Topics
Alignment Algorithms
Data Structures
- List
- Tree; trie; suffix tree
- Suffix array
- Graph
Algorithms
- Greedy algorithm
- Dynamic programming algorithm: Alignment, Sankoff algorithm to small parsimony problem
- Combinatorial algorithm: genome rearrangement
- Randomized algorithm: motif finding
Statistics
- t-test & chi-squared test
- Cluster analysis
- PCA
Information-theoretic approaches
- Entropy, relative entropy and mutual information
NGS applications
- Genomic variant
- RNA-seq
- ChIP-seq
- Metagenomics
Biological networks
- Gene regulatory network inference
- Protein-protein interaction network
Things good to know (not covered in this course)