Banu Dost, Tomer Shlomi, Nitin Gupta (auth.), Terry Speed, Haiyan Huang (eds.)3540716807, 9783540716808
The 37 revised full papers presented were carefully reviewed and selected from just under 170 submissions. As the top conference in computational molecular biology, RECOMB addresses all current issues in algorithmic, theoretical, and experimental bioinformatics.
Table of contents :
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 –
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