Research in Computational Molecular Biology: 16th Annual International Conference, RECOMB 2012, Barcelona, Spain, April 21-24, 2012. Proceedings (Lecture Notes in Computer Science, 7262)

This book constitutes the refereed proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, held in Barcelona, Spain, in April 2012. The 31 revised full papers presented together with 5 keynote lectures were carefully reviewed and selected from 200 submissions. The papers feature current research in all areas of computational molecular biology, including: molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; protein structure; structural genomics; analysis of gene expression; biological networks; sequencing and genotyping technologies; drug design; probabilistic and combinatorial algorithms; systems biology; computational proteomics; structural and functional genomics; information systems for computational biology and imaging. Front Matter....Pages - Protein Structure by Semidefinite Facial Reduction....Pages 1-11 Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models....Pages 12-28 Charge Group Partitioning in Biomolecular Simulation....Pages 29-43 Increased Methylation Variation in Epigenetic Domains across Cancer Types....Pages 44-44 Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising....Pages 45-59 Quantifying the Dynamics of Coupled Networks of Switches and Oscillators....Pages 60-61 lobSTR: A Short Tandem Repeat Profiler for Personal Genomes....Pages 62-63 Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data....Pages 64-78 Ballast : A Ball-Based Algorithm for Structural Motifs....Pages 79-93 Evolution of Genome Organization by Duplication and Loss: An Alignment Approach....Pages 94-112 LoopWeaver – Loop Modeling by the Weighted Scaling of Verified Proteins....Pages 113-126 A Robust Method for Transcript Quantification with RNA-seq Data....Pages 127-147 Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics....Pages 148-162 TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq....Pages 163-164 Synthetic Sequence Design for Signal Location Search....Pages 165-179 The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation....Pages 180-180 Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing....Pages 181-182 Network-Based Prediction and Analysis of HIV Dependency Factors....Pages 183-183 Structure-Guided Deimmunization of Therapeutic Proteins....Pages 184-198 Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures....Pages 199-199 Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly....Pages 200-212 Finding Maximum Colorful Subtrees in Practice....Pages 213-223 Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis....Pages 224-238 RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract)....Pages 239-240 Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies....Pages 241-243 A Model for Biased Fractionation after Whole Genome Duplication....Pages 244-244 Exact Pattern Matching for RNA Structure Ensembles....Pages 245-260 Reconstructing Boolean Models of Signaling....Pages 261-271 Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract....Pages 272-285 Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer....Pages 286-286 Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem....Pages 287-301 Function-Function Correlated Multi-Label Protein Function Prediction over Interaction Networks....Pages 302-313 Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization....Pages 314-325 CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping....Pages 326-340 Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs....Pages 341-341 Probabilistic Inference of Viral Quasispecies Subject to Recombination....Pages 342-354 Simultaneously Learning DNA Motif along with Its Position and Sequence Rank Preferences through EM Algorithm....Pages 355-370 Back Matter....Pages - This book constitutes the refereed proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011, held in Vancouver, Canada, in March 2011. The papers cover a wide range of topics including molecular sequence analysis; molecular evolution; molecular structural biology.