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BME 210 - Class Calendar

updated daily
Date
Session
Topics
Assigned Reading
(see Reading List page for links)
April 4, Wed

Course Overview

Administrative issues, background, goals, overview of course

April 6, Fri
Cancelled



Apr 9, Mon
Lecture
Introduction
Vocabulary
Basic types of DNA arrays: Spotted oligo/cDNA, Affymetrix
Oligos v. PCR products v. In situ oligo synthesis
Types of Array Experiments



Text: Chapters 1 & 2.4, Lockhart Nature review

Apr 11, Wed
Lecture
Introduction 2


Alternate Array platforms
Types of Data Analysis
Limitations of Arrays


Text: Rest of Chapter 2,
Eisen Methods in Enzymology review
Apr 13, Fri
Paper Discussion
Classic Yeast Papers
Spellman Yeast Cell Cycle paper,
Gasch Environmental Stress paper

Apr 16, Mon
Lecture
Spotted Array Design
Oligo v. PCR product arrays
Resources for making a spotting robot
Text Chapter 3
Apr 18, Wed

Lecture
Types of Experiments /
Databases

Types of Experiments
Choices of References
Microarray Databases

Text Chapter 4
Apr 20, Fri
Paper Discussion
Compendiums of array experiments


Hughes, Cell 2000 compendium paper
Scherf, Nat Genetics 2000 molecular pharmacology of cancer paper

Apr 23, Mon
Lab 1
GenePix Introductory Lab
Gridding
Data Extraction
Using a Print-list
GenePix Manual, chapters 1-4
[Download GenePix Software]
Apr 25, Wed
Lecture
Normalization


Apr 27, Fri
Paper Discussion Ammonium toxicity & use of chemostats in yeast
Hess et al., PLoS Biology, 2006 Ammonium toxicity paper
Apr 30, Mon
Lab 2
Bioconductor & normalization


May 2, Wed
Lecture Cancelled -rescheduled for May 3 makeup


May 4, Fri
Paper Discussion Cross-platform reproducibility of array data

See Reading List
May 7, Mon
Lab 3
More Normalization
For May 10: Cluster Analysis
Using Cluster and TreeView
May 9, Wed
Lecture Normalization

May 11,Fri
Lecture on
Clustering

More Clustering Lab
Clustering

May 14, Mon

Paper Discussion



May 16, Wed
Lecture Finding significant gene expression changes
Integrating microarray data with genomic data to find transcription control regions

May 17
Thurs
Lab 4
Using Microarray Web Resources:
Analysis: CARMAWeb
Data Retreival: Geo, Gene Xpress Databases

May 18, Fri
Paper Discussion Evolution of Gene Expression Khaitovich review
Gilad et al., Evolution of transcription factor expression
May 21, Mon
Lab 5
Guest Instructors
Using ClueGene

May 23, Wed
Group Presentation
Lab (Wed-Thurs group)
Group Presentation: Grant & Hongqing

Wed-Thurs Lab Group: Meet at 8:30am in 134 to start hybridizing arrays

May 24,
Thurs
Lab 6
Wed-Thurs Group: Meet at 8:30am to wash & scan arrays

Thurs-Fri Groups: Meet at 10am in Baskin 134 to hybridize arrays

May 25, Fri
Lab
Thurs-Fri Groups: Meet at 10am to wash & scan your arrays

May 28, Mon
Holiday
No class

May 30, Wed
Group Presentation
Pinal & Rachel

May 31
Thurs
Lab Time
Work on analyzing your array data from last week

Jun 1, Fri
Group Presentation
John & Marcos

Jun 4, Mon
Group Presentation
Nick & Kivanc
Jun 6, Wed
Group Presentation
Greg & Navya

Jun 8, Fri
Group Presentation
Jonathan & Dan

Jun 14, Thurs

Pseudo-grant & your array data analysis due 5pm