Algorithms in Bioinformatics

Measures of Codon Bias in Yeast, the tRNA Pairing Index and Possible DNA Repair Mechanisms.- Decomposing Metabolomic Isotope Patterns.- A Method to Design Standard HMMs with Desired Length Distribution for Biological Sequence Analysis.- Efficient Model-Based Clustering for LC-MS Data.- A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks.- Linear-Time Haplotype Inference on Pedigrees Without Recombinations.- Phylogenetic Network Inferences Through Efficient Haplotyping.- Beaches of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems.- On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model.- How Many Transcripts Does It Take to Reconstruct the Splice Graph?.- Multiple Structure Alignment and Consensus Identification for Proteins.- Procrastination Leads to Efficient Filtration for Local Multiple Alignment.- Controlling Size When Aligning Multiple Genomic Sequences with Duplications.- Reducing Distortion in Phylogenetic Networks.- Imputing Supertrees and Supernetworks from Quartets.- A Unifying View of Genome Rearrangements.- Efficient Sampling of Transpositions and Inverted Transpositions for Bayesian MCMC.- Alignment with Non-overlapping Inversions in O(n 3)-Time.- Accelerating Motif Discovery: Motif Matching on Parallel Hardware.- Segmenting Motifs in Protein-Protein Interface Surfaces.- Protein Side-Chain Placement Through MAP Estimation and Problem-Size Reduction.- On the Complexity of the Crossing Contact Map Pattern Matching Problem.- A Fuzzy Dynamic Programming Approach to Predict RNA Secondary Structure.- Landscape Analysis for Protein-Folding Simulation in the H-P Model.- Rapid ab initio RNA Folding Including Pseudoknots Via Graph Tree Decomposition.- Flux-Based vs. Topology-Based Similarity of Metabolic Genes.- Combinatorial Methods for Disease Association Search and Susceptibility Prediction.- Integer Linear Programs for Discovering Approximate Gene Clusters.- Approximation Algorithms for Bi-clustering Problems.- Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning.- Accelerating the Computation of Elementary Modes Using Pattern Trees.- A Linear-Time Algorithm for Studying Genetic Variation.- New Constructive Heuristics for DNA Sequencing by Hybridization.- Optimal Probing Patterns for Sequencing by Hybridization.- Gapped Permutation Patterns for Comparative Genomics.- Segmentation with an Isochore Distribution.