This book constitutes the refereed proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2014, held in Pittsburgh, PA, USA, in April 2014. The 35 extended abstracts were carefully reviewed and selected from 154 submissions. They report on original research in all areas of computational molecular biology and bioinformatics.

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Tractatus: An Exact and Subquadratic Algorithm for Inferring Identical-by-Descent Multi-shared Haplotype Tracts.- Hap Tree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data.- Change point Analysis for Efficient Variant Calling.- On the Representation of de Bruijn Graphs.- Exact Learning of RNA Energy Parameters from Structure.- An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data.- The Generating Function Approach for Peptide Identification in Spectral Networks.- Decoding Coalescent Hidden Markov Models in Linear Time.- AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application.- Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models.- On Sufficient Statistics of Least-Squares Superposition of Vector Sets.- IDBA-MTP: A Hybrid Meta Transcriptomic Assembler Based on Protein Information.- MRFalign: Protein Homology Detection through Alignment of Markov Random Fields.- An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.- PASTA: Ultra-Large Multiple Sequence Alignment.- Fast Flux Module Detection Using Matroid Theory.- Building a Pangenome Reference for a Population.-CSAX: Characterizing Systematic Anomalies in eXpression Data.-Whats Hap: Haplotype Assembly for Future-Generation Sequencing Reads.- Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data.- dip SPA des: Assembler for Highly Polymorphic Diploid Genomes.- An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes.- HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time.- Modeling Mutual Exclusivity of Cancer Mutations.-Viral Quasispecies Assembly via Maximal Clique Enumeration.-Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency.- Bayesian Multiple Protein Structure Alignment.- Gene-Gene Interactions Detection Using a Two-Stage Model.- A Geometric Clustering Algorithm and Its Applications to Structural Data.- A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation.- Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification.-Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers.- Reconciliation with Non-binary Gene Trees Revisited.- Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models.-Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion.