Zeitschriften
L. Fiedler, M. Bernt, M. Middendorf, P. Stadler
Detecting gene breakpoints in noisy genome sequences using position annotated colored de-Bruijn graphs
BMC Bioinformatics, 24:235, 2023.
T. Gernat, T. Jagla, B.M. Jones, M. Middendorf, G.E. Robinson
Automated monitoring of honey bees with barcodes and artificial intelligence reveals two distinct social networks from a single affiliative behavior
Scientific Reports, 13:1541, 2023.
H.T. Le, M. Middendorf, Y. Shi
An Improvement Heuristic Based on Variable Neighborhood Search for Dynamic Orienteering Problems with Changing Node Values and Changing Budgets
SN Computer Science, 3:326, 2022.
T. Hartmann, M. Bannach, M. Middendorf, P.F. Stadler, N. Wieseke, M. Hellmuth
Complete Edge-Colored Permutation Graphs
Advances in Applied Mathematics, 139: 102377, 2022
P. Geser, H. T. Le, T. Hartmann, M. Middendorf
On Permutation Schedules for Two-Machine Flow Shops With Buffer Constraints and Constant Processing Times on One Machine
European Journal of Operational Research, 303(2): 593-601, 2022
Q. Zhao, B. Yan, Y. Shi, M. Middendorf
Evolutionary Dynamic Multiobjective Optimization via Learning From Historical Search Process
IEEE Trans. Cybern., 52(7):6119-6130, 2022
Ö. Kayacan, M. Middendorf
Population dynamics for systems with cyclic predator-prey relations and pheromone dependent movement
Physica A: Statistical Mechanics and its Applications, 580: 126137, 2021.
H.T. Le, P. Geser, M. Middendorf
Iterated Local Search and Other Algorithms for Buffered Two-Machine Permutation Flow Shops with Constant Processing Times on One Machine
Evolutionary Computation, 29 (3): 415–439. 2021.
T. Hartmann, M. Bannach, M. Middendorf
Sorting Signed Permutations by Inverse Tandem Duplication Random Losses
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(6): 2177-2188, 2021
B.M. Jones, V. D. Rao, T. Gernat, T. Jagla, A. Cash-Ahmed, B.E.R. Rubin, T.J. Comi, S. Bhogale, S.S. Husain, C. Blatti, M. Middendorf, S. Sinha, S. Chandrasekaran, G.E. Robinson
Individual differences in honey bee (Apis mellifera) behavior enabled by plasticity in brain gene regulatory networks
eLife, 9:e62850, 2020
Y. Shen, M. Liu, J. Yang, Y. Shi, M. Middendorf
A Hybrid Swarm Intelligence Algorithm for Vehicle Routing Problem with Time Windows
IEEE Access, 8: 93882-93893, 2020.
S. Käfer, S. Paraskevopoulou, F. Zirkel, N. Wieseke, A. Donath, M.. Petersen, T. C. Jones, M. Middendorf, S. Junglen, B. Misof, C. Drosten
Re-assessing the diversity of negative strand RNA viruses in insects
PLOS Pathogens, 15(12): e1008224, 2019.
A. Donath, F. Jühling, M. Al-Arab,S.H. Bernhart, F. Reinhardt, P.F. Stadler, M. Middendorf, M. Bernt
Improved Annotation of Protein-Coding Genes Boundaries in Metazoan Mitochondrial Genomes
Nucleic Acids Research, 47(20):10543–10552, 2019
T. Hartmann, M. Bernt, M. Middendorf
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(1): 52-62, 2019.
M. Middendorf, N. Wieseke
A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
PLoS ONE 13(9): e0204907, 2018.
T. Hartmann, M. Bernt, M. Middendorf
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
BMC Bioinformatics, 19: 192, 2018.
T. Gernat, V. D. Rao, M. Middendorf, H. Dankowicz, N. Goldenfeld, G. E. Robinson
Automated monitoring of behavior reveals bursty interaction patterns and rapid spreading dynamics in honeybee social networks
Proceedings of the National Academy of Sciences (PNAS), 115 (7) 1433-1438, 2018.
N. de Villiers, G.C. van Rooyen, M. Middendorf
Sewer network design layout optimization using ant colony algorithms
SAICE Journal (Journal of the South African Institution of Civil Engineering), 60(9), pages 2-15, paper 1773, 2018
T. Hartmann, N. Wieseke, R. Sharan, M. Middendorf, M. Bernt
Genome Rearrangement with ILP
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(5):1585-1593, 2018.
T. Hartmann, A. Chu, M. Middendorf, M. Bernt
Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(1): 83-95, 2018.
N. de Villiers, G.C. van Rooyen, M. Middendorf
Sewer Network Design: Heuristic algorithm for hydraulic optimization
SAICE Journal (Journal of the South African Institution of Civil Engineering), 59(3): 48–56, 2017
M Al Arab, M Bernt, C Höner Zu Siederdissen, K Tout, and PF Stadler
Partially Local Three-Way Alignments and the Sequence Signatures of Mitochondrial Genome Rearrangements
Algorithms for Molecular Biology, 12:22, 2017
Y.-C. Cheng, T. Hartmann, P.-Y. Tsai, M. Middendorf
Population Based Ant Colony Optimization for Reconstructing ECG Signals
Evolutionary Intelligence, 9(3): 55-66, 2016
Y.-C. Lin, M. Clauß, M. Middendorf
Simple Probabilistic Population Based Optimization
IEEE Transactions on Evolutionary Computation, 20(2): 245 - 262, 2016.
M. Clauss, L. Lotzmann, M. Middendorf
A Population Based ACO Algorithm for the Combined Tours TSP Problem
EAI Endorsed Transactions on Self-Adaptive Systems, 16(7): e2, 2016.
A. Sahyoun, M. Hölzer, F. Jühling, C. Hoener zu Siederdissen, M. Al-Arab, K. Tout, M. Marz, M. Middendorf, P. Stadler, and M. Bernt
Towards a Comprehensive Picture of Alloacceptor tRNA Remolding in Metazoan Mitochondrial Genomes
Nucleic Acids Research, 43(16): 8044-8056, 2015.
Link
N. Wieseke, T. Hartmann, M. Bernt, M. Middendorf
Cophylogenetic Reconciliation with ILP
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(6): 1227-1235, 2015.
Link
T. Thalheim, B. Wagner, R. Kühne, M. Middendorf, G. Schüürmann
A Branch-and-Bound Approach for Tautomer Enumeration
Molecular Informatics, 34(5): 262-275, 2015.
M. Hellmuth, N. Wieseke, M. Lechner, H.-P. Lenhof, M. Middendorf, P. F. Stadler
Phylogenomics with Paralogs
Proceedings of the National Academy of Sciences (PNAS), 112(7): 2058–2063, 2015.
R. L.V. Moritz, M. Middendorf
Decentralized and Dynamic Group Formation of Reconfigurable Agents
Memetic Computing, 7:77-91, 2015.
D. Merkle, M. Middendorf, A. Scheidler
Task Allocation in Organic Computing Systems: Networks with Reconfigurable Helper Units
International Journal of Autonomous and Adaptive Communications Systems, 8(1):60-80, 2015.
R. L.V. Moritz, E. Reich, M. Schwarz, M. Bernt, and M. Middendorf
Refined Ranking Relations for Selection of Solutions in Multi Objective Metaheuristics
European Journal of Operational Research, 243: 454-464, 2015.
A. H. Sahyoun, M. Bernt, P. F. Stadler, K. Tout
GC Skew and Mitochondrial Origins of Replication
Mitochondrion, 17:56-66, 2014.
R. L.V. Moritz, M. Bernt, and M. Middendorf
Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes
Biology, special issue: Developments in Bioinformatic Algorithms, 3(1), 220-242, 2014.
Link
M. Marz, N. Beerenwinkel, C. Drosten, M. Fricke, D. Frishman, I. L. Hofacker, D. Hoffmann, M. Middendorf, T. Rattei, P. F. Stadler, A. Töpfer
Challenges in RNA Virus Bioinformatics
Bioinformatics, 30 (13): 1793-1799, 2014.
N. J. R. Plowes, K. Ramsch, M. Middendorf, B. Hölldobler
An empirically based simulation of group foraging in the harvesting ant, Messor pergandei
Journal of Theoretical Biology, 340: 186–198, 2014.
H. J. Osigus, M. Eitel, M. Bernt, A. Donath, B. Schierwater
Mitogenomics at the base of Metazoa
Molecular Phylogenetics and Evolution, 69(2):339-351, 2013.
link
M. Bernt, C. Bleidorn, A. Braband, J. Dambach, A. Donath, G. Fritzsch, A. Golombek, H. Hadrys, F. Jühling; K. Meusemann, M. Middendorf, B. Misof, M. Perseke, L. Podsiadlowski, B. von Reumont, B. Schierwater, M. Schlegel, M. Schrödl, S. Simon, P. F. Stadler, I. Stöger, T. H. Struck
A comprehensive analysis of bilaterian mitochondrial genomes and animal phylogeny
Molecular Phylogenetics and Evolution, 69(2):352-364, 2013.
link
S. Volke, M. Middendorf, M. Hlawitschka, J. Kasten, D. Zeckzer, G. Scheuermann
dPSO-Vis: Topological Visualization of Discrete Particle Swarm Optimization
Computer Graphics Forum, 32(3):351-360, 2013.
A. Scheidler, D. Merkle, M. Middendorf
Swarm Controlled Emergence for Ant Clustering
International Journal of Intelligent Computing and Cybernetics, 6(1):62-82, 2013.
M. Bernt, A. Braband, B. Schierwater, P. F. Stadler
Genetic aspects of mitochondrial genome evolution
Molecular Phylogenetics and Evolution, 69(2):328-338, 2013.
link
M. Bernt, A. Braband, M. Middendorf, B. Misof, O. Rota-Stabelli, P. F. Stadler
Bioinformatics Methods for the Comparative Analysis of Metazoan Mitochondrial Genome Sequences
Molecular Phylogenetics and Evolution 69(2):320-327, 2013.
link
M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Pütz, M. Middendorf, P. F. Stadler
MITOS: Improved de novo Metazoan Mitochondrial Genome Annotation
Molecular Phylogenetics and Evolution, 69(2):313-319, 2013.
link
F. Jühling, J. Pütz, M. Bernt, A. Donath, M. Middendorf, C. Florentz, P. F. Stadler
Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements.
Nucleic Acids Research, 40(7): 2833-2845, 2012.
A. Johansson, K. Ramsch, M. Middendorf, D.J. Sumpter
Tuning positive feedback for signal detection in noisy dynamic environments.
Journal of Theoretical Biology, 309: 88-95, 2012.
K. Ramsch, C. R. Reid, M. Beekman, M. Middendorf
A mathematical model of foraging in a dynamic environment by trail-laying Argentine ants
Journal of Theoretical Biology, 306:32-45, 2012.
A. Duò, R. Bruggmann, S. Zoller, M. Bernt, C. R. Gruenig
Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex
BMC Genomics, 13:166, 2012.
M. Dilcher, L. Hasib, M. Lechner, N. Wieseke, M. Middendorf, M. Marz, A. Koch, M. Spiegel, G. Dobler, F. T. Hufert, M. Weidmann
Genetic Characterisation of Tribec virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses
Virology, 423(1): 68-76, 2012.
M. Bernt, M. Middendorf
A Method for Computing an Inventory of Metazoan Mitochondrial Gene Order Rearrangements.
BMC Bioinformatics, 12(Suppl 9):S6, 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.
link
M. Geis, M. Middendorf
Particle Swarm Optimization for Finding RNA Secondary Structures
International Journal of Intelligent Computing and Cybernetics, 4(2): 160-186, 2011.
S. Lange, M. Middendorf
Multi-level Reconfigurable Architectures in the Switch Model
Journal of Systems Architecture, 56(2-3): 103-115, 2010.
D. Merkle, M. Middendorf, N. Wieseke
A Parameter-Adaptive Dynamic Programming Approach for Inferring Cophylogenies
BMC Bioinformatics 2010, 11(Suppl 1): S60, 2010.
Paper
M. Hellmuth, D. Merkle, M. Middendorf
Extended shapes for the combinatorial design of RNA sequences
International Journal of Computational Biology and Drug Design, 2(4): 371 - 384, 2009.
K. Diwold, D. Merkle, M. Middendorf
Adapting to Dynamic Environments: Polyethism in Response Threshold Models for Social Insects
Advances in Complex Systems, 12(3): 327-346, 2009.
M. Bernt, D. Merkle, M. Middendorf
Solving the Preserving Reversal Median Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(3): 332-347, 2008.
link
D. Merkle, M. Middendorf
Swarm Intelligence and Signal Processing
IEEE Signal Processing Magazine, 25(6): 152-158, 2008.
T. Thalheim, D. Merkle, M. Middendorf
Protein Folding in the HP-Model Solved With a Hybrid Population Based ACO Algorithm
IAENG International Journal of Computer Science, 35(3): 291-300, 2008.
A. Scheidler, D. Merkle, M. Middendorf
Stability and Performance of Ant Queue Inspired Task Partitioning Methods
Theory in Biosciences, 127(2): 149-161, 2008.
M. Geis, C. Flamm, M. T. Wolfinger, I. L. Hofacker, M. Middendorf, C. Mandl, P. F. Stadler, C. Thurner
Folding Kinetics of Large RNAs
Journal of Molecular Biology, 379(1): 160-173, 2008.
D. Merkle, M. Middendorf, A. Scheidler
Self-Organized Task Allocation for Service Tasks in Computing Systems with Reconfigurable Components
Journal of Mathematical Modelling and Algorithms, 7(2): 237-254, 2008.
M. Geis, M. Middendorf
Creating Melodies and Baroque Harmonies with Ant Colony Optimization
International Journal of Intelligent Computing and Cybernetics, 1(2): 213-238, 2008.
S. Janson, D. Merkle, M. Middendorf
A Decentralization Approach for Swarm Intelligence Algorithms in Networks Applied to Multi Swarm PSO
International Journal of Intelligent Computing and Cybernetics, 1(1): 25-45, 2008.
This paper has won the Highly Commended Award of IJICC.
M. Perseke, G. Fritzsch, K. Ramsch, M. Bernt, D. Merkle, M. Middendorf, D. Bernhard, P. F. Stadler, M. Schlegel
Evolution of Mitochondrial Gene Orders in Echinoderms
Molecular Phylogenetics and Evolution, 47: 855–864, 2008.
link
S. Lange, M. Middendorf
Design Aspects of Multi-level Reconfigurable Architectures
Journal of Signal Processing Systems for Signal, Image, and Video Technology, 51(1): 23-37, 2008.
S. Janson, D. Merkle, M. Middendorf
Molecular Docking with Multi-Objective Particle Swarm Optimization
Applied Soft Computing, 8(1): 666-675, 2008.
M. Bernt, D. Merkle, K. Ramsch, G. Fritzsch, M. Perseke, D. Bernhard, M. Schlegel, P. Stadler, M. Middendorf
CREx: Inferring Genomic Rearrangements Based on Common Intervals
Bioinformatics, 23(21): 2957-2958, 2007.
link
B. Scheuermann, S. Janson, M. Middendorf
Hardware-oriented Ant Colony Optimization
Journal of Systems Architecture, 53(7): 386-402, 2007.
M. Bernt, D. Merkle, M. Middendorf
Using Median Sets for Inferring Phylogenetic Trees
Bioinformatics, 23: e129-e135, 2007.
This paper won the 3rd prize in the Best Paper Competition of the 5th European Conference on Computational Biology (ECCB), Eilat, Israel, Jan. 21-24, 2007.
link
S. Janson, M. Middendorf, M. Beekman
Searching for a new home - scouting behaviour of honeybee swarms
Behavioral Ecology, 18(2): 384-392, 2007.
S. Janson, M. Middendorf
A Hierarchical Particle Swarm Optimizer for Noisy and Dynamic Environments
Genetic Programming and Evolvable Machines, 7(4): 329-354, 2006.
M. Bernt, D. Merkle, M. Middendorf
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3): 275-288, 2006.
link
D. Merkle, M. Middendorf, A. Scheidler
Modelling Ant Brood Tending Patterns with Cellular Automata
Journal of Cellular Automata 2(2): 183-194, 2006.
Preliminary version in: Proc. of the Workshop on Modelling of Complex Systems by Cellular Automata 2005 (ICCS 2005), LNCS 3515, pp. 412-419, 2005.
E. Alba, M. Middendorf
The ‘Decent’ Project: Decentralized Metaheuristics
ERCIM News No. 64, 51-51, 2006.
S. Lange, M. Middendorf
Multi Task Hyperreconfigurable Architectures: Models and Reconfiguration Problems
International Journal of Embedded Systems, 1(3/4): 154-164, 2005.
D. Merkle, M. Middendorf
Reconstruction of the Cophylogenetic History of Related Phylogenetic Trees with Divergence Timing Information
Theory in Biosciences 4: 277-299, 2005
Paper
D. Merkle, M. Middendorf
On solving permutation scheduling problems with ant colony optimization
International Journal of Systems Science, 36(5): 255-266, 2005
Paper
S. Lange, M. Middendorf
Hyperreconfigurable Architectures and the Partition into Hypercontexts Problem
Journal of Parallel and Distributed Computing, 65(6): 743-754, 2005.
Paper
S. Janson, M. Middendorf
A Hierarchical Particle Swarm Optimizer and its Adaptive Variant
IEEE Systems, Man and Cybernetics - Part B, 32(6): 1272- 1282, 2005.
Preliminary version in Proceedings of the Congress on Evolutionary Computation (CEC 2003), IEEE Press, 770--776, (2003).
Paper
D. Merkle, M. Middendorf, A. Scheidler
Decentralized Packet Clustering in Router-based Networks
International Journal of Foundations of Computer Science, 16(2): 321-341, 2005.
Preliminary version in: Proc. International Parallel and Distributed Processing Symposium (IPDPS-2004), Sixth International Workshop on Nature Inspired Distributed Computing (NIDISC'04), IEEE-CS Press, Santa Fe, 9 pp., 2004.
Preliminary version
S. Janson, M. Middendorf, M. Beekman
Honey bee swarms: How do scouts guide a swarm of uninformed bees?
Animal Behavior, 70: 349-358, 2005.
J. Branke, M. Middendorf, G. Noeth, M. Dessouky
Waiting Strategies for Dynamic Vehicle Routing
Transportation Science, 39(3): 298–312, 2005.
Paper
D. Merkle, M. Middendorf
Dynamic Polyethism and Competition for Tasks in Threshold Reinforcement Models of Social Insects
Adaptive Behavior, 12: 251-262, 2004.
Preliminary version
M. Middendorf, D. Manlove
Combined Super-Substring and Super-/Subsequence problems
Theoretical Computer Science, 320(2-3): 247-267, 2004.
Paper
B. Scheuermann, K. So, M. Guntsch, M. Middendorf, O. Diessel, H. ElGindy, H. Schmeck
FPGA Implementation of Population-based Ant Colony Optimization
Applied Soft Computing, 4(3): 303-322, 2004 (special issue on Hardware Implementations of Softcomputing Techniques)
S. Janson, D. Merkle, M. Middendorf, H. ElGindy, H. Schmeck
On Enforced Convergence of ACO and its Implementation on the Reconfigurable Mesh Architecture Using Size Reduction Tasks
Journal of Supercomputing, 26(3): 221-238, 2003.
Preliminary version in:Proceedings of the Second International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'02), Las Vegas, CSREA Press, 2002, 3-9.
D. Merkle and M. Middendorf
An Ant Algorithm with Global Pheromone Evaluation for Scheduling a Single Machine
Applied Intelligence, 18(1): 105-111, 2003.
M. Middendorf, B. Scheuermann, H. Schmeck, H. ElGindy
An Evolutionary Approach to Dynamic Task Scheduling on FPGAs
Journal of Parallel and Distributed Computing, 62(9): 1407-1420, September 2002.
D. Merkle and M. Middendorf
Modelling the Dynamics of Ant Colony Optimization Algorithms
Evolutionary Computation 10(3): 235-262, 2002.
Paper
D. Merkle and M. Middendorf
Fast Ant Colony Optimization on Runtime Reconfigurable Processor Arrays
Genetic Programming and Evolvable Machines, 3(4): 345-361, 2002.
Paper
D. Merkle, M. Middendorf, and H. Schmeck
Ant Colony Optimization for Resource-Constrained Project Scheduling
IEEE Transactions on Evolutionary Computation, 6(4): 333-346, 2002.
Preliminary version
M. Middendorf and V. Timkovsky
On scheduling cycle shops: classification, complexity and approximation
Journal of Scheduling, 5(2): 135-169, 2002.
Preliminary version
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
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.
Preliminary version
D. Merkle, Th. Worsch
Formal Language Recognition by Stochastic Cellular Automata
Fundamenta Informaticae 52(1-3): 183-201, 2002.
Konferenzen
L. Fiedler, M. Middendorf, M. Bernt
Fully automated annotation of mitochondrial genomes using a cluster-based approach with de-Brujin graphs
Proceedings Asia Pacific Bioinformatics Conference (APBC 2023)
E. Kupfer, H.T. Le, J. Zitt, Y.-C. Lin, M. Middendorf
A Hierarchical Simple Probabilistic Population-Based Algorithm Applied to the Dynamic TSP
IEEE Symposium Series on Computational Intelligence (SSCI 2021), 1-8, 2021.
H.T. Le, M. Middendorf, Y. Shi
An Improvement Heuristic Based on Variable Neighborhood Search for a Dynamic Orienteering Problem
in: Proceedings 21st European Conference on Evolutionary Computation in Combinatorial Optimization (EvoCOP 2021), Springer LNCS 12692, 68-83, 2021.
D. Abitz, T. Hartmann, M. MIddendorf
A Weighted Population Update Rule for PACO Applied to the Single Machine Total Weighted Tardiness Problem
GECCO '20: Proceedings of the 2020 Genetic and Evolutionary Computation Conference, 4–12, 2020.
H.T. Le, P. Geser, M. Middendorf
An Iterated Local Search Algorithm for the Two-Machine Flow Shop Problem with Bu ers and Constant Processing Times on One Machine
in: Proceedings of the 19th European Conference EvoCOP 2019, Springer LNCS 11452, 50-65, 2019.
T. Hartmann, M. Bannach, M. Middendorf
Sorting by Inverse Tandem Duplication Random Losses
accepted for the Seventhenth Asia Pacific Bioinformatics Conference (APBC2019)
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
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
Thirteenth Asia-Pacific Bioinformatics Conference (APBC 2015), Hsinchu, Taiwan, 2015.
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
link
N. Wieseke, M. Bernt, M. Middendorf
Unifying Parsimonious Tree Reconciliation
Proc. 13th Workshop on Algorithms in Bioinformatics (WABI 2013), LNBI 8126, 200-214, 2013
link
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, and M. Middendorf
Refined Ranking Relations for Multi Objective Optimization and Application to P-ACO
Proceedings of the Fifteenth Annual Conference on Genetic and Evolutionary Computation (GECCO '13), 65-72, 2013
link
Y.-C. 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
Link
M. Bernt, K.-M. Chao, J.-W. Kao, M. Middendorf, E. Tannier
Preserving Inversion Phylogeny Reconstruction
Algorithms in Bioinformatics 2012, Lecture Notes in Computer Science, Vol. 7534, Springer, pp. 1-13
appendix
link
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
accpeted for 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.
link
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
Accepted for 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, 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.
link
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), IEEE, 2006
M. Bernt, D. Merkle, M. Middendorf
The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders
Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006, Lecture Notes in Bioinformatics, M.R. Berthold, R. Glen, I. Fischer (eds.), Vol. 4216, Springer, pp. 52-63, 2006
link
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, Las Vegas, USA.
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 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.
link
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
Proc. 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.
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, 2004, 251-260.
Paper
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.
Paper
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.
Paper
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
Proc. International Parallel and Distributed Processing Symposium (IPDPS-2004), Reconfigurable Architectures Workshop (RAW-2004), IEEE-CS Press, 8 pp., 2004.
Paper
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.
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, 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.
Paper
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.
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.
Paper
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.
Paper
Buchbeiträge
S. Volke, M. Middendorf, G. Scheuermann
Coarse-Graining Large Search Landscapes using Massive Edge Collapse
In: Carr H., Fujishiro I., Sadlo F., Takahashi S. (eds) Topological Methods in Data Analysis and Visualization V, Springer, 55-69, 2020
T. Hartmann, M. Middendorf, M. Bernt
Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches
In: Setubal J., Stoye J., Stadler P. (eds) Comparative Genomics. Methods in Molecular Biology, Humana Press, New York, NY vol 1704:261-289 2018.
S. Volke, D. Zeckzer, M. Middendorf, and G. Scheuermann
Visualizing Topological Properties of the Search Landscape of Combinatorial Optimization Problems
In: Topological Methods in Data Analysis and Visualization IV: Theory, Algorithms, and Applications, H. Carr, C. Garth, T. Weinkauf (Eds.), Springer, Mathematics and Visualization, p.69-85, 2017
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
Link
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
Link
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
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
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, ISBN: 0-471-67806-6, 171-201, 2005.
D. Merkle, M. Middendorf
Ant Colony Optimization: Biological Motivation, Phase Structure, and Modelling
Proc. 4th International Symposium on Mathematical and Computational Biology (BIOMAT 2004), Vol. 2, 67-88, 2005.
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.
Special Issues (Hrsg.)
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
Bücher (Hrsg.)
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.
C. Blum, D. Merkle (Eds.)
Swarm Intelligence
Springer Verlag, 2008.
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
Tutorien
M. Middendorf
Tutorial on Ant Colony Optimization.
Genetic and Evolutionary Computation Conference (GECCO-2003), Chicago, Tutorial Proceedings, 556-580, 2003.
M. Middendorf
Tutorial on Ant Colony Optimization.
Genetic and Evolutionary Computation Conference (GECCO-2002), New York, Tutorial Proceedings, 416-436, 2002.
Andere
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.
D. Merkle, M. Middendorf, N. Wieseke
A Parameter-Adaptive Dynamic Programming Approach for Inferring Cophylogenies.
Working Paper PACOSY 09-01, August 10, 2009, submitted
Paper
M. Bernt
Inferring Genome Rearrangements in a Phylogenetic Tree
Abstracts of 2010 Information and Management of Application and Innovation Forum, Hwa Hsia Institute of Technology, Taipei, Taiwan
M. Bernt
Inferring Genome Rearrangements in a Phylogenetic Tree
Abstracts of 2010 Information and Management of Application and Innovation Forum, Hwa Hsia Institute of Technology, Taipei, Taiwan
A. Donath, F. Externbrink, F. Jühling, M. Bernd, G. Fritzsch, M. Middendorf and P. F. Stadler
Improved Automatic Annotation of Metazoan Mitochondrial Genomes.
Poster at German Conference on Bioinformatics 2009 (GCB'09).
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
Heuristics for the Reversal Median Problem: How to select good reversals?
Proc. of the 20th Dubrovnik International Course and Conference on the Interfaces Among Mathematics, Chemistry and Computer Sciences, Inter-University Centre Dubrovnik, 3, 2005
link
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.
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.
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
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.
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.