Mathematica for Bioinformatics

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 <4.5 Processing BLAST Output 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 Components 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 Packages< 13.2 Creating a Simple Bioinformatics Package 13.3 Dynamics, Manipulate and Interactive Interfaces