Location: Prince William II, Room 185, Prince William Campus

Textbooks:
Parmigiani, G, Garrett, E., Irizarry, R., and Zeger, S.,"The Analysis of Gene Expression Data,"
Springer, 2003.

Speed, Terry (Ed.), "Statistical Analysis of Gene Expression Microarry Data,"
Chapman and Hall/CRC, 2003.

Course Description: The student will learn concepts underlying experimental design for micro-array studies and numerous micro-array data analysis techniques including data normalization, visualization, discriminant analysis, dimensionality reduction, and clustering. Software packages utilized will include MATLAB, R, and BIOCONDUCTOR.

Grading Policy:
Quizes:           10%
Homework:    30% Several homework assignments will be given throughout the semester
Presentations: 20% Each student will make 1 presentation of a recent paper from the literature
Final Project: 20% A written report is required.
Final Project: 20% A presentation is required.

Presentations are to be of a paper or papers from the published literature, either from a suggested
pool of papers or a relevant paper that the instructors have approved. The paper presentation slides must be made available to the class on the Monday prior to the student presentations.

Projects are to involve independent analysis or visualization of a public dataset, with a discussion of the methods chosen, validation tests verifying the suitability of the data for the technique you are displaying, a summary of the results and a discussion of the implications and possible interpretations.

Tenative Lecture Schedule

Week 1 1/22/04
Primary Data Extraction (Jennifer)
Lecture1

Homework1

Week 2 1/29/04
Introduction to R and MATLAB (Jeff)
Lecture 2 - MATLAB

Lecture 2 - R

HW2

Week 3 2/5/04
Preprocessing Data With Bioconductor (Guest)
Lecture 3
Lab 3
HW 3

Week 4 2/12/04
Dimensionality Reduction - I (Jeff)

Lecture Dimensionality Reduction - I

HW4
Readings Chapter 3 of Speed
* Title and Authors for Presentation Paper Due

BINF733 Workshop on High-Dimensional Data

Here are two links to tutorials on principal components analysis.
A Principal Components Tutorial
Another Principal Components Tutorial

Here are a few papers on subset feature selection
A Nice Paper on Feature Subset Selection
A Paper of Mine on Simultaneous Feature/Metric Selection (to appear Communications in Statistics

Week 5 2/19/04
Experimental Design for Micro-Array Analysis (Jennifer)
Lecture 5
Lab 5
HW 5
Readings Chapters 1 and 2 of Speed along with Chapter 14 of AGED
* Project Outline Due

Week 6 2/26/04
Normalization (Jennifer)
Lecture 6
Lab 6
HW 6

Week 7 3/4/04
Lecture Dimensionality Reduction - II (Jeff)
HW 7

A power point hw solution file
Readings Chapter 15 of AGED

Week 8 3/18/04
Clustering (Jeff)
Lecture 8
HW 8
A power point hw solution file
Readings Chapter 15 of AGED and Chapter 18 of AGED

Week 9 3/25/04
Functional Notation (Jennifer)
Lecture 9
Lab 9
HW 9
Readings Chapters 8,9, and 20 of AGED

Week 10 4/1/04
Discriminant Analysis (Jeff)
Lecture 10
Lab 10
HW 10
Readings Chapter 3 of Speed

Week 11 4/8/04
Student Paper Presentations
Quiz # 1
Ming-Kuan Lin
Article(PDF)

Yan Xiang
Article(PDF)

Chun-Lung Wang
Article Website

Zhong Yin
Article(PDF)

* Presentation Slides Due to Jeff and Jennifer by 4/5/04

Week 12 4/15/04
Student Paper Presentations
Quiz # 2
Guozhong Ma
Article(PDF)

Kevin Thompson
Article(PDF)

Kishor Kumar Tappita
Article(PDF)

Vasuki Palanigobu
Article(PDF)

* Presentation Slides Due to Jeff and Jennifer by 4/12/04

Week 13 4/22/04
Student Project Presentations
Quiz # 3
Guozhong Ma
Kishor Kumartappita
Chun-Lung Wang
Ming-Kuan Lin
* Presentation Slides to Jeff and Jennifer by 4/19/04

Week 14 4/28/04
Student Project Presentations
Quiz # 4
Yan Xiang
Zhong Yin
Vasuki Palanigobu
Kevin Thompson
* Presentation Slides to Jeff and Jennifer by 4/16/04

BINF733 The study of microarray data: Methods and Data Analysis Spring 2004

BINF733 2003-Topics in Bioinformatics: Multidimensional Genome Analysis

A link to the 2002 course is given below.

CSI739 2002-Topics in Bioinformatics: Multidimensional Genome Analysis

A link to some interesting papers that Jeff would like to see presented is given below

Some papers of interest to Jeff.