QNet: A Tool for Querying Protein Interaction Networks -- Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology -- Reconstructing the Topology of Protein Complexes -- Network Legos: Building Blocks of Cellular Wiring Diagrams -- An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments -- A Feature-Based Approach to Modeling Protein-DNA Interactions -- Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking -- Nucleosome Occupancy Information Improves de novo Motif Discovery -- Framework for Identifying Common Aberrations in DNA Copy Number Data -- Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models -- GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data -- Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions -- Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide Binding -- Reconstructing the Phylogeny of Mobile Elements -- Beyond Galled Trees - Decomposition and Computation of Galled Networks -- Variational Upper Bounds for Probabilistic Phylogenetic Models -- Heuristics for the Gene-Duplication Problem: A ?(n) Speed-Up for the Local Search -- Support Vector Training of Protein Alignment Models -- Tools for Simulating and Analyzing RNA Folding Kinetics -- Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences -- Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data -- Multivariate Segmentation in the Analysis of Transcription Tiling Array Data -- A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements -- Rearrangements in Genomes with Centromeres Part I: Translocations -- Identification of Deletion Polymorphisms from Haplotypes -- Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation -- Minimizing and Learning Energy Functions for Side-Chain Prediction -- Protein Conformational Flexibility Analysis with Noisy Data -- Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules -- Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments -- Improved Ranking Functions for Protein and Modification-Site Identifications -- Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions -- A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data -- Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms -- An Efficient and Accurate Graph-Based Approach to Detect Population Substructure -- RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints -- Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs.