| Sequences / Part I： |
| Modern BLAST Programs / Jian Ma ; Louxin Zhang |
| Introduction / 1： |
| Available Implementations / 2： |
| Algorithm Description / 3： |
| BLAST Statistics / 4： |
| Examples / 5： |
| Advanced Topics / 6： |
| Exercises / 7： |
| Further Reading / 8： |
| References |
| Practical Multiple Sequence Alignment / Tobias Rausch ; Knut Reinert |
| History of the Problem |
| Sequence Alignment Statistics / John L. Spouge |
| Dynamic Programming with Independent Random Inputs |
| The Extreme-Value Distributions for Maxima |
| The Poisson Approximation for Counting Rare Events |
| Pairwise Sequence Alignment |
| Islands in Local Alignment |
| The Finite-Size Correction in Gapped Local Alignment |
| The Independent Diagonals Approximation |
| The Combinatorial Approximation / 9： |
| Phylogenetics / Part II： |
| Practical Implications of Coalescent Theory / Paul Marjoram ; Paul Joyce |
| Introduction - What is the coalescent? |
| Motivating Problems |
| Implications of the Coalescent |
| Software Review |
| Exercises for the reader |
| Graph Model of Coalescence with Recombinations / Laxmi Parida |
| Random Graph Framework: Pedigree Graph |
| Pedigree Subgraphs |
| Unilinear Transmission: Monochromatic Subgraphs |
| Genetic Exchange Model: Mixed Subgraph |
| Topological definition of GMRCA: Least Common Ancestor with Ancestry (LCAA) |
| Discussion |
| Phylogenetic Trees From Sequences / Paul Ryvkin ; Li-San Wang |
| Basics |
| Sequence evolution |
| Distance-based phylogeny reconstruction |
| Maximum parsimony |
| Maximum likelihood |
| Multiple phylogenies: comparison, consensus, and confidence |
| Software |
| Further reading |
| Exercise |
| Evolutionary Phylogenetic Networks: Models and Issues / Luay Nakhleh |
| Phylogenetic Networks and the Trees Within |
| Optimization Criteria for Inferring and Evaluating Phylogenetic Networks |
| To Network, or Not to Network, That Is the Question |
| Genome Wide Association Studies / Paola Sebastiani ; Nadia Solovieff |
| An overview of population genetics |
| Genome-Wide Association Studies |
| Resources |
| Proteins: Structure, Function, and Biochemistry / Part III： |
| Novel Perspectives on Protein Structure Prediction / Bonnie Berger ; Jérôme Waldispühl |
| Modeling transmembrane β-barrel structure |
| Energy model |
| Algorithms |
| Applications |
| Sampling the local neighborhood of 3D structures |
| Stochastic Simulation for Biochemical Systems / Yang Cao |
| Networks / Part IV： |
| Cellular Response Networks / Christopher D. Lasher ; Christopher L. Poirel ; T. M. Murali |
| Algorithm Descriptions |
| Advanced Topics: Comparing Response Networks |
| Outlook and Further Reading |
| Identification of Modules in Protein-Protein Interaction Networks / Sinan Erten ; Mehmet Koyutürk |
| Biological Data Management and Mining / Part V： |
| Designing Microarray Experiments / Jacqui Milton ; Ling Wang |
| Designed experiments versus observational studies |
| Discovery of Differentially Expressed Genes |
| Building prognostic models |
| Running the experiment |
| Advanced topics and further reading |
| Matrix and Tensor Decompositions / Karthik Devarajan |
| Non-negative Matrix Factorization |
| Singular Value Decomposition |
| Other Matrix Decompositions |
| Comparison of the Methods |
| Tensor Decompositions |
| Concluding Remarks |
| Practical Applications of the Gene Ontology Resource / Rachael P. Huntley ; Emily C. Dimmer ; Rolf Apweiler |
| GO Annotations |
| Viewing the GO and its annotations |
| Use of GO in the literature |
| Popular methods for supplementing and grouping GO annotations |
| The effective use of GO for large-scale analyses |
| Index |
| Sequences / Part I： |
| Modern BLAST Programs / Jian Ma ; Louxin Zhang |
| Introduction / 1： |
| Available Implementations / 2： |
| Algorithm Description / 3： |
| BLAST Statistics / 4： |
