Lecture Notes for Spring 2008

Graphs and Networks in Systems Biology

The lectures are divided into chapters. Each chapter is typically covered over multiple sessions. The handout is formatted with 4 pages of the PDF on a single handout page.

• Syllabus - PDF
• Introduction - PDF | Handout
• Graph Concepts - PDF | Handout
• Network Properties - PDF | Handout
• Biological Networks - PDF | Handout
• Random Graphs - PDF | Handout
• Network Models - PDF | Handout
• Biological Network Models - PDF | Handout
• Network Perturbations and Resilience - PDF | Handout
• Community Structures in Complex Networks - PDF | Handout
• Network Dynamics in Cellular Networks - PDF | Handout
• Chemical Kinetics - PDF | Handout
• Signal Transduction Modeling - PDF | Handout
• Discrete Dynamic Modeling - PDF | Handout
• Network Inference - PDF | Handout
• Boolean Modeling and Simulation (application)- PDF | Handout

Homework

Homework's: HW1, HW2, HW3, HW4, HW5, HW6, HW7, HW8, HW9 | HW10

Projects

Project topics will be selected from a list of suggestions or can be based on the research interests of participants. Work on terms projects will continue throughout the semester, with an abstract due in March and a draft paper due in April. Each participant will give a 10 minute project presentation during the last 3 classes. The final papers will be due on the last day of classes (May 4), at 5 pm. Project topics: Project 1, Project 2

See also the lecture notes from 2007