Session Key

L = Lecture
R = Recitation
P = Project session

L1Introduction: Course overview, biology, algorithms, machine learning

Problem Set 1 assigned

Project Profile assigned

R1Recitation 1: Biology and probability review 
L2Alignment I: Dynamic programming, global and local alignment 
L3Alignment II: Database search, rapid string matching, BLAST, BLOSUM 
R2Recitation 2: Deriving parameters of alignment, multiple alignment 
L4Hidden Markov Models Part 1: Evaluation / parsing, Viterbi, forward algorithms 
L5Hidden Markov Models Part 2: Posterior decoding, learning, Baum-Welch 
P1Project Introduction: About the projects, self-introductions, mentor introductions, example projects, teamwork 
L6Transcript 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

L7Expression Analysis: Clustering / classification, k-means, hierarchical, Bayesian 
R3Recitation 3: Affinity propagation clustering and random forest classification 
L8Networks I: Bayesian inference, deep learning, network dynamics

Project area / team due

Project proposal assigned

L9Networks II: Network learning, structure, spectral methods 
R4Recitation 4: Small and large regulatory RNAs: lincRNA, miRNA, piRNA, etc. 
P2Project Planning: Research areas, initial ideas, type of project, mentor matching, finding partners 
L10Regulatory Motifs: Discovery, representation, PBMs, Gibbs sampling, EM

Problem Set 2 due

Problem Set 3 assigned

R5Recitation 5: Gapped motif discovery, DNA shape, PBMs, SELEX 
L11Epigenomics: ChIP-seq, read mapping, peak calling, IDR, chromatin statesProject proposal due
L12RNA Modifications: RNA editing, translation regulation, splicing regulation 
R6Recitation 6: Dimensionality reduction 
P3Project Feedback: Prepare 2-3 slide presentation of your term project for your mentor. 
L13Resolving human ancestry and human history from genetic data

Problem Set 3 due

Problem Set 4 assigned

L14Disease association mapping, GWAS, organismal phenotypes 
R7Recitation 7: Robinson-Foulds distance and coalescent process 
P4Panel Discussion: Reconciling critiques, strategies for improvement, feedback to author 
L15Quantitative trait mapping, molecular traits, eQTLs 
L16Missing heritability, complex traits, interpret GWAS, rank-based enrichment 
R8Recitation 8: Suffix trees and arrays 
L17Comparative genomics and evolutionary signatures

Problem Set 4 due

Problem Set 5 assigned

R9Recitation 9: Review of phylogeny and molecular evolution 
L18Phylogenetics: Molecular evolution, tree building, phylogenetic inference 
L19Phylogenomics: Gene / species trees, reconciliation, recombination graphs 
R10Recitation 10: Linkage disequilibrium, haplotype phasing, and genotype imputation 
L20Personal genomics, disease epigenomics: Systems approaches to diseaseProblem Set 5 due
L21Three-dimensional chromatin interactions: 3C, 5C, HiC, ChIA-Pet 
R11Recitation 11: Project tips, write-up, slides, final presentation 
L22Genome engineering with CRISPR / Cas9 and related technologies 
 Final presentations