Algorithms in Bioinformatics

Comparative Genomics.- A Local Chaining Algorithm and Its Applications in Comparative Genomics.- Common Intervals of Two Sequences.- A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring.- Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specificity.- Gene Finding and Expression.- A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methods.- A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence.- Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency.- Genome Mapping.- New Algorithm for the Simplified Partial Digest Problem.- Noisy Data Make the Partial Digest Problem NP-hard.- Pattern and Motif Discovery.- Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions.- A Combinatorial Approach to Automatic Discovery of Cluster-Patterns.- Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology.- Phylogenetic Analysis.- Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees.- Efficient Generation of Uniform Samples from Phylogenetic Trees.- New Efficient Algorithm for Detection of Horizontal Gene Transfer Events.- Ancestral Maximum Likelihood of Evolutionary Trees Is Hard.- A Linear-Time Majority Tree Algorithm.- Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model.- Better Hill-Climbing Searches for Parsimony.- Computing Refined Buneman Trees in Cubic Time.- Distance Corrections on Recombinant Sequences.- Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks.- Polymorphism.- Identifying Blocks and Sub-populations in Noisy SNP Data.- Designing Optimally Multiplexed SNP Genotyping Assays.- Minimum Recombinant Haplotype Configuration on Tree Pedigrees.- Protein Structure.- Efficient Energy Computation for Monte Carlo Simulation of Proteins.- Speedup LP Approach to Protein Threading via Graph Reduction.- Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment.- Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Power.- Sequence Alignment.- A Large Version of the Small Parsimony Problem.- Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree.- Composition Alignment.- String Algorithms.- Match Chaining Algorithms for cDNA Mapping.- Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt.- Bounds for Resequencing by Hybridization.- Selecting Degenerate Multiplex PCR Primers.