Research in Computational Molecular Biology

Chapter 1 The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB)

Chapter 2 A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets

Chapter 3 Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast

Chapter 4 Multitask Matrix Completion for Learning Protein Interactions Across Diseases

Chapter 5 pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression

Chapter 6 Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data

Chapter 8 MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows

Chapter 9 LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency

Chapter 10 Improving Bloom Filter Performance on Sequence Data Using \(k\) -mer Bloom Filters

Chapter 11 Safe and Complete Contig Assembly Via Omnitigs

Chapter 12 Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants

Chapter 13 Structural Variation Detection with Read Pair Information—An Improved Null-Hypothesis Reduces Bias

Chapter 14 On Computing Breakpoint Distances for Genomes with Duplicate Genes

Chapter 15 New Genome Similarity Measures Based on Conserved Gene Adjacencies

Chapter 16 Fast Phylogenetic Biodiversity Computations Under a Non-uniform Random Distribution