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Bioinformatics |
Publications on Bioinformatics |
Journal articles |
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
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.
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, doi:10.1016/j.jmb.2008.02.064
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.
M. Bernt, D. Merkle, K. Ramsch, G. Fritzsch, M.
Perserke, D. Bernhard, M. Schlegel, P. Stadler, M.
Middendorf:
CREx: Inferring Genomic Rearrangements Based on Common Intervals
Bioinformatics, 23(21):2957-2958, 2007.
M. Bernt, D. Merkle, M. Middendorf:
Using Median Sets for Inferring Phylogenetic Trees
Bioinformatics 2007 23: e129-e135.
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:
Reconstruction of the Cophylogenetic History
of Related Phylogenetic Trees with Divergence Timing Information
Theory of Biosciences 4: 277-299, 2005
D. Merkle, M. Middendorf, A. Scheidler:
Modelling Ant Brood Tending Behaviour with Cellular Automata
accepted for International Journal of Unconventional Computing
Preliminary version in:
Proc. of the Workshop on Modelling of Complex Systems by Cellular Automata 2005 (ICCS 2005),
LNCS 3515, pp. 412-419, 2005.
S. Janson, M. Middendorf, M. Beekman:
Honey bee swarms: How do scouts guide a swarm of uninformed bees?
Animal Behavior, 70: 349-358, 2005.
D. Merkle, M. Middendorf:
Dynamic Polyethism and Competition for Tasks in Threshold Reinforcement Models of Social Insects.
Adaptive Behavior, 12: 251-262, 2004.
M. Middendorf, D. Manlove:
Combined Super-/Substring and Super/Subsequence problems.
Theoretical Computer Science, 320(2-3): 247-267, 2004.
Branke, M. Middendorf, and F. Schneider:
Improved heuristics and a genetic algorithm for finding short supersequences
OR-Spektrum 20 (1998) 39-46.
Preliminary versions: J. Branke, M. Middendorf: Searching for Shortest Common Supersequences by Means of a Heuristic
Based Genetic Algorithm, Proceedings of the Second Nordic Workshop on Genetic Algorithms and their Applications,
Finnish Artificial Intelligence Society, 1996, pp. 105-114.
M. Middendorf:
Shortest common superstrings and scheduling with coordinated starting times
Theoret. Comp. Sci. 191 (1998) 205-214.
E. Atkins and M. Middendorf:
On physical mapping and the consecutive ones property for sparse matrices
Discrete Applied Mathematics 71 (1996) 5-22 (Special Issue on Computational Molecular Biology).
C. Fraser, R. Irving, and M. Middendorf:
Maximal common subsequences and minimal common supersequences
Information and Computation 124 (1996) 145-153.
M. Middendorf:
On finding various minimal, maximal, and consistent sequences over a binary alphabet
Theoretical Computer Science 145 (1995) 317-327.
Preliminary version in: Proc. 5th International Symposium on Algorithms and Computation (ISAAC), LNCS 843, 306--314,
1994.
M. Middendorf:
More on the complexity of common superstring and supersequence problems
Theoretical Computer Science 125 (1994) 205-228.
M. Middendorf:
The shortest common nonsupersequence problem is NP-complete
Theoretical Computer Science 108 (1993) 365-369.
Book chapters |
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, to appear
Conference proceedings |
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.
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. 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), Barcelona,
Spain, August 29-31, 2005
D. Merkle, M. Middendorf, A. Scheidler:
Modelling Ant Brood Tending Behaviour with Cellular Automata
Accepted for the Workshop on Modelling of Complex Systems by Cellular Automata 2005, Atlanta, USA, 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.
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:
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. Middendorf and V. Timkovsky:
Consistent supersequences and transversal graphs: An extended abstract.
Workshop on Computational Biology, Udine, Italiy, 1998.
Diploma Thesises on Bioinformatics |
Markus Bautze:
planed
Hagen Jung:
Heuristiken zur Rekonstruktion der Geschichte von Genduplikationen
supervised together with P. Stadler
24.5.2005
Matthias Bernt:
Strukturerhaltende Rekonstruktion von Phylogenien auf der Basis
von Genomanordnungsdaten (Reconstruction of Phylogenies based on Genome Order Data)
13.8.2004
Gunnar Schau:
Modellierung und Simulation von Arbeitsteilungsprozessen in Multi-Agenten-Systemen
auf der Grundlage von Treshold-Response Modellen
13.2.2004
Ekkard Petzold:
Parallelized Parameter Estimation for Molecular Phylogenetics
Cosuperviser Prof. von Haeseler (Bioinformatik, Uni Düsseldorf)
18.6.2003
Thorsten Langspecht:
Untersuchungen zur Komplexität von koevolutionären Prozessen auf Basis assoziierter phylogenetischer Bäume.
27.2.2001 (Uni Hannover)
Roman Legat:
Datenstrukturen zur Analyse der Phylogenie von Parasit-Wirt-Beziehungen.
10.2.2001 (Uni Hannover)
Semester Thesises on Bioinformatics |
Michael Kaltenbach und Frederik Nagel:
Entwicklung eines Werkzeuges zur Lösung des HP-Proteinfaltungsproblems mit Ameisenalgorithmen.
21.6.2001 (Uni Hannover)
Program Committee |
GECCO-2004
Genetic and Evolutionary Computation Conference,
2004, Seattle, program track "Biological Applications and
Evolutionary Computation'' (BioGEC)
EvoBIO 2004
2bnd European Workshop on Evolutionary Computation
and Bioinformatics, 2004, Coimbra, Portugal
EvoBIO 2003
1st European Workshop on Evolutionary Bioinformatics, 2003, Essex, UK