12 7 Predictive Methods Using Protein Sequences Introduction One-Dimensional Prediction of Protein Structure Predicting Protein Function Summary Further Reading References
13 8 Multiple Sequence Alignments Introduction Measuring Multiple Alignment Quality Making an Alignment: Practical Issues Commonly Used Alignment Packages Viewing a Multiple Alignment Summary References
14 9 Molecular Evolution and Phylogenetic Analysis Introduction Early Classification Schemes Sequences As Molecular Clocks Background Terminology and the Basics How to Construct a Tree Marker-Based Evolution Studies Phylogenetic Analysis and Data Integration Future Challenges References
15 10 Expression Analysis Introduction Step 0: Choose an Expression Analysis Technology Step 1: Design the Experiment Step 2: Collect and Manage the Data – and Metadata Step 3: Data Pre-Processing Step 4: Quality Control Step 5: Normalization and Batch Effects Step 6: Exploratory Data Analysis Step 7: Differential Expression Analysis Step 8: Exploring Mechanisms Through Functional Enrichment Analysis Step 9: Developing a Classifier Single-Cell Sequencing Summary Further Reading References
16 11 Proteomics and Protein Identification by Mass Spectrometry Introduction Mass Spectrometry Tandem Mass Spectrometry for Peptide Identification Sample Preparation Bioinformatics Analysis for MS-based Proteomics Proteomics Strategies Peptide Mass Fingerprinting PMF on the Web Proteomics and Tandem MS PSM Software PSM on the Web Reporting Standards Proteomics Data Repositories Protein/Proteomics Databases Selected Applications of Proteomics Summary Acknowledgments Internet Resources Further Reading References
17 12 Protein Structure Prediction and Analysis Introduction to Protein Structures How Protein Structures are Determined How Protein Structures are Described Protein Structure Databases Visualizing Proteins Protein Structure Prediction Protein Structure Evaluation Protein Structure Comparison Summary Further Reading References
18 13 Biological Networks and Pathways Introduction