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7. ChIP-seq Analysis; DNA-protein Interactions
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Classroom Contents
Foundations of Computational and Systems Biology
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- 1 1. Introduction to Computational and Systems Biology
- 2 2. Local Alignment (BLAST) and Statistics
- 3 3. Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM)
- 4 4. Comparative Genomic Analysis of Gene Regulation
- 5 5. Library Complexity and Short Read Alignment (Mapping)
- 6 6. Genome Assembly
- 7 7. ChIP-seq Analysis; DNA-protein Interactions
- 8 8. RNA-sequence Analysis: Expression, Isoforms
- 9 9. Modeling and Discovery of Sequence Motifs
- 10 10. Markov and Hidden Markov Models of Genomic and Protein Features
- 11 11. RNA Secondary Structure; Biological Functions and Predictions
- 12 12. Introduction to Protein Structure; Structure Comparison and Classification
- 13 13. Predicting Protein Structure
- 14 14. Predicting Protein Interactions
- 15 15. Gene Regulatory Networks
- 16 16. Protein Interaction Networks
- 17 17. Logic Modeling of Cell Signaling Networks
- 18 18. Analysis of Chromatin Structure
- 19 19. Discovering Quantitative Trait Loci (QTLs)
- 20 20. Human Genetics, SNPs, and Genome Wide Associate Studies
- 21 21. Synthetic Biology: From Parts to Modules to Therapeutic Systems
- 22 22. Causality, Natural Computing, and Engineering Genomes
