Foundations of Computational and Systems Biology

Lecture Slides

Lecturer Key

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

LEC #	TOPICS	LECTURERS
1	Course Introduction: History of Computational Biology; Overview of the Course; Course Policies and Mechanics; DNA Sequencing Technologies (PDF - 5.0MB)	CB, DG, EF
Genomic Analysis
2	Local Alignment (BLAST) and Statistics (PDF - 2.0MB)	CB
3	Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM) (PDF)	CB
4	Comparative Genomic Analysis of Gene Regulation (PDF - 2.9MB)	CB
Genomic Analysis—Next Gen Sequencing
5	Library Complexity and Short Read Alignment (Mapping) (PDF - 1.4MB)	DG
6	Genome Assembly (PDF)	DG
7	ChIP-seq Analysis; DNA-protein Interactions (PDF - 2.0MB)	DG
8	RNA-sequence Analysis: Expression, Isoforms (PDF - 2.9MB)	DG
Modeling Biological Function
9	Modeling and Discovery of Sequence Motifs (Gibbs Sampler, Alternatives) (PDF)	CB
10	Markov and Hidden Markov Models of Genomic and Protein Features (PDF)	CB
11	RNA Secondary Structure–Biological Functions and Prediction (PDF - 1.6MB)	CB
Proteomics
12	Introduction to Protein Structure; Structure Comparison and Classification (PDF - 3.1MB)	EF
13	Predicting Protein Structure (PDF - 3.4MB)	EF
14	Predicting Protein Interactions (PDF - 4.7MB)	EF
Regulatory Networks
15	Gene Regulatory Networks (PDF - 6.1MB)	EF
16	Protein Interaction Networks (PDF - 7.6MB)	EF
17	Logic Modeling of Cell Signaling Networks (PDF - 3.1MB) Guest Lecture: Doug Lauffenburger	GL
18	Analysis of Chromatin Structure (PDF - 3.8MB)	DG
Computational Genetics
19	Discovering Quantitative Trait Loci (QTLs) (PDF - 2.8MB)	DG
20	Human Genetics, SNPs, and Genome Wide Associate Studies (PDF - 3.3MB)	DG
21	Synthetic Biology: From Parts to Modules to Therapeutic Systems. Guest Lecture: Ron Weiss Slides of this guest lecture are not available.	GL
22	Causality, Natural Computing, and Engineering Genomes. Guest Lecture: George Church Slides of this guest lecture are not available.	GL