Research in Computational Molecular Biology: 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings

Front Matter....Pages -
Bacterial Community Reconstruction Using Compressed Sensing....Pages 1-15
Constrained De Novo Sequencing of Peptides with Application to Conotoxins....Pages 16-30
Metabolic Network Analysis Demystified....Pages 31-33
Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes....Pages 34-37
Hapsembler: An Assembler for Highly Polymorphic Genomes....Pages 38-52
Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome....Pages 53-53
Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks....Pages 54-68
Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast....Pages 69-69
Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways....Pages 70-84
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels....Pages 85-103
Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes....Pages 104-105
Variable Selection through Correlation Sifting....Pages 106-123
Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions....Pages 124-133
PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling....Pages 134-135
Pedigree Reconstruction Using Identity by Descent....Pages 136-152
A Quantitative Model of Glucose Signaling in Yeast Reveals an Incoherent Feed Forward Loop Leading to a Specific, Transient Pulse of Transcription....Pages 153-153
Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut....Pages 154-167
IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly....Pages 168-188
Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals....Pages 189-203
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs....Pages 204-221
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs....Pages 222-237
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers....Pages 238-251
An Optimization-Based Sampling Scheme for Phylogenetic Trees....Pages 252-266
Multiplex De Novo Sequencing of Peptide Antibiotics....Pages 267-281
Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk....Pages 282-282
AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization....Pages 283-297
Blocked Pattern Matching Problem and Its Applications in Proteomics....Pages 298-319
A Three-Dimensional Model of the Yeast Genome....Pages 320-320
Optimization of Combinatorial Mutagenesis....Pages 321-335
Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets....Pages 336-336
T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome....Pages 337-338
Experiment Specific Expression Patterns....Pages 339-354
Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles....Pages 355-357
A Ribosome Flow Model for Analyzing Translation Elongation....Pages 358-360
Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm....Pages 361-376
Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data....Pages 377-391
Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction....Pages 392-407
Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models....Pages 408-423
Optimally Orienting Physical Networks....Pages 424-436
Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences....Pages 437-451
Increasing Power of Groupwise Association Test with Likelihood Ratio Test....Pages 452-467
Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection....Pages 468-482
Protein Loop Closure Using Orientational Restraints from NMR Data....Pages 483-498
 De Novo Discovery of Mutated Driver Pathways in Cancer....Pages 499-500
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure....Pages 501-515
Nonparametric Combinatorial Sequence Models....Pages 516-530
Algorithms for MDC-Based Multi-locus Phylogeny Inference....Pages 531-545
Rich Parameterization Improves RNA Structure Prediction....Pages 546-562
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data....Pages 563-578
Back Matter....Pages -