Algorithms in Bioinformatics

Table of Contents

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   Book Overview
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   Chapter 1 Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spaces
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   Chapter 2 Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Design
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   Chapter 3 Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem
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   Chapter 4 Methods for Inferring Block-Wise Ancestral History from Haploid Sequences
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   Chapter 5 Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks
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   Chapter 6 Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry
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   Chapter 7 Improved Approximation Algorithms for NMR Spectral Peak Assignment
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   Chapter 8 Efficient Methods for Inferring Tandem Duplication History
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    Chapter 9 Genome Rearrangement Phylogeny Using Weighbor
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    Chapter 10 Segment Match Refinement and Applications
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    Chapter 11 Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation
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    Chapter 12 Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics
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    Chapter 13 FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structures
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    Chapter 14 Efficient Unbound Docking of Rigid Molecules
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    Chapter 15 A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants
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    Chapter 16 A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding
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    Chapter 17 Comparative Methods for Gene Structure Prediction in Homologous Sequences
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    Chapter 18 MultiProt — A Multiple Protein Structural Alignment Algorithm
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    Chapter 19 A Hybrid Scoring Function for Protein Multiple Alignment
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    Chapter 20 Functional Consequences in Metabolic Pathways from Phylogenetic Profiles
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    Chapter 21 Finding Founder Sequences from a Set of Recombinants
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    Chapter 22 Estimating the Deviation from a Molecular Clock
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    Chapter 23 Exploring the Set of All Minimal Sequences of Reversals — An Application to Test the Replication-Directed Reversal Hypothesis
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    Chapter 24 Approximating the Expected Number of Inversions Given the Number of Breakpoints
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    Chapter 25 Invited Lecture — Accelerating Smith-Waterman Searches
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    Chapter 26 Sequence-Length Requirements for Phylogenetic Methods
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    Chapter 27 Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle
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    Chapter 28 NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks
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    Chapter 29 On the Control of Hybridization Noise in DNA Sequencing-by-Hybridization
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    Chapter 30 Restricting SBH Ambiguity via Restriction Enzymes
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    Chapter 31 Invited Lecture — Molecule as Computation: Towards an Abstraction of Biomolecular Systems
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    Chapter 32 Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search
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    Chapter 33 Rapid Large-Scale Oligonucleotide Selection for Microarrays
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    Chapter 34 Border Length Minimization in DNA Array Design *
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    Chapter 35 The Enhanced Suffix Array and Its Applications to Genome Analysis
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    Chapter 36 The Algorithmic of Gene Teams
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    Chapter 37 Combinatorial Use of Short Probes for Differential Gene Expression Profiling
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    Chapter 38 Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome
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    Chapter 39 K -ary Clustering with Optimal Leaf Ordering for Gene Expression Data
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    Chapter 40 Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
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    Chapter 41 Modified Mincut Supertrees