640:338 Discrete and Probabilistic Models in Biology:
Home Page, Spring 2006

Class meets: TTH6 (5:00-6:20), SEC, Room 218

Text: The text is available (free!) on-line at http://www.math.rutgers.edu/courses/338/coursenotes/coursetext.html.

Instructor: Daniel Ocone, ocone@math.rutgers.edu

Office Hours: Hill 518: Tuesday and Thursday, 3:15-4:45 (before class); Wednesday, 10:30-11:30; or by appointment.

Lecture schedule, problem sets and reading assignments, etc. Click here.

Syllabus by topic

Tests, homework, grades: There will be weekly, graded problem sets, two midterms, and a final.
The final grade will be computed from an average of the final grade (200 points), the midterm grades (100 points each),
and the homework grades (100 points).
The midterms are tentatively scheduled for Feb. 21 and March 30.

Course description

THE SPRING 2006 semester will focus on probabilistic and dynamic programming methods in the analysis of biological sequences and in genetics. The course introduces models from population biology for the study of the evolution of gene frequency, models from genomics for the statistical description and for the evolution of genomes and proteomes, and the mathematical tools for their analysis.

Here is a summary:

Basic populations genetics as an introduction to probabilistic models in biology.
Continuous random variables. Independent, identically distributed random sequences, geometric, exponential, and normal random variables, and Poisson processes. Application to coverage analysis in DNA sequencing strategies.
Likelihood functions, Maximum Likelihood Estimation, hypothesis testing, and application to models for biological sequences.
Dynamic Programming and sequence alignment.
Markov chain basics and Hidden Markov models for sequence evolution and applications to alignment.

640:338 Discrete and Probabilistic Models in Biology: Home Page, Spring 2006

Course description

640:338 Discrete and Probabilistic Models in Biology:
Home Page, Spring 2006