Computational Systems Biology:
G22.3033.004
- Lecturers:
-
Professor
B. Mishra
Office Hours: Mon 3:30 - 4:30 P.
Office Phone: 212.998.3464
Email Address: mishra@nyu.edu
- Day and Time:
-
Mondays, 5:00-6:50pm EST, Room 102, WWH.
- Credits for Course:
-
3
- Syllabus for Course:
Syllabus: Biology X
- (1) Evolutionary Biology
- (2) Computability in Biology
- (3) Reconstructibility in Biology
- (4) Biology of Cancer
- (5) Biology of Aging
Lecture 1
(1) Evolutionary Biology
.
(2) Computability in Biology
- Models in Biology: (Regulatory Networks; Metabolic Networks;
Signaling Networks)
Lecture 7;
- KMA Models: (ODE's describing Regulatory Networks; How to create
such models; Question of Reachability)
Lecture 8;
Lecture 9;
- Model Checking: (CTL and Basic Model Checking algorithms; TCTL
and RTL)
- Hybrid Models: (Basic Definitions; Classes of Hybrid Models)
Lecture 10;
(3) Reconstructibility in Biology
- Biological Networks:
- Protein-DNA and Protein-Protein Interactions: (Two hybrid
experiments; Motifs and Scale-Free Networks; Origin of structures)
- Network Reconstruction: (From Microarray Data; Techniques based
on Linear and non-linear regression; The issue of sparsity)
- Theory of Information Bottleneck: (Clustering using IB,
side-information and ontology; Analysis of Time-Course Data; GOALIE)
(4) Biology of Cancer
Lecture 11;
- Cancer: (A Genomic Disease)
- Cancer Data Analysis: (Genomic Data; Transcriptomic Data;
Proteomic Data)
- Cancer Gene Discovery: (Tumor Suppressor Genes and Oncogenes)
- Somatic Evolution in Cancer:
- Theories of Origin of Cancer:
(5) Biology of Aging
- Theories of Aging: (Hayflick's model; Mitochodria and Oxidative
Stress; Stem Cells & Niche-Clonality; Genome Evolution; Proteomic
Explanation: E.g, Protein Degradation)
- Key Experiments in Animals: (Examples: Deinococcus radiodurans;
Tradigrades; C. Elegans)
- Anti-Aging:
- Immortality:
- Midterm Date:
-
No Midterm.
- Final Date:
-
Class Project.
- Homework(s):
-
Class Presentation.
Bud Mishra
January 1 2006