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.