| LEC # | TOPICS AND SLIDES |
|---|---|
| 1 | Introduction: Course overview, biology, algorithms, machine learning (PDF - 7.9MB) |
| 2 | Alignment I: Dynamic programming, global and local alignment (PDF - 1.7MB) |
| 3 | Alignment II: Database search, rapid string matching, BLAST, BLOSUM (PDF - 1.8MB) |
| 4 | Hidden Markov Models Part 1: Evaluation/parsing, Viterbi, forward algorithms (PDF) |
| 5 | Hidden Markov Models Part 2: Posterior decoding, learning, Baum-Welch (PDF - 1.3MB) |
| 6 |
Transcript Structure: GENSCAN, RNA-seq, mapping, de novo assembly, diff expr (Lecture slides are not available for this lecture.) |
| 7 | Expression Analysis: Clustering/classification, k-means, hierarchical, Bayesian (PDF - 1.6MB) |
| 8 |
Networks I: Bayesian inference, deep learning, network dynamics (Lecture slides are not available for this lecture.) |
| 9 | Networks II: Network learning, structure, spectral methods (PDF - 2.2MB) |
| 10 | Regulatory Motifs: Discovery, representation, PBMs, Gibbs sampling, EM (PDF - 3.2MB) |
| 11 | Epigenomics: ChIP-seq, read mapping, peak calling, IDR, chromatin states (PDF - 9.8MB) |
| 12 |
RNA Modifications: RNA editing, translation regulation, splicing regulation (Lecture slides are not available for this lecture.) |
| 13 |
Resolving human ancestry and human history from genetic data (Lecture slides are not available for this lecture.) |
| 14 |
Disease association mapping, GWAS, organismal phenotypes (Lecture slides are not available for this lecture.) |
| 15 |
Quantitative trait mapping, molecular traits, eQTLs (Lecture slides are not available for this lecture.) |
| 16 |
Missing heritability, complex traits, interpret GWAS, rank-based enrichment (Lecture slides are not available for this lecture.) |
| 17 | Comparative genomics and evolutionary signatures (PDF - 5.1MB) |
| 18 | Phylogenetics: Molecular evolution, tree building, phylogenetic inference (PDF - 2.1MB) |
| 19 |
Phylogenomics: Gene/species trees, reconciliation, recombination graphs (Lecture slides are not available for this lecture.) |
| 20 | Personal genomics, disease epigenomics: Systems approaches to disease (PDF - 8.7MB) |
| 21 |
Three-dimensional chromatin interactions: 3C, 5C, HiC, ChIA-Pet (Lecture slides are not available for this lecture.) |
| 22 |
Genome engineering with CRISPR/Cas9 and related technologies (Lecture slides are not available for this lecture.) |
