This book constitutes the refereed proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2007, held in Oakland, CA, USA in April 2007.

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.