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Intermediate Courses

  
 

Co-sponsored by:
BTCI
DNASTAR, Inc.
NimbleGen Systems
Promega Corporation
Gene Expression Center, University of Wisconsin Biotechnology Center

Offered at BTCI in Madison, Wisconsin 
 

  
  TITLE  
 

Computational Approaches to Analyzing Microarray Data

  
DATES
 

July 13-17, 2009
 

  
  CONTENT  
 


Goals & Objectives:

Microarray technologies have become essential tools for experimental uses in the research laboratory and for the development of medical diagnostics. They offer the hope of understanding biological processes at the cellular level from a systematic, simultaneous survey of DNA and RNA variation, documenting gene expression levels, DNA mutation and repair. The high throughput nature of microarray data can be a challenge to biologists who need to incorporate techniques from statistics, bioinformatics and computer science into their routine tool kits.
 
This "hands on" computer course will call on the expertise of  instructors as varied as bench scientists, bioinformaticians, statisticians and computer scientists from Academic and Industry backgrounds. The course will comprise scholarly designed classes and state of the art presentations to review fundamental knowledge of statistics, microarray technologies, experimental design, data mining techniques, data diagnostics, using prior knowledge to constrain analyses and modeling techniques.  The course is geared towards molecular biologists and mathematical or computation scientists entering the field of bioinformatics. 
 
Students will run specific "hands on" worked examples and build self-sufficient competence using an open source software (R/Bioconductor) and a commercial package (ArrayStar) as "proof of concepts" to understand methods and algorithms presented in class.

Technical Program:

In general the format for each day will be equally divided between lecture and computer lab time. 
NEW for 2008: Optional evening labs will be provided at no extra charge; students may choose to work on their own data during this time.

Summary Goal:
To raise students' self-sufficient competence in applying fundamental statistics and bioinformatics methods to microarray data for efficient data mining.

Schedule:
NOTE: The schedule below was used in 2008; it will be modified for 2009.

Monday, July 14  
8:30 - 9:15 am Continental Breakfast & Introductions
Computer Set-Up & Course Overview		 A. Prevost, K. Borgh, J.Y. Sgro
9:15 - 10:45 am Microarray Technologies &  Platforms M. Hessner
11:00 am - 12:30 pm Data Analysis Algorithms I: Data Normalization and RMA Analysis R.Alexandridis, N. Jiang
12:30 - 1:30 pm Lunch
 
1:30 - 3:30 pm Data Analysis Algorithms II: Clustering Methods
Research: Genetic Regulatory Network Modeling and Genetic Linkage		 X. Wang
3:45 - 5:30 pm Statistics for Microarrays - Part I L. Chung
5:30 - 7:30 pm Dinner (with class)
 

Tuesday, July 15		  
8:30 - 10:20 am Statistics for Microarrays - Part II L. Chung
10:35 am - 12:30 pm Data Analysis Algorithms III: Selecting Differentially Expressed (DE) Genes L. Chung
 
12:30 - 1:30 pm Lunch
 
1:30 - 3:30 pm Genome Evolution - Pathways and Databases (GO/ KEGG/Marts) J. Glasner
3:30 - 4:30 pm
Cognate Site Identifier (CSI): High Throughput Technique to Determine DNA Sequence Specificity
C. Warren
 
4:30 - 5:30 pm Introduction to R and Bioconductor Analysis of Different Data Sets; RMA (hands-on) J.Y. Sgro, L. Chung
5:30 - 7:00 pm Dinner (on your own)
 
6:30 - 9:00 pm Open-lab: "Bring Your Own Data" J.Y. Sgro, L. Chung

Wednesday, July 16		  
8:30 am - 12:30 pm ArrayStar® v2.0 Gene Expression Analysis Software (hands-on demo) B. Anderson, T. Durfee, D. Nash
12:30 - 1:30 pm Lunch
 
1:30 - 5:30 pm Partek® Genomics Suite TM (hands-on demo) M. Lelivelt
5:30 - 7:00 pm Dinner (on your own)
 
6:30 - 9:00 pm Open-lab: "Bring Your Own Data" J.Y.Sgro, L. Chung

Thursday July 17		  
8:30 - 9:45 am Understanding Genome Structure & Function - Density Oligonucleotide Tiling Microarrays  T. Albert
10:00 - 11:15 am Combination of ChIP-chip and Expression Data  M. Hogan
11:30 am - 12:30 pm Whole Genome Alignments C. Dewey
 
12:30 - 1:30 pm Lunch
 
1:30 - 4:30 pm ChIP-chip Arrays/Nimblegen Platform
R-bioconductor Ringo Package Analysis
ChIP-seq studies		 M. Meyer
4:30 - 5:30 pm R Analysis (continued) - Limma Package (hands-on continued) J.Y. Sgro, L. Chung
 
5:30 - 7:00 pm Dinner (on your own)
 
6:30 - 9:00 pm Open-lab: "Bring Your Own Data" J.Y.Sgro, L. Chung
Friday July 18  
8:30 am - 10:30 am Localizing the Genetic Basis of Gene Expression: Theoretical  background and Intro to the eQTL R Package;
eQTL R Package Exercises in Class		 J. Dawson
10:45 am - 12:30 pm R & Bioconductor (hands-on continued) J.Y.Sgro, L. Chung
 
12:30 - 2:00 pm
Lunch
Course Review / Feedback & Closing
 		 A. Prevost, K. Borgh, J.Y. Sgro
 

 

  
  INSTRUCTORS  
 


Tom Albert, Ph.D., Director of Molecular Research, Roche NimbleGen, Inc.

Roxana Alexandridis, Ph.D., Biostatistician, Research Informatics, Roche NimbleGen, Inc.

 Brian Anderson, M.Sc., Technical Sales Scientist, DNASTAR, Inc.

Karin Borgh, Ph.D., Executive Director, BTCI

Lisa Chung, Graduate Student, Department of Statistics; NIGMS Biostat Trainee, Department of Biostatistics and Medical Informatics, UW-Madison

John Dawson, Ph.D., Student, Departments of Biostatistics & Medical Informatics and Computer Sciences, UW-Madison

Colin Dewey, Ph.D., Assistant Professor, Departments of Biostatistics & Medical Informatics and Computer Sciences, UW-Madison

Tim Durfee, Ph.D., Senior Scientist, DNASTAR, Inc.

Stephanie Ellenbecker, B.Sc., Director of Sales, Distribution and Technical Support, DNASTAR, Inc.

 Jeremy Glasner, Ph.D., Associate Scientist, Biotechnology Center AHABS, UW-Madison

 Martin Hessner, Ph.D., Associate Professor, Medical College of Wisconsin

Michael Hogan, Senior Director of Production Bioinformatics, Roche NimbleGen, Inc.

Nan Jiang, Ph.D., Biostatistician, Research Informatics, Roche NimbleGen, Inc.

Mike Lelivelt, Ph.D., Vice President of Genomics, Partek, Inc.

Mark Meyer, Ph.D., Research Associate, J.W. Pike Lab, Department of Biochemistry, UW-Madison

Dan Nash, Senior Software Engineer, DNASTAR, Inc.

Amy Prevost, M.S. Scientific Courses Coordinator, BTCI

Sandra Splinter BonDurant, M.S., Associate Researcher, University of Wisconsin Biotechnology Center

Jean-Yves Sgro, Ph.D., Senior Scientist, Institute for Molecular Virology, UW-Madison

 Xujing Wang, Ph.D., Assistant Professor, Medical College of Wisconsin

Christopher Warren, Ph.D., Research Associate, Integrated Program in Biochemistry, UW-Madison

  COST & REQUIREMENTS  
  $1000 Faculty, industry, medical, clinical laboratory professionals
$750   Graduate students, post-doctoral candidates.
This includes course materials, lab supplies, breakfast and lunch. Participants are responsible for their own lodging, transportation and dinner arrangements; a list of recommended hotels and restaurants will be provided.

Other Requirements:

  • Eligibility: No prior knowledge of bioinformatics or associated software packages is assumed.  Basic computer literacy is required, as are stated interests in receiving broader training in computational analysis of data, in current developments, and in the future of this dynamic field.
  • Application: Applicants are required to submit an application form and a succinct letter of interest, clarifying eligibility and professional need for the course content. Admission to the course will be based upon receipt of the application form and review of the letter of interest, with enrollment limited to 16 participants.  Admission to the course will be on a first-come, first-served basis, and applications will be accepted until the course is fully enrolled.
  • Confirmation: Registration will be confirmed based on receipt of payment or guarantee of payment.
  
 
  CANCELLATION  
 
  • If you have registered for a workshop but cannot attend, you may transfer the registration to a colleague within your organization, or you may transfer to another scheduled workshop within 12 months of the original.  There is no charge for transfers.
  • For cancellations made more than two weeks before the start of the workshop, you will be refunded the tuition fee minus a 5% fee.
  • For cancellations made within the two weeks prior to the workshop start date, half the tuition will be refunded.
  • No refunds will be made for non-attendance or withdrawals after the start of each workshop.

Note: BTCI may cancel or postpone any workshop due to unforeseen circumstances. If this occurs, we will provide full tuition reimbursement.  We are not responsible for any related costs, charges, or expenses including imposed penalties by airlines, hotels, or travel agents.
 

  
  FOR MORE INFORMATION  
 
  • For more information regarding registration, contact: Dr. Karin Borgh, Executive Director
    BioPharmaceutical Technology Center Institute (BTCI)
    608-277-2508;e-mail: karin.borgh@btci.org
  • For more information regarding course content, please contact Jean-Yves Sgro, Ph.D., Senior Scientist, Institute for Molecular Virology, UW-Madison; e-mail: jsgro@wisc.edu .

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