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Scientific Publications Daniel Merkle, 1. July 2009 (just write me a mail if you want an article as a pdf; to the best of my knowledge my Erdös number is still 3, but who knows) Books [KMO09a] Klemm, K., D. Merkle   E. Olbrich (editors): Proceedings of the 8th German Workshop on Artificial Life. IOS Press, 2009. [BM08] Blum, C.   D. Merkle (editors): Swarm Intelligence - Introduction and Application. Natural Computing Series, Springer, 2008. [Mer02] Merkle, D.: Ameisenalgorithmen - Optimierung und Modellierung. , Institut für Angewandte Informatik und Formale Beschreibungsverfahren, Universität Karlsruhe (TH), 2002. 211 pages. Editorials [DMS09] Doerner, K., D. Merkle,   T. Stützle: Special issue in: Swarm Intelligence. 2009. to be published.   International Journals [DMM09a] Diwold, K., D. Merkle   M. Middendorf: Adapting to Dynamic Environments: Polyethism in Response Threshold Models for Social Insects. Advances in Complex Systems, 2009. accepted. [BMM08] Bernt, M., D. Merkle   M. Middendorf: Solving the Preserving Reversal Median Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(3): 332-347, 2008. [PRB+08] Perseke, M., K. Ramsch, M. Bernt, D. Merkle, M. Middendorf, D. Bernhard, P.F. Stadler   M. Schlegel: Phylogenetic analyses of mitochondrial genomes of echinoderms challenge the monophyly of Eleutherozoa. Molecular Phylogenetics and Evolution, 47:855-864, 2008. [MM08a] Merkle, D.   M. Middendorf: Swarm Intelligence and Signal Processing. IEEE Signal Processing Magazine, 25(6): 152-158, 2008. [TMM08a] Thalheim, T., 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. [JMM08a] Janson, S., 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. [JMM08b] Janson, S., D. Merkle   M. Middendorf: Molecular Docking with Multi-Objective Particle Swarm Optimization. Applied Soft Computing, 8(1):666-675, 2008. [SMM08b] Scheidler, A., D. Merkle   M. Middendorf: Stability and Performance of Ant Queue Inspired Task Division Methods. Theory in Biosciences, 127(2):149-161, 2008. [MMS08c] Merkle, D., M. Middendorf   A. Scheidler: Self-Organized Task Allocation for Service Tasks in Computing Systems with Reconfigurable Components. Journal Mathematical Modelling and Algorithms, 7(2):237-254, 2008. [BMR+07] Bernt, M., D. Merkle, K. Ramsch, M. Perseke, D. Bernhard, M. Schlegel, P.F. Stadler   M. Middendorf: CREx: Inferring Genomic Rearrangements Based on Common Intervals. Bioinformatics, 23(21):2957-2958, 2007. [BMM07b] Bernt, M., D. Merkle   M. Middendorf: Using Median Sets for Inferring Phylogenetic Trees. Bioinformatics, 23:e129-e135, 2007. This paper won the 3rd best paper award at the European Conference on Computational Biology 2006. [BMM06b] Bernt, M., 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. [MMS06a] Merkle, D., M. Middendorf   A. Scheidler: Modelling Ant Brood Tending Behaviour with Cellular Automata. Journal of Cellular Automata, 2(2):183-194, 2006. preliminary version in [, ]. [MB05] Merkle, D.   C. Blum: Swarm Intelligence - An optimization-based introduction. Künstliche Intelligenz, 4:5-10, 2005. [MM05b] Merkle, D.   M. Middendorf: Reconstruction of the Cophylogenetic History of Related Phylogenetic Tree with Divergence Timing Information. Theory in Biosciences, 123(4):277-299, 2005. [MMS05a] Merkle, D., M. Middendorf   A. Scheidler: Decentralized Packet Clustering in Router-based Networks. International Journal of Foundations of Computer Science, 16(2):321-341, 2005. [MM05a] Merkle, D.   M. Middendorf: On solving permutation scheduling problems with ant colony optimization. International Journal of Systems Science, 36(5):255-266, 2005. [MM04c] Merkle, D.   M. Middendorf: Dynamic Polyethism and Competition for Tasks in Threshold Reinforcement Models of Social Insects. Adaptive Behavior, 12:251-262, 2004. preliminary version in [, ]. [MM02e] Merkle, D.   M. Middendorf: Modelling the dynamics of ant colony optimization. Evolutionary Computation, 10(3):235-265, 2002. preliminary version in [, ]. [MMS02] Merkle, D, M. Middendorf   H. Schmeck: Ant colony optimization for resource-constrained project scheduling. IEEE Transactions on Evolutionary Computation, 6(4):333-346, 2002. preliminary version in [, ]. [MM02c] Merkle, D.   M. Middendorf: Fast ant colony optimization on runtime reconfigurable processor arrays. Genetic Programming and Evolvable Machines, 3(4):345-361, 2002. [MW02] Merkle, D. and Th. Worsch Formal language recognition by stochastic cellular automata. Fundamenta Informaticae, 52(1-3):183-201, 2002. preliminary version in [, ]. [JMM+03] Janson, S., 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 Supercomuting, 26(3): 221-238,2003. preliminary version in [, ]. [MM02a] Merkle, D   M. Middendorf: An ant algorithm with global pheromone evaluation for scheduling a single machine. Applied Intelligence., 18(1):105-111, 2002.   Book Chapters [MMS08a] Merkle, D., M. Middendorf   A. Scheidler: Organic Computing,  Self-Adaptive Worker-Helper Systems with Self-Organized Task Allocation,   Würtz, R.P. (editor): Organic Computing,  221-240. Springer, 2008. [MMS08b] Merkle, D., M. Middendorf   A. Scheidler: Organic Computing and Swarm Intelligence.   Blum, C.   D. Merkle (editors): Swarm Intelligence,  253-281. Springer, 2008. [PvHM+06] Petzold, E., A. von Haeseler, D. Merkle, M. Middendorf   H.A. Schmidt: Phylogenetic Parameter Estimation on COWs.   Zomaya, A. (editor): Parallel Computing in Bioinformatics and Computational Biology,   347-368. Wiley, 2006. [MM05b] Merkle, D.   M. Middendorf: Swarm Intelligence.   Burke, E.   G. Kendall  (editors): Introductory Tutorials in Optimisation, Search and Decision Support Methodology,  401-435. Springer, 2005. [JMM05b] Janson, S., D. Merkle   M. Middendorf: Parallel Ant Colony Algorithms.   Alba, E. (editors): Parallel Metaheuristics, Wiley Book Series on Parallel and Distributed Computing,  171 - 201. Wiley, 2005. [MM03a] Merkle, D.   M. Middendorf: On the behaviour of ant algorithms: Studies on simple problems.   Resende, M.G.C.   J.P. de Sousa (editors): Metaheuristics: Computer Decision-Making. pages 465-480, Kluwer Academic Publisher, 2003.   Publications in Conference Proceedings [BCM+09] Bernt, M, , M.-C. Chen, D. Merkle, H.-L. Wang, K.-M. Chao, M. Middendorf: Finding All Sorting Tandem Duplication Random Loss Operations.  Lecture Notes in Bioinformatics (LNBI), Accepted for 20th Annual Symposium on Combinatorial Pattern Matching (CPM 2009). [HMM09] Hellmuth, M., D. Merkle   M. Middendorf: On the Design of RNA Sequences for Realizing Extended Shapes accepted for International Joint Conferences on System Biology, Bioinformatics and Intelligent Computing (IJCBS 2009), Shanghai, China, August 3-5th, 2009. [DMM09b] Diwold, K., D. Merkle   M. Middendorf: The Influence of Dynamic Environments on Polyethism in Response Threshold Models for Social Insects.  Proc. of the 8th German Workshop on Artificial Life (GWAL),  37-48. IOS Press, 2009. [BSMM08] Brutschy, A., A. Scheidler, D. Merkle   M. Middendorf: Learning from House-Hunting Ants: Collective Decision-Making in Organic Computing Systems.  Proc. of the 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008),  5217  LNCS,  96-107. Springer, Berlin, 2008. This paper won the paper award at ANTS 2008. [SBMM08] Scheidler, A., C. Blum, D. Merkle   M. Middendorf: Emergent Sorting in Networks of Router Agents.  Proc. of the 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008),  5217  LNCS,  299-306. Springer, Berlin, 2008. [BMM08a] Bernt, M., D. Merkle   M. Middendorf: An Algorithm for Inferring Mitochondrial Genome Rearrangements in a Phylogenetic Tree.  Proc. 2008 of the 6th RECOMB Comparative Genomics Satellite Workshop,  5267  Lecture Notes in Bioinformatics (LNBI),  143-157, 2008. [TMM08b] Thalheim, T., D. Merkle   M. Middendorf: A Hybrid Population based ACO Algorithm for Protein Folding.  Proc. 2008 IAENG International Conference on Bioinformatics, 2008. [SMM08] Scheidler, A., D. Merkle   M. Middendorf: Congestion Control in Ant Like Moving Agent Systems.  2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC), 2008. [MMS07a] Merkle, D., M. Middendorf   A. Scheidler: Swarm Controlled Emergence - Designing an Anti-Clustering Ant System.  Proc. of the IEEE Swarm Intelligence Symposium 2007,  242-249. IEEE Press, 2007. [SMM07] Scheidler, A., D. Merkle   M. Middendorf: Stability and Performance of Ant Queue Inspired Task Division Methods.  Proc. of the European Conference on Complex Systems (ECCS), 2007. [BMM07a] Bernt, M., D. Merkle   M. Middendorf: A Fast and Exact Algorithm for the Perfect Reversal Median Problem.   Mandoiu, Ion   Alexander Zelikovsky (editors): Bioinformatics Research and Applications,  4463  Lecture Notes in Bioinformatics (LNBI),  305-316, 2007. [BMM06e] Bernt, M., D. Merkle   M. Middendorf: The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders.   Berthold, M.R., R. Glen   I. Fischer (editors): Computational Life Sciences II - Proc. 2nd International Symposium CompLife,  4216  Lecture Notes in Bioinformatics (LNBI),  52-63, 2006. [MMS06c] Merkle, D., M. Middendorf   A. Scheidler: Using Decentralized Clustering for Task Allocation in Networks with Reconfigurable Helper Units.  Proceedings of the International Workshop on Self-Organizing Systems 2006 (IWSOS 2006),  4124  LNCS,  137-147. Springer, Berlin, 2006. [MMS06b] Merkle, D., M. Middendorf   A. Scheidler: Self-Organized Task Allocation for Computing Systems with Reconfigurable Components.  Proceedings of the 9th International Workshop on Nature Inspired Distributed Computing (NIDISC'06), 2006. [SMM06] Scheidler, A., D. Merkle   M. Middendorf: Emergent Sorting Patterns and Individual Differences of Randomly Moving Ant Like Agents.  Proceedings of the 7th German Workshop on Artificial Life (GWAL-7), 2006. [BMM06c] Bernt, M., D. Merkle   M. Middendorf: A Parallel Algorithm for Solving the Reversal Median Problem.  Proceedings of the Parallel Processing and Applied Mathematics - Bio-Computing Workshop (PBC 2005),  3911  LNCS,  1089-1096, Berlin, 2006. Springer. [MMS05b] Merkle, D., M. Middendorf   A. Scheidler: Dynamic Decentralized Packet Clustering in Networks.   Rothlauf et al., F. (editors): Proceedings of the 2nd European Workshop on Evolutionary Algorithms in Stochastic and Dynamic Environments,  3449  LNCS,  574-583, Berlin, 2005. Springer. [JMM05a] Janson, S., D. Merkle   M. Middendorf: Decentralized Packet Clustering in Networks Applied to Particle Swarm Optimization.  Proceedings of the Conference on Design, Analysis, and Simulation of Distributed Systems 2005 (DASD 2005),   3-10, 2005. [JM05] Janson, S.   D. Merkle: A New Multi-objective Particle Swarm Optimization Algorithm Using Clustering Applied to Automated Docking.  Proc. of the Second International Workshop on Hybrid Metaheuristics (HM),  3636   Lecture Notes in Computer Science (LNCS),  128-141, 2005. [MMS05c] Merkle, D., M. Middendorf   A. Scheidler: Modelling Ant Brood Tending with Cellular Automata.  Proceedings of the Workshop on Modelling of Complex Systems by Cellular Automata 2005 (ICCS 2005),   3515  LNCS,  412-419. Springer, Berlin, 2005. [MM05a] Merkle, D.   M. Middendorf: Ant Colony Optimization: Biological Motivation, Phase Structure, and Modelling.  Proceedings of the first International Symposium on Mathematical and Computational Biology (BIOMAT 2004), 2005. [MMS04] Merkle, D., M. Middendorf   A. Scheidler: Decentralized Packet Clustering in Networks.  Proceedings of the International Parallel and Distributed Processing Symposium (IPDPS-2004), Sixth International Workshop on Nature Inspired Distributed Computing (NIDISC'04). IEEE-CS Press, 9 pages, 2004. [MM04b] Merkle, D.   M. Middendorf: Competition Controlled Pheromone Update for Ant Colony Optimization.   Dorigo, M., M. Birattari, C. Blum, L. M. Gambardella, F. Mondada   T. Stützle  (editors): Proceedings of the Fourth International Workshop on Ant Colony and Swarm Intelligence (ANTS 2004),  3172  LNCS,  95-105, Berlin, 2004. Springer. [MM03b] Merkle, D.   M. Middendorf: Dynamic Polyethism in Social Insect Societies - A Simulation Study.   Balch, T.   C. Anderson.  (editors): Proceedings of the 2nd International Workshop on the Mathematics and Algorithms of Social Insects,  99-106, Georgia Institute of Technology, Atlanta, 2003. [MMS00a] Merkle, D., M. Middendorf   H. Schmeck: Ant colony optimization for resource-constrained project scheduling.   Whitley, D., D. Goldberg, E. Cantu-Paz, L. Spector, I. Parmee   H.-G. Beyer (editors): Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2000),  893-900, San Francisco, CA, USA, 2000. Morgan Kaufmann. [MM00] Merkle, D.   M. Middendorf: An ant algorithm with a new pheromone evaluation rule for total tardiness problems.  Proceeding of the EvoWorkshops 2000,  1803  Lecture Notes in Computer Science (LNCS),  287-296. Springer Verlag, 2000. [IMM01] Iredi, S., D. Merkle   M. Middendorf: Bi-criterion optimization with multi colony ant algorithms.   Zitzler, E., K. Deb, L. Thiele, C.A. Coello Coello   D. Corne (editors): First International Conference on Evolutionary Multi-Criterion Optimization (EMO'01),  1993   Lecture Notes in Computer Science (LNCS),  359-372, Berlin, 2001. Springer. [MM02g] Merkle, D.   M. Middendorf: Studies on the dynamics of ant colony optimization algorithms.  Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2002),  105-112, San Francisco, CA, USA, 2002. Morgan Kaufmann. [MM02d] Merkle, D.   M. Middendorf: Modelling ACO: Composed permutation problems.   Dorigo, M, G. Di Caro   M. Sampels (editors): Proceedings of 3rd International Workshop on Ant Algorithms (ANTS'2002),  2463  Lecture Notes in Computer Science (LNCS),  149-162, Berlin, 2002. Springer. [MM01d] Merkle, D.   M. Middendorf: A new approach to solve permutation scheduling problems with ant colony optimization.  Second European Workshop on Scheduling and Timetabling (EvoStim2001),  2037   Lecture Notes in Computer Science (LNCS),  484-493. Springer Verlag, 2001. [MM02b] Merkle, D.   M. Middendorf: Ant colony optimization with the relative pheromone evaluation method.  Proceedings of the 3rd European Workshop on Scheduling and Timetabling and 3rd European Workshop on Evolutionary Methods for AI Planning,  2279  Lecture Notes in Computer Science (LNCS),  325-333, 2002. [BDM02] Branke, J., M. Decker   D. Merkle: Coevolutionary Ant Algorithms for Playing Games.   Dorigo, M, G. Di Caro   M. Sampels (editors): Proceedings of 3rd International Workshop on Ant Algorithms (ANTS'2002),  2463  Lecture Notes in Computer Science (LNCS),  298-299, Berlin, 2002. Springer. [JMM+02] Janson, S., 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.  Proceedings of the Second International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'02),  3-9, 2002. [MM03c] Merkle, D.   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, Atlanta, USA, 2003. [MM01a] Merkle, D.   M. Middendorf: Collective optimization: The artificial ants way.  Abstracts of the Workshop From Worker to Colony: Understanding the Organisation of Insect Societies, Cambridge, UK, 2001. Isaac Newton Institute for Mathematical Sciences. [MM01b] Merkle, D.   M. Middendorf: Fast ant colony optimization on reconfigurable processor arrays.  Proceedings of the 15th International Parallel and Distributed Processing Symposium (IPDPS-01). IEEE Computer Society Press, 2001. [MM01e] Merkle, D.   M. Middendorf: On the behaviour of ant algorithms: Studies on simple problems.  Proceedings of the 4th Metaheuristics International Conference (MIC' 2001), Porto, Portugal,  573-577, 2001. [MM01f] Merkle, D.   M. Middendorf: Prospects for dynamic algorithm control: Lessons from the phase structure of ant scheduling algorithms.   Heckendorn, R.B. (editors): Proceedings of the 2001 Genetic and Evolutionary Computation Conference - Workshop Program,  121-126, San Francisco, CA, USA, 2001. Morgan Kaufmann. [MMS00b] Merkle, D., M. Middendorf   H. Schmeck: Ant colony optimization for the RCPSP using weighted summation evaluation.  Abstract Proceedings of the ANTS'2000 - From Ant Colonies to Artificial Ants: Second International Workshop on Ant Algorithms,  84-87, 2000. [MMS00c] Merkle, D., 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),  2726-2731, Piscataway, USA, 2000. IEEE Press.   Book Review [MM05a] Merkle, D.   M. Middendorf: Bookreview on "Ant Colony Optimization" by M. Dorigo, T. Stützle. European Journal of Operations Research, 168(1):269-271, 2005.   Other Publications [JMM06] Janson, S., D. Merkle   M. Middendorf: Solving Molecular Docking Problems with Particle Swarm Optimization.  Abstracts of 3rd Biotechnolgy Symposium 2006, Center of Biotechnolgy and Biomedicine, University of Leipzig,  77, 2006. [BMM06a] Bernt, M., D. Merkle   M. Middendorf: From Genome Rearrangements to Phylogenies.  Abstracts of 3rd Biotechnolgy Symposium 2006, Center of Biotechnolgy and Biomedicine, University of Leipzig,  59, 2006. [PvHMM04] Petzold, E., 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. [MML04] Merkle, D., 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. [BMM04] Bernt, M., D. Merkle   M. Middendorf: Solving the Multiple Genome Rearrangement Problem.  Abstract Proceedings of the 19th Dubrovnik International Course and Conference on the Interfaces Among Mathematics, Chemistry and Computer Sciences (MCC 2004),  6. 2004. [MM04a] Merkle, D.   M. Middendorf: Combined Phylogenies: Hosts and Their Parasites.  Abstract Proceedings of the 19th Dubrovnik International Course and Conference on the Interfaces Among Mathematics, Chemistry and Computer Sciences (MCC 2004),  46, 2004. [MM01c] Merkle, D.   M. Middendorf: Modelling the dynamics of ant colony optimization.  412, Institut AIFB, Universität Karlsruhe, 2001. published as [, ]. [MMS01] Merkle, D., M. Middendorf   H. Schmeck: Ant colony optimization for resource-constrained project scheduling.  409, Institut AIFB, Universität Karlsruhe, 2001. published as [, ]. [MW99] Merkle, D.   Th. Worsch: Formal language recognition by stochastic cellular automata.  392, Institut AIFB, Universität Karlsruhe, 1999. published as [, ]. File translated from TEX by TTH, version 3.85. On 6 Jul 2009, 14:01.

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