Research in Computational Molecular Biology: 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings

Front Matter....Pages -
Tractatus: An Exact and Subquadratic Algorithm for Inferring Identical-by-Descent Multi-shared Haplotype Tracts....Pages 1-17
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data....Pages 18-19
Changepoint Analysis for Efficient Variant Calling....Pages 20-34
On the Representation of de Bruijn Graphs....Pages 35-55
Exact Learning of RNA Energy Parameters from Structure....Pages 56-68
An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data....Pages 69-84
The Generating Function Approach for Peptide Identification in Spectral Networks....Pages 85-99
Decoding Coalescent Hidden Markov Models in Linear Time....Pages 100-114
AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application....Pages 115-128
Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models....Pages 129-143
On Sufficient Statistics of Least-Squares Superposition of Vector Sets....Pages 144-159
IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information....Pages 160-172
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields....Pages 173-174
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding....Pages 175-176
PASTA: Ultra-Large Multiple Sequence Alignment....Pages 177-191
Fast Flux Module Detection Using Matroid Theory....Pages 192-206
Building a Pangenome Reference for a Population....Pages 207-221
CSAX: Characterizing Systematic Anomalies in eXpression Data....Pages 222-236
 WhatsHap : Haplotype Assembly for Future-Generation Sequencing Reads....Pages 237-249
Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data....Pages 250-264
 dipSPAdes : Assembler for Highly Polymorphic Diploid Genomes....Pages 265-279
An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes....Pages 280-292
HIT’nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time....Pages 293-306
Modeling Mutual Exclusivity of Cancer Mutations....Pages 307-308
Viral Quasispecies Assembly via Maximal Clique Enumeration....Pages 309-310
Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency....Pages 311-325
Bayesian Multiple Protein Structure Alignment....Pages 326-339
Gene-Gene Interactions Detection Using a Two-Stage Model....Pages 340-355
A Geometric Clustering Algorithm and Its Applications to Structural Data....Pages 356-370
A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation....Pages 371-384
Traversing the k -mer Landscape of NGS Read Datasets for Quality Score Sparsification....Pages 385-399
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers....Pages 400-417
Reconciliation with Non-binary Gene Trees Revisited....Pages 418-432
Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models....Pages 433-447
Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion....Pages 448-462
Back Matter....Pages -