Algorithms in Bioinformatics: 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings

Front Matter....Pages -
Multichromosomal Genome Median and Halving Problems....Pages 1-13
A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem....Pages 14-24
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem....Pages 25-37
Read Mapping Algorithms for Single Molecule Sequencing Data....Pages 38-49
Exact Transcriptome Reconstruction from Short Sequence Reads....Pages 50-63
Post-Hybridization Quality Measures for Oligos in Genome-Wide Microarray Experiments....Pages 64-75
NAPX: A Polynomial Time Approximation Scheme for the Noah’s Ark Problem....Pages 76-86
Minimum Common String Partition Parameterized....Pages 87-98
Hardness and Approximability of the Inverse Scope Problem....Pages 99-112
Rapid Neighbour-Joining....Pages 113-122
Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices....Pages 123-134
Efficient Genome Wide Tagging by Reduction to SAT....Pages 135-147
Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming....Pages 148-161
An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem....Pages 162-173
A Faster Algorithm for RNA Co-folding....Pages 174-185
An Automated Combination of Kernels for Predicting Protein Subcellular Localization....Pages 186-197
Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach....Pages 198-209
Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles....Pages 210-221
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks....Pages 222-232
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network....Pages 233-244
Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach....Pages 245-258
Fast Bayesian Haplotype Inference Via Context Tree Weighting....Pages 259-270
Genotype Sequence Segmentation: Handling Constraints and Noise....Pages 271-283
Constructing Phylogenetic Supernetworks from Quartets....Pages 284-295
Summarizing Multiple Gene Trees Using Cluster Networks....Pages 296-305
Fast and Adaptive Variable Order Markov Chain Construction....Pages 306-317
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata....Pages 318-329
The Relation between Indel Length and Functional Divergence: A Formal Study....Pages 330-341
Detecting Repeat Families in Incompletely Sequenced Genomes....Pages 342-353
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models....Pages 354-368
A Local Move Set for Protein Folding in Triangular Lattice Models....Pages 369-381
Protein Decoy Generation Using Branch and Bound with Efficient Bounding....Pages 382-393
Back Matter....Pages -