP
accepted for Thirteenth Asia-Pacific Bioinformatics Conference (APBC 2015), Hsinchu, Taiwan

S. Bin, S. Volke, G. Scheuermann, M. Middendorf
Comparing the Optimization Behaviour of Heuristics with Topology Based Visualization
Proc. 3rd International Conference on the Theory and Practice of Natural Computing (TPNC 2014), LNCS 8890, 47 - 58, 2014

R. L.V. Moritz, E. Reich, M. Bernt, M. Middendorf
The Influence of Correlated Objectives on Different Types of P-ACO Algorithms
Proc. 14th European Conference on Evolutionary Computation in Combinatorial Optimisation (EvoCOP 2014), LNCS 8600,230-241.

M. Bernt, N. Wieseke, and M. Middendorf
On Weighting Schemes for Gene Order Analysis
Proc. of the German Conference on Bioinformatics (GCB 2013), OASIcs Vol. 34, 14-23, 2013

N. Wieseke, M. Bernt, M. Middendorf
Unifying Parsimonious Tree Reconciliation
Proc. 13th Workshop on Algorithms in Bioinformatics (WABI 2013), LNBI 8126, 200-214, 2013

R. L. V. Moritz, M. Middendorf
Self-adaptable Group Formation of Reconfigurable Agents in Dynamic Environments
Proceedings of the Workshop on Nature Inspired Cooperative Strategies for Optimization (NICSO 2013), Springer, Studies in Computational Intelligence, Vol. 512, 287 - 301, 2013

R. L. V. Moritz, E. Reich, M. Schwarz, M. Bernt, M. Middendorf
Refined Ranking Relations for Multi Objective Optimization and Application to P-ACO
Proceeding of the Fifteenth Annual Conference on Genetic and Evolutionary Computation (GECCO '13), 65-72, 2013

Ying-Chi Lin. Martin Middendorf
Simple Probabilistic Population Based Optimization for Combinatorial Optimization
Proc. IEEE Symposium on Swarm Intelligence, 213-220, 2013

M. Clauss, M. Bernt. M. Middendorf
A Common Interval Guided ACO Algorithm for Permutation Problems
Proc. IEEE Symposium on Swarm Intelligence, 64-71, 2013

R. L. V. Moritz, M. Middendorf
Self-Organized Cooperation between Agents that have to Solve Resource Collection Tasks
Proc. IEEE Symposium on Swarm Intelligence, 206-212, 2013

R. L. V. Moritz, M. Bernt, and M. Middendorf
Annotation Guided Local Similarity Search in Multiple Sequences and its Application to Mitochondrial Genomes
Proc. 12th IEEE International Conference on Bioinformatics & Bioengineering (BIBE),157-162, 2012

M. Bernt, K.-M. Chao, J.-W. Kao, M. Middendorf, E. Tannier
Preserving Inversion Phylogeny Reconstruction
Proc. of the Workshop on Algorithms in Bioinformatics 2012 (WABI 2012), LNCS 7534, 1-13, 2012.

M. Bernt, M. Middendorf
A Method for Computing an Inventory of Metazoan Mitochondrial Gene Order Rearrangements.
Ninth Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB CG), 2011.

K. Diwold, D. Himmelbach, R. Meier, C. Baldauf, M. Middendorf
Bonding as a Swarm: Applying Bee Nest-Site Selection Behaviour to Protein Docking
Proc. 13th Annual Conference on Genetic and Evolutionary Computation (GECCO 2011), 2011.

R. Moritz, K. Ramsch, M. Middendorf
Trophallaxis-Inspired Self-Organised Task Exchange in Heterogeneous Swarms
Proc. IEEE Swarm Intelligence Symposium (SIS2011), pp. 8, 2011.

W. Cheng, M. Middendorf, B. Scheuermann
Quick-ACO: Accelerating Ant Decisions and Pheromone Updates in ACO
Proc. EvoCOP'11, LNCS 6622, 238-249, 2011.

K. Diwold, T. Ruhnke, M. Middendorf
Sensor Placement in Water Networks Using a Population-Based Ant Colony Optimization Algorithm
Proc. Second International Conference on Computational Collective Intelligence - Technologies and Applications (ICCCI-2010), Springer, LNAI 6423, 426-437, 2010.

K. Diwold, M. Beekman, M. Middendorf
Bee Nest Site Selection as an Optimization Process
Proc. 12th International Conference on the Synthesis and Simulation of Living Systems (Alife XII), The MIT Press, 626-633, 2010.

M. Middendorf, B. Scheuermann
Perspectives of Extending Runtime Reconfigurable Computing to the Enterprise Application Domain
Accepted for 8th IEEE International Conference on Indutstrial Informatics (INDIN 2010), July 13-16, Osaka, Japan.

A. Aderhold, K. Diwold, A. Scheidler, and M. Middendorf
Artificial Bee Colony Optimization: A new Selection Scheme and its Performance
Proc. International Workshop on Nature Inspired Cooperative Strategies for Optimization (NICSO 2010), Springer, Studies in Computational Intelligence, Vol. 284/2010, 283-294, 2010.

A. Scheidler, M. Middendorf
Invited Talk: Communication Patterns in Decentralized Learning Classifier Systems
Proc. Autonomics 2009, Lecture Notes of ICST (LNICST)

K. Diwold, A. Scheidler, M. Middendorf
The Effect of Spatial Organisation in Response Threshold Models for Social Insects
Proc. European Conference on Complex Systems (ECCS’09), 21-25 September 2009, University of Warwick, UK

M. Hellmuth, D. Merkle, M. Middendorf
On the Design of RNA Sequences for Realizing Extended Shapes
Proc. International Joint Conferences on System Biology, Bioinformatics and Intelligent Computing (IJCBS 2009), IEEE,167 - 173, 2009.

A. Scheidler, M. Middendorf
Evolved cooperation and emergent communication structures in learning classifier based organic computing systems.
Proc. 11th Annual Conference Companion on Genetic and Evolutionary Computation Conference: Late Breaking Papers, 2633-2640, 2009.

M. Bernt, M.-C. Chen, D. Merkle, H.-L. Wang, K.-M. Chao, M. Middendorf
Finding All Sorting Tandem Duplication Random Loss Operations
Proc. 20th Annual Symposium on Combinatorial Pattern Matching (CPM 2009), LNCS 5577, 301-313, 2009.

H. Hernandez, C. Blum, M. Middendorf, K. Ramsch, A, Scheidler
Self-Synchronized Duty-Cycling for Mobile Sensor Networks with Energy Harvesting Capabilities: A Swarm Intelligence Study
Proc. IEEE Swarm Intelligence Symposium (SIS 2009), 153 – 159, 2009.

M. Bernt, D. Merkle, M. Middendorf
An Algorithm for Inferring Mitochondrial Genome Rearrangements in a Phylogenetic Tree
Proc. 6th Annual RECOMB Satellite Meeting on Comparative Genomics, LNCS 5267, 143-157, 2008.

S. Lange, M. Middendorf
SPP1148 booth: Hyperreconfigurable architectures
Proc. International Conference on Field Programmable Logic and Applications (FPL 2008), 353, 2008.

A. Brutschy, A. Scheidler, D. Merkle, M. Middendorf
Learning from House-Hunting Ants: Collective Decision-Making in Organic Computing Systems
Proc. 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008), LNCS 5217, 96-107, 2008.
This paper won the Best Paper Award of ANTS 2008.

A. Scheidler, C. Blum, D. Merkle, M. Middendorf
Emergent Sorting in Networks of Router Agents
Proc. 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008), LNCS 5217, 299-306, 2008.

K. Diwold, D. Merkle, M. Middendorf
The Influence of Dynamic Environments on Polyethism in Response Threshold Models for Social Insects
Proc. 8th German Workshop on Artificial Life (GWAL-8 2008), Leipzig, Germany, July 30 - August 01, 2008.

A. Scheidler, D. Merkle, M. Middendorf
Congestion Control in Ant Like Moving Agent Systems
Proc. 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC), Springer, 33-44, 2008.

T. Basuki Kurniawan, N. Khafifah Khalid, Z. Ibrahim, M. Khalid, M. Middendorf
Evaluation of Ordering Methods for DNA Sequence Design Based on Ant Colony System
Asia International Conference on Modelling and Simulation 2008: 905-910.

T. Thalheim, D. Merkle, M. Middendorf
A Hybrid Population based ACO Algorithm for Protein Folding
Proc. 2008 IAENG International Conference on Bioinformatics Hong Kong, 19-21 March, 2008.

S. Lange, M. Middendorf
On the Reconfiguration Costs of Models for Partially Reconfigurable FPGAs
Proc. IV Southern Programmable Logic Conference (SPL'08), IEEE, 111-118, 2008.

A. Scheidler, D. Merkle, M. Middendorf
Stability and Performance of Ant Queue Inspired Task Division Methods
Proc. European Conference on Complex Systems 2007 (ECCS 2007), Dresden, October 1-5, 2007.

M. Geis, M. Middendorf
An Ant Colony Optimizer for Melody Creation with Baroque Harmony
Proc. IEEE Congress on Evolutionary Computation (CEC 2007), Singapore, September 25-28, 2007.

M. Bernt, D. Merkle, M. Middendorf
A Fast and Exact Algorithm for the Perfect Reversal Median Problem
Proc. International Symposium on Bioinformatics Research and Applications (ISBRA), Georgia, USA, May 7-10, 2007.

S. Lange, M. Middendorf
Online Strategies for the Reconfiguration of Two-Level Reconfigurable Architectures
Proc. Workshop Workshop on Dynamically Reconfigurable Systems (DRS), Zurich, 2007.

D. Merkle, M. Middendorf, A. Scheidler
Swarm Controlled Emergence - Designing an Anti-Clustering Ant System
Proc. IEEE Swarm Intelligence Symposium, Honolulu, Hawaii, 2007.

S. Janson, M. Middendorf
On Trajectories of Particles in PSO
Proc. IEEE Swarm Intelligence Symposium, Honolulu, Hawaii, 2007.

M. Geis, M. Middendorf
A Particle Swarm Optimizer for Finding Minimum Free Energy RNA Secondary Structures
Proc. IEEE Swarm Intelligence Symposium, Honolulu, Hawaii, 2007.

S. Lange, M. Middendorf
Granularity Aspects for the Design of Multi-level Reconfigurable Architectures
Proc. IEEE International Conference on Field Programmable Technology (ICFPT 06), Bangkok, Thailand, 2006.

M. Bernt, D. Merkle, M. Middendorf
The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders
Computational Life Sciences II - Proc. 2nd International Symposium CompLife, LNCS 4216, 52-63, 2006.

D. Merkle, M. Middendorf, A. Scheidler
Using Decentralized Clustering for Task Allocation in Networks with Reconfigurable Helper Units
Proc. International Workshop on Self-Organizing Systems 2006 (IWSOS 2006), LNCS 4124, 137-147, 2006.

A. Scheidler, D. Merkle, M. Middendorf
Emergent Sorting Patterns and Individual Differences of Randomly Moving Ant Like Agents
Proc. 7th German Workshop on Artificial Life (GWAL-7), IOS Press, 11 pp., 2006.

S. Lange, M. Middendorf
Cache Architectures for Reconfigurable Hardware
Proc. 2006 International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'06), IEEE, 2006.

D. Merkle, M. Middendorf, A. Scheidler
Self-Organized Task Allocation for Computing Systems with Reconfigurable Components
Proc. 9th International Workshop on Nature Inspired Distributed Computing (NIDISC'06), IEEE, 8 pp., 2006.

S. Lange, M. Middendorf
On Multi-level Reconfigurable Architectures
Proc. 13th Reconfigurable Architectures Workshop (RAW 2006), IEEE, 8 pp., 2006.

S. Janson, E. Alba, B. Dorronsoro, M. Middendorf
Hierarchical Cellular Genetic Algorithm
Proc. 6th European Conference on Evolutionary Computation in Combinatorial Optimization, Springer, LNCS 3906, 111-122, 2006.
Paper

S. Lange, M. Middendorf
Heuristics for Context-Caches in 2-Level Reconfigurable Architectures
Proc. of the IEEE 2005 Conference on Field-Programmable Technology (FPT' 05), 293-294, 2005.

M. Bernt, D. Merkle, M. Middendorf
A Parallel Algorithm for Solving the Reversal Median Problem
Proc. Parallel Processing and Applied Mathematics - Bio-Computing Workshop (PBC'5), LNCS 3911, 1089-1096, 2005.

S. Lange, M. Middendorf
On the Design of Two-Level Reconfigurable Architectures
Proceedings of the 2005 International Conference on Reconfigurable Computing and FPGAs (ReConFig05), IEEE Computer Society, 9 p., 2005.

S. Janson, D. Merkle, M. Middendorf
Decentralized Packet Clustering in Networks Applied to Particle Swarm Optimization
Proc. of the Conference on Design, Analysis, and Simulation of Distributed Systems 2005 (DASD 2005), 3-10, 2005.

S. Janson, M. Middendorf
Flexible Particle Swarm Optimization Tasks for Reconfigurable Processor Arrays
Proc. 8th International Workshop on Nature Inspired Distributed Computing (NIDISC’05), IEEE Computer Society , 8 p., 2005.
Paper

D. Merkle, M. Middendorf, A. Scheidler
Dynamic Decentralized Packet Clustering in Networks
Proc. EvoWorkkshops 2005, 2nd European Workshop on Evolutionary Algorithms in Stochastic and Dynamic Environments, Springer, LNCS 3449, 574-583, 2005.

B. Scheuermann, M. Middendorf
Counter-based Ant Colony Optimization as a Hardware-oriented Meta-Heuristic
Proc. EvoWorkkshops 2005, 2nd European Workshop on Evolutionary Computation in Hardware Optimisation, Springer, LNCS 3449, 235-244, 2005.

S. Lange, M. Middendorf
The Partition into Hypercontexts Problem for Hyperreconfigurable Architectures
Proc. of the International Conference on Field Programmable Logic and Applications (FPL 2004), Springer Verlag, LNCS 3205, 251-260, 2004..

D. Merkle, M. Middendorf
Competition Controlled Pheromone Update for Ant Colony Optimization
Proc. Fourth International Workshop ANTS 2004, Springer, LNCS 3172, 95-105, 2004.

B. Scheuermann, M. Guntsch, M. Middendorf, H. Schmeck
Time-Scattered Heuristic Guidance for a Hardware Implementation of ACO
Proc. Fourth International Workshop ANTS 2004, Springer, LNCS 3172, 250-261, 2004.

S. Lange, M. Middendorf
Hyperreconfigurable Architectures for Fast Runtime Reconfiguration
Proc. 2004 IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM´04), 304-305, 2004.

S. Lange, M. Middendorf
Hyperreconfigurable Architectures as Flexible Control Systems
ARCS 2004 Workshop "Dynamically Reconfigurable Systems", Lecture Notes in Informatics, Vol. P-41, 175-184, 2004.

S. Janson, M. Middendorf
A Hierarchical Particle Swarm Optimizer for Dynamic Optimization Problems
Proc. Evoworkshops 2004: 1st European Workshop on Evolutionary Algorithms in Stochastic and Dynamic Environments, Springer, LNCS 3005, 513-524, 2004.

S. Lange, M. Middendorf
Models and Reconfiguration Problems for Multi Task Hyperreconfigurable Architectures
Proc. International Parallel and Distributed Processing Symposium (IPDPS-2004), Reconfigurable Architectures Workshop (RAW-2004), IEEE-CS Press, 8 pp., 2004.

D. Merkle, M. Middendorf
Dynamic Polyethism in Social Insect Societies - A Simulation Study
Proceedings of the 2nd International Workshop on the Mathematics and Algorithms of Social Insects, Georgia Institute of Technology, 99-106, 2003.

M. Guntsch, M. Middendorf
Solving Multi-Objective Permutation Problems with Population Based ACO
Proceedings of the Second International Conference on Evolutionary Multi-Criterion Optimization (EMO 2003), C.M. Fonseca, P.J. Fleming, E. Zitzler, K. Deb, L. Thiele (Eds.), Springer, LNCS 2636, 464-478, 2003.
Paper

M. Guntsch, M. Middendorf, B. Scheuermann, O. Diessel, H. ElGindy, H. Schmeck, K. So
Population based Ant Colony Optimization on FPGA
Proceedings 2002 IEEE International Conference on Field-Programmable Technology (FPT'02), P. Leong, W. Luk (Eds.), IEEE, Hong Kong, 125-132, 2002.

M. Guntsch, M. Middendorf
Applying Population Based ACO to Dynamic Optimization Problems
Ant Algorithms, Proceedings of Third International Workshop ANTS 2002, Brussels, Belgium, Springer Verlag, LNCS 2463, 111-122, 2002.
Paper

D. Merkle, M. Middendorf
Modelling ACO: Composed Permutation Problems
Ant Algorithms, Proceedings of Third International Workshop ANTS 2002, Brussels, Belgium, Springer Verlag, LNCS 2463, 149-162, 2002.

M. Guntsch, M. Middendorf
A Population Based Approach for ACO
Proc. 2nd European Workshop on Evolutionary Computation in Combinatorial Optimization (EvoCOP-2002), Kinsale, Ireland, Springer Verlag, LNCS 2279, 72-81, 2002.
Paper

D. Merkle, M. Middendorf
Ant Colony Optimization with the Relative Pheromone Evaluation Method
Proc. 3rd European Workshop on Scheduling and Timetabling and 3rd European Workshop on Evolutionary Methods for AI Planning (EvoSTIM/EvoPLAN-2002), Kinsale, Ireland, LNCS 2279, 325-333, 2002.
Paper

D. Merkle, M. Middendorf
Collective Optimization: The Artificial Ants Way
Abstracts of the Workshop From Worker to Colony: Understanding the Organisation of Insect Societies, Isaac Newton Institute, Cambridge, 2001.

M. Guntsch, M. Middendorf, and H. Schmeck
An Ant Colony Optimization Approach to Dynamic TSP
In: L. Spector et al. (eds.) Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001), San Francisco, CA: Morgan Kaufmann Publishers, 860-867, 2001.

D. Merkle, M. Middendorf
Prospects for Dynamic Algorithm Control: Lessons from the Phase Structure of Ant Scheduling Algorithms
In: Robert B. Heckendorn (Ed.), Proceedings of the 2001 Genetic and Evolutionary Computation Conference -- Workshop Program. Workshop "The Next Ten Years of Scheduling Research", San Francisco, CA, July 7, 121-126, 2001.

M. Guntsch, M. Middendorf
Pheromone Modification Strategies for Ant Algorithms applied to Dynamic TSP
In: E.J.W. Boers et al. (Eds.) Applications of Evolutionary Computing: Proceedings of EvoWorkshops 2001, Lake Como, Italy, Springer Verlag, LNCS 2037, 213-222, 2001.

D. Merkle, M. Middendorf
A New Approach to Solve Permutation Scheduling Problems with Ant Colony Optimization
In: E.J.W. Boers et al. (Eds.) Applications of Evolutionary Computing: Proceedings of EvoWorkshops 2001, Lake Como, Italy, Springer Verlag, LNCS 2037, 484-493, 2001.

S. Iredi, D. Merkle, M. Middendorf
Bi-Criterion Optimization with Multi Colony Ant Algorithms
In: E. Zitzler et al. (Eds.) Evolutionary Multi-Criterion Optimization, First International Conference (EMO'01), Zurich, Springer Verlag, LNCS 1993, 359-372, 2001.

D. Merkle, M. Middendorf, H. Schmeck
Pheromone Evaluation in Ant Colony Optimization
Proceedings of the 26th Annual Conference of the IEEE Electronics Society IECON-2000 (2000 IEEE International Conference on Industrial Electronics, Control and Instrumentation), Third Asia-Pacific Conference on Simulated Evolution and Learning (SEAL2000), October 22-28, 2000, Nagoya, Japan, IEEE Press, 2726-2731.

M. Guntsch, J. Branke, M. Middendorf, H. Schmeck
ACO Strategies for Dynamic TSP
In: Abstract Proceedings of the ANTS'2000 - From Ant Colonies to Artificial Ants: Second International Workshop on Ant Algorithms, Brussels, Belgium, September 8-9, 59-62, 2000.

D. Merkle, M. Middendorf, H. Schmeck
Ant Colony Optimization for the RCPSP using Weighted Summation Evaluation
In: Abstract Proceedings of the ANTS'2000 - From Ant Colonies to Artificial Ants: Second International Workshop on Ant Algorithms, Brussels, Belgium, September 8-9, 84-87, 2000.

M. Middendorf
Evolutionary Methods for AI Planning - A Short Overview
Proceedings of the 2000 Genetic and Evolutionary Computation Conference - Workshop Program, Las Vegas, Nevada, 187-188, July 8. 2000.

M. Middendorf, V. Timkovsky
On Scheduling Cycle Shops
In: Extended Abstracts of 7th International Workshop on Project Management and Scheduling, Osnabrück, April 2000, Faculty of Mathematics, 214-216, 2000.

M. Middendorf
Bit-summation on the reconfigurable mesh
In: J. Rolim et al. (Eds.) Parallel and Distributed Computing, Proceedings of the 11 IPPS/SPDP`99 Workshops, 6th Reconfigurable Architectures Workshop RAW-99, Springer Verlag, LNCS 1586, 625-633, 1999.

R. Michels, M. Middendorf
An Ant System for Plan Merging
First International Workshop on Ant Colony Optimization (Ants'98), Brussels, Belgium, 1998.

M. Middendorf, V. Timkovsky
Consistent supersequences and transversal graphs: An extended abstract
Workshop on Computational Biology, Udine, Italiy, 1998.

M. Middendorf, V. Timkovsky
Transversal graphs in Plan Merging and related problems
Third International Symposium on Operations Research and Its Applications (ISORA'98), World Publishing Corp., Beijing, Lecture Notes in Operations Research 3, 60-74, 1998.

W. Zimmermann, M. Middendorf, W. Löwe
On optimal k-linear scheduling of tree-like task graphs for LogP-machines
In: D. Pritchard, J. Reeve (Eds.), Euro-Par"98 Parallel Processing, Springer Verlag, LNCS 1470, 328-336, 1998.

C. Steckel, M. Middendorf, H. ElGindy, H. Schmeck
A simulator for the reconfigurable mesh architecture
In: J. Rolim (Ed.) Parallel and Distributed Computing, Proceedings of the 10 IPPS/SPDP`98 Workshops, 5th Reconfigurable Architectures Workshop RAW-98, Springer Verlag, LNCS 1388, 99-104, 1998.
Preliminary version: Technical Report 374, Institute AIFB, University of Karlsruhe, Germany, December 1997.

M. Middendorf, H. Schmeck
A local and dynamic algorithm for reconfiguring a faulty processor array into a maximal fault-free subarray
In: N. Sharda, A. Tam (Eds.), Proceedings of the 4th Australasian Conference on Parallel and Real-Time Systems (PART '97), Springer Verlag, Singapore, 191-201, 1997.
Preliminary version: Technical Report 369, Institute AIFB, University of Karlsruhe, Germany, November 1997.

M. Middendorf
Supersequences, runs, and CD grammar systems
In: J. Dassow, A. Kelemenova (Eds.), Developments in Theoretical Computer Science, 101-114, (Topics in Computer Science, Vol. 6), Gordon and Breach, Amsterdam, 101-114, 1994.
Preliminary version: Technical Report 275, Institute AIFB, University of Karlsruhe, Germany, Mai 1993.

N. Kuck, M. Middendorf, H. Schmeck
Generic branch-and-bound on a network of transputers
In: R. Grebe, J. Hector, S.C. Hilton, M.R. Jane, P.H. Welch (Eds.), Transputer Applications and Systems `93, IOS Press, 306-314, 1993.

Proceedings (Editor)


Martin Middendorf, Hartmut Schmeck, and Detlev Seese
24. Workshop Komplexitätstheorie, Datenstrukturen und effiziente Algorithmen
Technical Report 310, Institute AIFB, November 1994.

Martin Middendorf
Workshop on Evolutionary Methods of AI Planning
In Annie S. Wu (Ed.), Proceedings of the 2000 Genetic and Evolutionary Computation Conference - Workshop Program. Las Vegas, Nevada, July 8, 2000.

Marco Dorigo, Martin Middendorf, and Thomas Stützle (Eds.)
Abstract Proceedings of ANTS'2000 - From Ant Colonies to Artificial ANTS: Second International Workshop on Ant Colony Optimization
Brussels, Belgium, September 7-9, 2000.

Tutorial


Tutorial on Ant Colony Optimization.
In: Tutorial Proceedings of Genetic and Evolutionary Computation Conference (GECCO-2001), San Francisco, 236-255, 2001.
Updated version in: Tutorial Proceedings of Genetic and Evolutionary Computation Conference (GECCO-2002), New York, 416-436, 2002.
Updated version in: Tutorial Proceedings of Genetic and Evolutionary Computation Conference (GECCO-2003), Chicago, 556-580, 2003.

Working paper


D. Merkle, M. Middendorf, N. Wieseke
A Parameter-Adaptive Dynamic Programming Approach for Inferring Cophylogenies
Working Paper PACOSY 09-01, August 10, 2009, submitted.

Book reviews


D. Merkle, M. Middendorf
Bookreview on "Ant Colony Optimization'' by M. Dorigo, T. Stützle, MIT Press, 2004
European Journal of Operations Research, 168(1): 269-271, 2006.

Other publications


A. Donath, F. Externbrink, F. Jühling, M. Bernd, G. Fritzsch, M. Middendorf, P. F. Stadler
Improved Automatic Annotation of Metazoan Mitochondrial Genomes
Poster at German Conference on Bioinformatics 2009 (GCB'09).

M. Bernt, D. Merkle, M. Middendorf
Solving the Multiple Genome Rearrangement Problem
Proc. of the 19th Dubrovnik International Course and Conference on the Interfaces Among Mathematics, Chemistry and Computer Sciences, Inter-University Centre Dubrovnik, 6, 2004.

D. Merkle, M. Middendorf
Combined Phylogenies: Hosts and Their Parasites
Proc. of the 19th Dubrovnik International Course and Conference on the Interfaces Among Mathematics, Chemistry and Computer Sciences, Inter-University Centre Dubrovnik, 46, 2004.

E. Petzold, A. von Haeseler, D. Merkle, M. Middendorf
Efficient Parallel Parameter Estimation for Maximum Likelihood Reconstruction of Phylogenetic Trees.
Abstracts of 3rd Biotechnolgy Symposium 2004, Center of Biotechnolgy and Biomedicine, University of Leipzig, 228, 2004.

D. Merkle, M. Middendorf, R. Legat
Reconstruction of Host-Parasite Phylognies with Extinction Events
Abstracts of 3rd Biotechnolgy Symposium 2004, Center of Biotechnolgy and Biomedicine, University of Leipzig, 227, 2004.