Lecture Slides

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.)

Course Info

Learning Resource Types

assignment Problem Sets
menu_book Online Textbook
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