Réka Albert - Teaching

Lecture Notes from Spring 2007

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 Topology - PDF | Handout
Detour into Scientific Programming (guest speaker Istvan Albert) - PDF | Handout
Biological Networks - PDF | Handout
Random Graphs - PDF | Handout
Network Models - PDF | Handout
Network Perturbations and Resilience - PDF | Handout
Graph Processing and Algorithms (guest speaker Istvan Albert) - PDF
Community Structures in Complex Networks (guest speaker Usha Nandini Raghavan) - PDF
Search in Complex Networks (guest speaker Hari Prasad Thadakamalla) - PDF
Disease Spreading on Complex Networks - PDF | Handout
Reaction Dynamics - PDF | Handout
Signal Transduction Modeling - PDF | Handout
Network Inference - PDF | Handout
Boolean Modeling and Simulation - PDF | Handout

Homework

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

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.

An Optimization-Based Approach for Reverse Engineering Gene Regulatory Networks (Alireza Zomorrodi) - PDF
Using Social Network Characteristics to Describe Disease Spread (Ruth M Hummel) - PDF
Cool Applications of Network Theory to Molecular Evolution (Melissa Wilson) - PDF
Boolean Modeling of Serotonin mediated Ca2+ Signaling pathway (Gaurav Bhardwaj) - PDF
Light Induced Guard Cell Signaling (Sunando Roy) - PDF
TOR Signaling Pathway for Nutrient-Regulated Transcription Factors (Kyung Dae Ko) - PDF
Cis-Regulatory Module Network (Swathi Ashok Kumar) - PDF
Investigating Statistical Mechanics of Complex Supply Chain Networks under Potential Risks (Satama Sirivunnabood) - PDF
Wikipedia as Semantic Network. What does Knowledge look like? (Sooyoung Oh) - PDF
A Context Based Growth and Preferential Attachment Network (Manini Madireddy) - PDF
Hierarchy Modeling in Complex Networks - PDF
The Topology and Evolution of a Network Model for Genome Evolution in Polyploids (Gue Su Chang) - PDF
A Study on Netflix Movie-User Network (Baojun Qiu) - PDF
Optimization Based Network Modeling and Analysis of Stochastic Processes (Sridhar Ranganathan) - PDF
A Networks Perspective On Duplication And Divergence (Guruprasad Ananda) - PDF