Time & Place: not determined yet.

Instructor:
Jun Ni, Ph.D.
Department of Computer Science
Tel: (319) 335-5486, Fax: (319) 335-5505
E-mail: jni@cs.uiowa.edu;

Office Hours: not determined yet.

Textbook:
Pierre Baldi and Soren Brunak, "Bioinformatics: The Machine Learning Approach", The MIT Press. ISBN: 026202442x.
The information about the textbook can be obtained at http://www.books24x7.com/book/id_1287/toc.asp; Author's web page is http://www.ics.uci.edu/~pfbaldi/

Class Lecture Notes:
Additional notes or handouts may be available in classroom.

Course Description:

This is a graduate level course on probabilistic modeling of biological data. The course covers computational approaches to understanding and predicting the structure, function, interactions, and evolution of DNA, RNA, proteins, and related molecules and processes. The emphasis is on providing a unified Bayesian statistical framework to mine large noisy data sets that are becoming the hallmark of modern biology. The methods taught focus on developing the structure of the models, on model fitting algorithms (machine learning), and on the application of the resulting models (data mining). Most applications will revolve around DNA, RNA, protein sequence, and gene-expression-array data, but other types of data will also be considered depending on participants interests.

Prerequisites:
A basic course in Computer Science's algorithms, in Biological Science's molecular biology, in Statistics' probability and statistics, or consent of instructor. Course assumes some background in biology, and basic knowledge of probability, statistics, and programming.

Objectives:

It provides great learning opportunity for students who are computer/computational science or engineering major to understand the needs of advanced probabilistic algorithms in computational biology, especially in bioinformatics. It also provides potentials for graduate students who are enthusiastic in learning statistical approaches and algorithms to bioinformatics, which can be directly used to their research in biological science.

 

Grading:
4 team-based projects (reading, development, and presentation) 80%, and final project 20%.

Disability Issue:

I need to hear from anyone who has a disability which may require some modification of seating, testing or other class requirements so that appropriate arrangements may be made. Please see me after class or during my office hours.

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