Analysis of Biological Networks (BE.440)

Lecture Notes

LEC #	TOPICS
1	Course Introduction Model networks involved in signaling - Signals that start outside of the cell (role of the ECM) and trigger cascades inside the cell, ultimately affecting gene expression
2	Information flow in the reverse direction - from DNA to RNA to protein (the central dogma) Review of regulatory circuits and introduction to the concept of evolutionary genomics (PDF) Key Issues: DNA replication and repair errors lead to mutations. Loss of mismatch repair leads to a hyper-Rec phenotype, which facilitates horizontal gene transfer (antibiotic resistance, etc.)
3	Decoding Information I (Transcription Regulation) (PDF)
4	Modeling Macromolecular Structure I Individual Homework Assignments
5	Decoding Information II (Translation) (PDF)
6	Modeling Macromolecular Structure II Students Present Homework
7	Roundtable Discussion
8	How to Write an NIH Grant Proposal
9	Analysis of the Interferon Network (The JAK/STAT system) (PDF)
10	Analysis of the Interferon Network (PDF)
11	Analysis of the Interferon Network (cont.)
12	Analysis of the Interferon Network (cont.) (PDF)
13	Roundtable 1: Students Present Model Projects on Apoptosis
14	Chemotaxis I - How Salvage Pathways Supplement Core Biochemical Pathways (PDF) The Che System Receptor Methylation as a Mechanism of Control of Chemotaxis
15	Chemotaxis II - How CheY(P) Signals to the Flagellar Motor Chemiosmotic Coupling Chemotaxis III - Proton Pumps
16	Introduction to the Extracellular Matrix
17	Epithelial Cell Morphogenesis Signaling Hierarchy I
18	Epithelial Cell Morphogenesis Signaling Hierarchy II
19	Round Table Discussion
20	Epithelial Cell Morphogenesis Signaling Hierarchy III
21	Roundtable 3
22	Changes in Lung Epithelium During Pathogenesis I
23	Changes in Lung Epithelium During Pathogenesis II
24	Network Example: Functional Glycomics