Algorithms in Bioinformatics

Table of Contents

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   Book Overview
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   Chapter 1 Shotgun Protein Sequencing
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   Chapter 2 Locality Kernels for Protein Classification
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   Chapter 3 When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features
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   Chapter 4 Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps
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   Chapter 5 Bringing Folding Pathways into Strand Pairing Prediction
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   Chapter 6 A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
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   Chapter 7 Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies
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   Chapter 8 Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity
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    Chapter 9 Haplotype Inference Via Hierarchical Genotype Parsing
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    Chapter 10 Seeded Tree Alignment and Planar Tanglegram Layout
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    Chapter 11 Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion
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    Chapter 12 An Ω ( n 2 /log n ) Speed-Up of Heuristics for the Gene-Duplication Problem
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    Chapter 13 Incremental Discovery of Irredundant Motif Bases in Time O (| Σ | n 2 log n )
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    Chapter 14 A Graph Clustering Approach to Weak Motif Recognition
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    Chapter 15 Informative Motifs in Protein Family Alignments
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    Chapter 16 Topology Independent Protein Structural Alignment
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    Chapter 17 Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction
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    Chapter 18 Alignment-Free Local Structural Search by Writhe Decomposition
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    Chapter 19 Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment
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    Chapter 20 Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding
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    Chapter 21 Genomic Signatures in De Bruijn Chains
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    Chapter 22 Fast Kernel Methods for SVM Sequence Classifiers
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    Chapter 23 On-Line Viterbi Algorithm for Analysis of Long Biological Sequences
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    Chapter 24 Predicting Protein Folding Kinetics Via Temporal Logic Model Checking
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    Chapter 25 Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops
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    Chapter 26 Algorithms for the Extraction of Synteny Blocks from Comparative Maps
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    Chapter 27 Computability of Models for Sequence Assembly
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    Chapter 28 Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data
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    Chapter 29 RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound
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    Chapter 30 HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding
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    Chapter 31 Homology Search with Fragmented Nucleic Acid Sequence Patterns
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    Chapter 32 Fast Computation of Good Multiple Spaced Seeds
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    Chapter 33 Inverse Sequence Alignment from Partial Examples
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    Chapter 34 Novel Approaches in Psychiatric Genomics
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    Chapter 35 The Point Placement Problem on a Line – Improved Bounds for Pairwise Distance Queries
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    Chapter 36 Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach
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    Chapter 37 Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data
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    Chapter 38 A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence
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    Chapter 39 Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation