6.047 | Fall 2015 | Undergraduate

Computational Biology


Session Key

L = Lecture
R = Recitation
P = Project session

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  
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  
Learning Resource Types
Problem Sets
Online Textbook