About the Book
1 Introduction to Bioinformatics
1.1 Principles of Genomics
1.2 Beyond the Genomes: Multiple Omics
1.3 Systems and Networks
1.4 Bioinformatics in modern genetics
2. A Mathematica Primer for Bioinformaticians
2.1 Getting Started
2.2 Variables
2.3 Lists
2.4 Functions
2.4 Importing and Exporting Data
2.5 Graphics
2.6 Associations and Query
2.7 Wolfram Alpha
2.8 Wolfram Language Resources
3. Statistics for Genomic Analysis
3.1 Probability
3.2 Distributions
3.3 Hypotheses
3.4 Parametric Testing
3.5 Non-parametric Testing
3.6 Markov Chains
3.7 Exploratory Data Analysis
4. Genomic Sequences
4.1 Sequence Alignments
4.2 Pairwise Alignment
4.3 Dynamic Programming
4.4 Processing Sequencing Files
5. Databases
5.1 Connecting to Databases
5.2 UCSC Browser and MySQL
5.3 Gene Ontology Annotations
5.4 Biological Pathways
5.5 Genomic Medicine Data Sources
6. Transcriptomics
6.1 Transcriptomic Data
6.2 Quality Control
6.3 Normalization
6.4 Differential Gene Expression
6.5 Visualization
6.6 Classification and Biological Significance
7. Proteomics
7.1 Proteomics Data
7.2 Spectral Visualization
7.3 Quality Control
7.4 Normalization
7.5 Differential Protein Expression
7.6 Visualization
8. Metabolomics
8.1 Metabolomics Data
8.2 Metabolomics Databases
8.3 Metabolomics Data Analysis
8.4 Putative Identification of Compounds
8.5 Clustering and Principal Co
mponents Analysis
9. Systems Biology
9.1 Introduction to Systems Biology
9.2 Basic Models
9.3 Visualization of Data
9.4 Beyond Basic Models
10. Networks
10.1 Introduction to Network Analysis
10.2 Basic Network Construction
10.3 Network Properties
10.4 Network Comparison
10.5 Scale Free Networks
11. Time Series Analysis
11.1 Introduction to Time Series
11.2 Regularly Sampled Time Series
11.3 Frequency Representation of Longitudinal Data
11.4 Uneven Sampling
12. Omics Integration and Systems Medicine
12.1 Introduction to Multiple Omics Integration
12.2 Systems Medicine Approaches
12.3 Example Integration of Omics Datasets
13. Bioinformatics Development with Mathematica
13.1 Introduction to Pa
ckages
13.2 Creating a Simple Bioinformatics Package
13.3 Dynamics, Manipulate and Interactive Interfaces
