Expression -- Spectral Clustering Gene Ontology Terms to Group Genes by Function -- Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression -- Clustering Gene Expression Series with Prior Knowledge -- A Linear Time Biclustering Algorithm for Time Series Gene Expression Data -- Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds -- Phylogeny -- A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem -- Computing the Quartet Distance Between Trees of Arbitrary Degree -- Using Semi-definite Programming to Enhance Supertree Resolvability -- An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree -- Pattern Identification in Biogeography -- On the Complexity of Several Haplotyping Problems -- A Hidden Markov Technique for Haplotype Reconstruction -- Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event -- Networks -- A Faster Algorithm for Detecting Network Motifs -- Reaction Motifs in Metabolic Networks -- Reconstructing Metabolic Networks Using Interval Analysis -- Genome Rearrangements -- A 1.375-Approximation Algorithm for Sorting by Transpositions -- A New Tight Upper Bound on the Transposition Distance -- Perfect Sorting by Reversals Is Not Always Difficult -- Minimum Recombination Histories by Branch and Bound -- Sequences -- A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds -- Generalized Planted (l,d)-Motif Problem with Negative Set -- Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI) -- The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity -- Multiple Structural RNA Alignment with Lagrangian Relaxation -- Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons -- Ortholog Clustering on a Multipartite Graph -- Linear Time Algorithm for Parsing RNA Secondary Structure -- A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance -- Structure -- Optimal Protein Threading by Cost-Splitting -- Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment -- Rotamer-Pair Energy Calculations Using a Trie Data Structure -- Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity -- The Main Structural Regularities of the Sandwich Proteins -- Discovery of Protein Substructures in EM Maps.