DIMACS Workshop on Analysis of Gene Expression Data

October 24 - 26, 2001
DIMACS Center, Rutgers University, Piscataway, NJ

Organizers:

Laurie Heyer, Davidson College, laheyer@davidson.edu

Gustavo Stolovitzky, IBM, gustavo@us.ibm.com

Shibu Yooseph, Celera Genomics, shibu.yooseph@celera.com

Program:

Wednesday, October 24, 2001

1:30-2:00     Registration

2:00-2:05     Welcome and Greeting:
              Mel Janowitz, DIMACS Associate Director

2:05-2:15     Welcome and Greeting:
              Workshop Organizers

2:15-3:45     Tutorial: Peter Tolias, Center for Applied Genomics, 
              Public Health Research Institute
   	      Emerging Technologies for Gene Expression Analysis

3:45-4:15     Break

4:15-5:45     Tutorial: Yuhai Tu, IBM
	      A Brief Review of Methods Used in the Analysis of Gene
              Expression Data


Thursday, October 25, 2001

8:15-9:00     Breakfast and Registration

9:00-10:00    Richard Karp, University of California, Berkeley
              Combinatorial and Information-Theoretic Approaches to Mining Gene Expression Data

10:00-10:30   Vladimir Filkov and Sorin Istrail, Celera Genomics
	      Inferring Gene Transcription Networks: The Davidson Model

10:30-11:00   Break

11:00-11:30   Felix Naef, Daniel Lim, Nila Patil and Marcelo Magnasco=20
              The Laboratories of Mathematical Physics and Neurogenesis,
              The Rockefeller University, Perlegen Sciences Inc. and
              Affymetrix Inc.
              From features to expression: High-density oligonucleotide
              array analysis revisited

11:30-12:00   Chao Deng, Aili Wang, Denong Wang, and Peisen Zhang,
              Columbia University
              A Nonlinear Channel Normalization Approach for cDNA
              Microarray Data and its Performance Analysis

12:00-2:15    Lunch

2:15-2:45     Alvaro Mateos, Joaquin Dopazo, Yuhai Tu, Ronald Jansen, 
              Mark Gerstein and Gustavo Stolovitzky
              Centro Nacional de Investigaciones Oncologicas (CNIO) - Madrid,
              IBM Computational Biology Center, and Yale University
              What can be "learned" from Gene Expression Arrays? 

2:45-3:30     DIMACS - Celera Genomics/Applied Biosystems Graduate Student Award Presentation
              Winner: Itsik Pe'er, Tel Aviv University

              Award Presenters: 
              Fred S. Roberts, DIMACS Director
              Sorin Istrail, Celera Genomics

              Award lecture by award winner, Itsik Pe'er
              Computational Resequencing by Universal Microarrays

3:30-4:00     Gregory Dewey, David Galas and Ashish Bhan,
              Keck Graduate Institute of Applied Life Sciences and
              Claremont Graduate University
              A Network Analysis of Expression Time Series

4:00-4:30     Break

4:30-5:30     Gary Stormo, Washington University Medical School
              Using Expression Data to Learn About Regulatory Networks
              Via Promoter Analysis

5:30-6:00     Thomas Heiman, George Mason University
	      Lessons from the Analysis of Gene Expression Data:
              A comparison of methods for inferring gene networks and
              different data sets
           

Friday, October 26, 2001

8:30-9:00    Breakfast and Registration

9:00-10:00   Amir Ben-Dor, Agilent Laboratories
             Overabundance Analysis with Applications in Cancer
             Sub-CLassification

10:00-10:30  Mat Soukup and Jae K. Lee, Univeristy of Virginia
             Identifying Multiple-Factor Genes and Evaluating
             Classification Probability for Distinct Biological Groups
             Based on Gene Expression Data: Stepwise Cross-Validated
             Discriminant Analysis

10:30-11:00  Break

11:00-11:30  Rebecka Jornsten, University of California, Berkeley
             MDL Gene Subset Selection for Classification

11:30-12:00  Virginie Aris, Peter Tolias and Michael Recce,
             Center for Applied Genomics, Public Health Research
             Institute, and Center for Computational Biology and 
             Bioengineering, NJIT
             Selective Expression Algorithm for Class Separation
             for DNA Microarrays

12:00-2:00   Lunch

2:00-3:00    Yidong Chen, Cancer Genetics Branch, National Human Genome 
             Research Institute, National Institutes of Health, 
             Bethesda, Maryland
             Microarray Image Analysis and Expression Ratio Statistics

3:00-3:30    N. Ge, F. Huang, P. Shaw and C. Wu,
             Aventis Pharmaceuticals, Bristol-Myers Squibb, and University 
             of Michigan
             PIDEX: a Statistical Approach for Screening Differentially
             Expressed Genes Using Microarray Analysis

3:30-4:00    Break

4:00-5:00    Honghui Wan, NCGR, NIH
             Gene Expression Analysis System from Multiple Biological
             Information Resources

5:00-5:30    S. Rifkin and J. Kim, Yale University
             Geometry of Gene Expression Dynamics

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