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Analysis of Biological Networks (BE.440) >> Content Detail



Lecture Notes



Lecture Notes

LEC #TOPICS
1Course 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
2Information 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.)
3Decoding Information I (Transcription Regulation) (PDF)
4Modeling Macromolecular Structure I

Individual Homework Assignments
5Decoding Information II (Translation) (PDF)
6Modeling Macromolecular Structure II

Students Present Homework
7Roundtable Discussion
8How to Write an NIH Grant Proposal
9Analysis of the Interferon Network (The JAK/STAT system) (PDF)
10Analysis of the Interferon Network (PDF)
11Analysis of the Interferon Network (cont.)
12Analysis of the Interferon Network (cont.) (PDF)
13Roundtable 1: Students Present Model Projects on Apoptosis
14Chemotaxis I - How Salvage Pathways Supplement Core Biochemical Pathways (PDF)

The Che System

Receptor Methylation as a Mechanism of Control of Chemotaxis
15Chemotaxis II - How CheY(P) Signals to the Flagellar Motor

Chemiosmotic Coupling

Chemotaxis III - Proton Pumps
16Introduction to the Extracellular Matrix
17Epithelial Cell Morphogenesis Signaling Hierarchy I
18Epithelial Cell Morphogenesis Signaling Hierarchy II
19Round Table Discussion
20Epithelial Cell Morphogenesis Signaling Hierarchy III
21Roundtable 3
22Changes in Lung Epithelium During Pathogenesis I
23Changes in Lung Epithelium During Pathogenesis II
24Network Example: Functional Glycomics

 








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