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Table of Contents

Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spaces.- Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Design.- Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem.- Methods for Inferring Block-Wise Ancestral History from Haploid Sequences.- Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks.- Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry.- Improved Approximation Algorithms for NMR Spectral Peak Assignment.- Efficient Methods for Inferring Tandem Duplication History.- Genome Rearrangement Phylogeny Using Weighbor.- Segment Match Refinement and Applications.- Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation.- Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics.- FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structures.- Efficient Unbound Docking of Rigid Molecules.- A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants.- A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding.- Comparative Methods for Gene Structure Prediction in Homologous Sequences.- MultiProt — A Multiple Protein Structural Alignment Algorithm.- A Hybrid Scoring Function for Protein Multiple Alignment.- Functional Consequences in Metabolic Pathways from Phylogenetic Profiles.- Finding Founder Sequences from a Set of Recombinants.- Estimating the Deviation from a Molecular Clock.- Exploring the Set of All Minimal Sequences of Reversals — An Application to Test theReplication-Directed Reversal Hypothesis.- Approximating the Expected Number of Inversions Given the Number of Breakpoints.- Invited Lecture — Accelerating Smith-Waterman Searches.- Sequence-Length Requirements for Phylogenetic Methods.- Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle.- NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks.- On the Control of Hybridization Noise in DNA Sequencing-by-Hybridization.- Restricting SBH Ambiguity via Restriction Enzymes.- Invited Lecture — Molecule as Computation: Towards an Abstraction of Biomolecular Systems.- Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search.- Rapid Large-Scale Oligonucleotide Selection for Microarrays.- Border Length Minimization in DNA Array Design*.- The Enhanced Suffix Array and Its Applications to Genome Analysis.- The Algorithmic of Gene Teams.- Combinatorial Use of Short Probes for Differential Gene Expression Profiling.- Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome.- K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data.- Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data.- Modified Mincut Supertrees.