Research in Computational Molecular Biology

Table of Contents

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   Book Overview
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   Chapter 1 Protein Structure by Semidefinite Facial Reduction
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   Chapter 2 Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models
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   Chapter 3 Charge Group Partitioning in Biomolecular Simulation
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   Chapter 4 Increased Methylation Variation in Epigenetic Domains across Cancer Types
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   Chapter 5 Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising
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   Chapter 6 Quantifying the Dynamics of Coupled Networks of Switches and Oscillators
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   Chapter 7 lobSTR: A Short Tandem Repeat Profiler for Personal Genomes
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   Chapter 8 Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data
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    Chapter 9 Ballast : A Ball-Based Algorithm for Structural Motifs
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    Chapter 10 Evolution of Genome Organization by Duplication and Loss: An Alignment Approach
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    Chapter 11 LoopWeaver – Loop Modeling by the Weighted Scaling of Verified Proteins
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    Chapter 12 A Robust Method for Transcript Quantification with RNA-seq Data
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    Chapter 13 Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics
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    Chapter 14 TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq
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    Chapter 15 Synthetic Sequence Design for Signal Location Search
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    Chapter 16 The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation
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    Chapter 17 Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing
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    Chapter 18 Network-Based Prediction and Analysis of HIV Dependency Factors
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    Chapter 19 Structure-Guided Deimmunization of Therapeutic Proteins
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    Chapter 20 Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures
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    Chapter 21 Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly
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    Chapter 22 Finding Maximum Colorful Subtrees in Practice
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    Chapter 23 Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
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    Chapter 24 RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract)
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    Chapter 25 Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies
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    Chapter 26 A Model for Biased Fractionation after Whole Genome Duplication
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    Chapter 27 Exact Pattern Matching for RNA Structure Ensembles
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    Chapter 28 Reconstructing Boolean Models of Signaling
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    Chapter 29 Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract
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    Chapter 30 Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer
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    Chapter 31 Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem
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    Chapter 32 Function-Function Correlated Multi-Label Protein Function Prediction over Interaction Networks
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    Chapter 33 Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization
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    Chapter 34 CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping
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    Chapter 35 Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs
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    Chapter 36 Probabilistic Inference of Viral Quasispecies Subject to Recombination
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    Chapter 37 Simultaneously Learning DNA Motif along with Its Position and Sequence Rank Preferences through EM Algorithm