 |
Problem solving handbook in computational biology and bioinformatics / edited by Lenwood S. Heath, Naren Ramakrishnan. — New York : Springer, 2011. – (58.17115/P962) |
Contents
Contents
Part I Sequences
Modern BLAST Programs
1 Introduction
2 Available Implementations
3 Algorithm Description
4 BLAST Statistics
5 Examples
6 Advanced Topics
7 Exercises
8 Further Reading
References
Practical Multiple Sequence Alignment
1 History of the Problem
2 Algorithm Description
3 Available Implementations
4 Advanced Topics
5 Exercises
6 Further Reading
References
Sequence Alignment Statistics
1 Introduction
2 Dynamic Programming with Independent Random Inputs
3 The Extreme-Value Distributions for Maxima
4 The Poisson Approximation for Counting Rare Events
5 Pairwise Sequence Alignment
6 Islands in Local Alignment
7 The Finite-Size Correction in Gapped Local Alignment
8 The Independent Diagonals Approximation
9 The Combinatorial Approximation
References
Part II Phylogenetics
Practical Implications of Coalescent Theory 63
1 Introduction -- What is the coalescent? 63
2 Motivating Problems 66
3 Implications of the Coalescent 69
4 Software Review 76
5 Further Reading 79
6 Exercises for the reader 79
References 80
Graph Model of Coalescence with Recombinations
1 Introduction 85
2 Random Graph Framework: Pedigree Graph 87
3 Pedigree Subgraphs 90
4 Unilinear Transmission: Monochromatic Subgraphs 92
5 Genetic Exchange Model: Mixed Subgraph 93
6 Topological definition of GMRCA: Least Common Ancestor with Ancestry (LCAA) 96
7 Discussion 97
References 99
Phylogenetic Trees From Sequences
1 Basics
2 Sequence evolution
3 Distance-based phylogeny reconstruction
4 Maximum parsimony
5 Maximum likelihood
6 Multiple phylogenies: comparison， consensus， and confidence..
7 Software
8 Further reading
9 Exercise
References
Evolutionary Phylogenetie Networks: Models and Issues
1 Introduction
2 Phylogenetic Networks and the Trees Within
3 Optimization Criteria for Inferring and Evaluating Phylogenetic Networks
4 To Network， or Not to Network， That is the Question
5 Exercises
6 Further Reading
References
Genome Wide Association Studies 159
1 An overview of population genetics 159
2 Genome-Wide Association Studies 162
3 Resources 172
4 Advanced Topics 172
5 Exercise 173
References 174
Part III Proteins: Structure， Function， and Biochemistry
Novel Perspectives on Protein Structure Prediction 179
1 Introduction 179
2 Modeling transmembrane β-barrel structure 182
3 Energy model 186
4 Algorithms 188
5 Applications 193
6 Sampling the local neighborhood of 3D structures 200
7 Exercises 203
8 Further reading 203
References 204
Stochastic Simulation for Biochemical Systems 209
l History of the Problem 209
2 Algorithm Description 211
3 Available Implementations 216
4 Examples 221
5 Advanced Topics 223
6 Exercises 227
7 Further Reading 228
References 228
Part IV Networks
Cellular Response Networks
1 History of the Problem
2 Algorithm Descriptions
3 Available Implementations
4 Examples
5 Advanced Topics: Comparing Response Networks
6 Exercises
7 Outlook and Further Reading
References
Identification of Modules in Protein-Protein Interaction Networks 253
1 History of the Problem
2 Algorithm Description
3 Available Implementations
4 Examples
5 Advanced Topics
6 Exercises
7 Further Reading
References
Part V Biological Data Management and Mining
Designing Microarray Experiments
1 Designed experiments versus observational studies
2 Discovery of Differentially Expressed Genes
3 Building prognostic models
4 Running the experiment
5 Advanced topics and further reading
6 Exercise
References
Matrix and Tensor Decompositions
1 Introduction
2 Non-negative Matrix Factorization
3 Singular Value Decomposition
4 Other Matrix Decompositions
5 Comparison of the Methods
6 Tensor Decompositions
7 Concluding Remarks
8 Exercises
References
Practical Applications of the Gene Ontology Resource 319
1 Introduction 319
2 GO Annotations 320
3 Viewing the GO and its annotations 324
4 Use of GO in the literature 326
5 Popular methods for supplementing and grouping GO annotations 328
6 The effective use of GO for large-scale analyses 334
7 Exercises 335
8 Further Reading 338
References 338
Index 341
