Advanced Bioinformatics

 

Time & Place:
TBD

Instructor:
Jun Ni, Ph.D., Associate Professor
Department of Radiology, Carver College of Medicine,
Biomedical Engineering
Mechanical Engineering
University of Iowa, Iowa City, IA, USA
Tel: (319) 335-9490
E-mail: jun-ni@uiowa.edu

Office Hours and Place:
TBD

Textbook: Pierre Baldi and Soren Brunak, "Bioinformatics: The Machine Learning Approach", Second Edition, The MIT Press. ISBN: ISBN-10:
0-262-02506-X; ISBN-13:978-0-262-02506-5
The information about the textbook can be obtained MIT Press
; 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.cc

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.

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.

Course Contents:

1 Introduction

2 Machine-Learning Foundations: The Probabilistic Framework

3 Probabilistic Modeling and Inference: Examples

4 Machine Learning Algorithms

5 Neural Networks: The Theory

6 Neural Networks: Applications

7 Hidden Markov Models: The Theory

8 Hidden Markov Models: Applications

9 Probabilistic Graphical Models in Bioinformatics

10 Probabilistic Models of Evolution: Phylogenetic Trees

11 Stochastic Grammars and Linguistics

12 Microarrays and Gene Expression

13 Internet Resources and Public Databases

Hawkeye Radiology Informatics Division (HawkRID)
Department of Radiology || Carver College of Medicine || The University of Iowa
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