Research in Computational Molecular Biology: 11th Annual International Conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007. Proceedings

Front Matter....Pages -
QNet: A Tool for Querying Protein Interaction Networks....Pages 1-15
Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology....Pages 16-31
Reconstructing the Topology of Protein Complexes....Pages 32-46
Network Legos: Building Blocks of Cellular Wiring Diagrams....Pages 47-61
An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments....Pages 62-76
A Feature-Based Approach to Modeling Protein-DNA Interactions....Pages 77-91
Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking....Pages 92-106
Nucleosome Occupancy Information Improves de novo Motif Discovery....Pages 107-121
Framework for Identifying Common Aberrations in DNA Copy Number Data....Pages 122-136
Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models....Pages 137-150
GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data....Pages 151-165
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions....Pages 166-180
Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide Binding....Pages 181-195
Reconstructing the Phylogeny of Mobile Elements....Pages 196-210
Beyond Galled Trees - Decomposition and Computation of Galled Networks....Pages 211-225
Variational Upper Bounds for Probabilistic Phylogenetic Models....Pages 226-237
Heuristics for the Gene-Duplication Problem: A Θ ( n ) Speed-Up for the Local Search....Pages 238-252
Support Vector Training of Protein Alignment Models....Pages 253-267
Tools for Simulating and Analyzing RNA Folding Kinetics....Pages 268-282
Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences....Pages 283-295
Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data....Pages 296-310
Multivariate Segmentation in the Analysis of Transcription Tiling Array Data....Pages 311-324
A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements....Pages 325-338
Rearrangements in Genomes with Centromeres Part I: Translocations....Pages 339-353
Identification of Deletion Polymorphisms from Haplotypes....Pages 354-365
Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation....Pages 366-380
Minimizing and Learning Energy Functions for Side-Chain Prediction....Pages 381-395
Protein Conformational Flexibility Analysis with Noisy Data....Pages 396-411
Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules....Pages 412-429
Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments....Pages 430-443
Improved Ranking Functions for Protein and Modification-Site Identifications....Pages 444-458
Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions....Pages 459-472
A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data....Pages 473-487
Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms....Pages 488-502
An Efficient and Accurate Graph-Based Approach to Detect Population Substructure....Pages 503-517
RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints....Pages 518-532
Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs....Pages 533-547
Back Matter....Pages -