COMP 572: BIOINFORMATICS: NETWORK ANALYSIS

[THIS WEBSITE IS UPDATED FREQUENTLY]

COMP 572 BIOINFORMATICS: NETWORK ANALYSIS
Spring 2008

[Staff] [Information] [Materials]

Staff

.	Name	Email address	Office hours
Instructor	Luay K. Nakhleh	nakhleh@cs.rice.edu	by appointment, DH 3119
Teaching Assistant	Evan Huston	ehuston@rice.edu	by appointment, DH 3117

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Course Information

MEETING PLACE AND TIME: Duncan Hall (DH) 1046 (DH is building #20 on the map), Monday and Wednesday, 3:00-4:20.
TEXTBOOK: None.
INTENDED AUDIENCE: anyone who's interested in learing about exciting applications at the intersection of biology and computation. Knowledge of biology, math, and algorithms is a plus; yet, the course will be taught in a way that is equally accessible to students from computer science, engineering, natural sciences, and medical institutions.
TOPICS TO BE COVERED:
1. Graph-theoretic techniques for analyzing biological networks.
2. Network motifs.
3. Robustness of biological networks.
4. Analysis of protein-protein interaction networks.
5. Comparative network analysis (network alignment).
6. Analysis of signal transduction networks.
7. Analysis of metabolic networks.
8. Network integration.
GRADING:
- A set of homework assignments: 30%.
- Course project: 70%.
STUDENTS WITH DISABILITY: Any student with a documented disability needing academic adjustments or accommodations is requested to speak with me during the first two weeks of class. All discussions will remain confidential. Students with disabilities will need to also contact Disability Support Services in the Ley Student Center.

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Course Material

Slides Set #	Topic	Slides	Additional material
1	Staff, grading, and schedule	PDF
2	The Emergence of Systems Biology	PDF	[1]
3	Molecular Cell Biology: A Brief Review	PDF
4	Computational Techniques: A Brief Review	PDF
5	Biological Sequence Analysis: A Brief Overview	PDF
6	General Network Analysis: Graph-theoretic Techniques	PDF	[1] , [2]
7	Graph-Theoretic Properties of Biological Networks	PDF	[1] , [2] , [3]
8	Network Motifs	PDF	[1] , [2] , [3] , [4] , [5] , [6] , [7]
9	Robustness of Biological Networks	PDF	[1] , [2] , [3] , [4] , [5] , [6] , [7]
10	Network modules: clustering and biclustering	PDF	[1] , [2] , [3] , [4] , [5]
11	Comparative Network Analysis	PDF	[1] , [2] , [3] , [4] , [5] , [6] , [7] , [8] , [9] , [10] , [11]
12	Analyzing Network Dynamics Using Petri Nets	PDF	[1] , [2] , [3] , [4] , [5]
13	Convex Analysis of Regulatory Networks	PDF	[1] , [2] , [3] , [4]

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