Session Key

[L] = Lecture
[R] = Recitation
[E] = Exam
[P] = Presentation 

Lecturer Key

[CB] = Christopher Burge
[DG] = David Gifford
[EF] = Ernest Fraenkel
[TA] = Teaching Assistant
[GL] = Guest Lecturer

L1 Course Introduction: History of Computational Biology; Overview of the Course; Course Policies and Mechanics; DNA Sequencing Technologies CB, DG, EF  
Genomic Analysis
L2 Local Alignment (BLAST) and Statistics CB  
R1 Statistics; Significance Testing; Bonferroni Correction TA  
L3 Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM) CB Project: Interests Due
L4 Comparative Genomic Analysis of Gene Regulation CB  
R2 Clustering, Model Selection, and BIC Scores TA  
Genomic Analysis—Next Gen Sequencing
L5 Library Complexity and Short Read Alignment (Mapping) DG Problem Set 1 Due
R3 Burrows–Wheeler Transform (BWT) and Alignments. Guest Lecture: Heng Li (Broad Institute) GL  
L6 Genome Assembly DG Project: Teams Due
L7 ChIP-seq Analysis; DNA-protein Interactions DG  
R4 Simultaneous ChIP-seq Peak Discovery and Motif Sampling TA  
L8 RNA-sequence Analysis: Expression, Isoforms DG  
Modeling Biological Function
L9 Modeling and Discovery of Sequence Motifs (Gibbs Sampler, Alternatives) CB  
R5 Gene Expression Program Discovery Using Topic Models TA  
L10 Markov and Hidden Markov Models of Genomic and Protein Features CB  
L11 RNA Secondary Structure—Biological Functions and Prediction CB Problem Set 2 Due
R6 Probabilistic Grammatical Models of RNA Structure TA  
E1 Exam 1
L12 Introduction to Protein Structure; Structure Comparison and Classification EF  
R7 Protein Amino Acid Sidechain Packing Using Markov Random Fields TA Project: Research Strategy Due
L13 Predicting Protein Structure EF  
L14 Predicting Protein Interactions EF Problem Set 3 Due
R8 Protein / Protein Interaction Prediction Using Threading TA  
Regulatory Networks
L15 Gene Regulatory Networks EF  
L16 Protein Interaction Networks EF  
R9 Regression Trees TA  
L17 Logic Modeling of Cell Signaling Networks. Guest Lecture: Doug Lauffenburger GL  
L18 Analysis of Chromatin Structure DG Problem Set 4 Due
R10 BayesNets TA  
Computational Genetics
L19 Discovering Quantitative Trait Loci (QTLs) DG Project: Written Report Due
R11 Narrow Sense Heritability TA  
L20 Human Genetics, SNPs, and Genome Wide Associate Studies DG  
L21 Synthetic Biology: From Parts to Modules to Therapeutic Systems. Guest Lecture: Ron Weiss GL Problem Set 5 Due
R12 Exam Review TA  
E2 Exam 2
L22 Causality, Natural Computing, and Engineering Genomes. Guest Lecture: George Church GL  
P1 Presentations
P2 Presentations (cont.)