Research in Computational Molecular Biology

Table of Contents

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   Book Overview
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   Chapter 1 Computing the Rearrangement Distance of Natural Genomes
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   Chapter 2 Deep Large-Scale Multi-task Learning Network for Gene Expression Inference
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   Chapter 3 A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets
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   Chapter 4 Multiple Competition-Based FDR Control and Its Application to Peptide Detection
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   Chapter 5 Supervised Adversarial Alignment of Single-Cell RNA-seq Data
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   Chapter 6 Bagging MSA Learning: Enhancing Low-Quality PSSM with Deep Learning for Accurate Protein Structure Property Prediction
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   Chapter 7 AStarix : Fast and Optimal Sequence-to-Graph Alignment
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   Chapter 8 Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
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    Chapter 9 RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy
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    Chapter 10 Representation of $$k$$ -mer Sets Using Spectrum-Preserving String Sets
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    Chapter 11 NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks
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    Chapter 12 Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification
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    Chapter 13 Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
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    Chapter 14 Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs
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    Chapter 15 Spectral Jaccard Similarity: A New Approach to Estimating Pairwise Sequence Alignments
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    Chapter 16 MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads
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    Chapter 17 Bayesian Non-parametric Clustering of Single-Cell Mutation Profiles
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    Chapter 18 PaccMann RL : Designing Anticancer Drugs From Transcriptomic Data via Reinforcement Learning
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    Chapter 19 CluStrat: A Structure Informed Clustering Strategy for Population Stratification
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    Chapter 20 PWAS: Proteome-Wide Association Study
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    Chapter 21 Estimating the Rate of Cell Type Degeneration from Epigenetic Sequencing of Cell-Free DNA
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    Chapter 22 Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection
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    Chapter 23 Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs
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    Chapter 24 Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning
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    Chapter 25 A Guided Network Propagation Approach to Identify Disease Genes that Combines Prior and New Information
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    Chapter 26 A Scalable Method for Estimating the Regional Polygenicity of Complex Traits
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    Chapter 27 Efficient and Accurate Inference of Microbial Trajectories from Longitudinal Count Data
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    Chapter 28 Identifying Causal Variants by Fine Mapping Across Multiple Studies
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    Chapter 29 MONN: A Multi-objective Neural Network for Predicting Pairwise Non-covalent Interactions and Binding Affinities Between Compounds and Proteins
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    Chapter 30 Evolutionary Context-Integrated Deep Sequence Modeling for Protein Engineering
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    Chapter 31 Log Transformation Improves Dating of Phylogenies
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    Chapter 32 Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores
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    Chapter 33 d-PBWT: Dynamic Positional Burrows-Wheeler Transform
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    Chapter 34 A Mixture Model for Signature Discovery from Sparse Mutation Data
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    Chapter 35 Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses
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    Chapter 36 Reconstruction of Gene Regulatory Networks by Integrating Biological Model and a Recommendation System
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    Chapter 37 Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning