Research in Computational Molecular Biology

Table of Contents

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   Book Overview
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   Chapter 1 Searching Protein 3-D Structures in Linear Time
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   Chapter 2 Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
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   Chapter 3 Boosting Protein Threading Accuracy
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   Chapter 4 New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees
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   Chapter 5 A Probabilistic Graphical Model for Ab Initio Folding
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   Chapter 6 Topology-Free Querying of Protein Interaction Networks
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   Chapter 7 Cross Species Expression Analysis of Innate Immune Response
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   Chapter 8 Haplotype Inference in Complex Pedigrees
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    Chapter 9 Storage and Retrieval of Individual Genomes
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    Chapter 10 An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
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    Chapter 11 Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology
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    Chapter 12 Spatial Clustering of Multivariate Genomic and Epigenomic Information
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    Chapter 13 How Many Bootstrap Replicates Are Necessary?
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    Chapter 14 A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
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    Chapter 15 Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation
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    Chapter 16 Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes
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    Chapter 17 Optimizing PCR Assays for DNA Based Cancer Diagnostics
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    Chapter 18 The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory
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    Chapter 19 COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study
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    Chapter 20 Overlapping Pools for High Throughput Targeted Resequencing
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    Chapter 21 Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction
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    Chapter 22 Lifting Prediction to Alignment of RNA Pseudoknots
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    Chapter 23 Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks
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    Chapter 24 Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination
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    Chapter 25 Research in Computational Molecular Biology
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    Chapter 26 Shared Peptides in Mass Spectrometry Based Protein Quantification
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    Chapter 27 Evaluating Between-Pathway Models with Expression Data
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    Chapter 28 Sorting Signed Permutations by Inversions in O ( n log n ) Time
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    Chapter 29 Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information
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    Chapter 30 Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data
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    Chapter 31 On the Relationship between DNA Periodicity and Local Chromatin Structure
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    Chapter 32 Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
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    Chapter 33 Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples
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    Chapter 34 An Adaptive and Memory Efficient Algorithm for Genotype Imputation
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    Chapter 35 A Statistical Framework for the Functional Analysis of Metagenomes
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    Chapter 36 Learning Models for Aligning Protein Sequences with Predicted Secondary Structure