Computational Systems Biology:


Professor B. Mishra

Office Hours: Mon 4:00 PM - 5:00 PM
Office Phone: 212.998.3464
Email Address:

Day and Time:
Thursdays, 5::00 PM - 6:50 PM EST, Room 1221, 719 Broadway.

Credits for Course:

Syllabus for Course: Syllabus: Biology X

Lecture 1: Evolutionary Biology

Lecture 2: Genome Evolution: (Point Mutations; Rearrangements; Evolution by Duplication)

Lecture 3, & 4: Phylogeny: (Algorithms for Phylogenetic Trees)

Lecture 5 & 6: Genome Structure: (Retro-Elements and their distributions; Physical Properties of a genome; Large Segmental Duplications; Models of Segmental Duplications); Evidence for Evolution: (Luria-Delbruck Jackpot); Polymorphisms: (SNPS & CNPS; Haplotyping and Haplotype phasing); Genetics: (Linkage Analysis; Association Studies)

Lecture 7 & 8: KMA Models: (ODE's describing Regulatory Networks; How to create such models; Question of Reachability)

Lecture 9 & 10: Model Checking: (CTL and Basic Model Checking algorithms; TCTL and RTL); Hybrid Models: (Basic Definitions; Classes of Hybrid Models)

Lecture 11 & 12: 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)

Lecture 13 & 14: Biology of Cancer; 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:

Recommended Text(s):

Midterm Date:
No Midterm.
Final Date:
Class Project.
Class Presentation.

Bud Mishra
January 1 2008