Research in Computational Molecular Biology

Table of Contents

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   Book Overview
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   Chapter 1 Tractatus: An Exact and Subquadratic Algorithm for Inferring Identical-by-Descent Multi-shared Haplotype Tracts
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   Chapter 2 HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data
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   Chapter 3 Changepoint Analysis for Efficient Variant Calling
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   Chapter 4 On the Representation of de Bruijn Graphs
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   Chapter 5 Exact Learning of RNA Energy Parameters from Structure
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   Chapter 6 An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data
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   Chapter 7 The Generating Function Approach for Peptide Identification in Spectral Networks
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   Chapter 8 Decoding coalescent hidden Markov models in linear time.
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    Chapter 9 AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application
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    Chapter 10 Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models
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    Chapter 11 On Sufficient Statistics of Least-Squares Superposition of Vector Sets
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    Chapter 12 IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information
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    Chapter 13 MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
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    Chapter 14 An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
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    Chapter 15 PASTA: Ultra-Large Multiple Sequence Alignment
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    Chapter 16 Fast Flux Module Detection Using Matroid Theory
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    Chapter 17 Building a Pangenome Reference for a Population
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    Chapter 18 CSAX: Characterizing Systematic Anomalies in eXpression Data
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    Chapter 19 WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads
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    Chapter 20 Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data
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    Chapter 21 dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes
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    Chapter 22 An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes
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    Chapter 23 HIT’nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time
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    Chapter 24 Modeling Mutual Exclusivity of Cancer Mutations
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    Chapter 25 Viral Quasispecies Assembly via Maximal Clique Enumeration
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    Chapter 26 Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency
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    Chapter 27 Bayesian Multiple Protein Structure Alignment
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    Chapter 28 Gene-Gene Interactions Detection Using a Two-Stage Model
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    Chapter 29 A Geometric Clustering Algorithm and Its Applications to Structural Data
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    Chapter 30 A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation
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    Chapter 31 Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification
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    Chapter 32 Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers
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    Chapter 33 Reconciliation with Non-binary Gene Trees Revisited
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    Chapter 34 Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models
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    Chapter 35 Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion