Session Key
L = Lecture
R = Recitation
P = Project session
| SES # | TOPICS | KEY DATES (PSETS) |
|---|---|---|
| L1 | Introduction: Course overview, biology, algorithms, machine learning |
Problem Set 1 assigned Project Profile assigned |
| R1 | Recitation 1: Biology and probability review | |
| L2 | Alignment I: Dynamic programming, global and local alignment | |
| L3 | Alignment II: Database search, rapid string matching, BLAST, BLOSUM | |
| R2 | Recitation 2: Deriving parameters of alignment, multiple alignment | |
| L4 | Hidden Markov Models Part 1: Evaluation / parsing, Viterbi, forward algorithms | |
| L5 | Hidden Markov Models Part 2: Posterior decoding, learning, Baum-Welch | |
| P1 | Project Introduction: About the projects, self-introductions, mentor introductions, example projects, teamwork | |
| L6 | Transcript Structure: GENSCAN, RNA-seq, mapping, de novo assembly, diff expr |
Problem Set 1 due Problem Set 2 assigned Project Profile due Project area / team assigned |
| L7 | Expression Analysis: Clustering / classification, k-means, hierarchical, Bayesian | |
| R3 | Recitation 3: Affinity propagation clustering and random forest classification | |
| L8 | Networks I: Bayesian inference, deep learning, network dynamics |
Project area / team due Project proposal assigned |
| L9 | Networks II: Network learning, structure, spectral methods | |
| R4 | Recitation 4: Small and large regulatory RNAs: lincRNA, miRNA, piRNA, etc. | |
| P2 | Project Planning: Research areas, initial ideas, type of project, mentor matching, finding partners | |
| L10 | Regulatory Motifs: Discovery, representation, PBMs, Gibbs sampling, EM |
Problem Set 2 due Problem Set 3 assigned |
| R5 | Recitation 5: Gapped motif discovery, DNA shape, PBMs, SELEX | |
| L11 | Epigenomics: ChIP-seq, read mapping, peak calling, IDR, chromatin states | Project proposal due |
| L12 | RNA Modifications: RNA editing, translation regulation, splicing regulation | |
| R6 | Recitation 6: Dimensionality reduction | |
| P3 | Project Feedback: Prepare 2-3 slide presentation of your term project for your mentor. | |
| L13 | Resolving human ancestry and human history from genetic data |
Problem Set 3 due Problem Set 4 assigned |
| L14 | Disease association mapping, GWAS, organismal phenotypes | |
| R7 | Recitation 7: Robinson-Foulds distance and coalescent process | |
| P4 | Panel Discussion: Reconciling critiques, strategies for improvement, feedback to author | |
| L15 | Quantitative trait mapping, molecular traits, eQTLs | |
| L16 | Missing heritability, complex traits, interpret GWAS, rank-based enrichment | |
| R8 | Recitation 8: Suffix trees and arrays | |
| L17 | Comparative genomics and evolutionary signatures |
Problem Set 4 due Problem Set 5 assigned |
| R9 | Recitation 9: Review of phylogeny and molecular evolution | |
| L18 | Phylogenetics: Molecular evolution, tree building, phylogenetic inference | |
| L19 | Phylogenomics: Gene / species trees, reconciliation, recombination graphs | |
| R10 | Recitation 10: Linkage disequilibrium, haplotype phasing, and genotype imputation | |
| Quiz | ||
| L20 | Personal genomics, disease epigenomics: Systems approaches to disease | Problem Set 5 due |
| L21 | Three-dimensional chromatin interactions: 3C, 5C, HiC, ChIA-Pet | |
| R11 | Recitation 11: Project tips, write-up, slides, final presentation | |
| L22 | Genome engineering with CRISPR / Cas9 and related technologies | |
| Final presentations | ||