BIOL 210: Application and Analysis of (Biological) Microarrays

Winter Quarter, 2003

 
Time: MWF 2-3:10pm
Location: Lectures: Baskin 372
Computer Labs: Baskin 109
Course Info Link: www.soe.ucsc.edu/~lowe/courses/MicroarrayW03/

InstructorTodd Lowe
Email lowe@soe
Phone 459-1511
Office 227 Sinsheimer
Office Hours Wed 3:30-4:30, Thur 2-3pm & by appt.

Announcements / Updates

Reading List

Problem Set Teams

Problem Sets

Final Project Data

Class-related Web links (mentioned in class)


Grading

50% Problem sets
50% Final Project - Data Set Analysis Write-up

Lecture Topics

Date Lecture Topics
January 3   Overview of Course  
January 6   Introduction Vocabulary
Basic types of DNA arrays: Spotted oligo/cDNA, Affymetrix
Oligos v. PCR products v. In situ oligo synthesis
Types of Array Experiments
January 8  Introduction II Types of Data Analysis
Limitations of Arrays
Array + Sequence Analysis
January 10  Experimental Design Time-resolved data
Comparison of different genetic backgrounds
Comparison of different developmental stages
Cancer/Tumor Classification
Comparison of different genomes
Human SNP Mapping
Spellman Yeast Cell-Cycle Paper
(please read before class)
January 13    Spotted DNA Array Design
& Construction 
PCR fragment / Oligo Feature Design
Building a spotting robot
Preparing slides
Preparing DNA samples
Spotting
January 15  Spotted DNA Array Design (cont)
Demos
Post-processing and care of arrays
Scanning Demo
Spotting Robot Demo
January 17  Lab #1: Using GenePix  GenePix Tutorial
Meet in Kresge computer lab

Gridding
Data Extraction
Using a Print-list
January 20  Holiday - No class
January 22  Introduction to R and Bioconductor   Guest Lecturer: Andy Pohl
January 24  Using Arrays to Study RNA Processing   Guest Lecturer: Manny Ares
January 27  Lab #2: Introduction to R & Bioconductor   Lab exercise
Meet in Baskin 109 Computer lab 
January 29  Microarray Club Guest Lecture:
Sandrine Dudoit  
Bioconductor & other cool stuff
  Basic Analysis Clustering
Self-organizing maps
K-means
mRNA expression
DNA copy number changes / footprinting
Cross-species hybridization
  Advanced Analysis Singular value decomposition
Support Vector machines
Correspondence analysis / Principle component analysis
Gene Shaving
Cross-Experiment Analyses
Identifying regulatory networks, Church et al.
Promotor sequence discovery, Gibbs sampling techniques
  Other Kinds of Arrays
Protein arrays
Tissue arrays
 
  New Array Technologies