SAGE 2004 Conference Program Thursday, September 30 4:00 PM- 6:00 PM

Registration, set up posters

6:00 PM-

Opening reception

Friday, October 1 7:00- 8:00 AM 8:00- 8:10 AM

Breakfast Welcome and introduction Kornelia Polyak/Eric Suh

8:10- 9:00 AM

Keynote Talk, George Church, Harvard Medical School, Boston, MA New technologies and models for integrative systems biology SESSION 1 SEQUENCING THE “OMES” Chair: Kornelia Polyak, Dana-Farber Cancer Institute 9:00- 9:25 AM Victor Velculescu, Johns Hopkins University, Baltimore, MD Mutational analysis of the colorectal cancer genome 9:25-9:50 AM

William Sellers, Dana-Farber Cancer Institute, Boston, MA

9:50-10:15 AM Andy Futreal, Wellcome Trust Sanger Institute, UK Large scale investigations of human cancer somatic genetics 10:15-10:40 AM

Coffee Break

10:40-11:05 AM Heiko Hermeking, Max-Planck Institute, Munich, Germany Digital karyotyping of cancer cell genomes 1

11:05-11:55 AM

3 short talks selected from abstracts:

Patrick W.P. Ng-Genome Center Singapore, Singapore Gene Identification Signature (G.I.S.) Analysis for Transcriptome Chracterization Colin Collins- End sequence profiling (ESP), End sequence profiling (ESP): a sequence-based approach to structural analysis of tumor genomes Keji Zhao- Laboratory of Molecular Immunology, NHLBI, NIH, Bethesda, MD Genome-wide Mapping of Histone Modifications 12:00- 1:30 PM

Lunch

SESSION 2 Technical developments in SAGE and sequencing Chair: Kevin McKernan, Agencourt 1:30- 1:55 PM Matthew Meyerson, Dana-Farber Cancer Institute, Boston, MA Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments 1:55- 2:20 PM John Dunn, Brookhaven National Laboratory, Upton, NY SACO: a High-throughput, SAGE-based Method for Identifying In Vivo Functional Protein Binding Sites in Whole Genomes 2:20- 2:45 PM ChiaLin Wei, Genome Institute of Singapore, Singapore Gene Identification Signature (G.I.S.) Analysis for Transcriptome Characterization and Genome Annotation 2:45- 3:10 PM

Coffee break

3:10- 3:35 PM Gina Costa, Agencourt, Beverly, MA BEAD-BASED POLONY SEQUENCING 3:35- 4:00 PM Kornelia Polyak, Dana-Farber Cancer Institute, Boston, MA Using digital karyotyping for global methylation profiling 4:00- 4:50 PM

3 short talks selected from abstracts:

Ryohei Terauchi, Iwate Biotechnology Research Center, Iwate, Japan SuperSAGE: a powerful SAGE variant suitable for gene function analysis Shin-Ichi Hashimoto, University of Tokyo, Tokyo, Japan SAGE for 5’-ends transcriptome Guo-Liang Wang, Ohio State University, Columbus, OH Deep Transcriptome Analysis of the Rice and Rice Blast Genomes Using LongSAGE and MPSS Technologies 5:00- 7:00 PM

Poster session 2

Saturday, October 2 7:00- 8:00 AM

Breakfast

SESSION 3 BIOINFORMATICS, INTEGRATION OF RNA AND DNA LEVELS Chair: Greg Riggins, Johns Hopkins University 8:00- 8:25 AM Robert Gentleman, Dana-Farber Cancer Institute, Boston, MA SAGELzyer: and interactive query tool for SAGE databases 8:25- 8:50 AM Sandro de Souza, Ludwig Institute, Sao Paolo, Brazil The effect of alternative splicing and SNPs in the interpretation of SAGE and MPSS data 8:50- 9:15 AM Frank Baas, University of Amsterdam, Netherlands The transcriptome of rhabdomyosarcoma 9:15- 9:40 AM Michael Hauser, Duke University, Durham, NC Identification of candidate genes for Parkinson Disease (PD) using Genomic Convergence 9:40-10:00 AM

Coffee Break

10:00-10:25 AM Robert Vertseeg, University of Amsterdam, Netherlands Comparison of the Human and Mouse Transcriptome Maps 10:25-10:50 AM Haiyan Huang, University of California Berkeley, Berkeley, CA Analyzing SAGE data using a Poisson approach 10:50-11:40 AM

3 short talks selected from abstracts:

Kuo Ping Chiu-Genome Center Singapore, Singapore Applications of Compressed Suffix Array and GISditagTool for Ditag Based Transcriptome Analysis Yuri Nikolsky-GenGeo Inc., St. Joseph, MI System-level analysis of SAGE and other high-throughput data in the context of functional networks Xijin Ge- Northwestern University, Evanston, IL Using tissue-specific SAGE reference database to identify the original genes for SAGE tags shared by multiple genes 12:00- 1:30 PM

Lunch

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SESSION 4 MODEL ORGANISMS AND DEVELOPMENT Chair: Frank Baas, University of Amsterdam 1:30- 1:55 PM San Min Wang, Northwestern University, Evanston, IL Detecting novel transcripts in the Drosophila genome 1:55- 2:20 PM Allan Delaney, British Columbia Cancer Res. Center, Vancouver B.C Quantitative and comprehensive gene expression profiles in developing mouse tissues and in human embryonic stem cell lines 2:20- 2:45 PM Jean-Marc Elalouf, CEA Saclay, France The long SAGE story of the mouse brain 2:45- 3:10 PM

Hamish Scott, University of Melbourne, Australia

3:10- 3:30 PM

Coffee Break

3:30- 3:55 PM

Ramesh Shivdasani Dana-Farber Cancer Institute, Boston, MA

3:55- 4:20 PM Seth Blackshaw, Johns Hopkins University, Baltimore, MD Genomic Analysis of Mouse Retinal Development 4:20- 5:10 PM

3 short talks selected from abstracts:

Yijun Ruan - Genome Center Singapore, Singapore Comparative Transcriptome Analysis of Murine and Human ES Cells Kay Werner- University of Bristol, Bristol, UK Exploiting environment – genotype interactions in the developing wheat grain via SAGE technology N.S. Cai - National Institute on Drug Abuse-Intramural Research Program, Baltimore, MD Serial Analysis of Gene Expression (SAGE) In the Rat Striatum After Methamphetamine Treatment 6:00 PM

Closing dinner

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Sunday, October 3 7:00- 8:00 AM

Breakfast

SESSION 5 CANCER TRANSCRIPTOMES Chair: Jean-Marc Elalouf, CEA Saclay, France 8:00- 8:50 AM keynote talk- Mariana Nacht, Genzyme, Framingham, MA Identification of regulators of vascular growth using SAGE 8:50- 9:15 AM

Daniela Gerhard, National Cancer Institute, Bethesda, MD

9:15- 9:40 AM Sara Sukumar, Johns Hopkins University, Baltimore, MD SAGE analysis reveals alterations in vascular gene expression in invasive breast carcinoma 9:40-10:00 AM

Coffee break

10:00-10:25 AM Pat Morin, National Institute of Ageing, Baltimore, MD Identification of Genes Differentially Expressed in Cisplatin-Resistant Ovarian Cancer Using Serial Analysis of Gene Expression 10:25-10:40 AM Greg Riggins, Johns Hopkins University, Baltimore, MD Locating Cancer Related Genes Using SAGE 10:40-11:05 AM Karin Oien, University of Glasgow, Glasgow, UK Gene expression profiling and classification of adenocarcinoma 11:05-11:55 AM

3 short talks selected from abstracts:

Malchenko S- University of Iowa, Iowa City, IA Global analysis of gene expression in metastatic chondrosarcoma N. Güngör- Universiteit Limburg, Diepenbeek, Belgium Gene expression profiling of pregnancy induced mammary gland differentiation Rodrigo A. Panepucci- Center for Cell-Therapy, Ribeirão Preto, Brazil Using SAGE and cluster analysis as a tool to define functional and/or ontological relationship of cells of distinct origin 12:00-12:10 PM

Closing remarks, Kornelia Polyak/Eric Suh

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