Research - Parallel Computing and Complex Systems

Faculty of Mathematics and Computer Science	Department of Computer Science
Parallel Computing and Complex Systems

Publications (since 2002)

Older publications see homepages of the members of our group.

Journals:

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.

T. Thalheim, D. Merkle, M. Middendorf:
Protein Folding in the HP-Model Solved With a Hybrid Population Based ACO Algorithm
accepted for IAENG International Jorunal

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
Journal of Intelligent Computing and Cybernetics, 1(1): 25-45, 2008.

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. Perseke, 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 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.
Paper (pdf)

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 (pdf)

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

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

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.
Paper (pdf)

Preliminary version in Proceedings of the Congress on Evolutionary Computation (CEC 2003), IEEE Press, 770--776, (2003).

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 (pdf)

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(pdf)

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 (pdf)

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

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: 303-322, 2004 (special issue on Hardware Implementations of Softcomputing Techniques)
Preliminary version (pdf)<

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.

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

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

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.
(pdf)

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

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 (pdf)

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) (2002) 59-63.

Journals (Guest Editorials):

IEEE Transactions on Evolutionary Computation, Special issue on Swarm Intelligence, in preparation.
Guest editors: A. Engelbrecht, L. M. Gambardella, X. Li, M. Middendorf

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

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

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

Books (Editor):

A. Engelbrecht, M. Middendorf (Eds.):
Applied Swarm Intelligence
Springer Verlag, in preperation.

S. Cagnoni, D. Corne, J. Gottlieb, A. Guillot, E. Hart, E. Marchiori, J.-A. Meyer, M. Middendorf, G.R. Raidl (Eds.):
Applications of Evolutionary Computing - EvoWorkshops 2003: EvoBIO, EvoCOP, EvoIASP, EvoSTIM/EvoPLAN, EvoROB,
Springer Verlag, 2003.

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.

Bookchapters:

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

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, 171-201, 2005.
Preliminary vrsion (pdf)

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.

Conferences:

M. Bernt, D. Merkle, M. Middendorf:
An Algorithm for Inferring Mitochondrial Genome Rearrangements in a Phylogenetic Tree
accepted for the 6th Annual RECOMB Satellite Meeting on Comparative Genomics, October 13-15, 2008.

A. Brutschy, A. Scheidler, D. Merkle, M. Middendorf:
Learning from House-Hunting Ants: Collective Decision-Making in Organic Computing Systems
accepted for 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008), September 22-24, 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
accepted for 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008), September 22-24, 2008.

K. Diwold, D. Merkle, M. Middendorf:
The Influence of Dynamic Environments on Polyethism in Response Threshold Models for Social Insects
accepted for 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
Accepted for 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC), Milan, Italy, 7-10 September 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, IEEE, 8 pp., 2007.

S. Janson, M. Middendorf
On Trajectories of Particles in PSO
Proc. IEEE Swarm Intelligence Symposium, IEEE, 8 pp., 2007.

M. Geis, M. Middendorf
A Particle Swarm Optimizer for Finding Minimum Free Energy RNA Secondary Structures
Proc. IEEE Swarm Intelligence Symposium, IEEE, 8 pp., 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), IEEE, 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.

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:
A New Multi-Objective Particle Swarm Optimization Algorithm Using Clustering Applied to Automated Docking
Accepted for Second Int. Workshop on Hybrid Metaheuristics (HM 2005), Springer, LNCS 3636, 128-140, 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.

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. International Conference on Field Programmable Logic and Applications (FPL 2004), Springer Verlag, LNCS 3205, 2004, 251-260.
Preliminary version (PDF)

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 an 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
Preliminary version (PDF)

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.
Preliminary version (PDF)

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, LNCS 3005, 2004, 513-524.

S. Lange, M. Middendorf:
Models and Reconfiguration Problems for Multi Task Hyperreconfigurable Architectures
Accepted for the 11th Reconfigurable Architectures Workshop (RAW 2004), Santa Fe, 2004.
Preliminary version (PDF)

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, 2003, 464-478.
Preliminary version (pdf)

M. Guntsch, M. Middendorf, B. Scheuermann, O. Diesel, 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, 2002, 125-132.

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

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, 2002, 111-122.
Preliminary version (gzipped postscript)

J. Branke, M. Decker, D. Merkle and H. Schmeck:
Coevolutionary Ant Algorithms Playing Games
Proceedings of Third International Workshop ANTS 2002, Springer Verlag, LNCS 2463, 2002, 298-299.

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

M. Guntsch and 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, 2002, 72-81.
Preliminary version (gzipped postscript)

D. Merkle and 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, 2002, 325-333.
Abstract Preliminary version (postscript)

Tutorials:

Martin Middendorf:
Tutorial on Ant Colony Optimization.
Genetic and Evolutionary Computation Conference (GECCO-2003), Chicago, Tutorial Proceedings, 556-580, 2003.

Martin Middendorf:
Tutorial on Ant Colony Optimization.
Genetic and Evolutionary Computation Conference (GECCO-2002), New York, Tutorial Proceedings, 416-436, 2002.

Book review:

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:

M. Bernt, D. Merkle, K. Ramsch, G. Fritzsch, M. Perseke, D. Bernhard, M. Schlegel, P. F. Stadler, M. Middendorf:
CREx - A Tool for Analyzing Genomic Rearrangement Operations Based on Common Intervals.
Abstracts of Saxon Biotechnology Symposium 2007, Biotechnolgy Center, Technische Universität Dresden, 115, 2007.

M. Bernt, D. Merkle, M. Middendorf:
A method for Solving the Preservation Reversal Median Problem.
Abstracts of Saxon Biotechnology Symposium 2007, Biotechnolgy Center, Technische Universität Dresden, 116, 2007.

M. Bernt, D. Merkle, M. Middendorf:
From genome rearrangements to phylogenies.
Abstracts of 5th Biotechnolgy Symposium 2006, Center of Biotechnolgy and Biomedicine, University of Leipzig, 59, 2006.

S. Janson, D. Merkle, M. Middendorf:
Solving molecular docking with particle swarm optimization.
Abstracts of 5th Biotechnolgy Symposium 2006, Center of Biotechnolgy and Biomedicine, University of Leipzig, 77, 2006.

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.

M. Bernt, D. Merkle, M. Middendorf:
Multiple Genome Rearrangement with conserved intervals.
Abstracts of 4th Biotechnolgy Symposium 2005, Center of Biotechnolgy and Biomedicine, University of Leipzig, 202, 2005.

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.

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