Algorithms in Bioinformatics

Table of Contents

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   Book Overview
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   Chapter 1 Preserving Inversion Phylogeny Reconstruction
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   Chapter 2 Fast Phylogenetic Tree Reconstruction Using Locality-Sensitive Hashing
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   Chapter 3 Efficient Computation of Popular Phylogenetic Tree Measures
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   Chapter 4 SibJoin: A Fast Heuristic for Half-Sibling Reconstruction
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   Chapter 5 Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models
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   Chapter 6 Estimating Population Size via Line Graph Reconstruction
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   Chapter 7 Extracting Conflict-Free Information from Multi-labeled Trees
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   Chapter 8 Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs
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    Chapter 9 An Optimal Reconciliation Algorithm for Gene Trees with Polytomies
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    Chapter 10 Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference
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    Chapter 11 RNA Tree Comparisons via Unrooted Unordered Alignments
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    Chapter 12 Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots
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    Chapter 13 δ-TRIMAX: Extracting Triclusters and Analysing Coregulation in Time Series Gene Expression Data
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    Chapter 14 CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population
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    Chapter 15 Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters
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    Chapter 16 Succinct Multibit Tree: Compact Representation of Multibit Trees by Using Succinct Data Structures in Chemical Fingerprint Searches
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    Chapter 17 Comparing DNA sequence collections by direct comparison of compressed text indexes
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    Chapter 18 Succinct de Bruijn Graphs
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    Chapter 19 Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter
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    Chapter 20 From de Bruijn Graphs to Rectangle Graphs for Genome Assembly
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    Chapter 21 MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing
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    Chapter 22 How Accurately Can We Model Protein Structures with Dihedral Angles?
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    Chapter 23 Resolving Spatial Inconsistencies in Chromosome Conformation Data
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    Chapter 24 MS-DPR: An Algorithm for Computing Statistical Significance of Spectral Identifications of Non-linear Peptides
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    Chapter 25 FinIS: Improved in silico Finishing Using an Exact Quadratic Programming Formulation
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    Chapter 26 Lightweight LCP Construction for Next-Generation Sequencing Datasets
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    Chapter 27 Sign Assignment Problems on Protein Networks
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    Chapter 28 Sparse Learning Based Linear Coherent Bi-clustering
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    Chapter 29 A Simplified View of DCJ-Indel Distance
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    Chapter 30 DCJ-indel Distance with Distinct Operation Costs
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    Chapter 31 Hidden Breakpoints in Genome Alignments
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    Chapter 32 A Probabilistic Approach to Accurate Abundance-Based Binning of Metagenomic Reads
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    Chapter 33 Tandem Halving Problems by DCJ
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    Chapter 34 A Practical Approximation Algorithm for Solving Massive Instances of Hybridization Number
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    Chapter 35 Distributed String Mining for High-Throughput Sequencing Data