Algorithms in Bioinformatics

Multichromosomal Genome Median and Halving Problems.- A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem.- Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem.- Read Mapping Algorithms for Single Molecule Sequencing Data.- Exact Transcriptome Reconstruction from Short Sequence Reads.- Post-Hybridization Quality Measures for Oligos in Genome-Wide Microarray Experiments.- NAPX: A Polynomial Time Approximation Scheme for the Noah's Ark Problem.- Minimum Common String Partition Parameterized.- Hardness and Approximability of the Inverse Scope Problem.- Rapid Neighbour-Joining.- Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices.- Efficient Genome Wide Tagging by Reduction to SAT.- Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming.- An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem.- A Faster Algorithm for RNA Co-folding.- An Automated Combination of Kernels for Predicting Protein Subcellular Localization.- Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach.- Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles.- An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks.- Enumerating Precursor Sets of Target Metabolites in a Metabolic Network.- Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach.- Fast Bayesian Haplotype Inference Via Context Tree Weighting.- Genotype Sequence Segmentation: Handling Constraints and Noise.- Constructing Phylogenetic Supernetworks from Quartets.- Summarizing Multiple Gene TreesUsing Cluster Networks.- Fast and Adaptive Variable Order Markov Chain Construction.- Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata.- The Relation between Indel Length and Functional Divergence: A Formal Study.- Detecting Repeat Families in Incompletely Sequenced Genomes.- Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models.- A Local Move Set for Protein Folding in Triangular Lattice Models.- Protein Decoy Generation Using Branch and Bound with Efficient Bounding.