Research in Computational Molecular Biology

Table of Contents

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   Book Overview
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   Chapter 1 Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks
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   Chapter 2 Towards an Integrated Protein-Protein Interaction Network
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   Chapter 3 The Factor Graph Network Model for Biological Systems
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   Chapter 4 Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution
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   Chapter 5 Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model
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   Chapter 6 Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis
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   Chapter 7 A Regulatory Network Controlling Drosophila Development
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   Chapter 8 Yeast Cells as a Discovery Platform for Neurodegenerative Disease
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    Chapter 9 RIBRA–An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem
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    Chapter 10 Avoiding Local Optima in Single Particle Reconstruction
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    Chapter 11 A High-Throughput Approach for Associating microRNAs with Their Activity Conditions
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    Chapter 12 RNA-RNA Interaction Prediction and Antisense RNA Target Search
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    Chapter 13 Consensus Folding of Unaligned RNA Sequences Revisited
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    Chapter 14 Discovery and Annotation of Genetic Modules
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    Chapter 15 Efficient q -Gram Filters for Finding All ε -Matches over a Given Length
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    Chapter 16 A Polynomial Time Solvable Formulation of Multiple Sequence Alignment
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    Chapter 17 A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters
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    Chapter 18 Reconstruction of Reticulate Networks from Gene Trees
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    Chapter 19 A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction
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    Chapter 20 Constructing a Smallest Refining Galled Phylogenetic Network
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    Chapter 21 Mapping Molecular Landscapes Inside Cells
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    Chapter 22 Information Theoretic Approaches to Whole Genome Phylogenies
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    Chapter 23 Maximum Likelihood of Evolutionary Trees Is Hard
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    Chapter 24 Graph Theoretical Insights into Evolution of Multidomain Proteins
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    Chapter 25 Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry
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    Chapter 26 A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search
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    Chapter 27 EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning
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    Chapter 28 Biology as Information
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    Chapter 29 Using Multiple Alignments to Improve Gene Prediction
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    Chapter 30 Learning Interpretable SVMs for Biological Sequence Classification
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    Chapter 31 Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition
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    Chapter 32 Rapid Protein Side-Chain Packing via Tree Decomposition
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    Chapter 33 Recognition of Binding Patterns Common to a Set of Protein Structures
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    Chapter 34 Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions
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    Chapter 35 Amino Acid Sequence Control of the Folding of the Parallel β -Helix, the Simplest β -Sheet Fold
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    Chapter 36 A Practical Approach to Significance Assessment in Alignment with Gaps
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    Chapter 37 Alignment of Optical Maps
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    Chapter 38 Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology
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    Chapter 39 Modeling the Combinatorial Functions of Multiple Transcription Factors
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    Chapter 40 Predicting Transcription Factor Binding Sites Using Structural Knowledge
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    Chapter 41 Motif Discovery Through Predictive Modeling of Gene Regulation
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    Chapter 42 HAPLOFREQ – Estimating Haplotype Frequencies Efficiently
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    Chapter 43 Improved Recombination Lower Bounds for Haplotype Data
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    Chapter 44 A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem
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    Chapter 45 Human Genome Sequence Variation and the Inherited Basis of Common Disease
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    Chapter 46 Stability of Rearrangement Measures in the Comparison of Genome Sequences
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    Chapter 47 On Sorting by Translocations