The Transcriptiome 2002 meeting was held March 11-13,2002 in Seattle, Washington with attendance by more than 300 scientists representing the international community. The scientific program (see attached) was developed by an international organizing committee consisting of Yoshihide Hayashizaki of The Institute for Physical and Chemical Research (RIKEN), Winston Hide from the South African National Bioinformatics Institute, John Quackenbush of The Institute for Genomic Research (TIGR), Andrew Simpson of the Ludwig Institute for Cancer Research, and Stefan Wiemann from the German Cancer Research Center, with assistance from Roger Bumgarner of the University of Washington. In association with the main meeting, an IMAGE Consortium invitational meeting was organized by Charles Auffrey of CNRS and held with approximately 40 participants immediately following the conclusion of the Transcriptome meeting.

Funds from this grant from the Department of Energy to support this meeting were supplemented by additional funds obtained through a grant from the National Cancer Institute and corporate donations from Amersham Biosciences, Mergen Ltd., Arcturus, Novartis, Agilent, and Affymetrix, as well as through registration fees collected from the participants.

Overall, the feedback from participants was extremely positive and plans were made to hold a Transcriptome 2003 meeting in October in Shanghai, China, to be organized by Zhu Chen of the Chinese Academy of Sciences.

DISCLAIMER

This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency Thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

DISCLAIMER Portions of this document may be illegible in electronic image products. Images are produced from the best available original document.

Transcriptome 2002 Agenda

Sunday, March 10

12:OO-8:OO pm Registration (Grand Registration)

2:OO-5:00 pm Exhibit Set Up (Fifth Avenue Room)

4:OO-6:30 pm Plenary Session 1: The Role of Transcription (Grand Ballroom 111)

Chair: John Quackenbush, The Institute for Genomic Research Introduction and Welcome Keynote Lectures: Leroy Hood, Institute of Systems Biology Systems Biology: Integrating Genomics, Proteomics, Computation and Biology

Mark Boguski, Fred Hutchinson Cancer Research Center Bioinformatics and Genome Sciences

6:30 -8:OO pm Welcome Reception (Elliot Bay Room, Lower Level)

Monday, March 11

7:OO am-6:00 pm Registration (Grand Registration)

7:OO-8:OO am Breakfast (Grand Ballroom 11)

7:OO am-1:30 pm Poster Set Up (Fifth Avenue Room)

8:OO-1O:OO am Plenary Session 2: Transcription and Processing I (Grand Ballroom 111)

Chair: Stefan Wiemann, German Cancer Research Center Frank Grosveld, Erasmus University Globin Gene Activation: a Stochastic Process

Juan Valcarcel, European Molecular Biology Laboratory Molecular Mechanisms of Splicing Regulation

Winston Hide, South African National Bioinformatics Institute Alternate Splicing and Gene Expression States: Using cDNAs To Explore the Human Genome

Vladimir Kuznetsov, National Institute of Child Health and Human Development Size-Dependent Pareto-like Distributions in Genomics and Prediction of the Number of Protein-Coding Genes in Human Genome

'

1O:OO-10:30 am BREAK (Fifth Avenue Room)

10:30 am-1:00 pm Plenary Session 3: Transcription and Processing I1 (Grand Ballroom 111)

Chair: Bento Soares, University of Iowa Jonathan Gott, Case Western Multiple Determinants of RNS Editing in Phsarum Mitochondria

Thomas Preiss, European Molecular Biology Laboratory Employing DNA Microarrays to Study Eukaryotic Translation

Tom Gingeras, Affymetrix RNA Transcription Detected on Chromosomes 21 and 22 Using High Density Oligonucleotide Arrays

Eric Schadt, Rosetta Inpharmatics The Genetics of Gene Expression

Mark Carter, National Institute on Aging A Novel 22,000 Featureih Situ-Synthesized 60-Mer Oligonucleotide Microarray: Expression Profiling Of E12.5 Mouse Embryo and Placenta

1:OO-2:00 pm Lunch (Grand Ballroom 11)

2:OO-3:00 pm Formal Poster Session for ODD Numbered Posters and Exhibit Session (Fifth Avenue Room)

3:OO-5:OO pm Plenary Session 4: cDNA Based Gene Discovery I (Grand Ballroom 111)

Chair: Charles Auffray, CNRS Robert Strausberg, National Cancer Institute The NIH Mammalian Gene Collection

Osamu Ohara, Kazusa DNA Research Institute Kazusa cDNA Project 2002; From Transcript to Protein

Sumio Sugano, University of Tokyo FLJ cDNA Project in Japan

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Stefan Wiemann, German Cancer Research Center The German cDNA Network -cDNAs for Functional Genomics and Proteomics

5:OO-5:30 pm BREAK (Fifth Avenue Room)

5:30-7:30 pm Plenary Session 5: cDNA Based Gene Discovery I1 (Grand Ballroom 111)

Chair: Winston Hide, South African National Bioinformatics Institute Yoshihide Hayashizaki, RIKEN Genomic Sciences Center RIKEN Mouse Genome Encyclopedia

Minuro KO, National Institute on Aging Gene Catalog of Mouse Stem Cells and Early Embryos

Andrew Simpson, Ludwig Institute Definition of Human Transcriptomes Using ORESTES

Bento Soares, University of Iowa The University of Iowa Mammalian Gene Discovery and Expression Program

Evening Free Night

Tuesday, March 12

7:OO-8:OO am Breakfast (Grand Ballroom 11)

7:30 am-6:00 pm Registration (Grand Registration)

8:OO-1O:OO am Plenary Session 6: Transcription and Processing I11 (Grand Ballroom 111)

Chair: Yoshihide Hayashizaki, RIKEN Genomic Sciences Center Joakim Lundeberg, Royal Institute of Technology Microarray Technology for Transcript Profiling and Analysis of Genetic Variability

Claudio Schneider, LNCIB cDNA-Microarray Profiling of Ovarian Cancer

Zhu Chen, Chinese Academy of Sciences Transcriptome Study in China

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Lukas Wagner, National Institutes of Health Clone Selection and Analysis Methods for Full-Insert cDNA Sequencing

1O:OO-10:30 am BREAK (Fifth Avenue Room)

10:30 am-12:30 pm Plenary Session 7: Sequence-Based Tools for Gene Discovery I (Grand Ballroom 111)

Chair: Andrew Simpson, Ludwig Institute for Cancer Research

Yudan Lee, The Institute for Genomic Research Comparative Genomics Tools: TIGR Gene Indices and TIGR Orthologous Gene Alignments (TOGA)

Graziano Pesole, University of Milan UTRDB and UTRSITE: Specialized Databases of Sequences and Functional Elements of 5? And 3? Untrunslated Regions of Eukaryotic MRNAS

Peg Folta, Lawrence Livermore National Laboratory I.M.A.G.E. Data Mining Tools

Kim Pruitt, NCBI Using NCBI Resources for Gene Discovery

12:30-1:30 pm Lunch (Grand Ballroom 11)

1:30-2:30 pm Formal Poster for EVEN Numbered Posters and Exhibit Session (Fifth Avenue Room)

2:30-4:30 pm Plenary Session 8: Sequence-Based Tools for Gene Discovery I1 (Grand Ballroom 111)

Chair: Greg Lennon, Cell Logic, Inc.

Tim Hubbard, The Sanger Centre

Roger Bumgarner, University of Washington, Extraction of Biological Meaning from Array Data: What is Required?

Len Pennacchio, Lawrence Berkeley National Laboratory, Comparative and Functional Analysis of Cardiovascular-Related Genes

Essam Zaki, The Detection of Env-Transcripts in Gossypium

‘’ 4:30-5:OO pm BREAK (Fifth Avenue Room)

5:OO-7:00 pm Plenary Session 9: Gene Expression - Transcript Abundance and Disease (Grand Ballroom 111)

Chair: John Quackenbush, The Institute for Genomic Research

Eric Hoffman, Children’s National Medical Center Delineation of Transcriptional Pathways in Vivo: Temporal Profiling in Muscle Regeneration

Timothy J. Yeatman, H. Lee Moffitt Cancer Center and Research Institute Application of Arrays to the Study of Colon Cancer

Saurabh Saha, Johns Hopkins School of Medicine Using SAGE to Explore the Genome

Howard Jacob, Medical College of Wisconsin System Biology: From Genome to Physiology

7:30-1O:OO pm “Seattle at Night”-Dinner at the Space Needle (Free for attendees)

Wednesday, March 13

7:OO-8:00 am Breakfast (Grand Ballroom 11)

7:30 am-1 :00 pm Registration (Grand Registration)

8:OO-10:30 am Plenary Session 10: Alternate Measures of Expression (Grand Ballroom 111)

Chair: Winston Hide, South African National Bioinformatics Institute

N. Leigh Anderson, Large Scale Biology Corporation Gels, Mass Spectrometry and Chips: Large Scale Acquisition of Protein Abundance Fingerprints

Marc Vidal, Harvard Medical School Toward a Proteome Atlas for C-elegans

' Frank Holstege, University Medical Center-Utrecht Protein Interaction Verzfication and Functional Annotation by Integrated Analysis of Genome-Scale Data

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Mihael Polymeropoulos, Novartis Pharmaceuticals Corporation

Moncef Jendoubi, Miligen, Inc. Breaking the Bottle Neck of Genomics and Proteomics

10:30-11:OO am BREAK (Fifth Avenue Room)

11 :00 am-1 :00 pm Plenary Session 11 : The Future (Grand Ballroom 111)

Chair: Zhu Chen, Chinese Academy of Sciences

John Quackenbush, The Institute for Genomic Research Back to the Future: Integrating Expression with Genomic, Genetic, and Metabolic Data

Ken Buetow, National Cancer Institute Combining Bioinformatics and Genomics to Gain Insight into the Etiology of Cancer

Helen Parkinson, European Bioinformatics Insitute ArrayExpress - A Public Database for Microarray Data

Rajiv Raja, Arcturus, Inc. A Novel Platform for High-Sensitivity Analysis of Cell-SpeciJic Gene Expression Using Microarrays

1:OO-2:00 pm Lunch (Grand Ballroom 11)

2:OO-4:00 pm Poster and Exhibit Removal (Fifth Avenue Room)

**Conference Officially Ends

Thursday, March 14

8:OO am-5:00 pm IMAGE Consortium Invitational 2002 (by invitation only) (Elliott Bay Room, Lobby Level)