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Stein Lab

Stein Lab. In-House Symposium 2002. The Plan. Overview of my lab’s activities Detailed look at the Gramene Database Run out of time Talk really fast Thunderous applause. The HapMap Project. Gudmundur Thorisson. Ravi Sachidanandam. WormBase. Peter D’Eustachio. Todd Harris. Jason

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Stein Lab

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  1. Stein Lab In-House Symposium 2002

  2. The Plan • Overview of my lab’s activities • Detailed look at the Gramene Database • Run out of time • Talk really fast • Thunderous applause

  3. The HapMap Project Gudmundur Thorisson Ravi Sachidanandam

  4. WormBase Peter D’Eustachio Todd Harris Jason Stajich Fiona Cunningham Jack Chen

  5. Genome KnowledgeBase Peter D’Eustachio Geeta Joshi-Tope Marcela Tello-Ruiz

  6. Maize & Arabidopsis Insertion Databases Xiaokang Pan

  7. Generic Model Organism Database Scott Cain Shulamit Avraham

  8. Gramene Doreen Ware Chris Mahr Xiaokang Pan, Steve Schmidt, Lenny Teytelman, Wei Zhang Ken Clark (Dallas)

  9. Rice as a Model Monocot • Rice genome is 400 Mbp • Maize is 2.8 Gbp • Wheat is 16 Gbp • Large-scale & microsynteny among grasses

  10. Genomics by Proxy Maize, Barley, Sorghum, Oat, Wheat… Rice trait candidate1 candidate2 candidate3

  11. What’s in Gramene • High-throughput data • Rice genome (two cultivars) • Gene predictions • Rice proteins • Functional annotation of gene products • EST collections (rice & other cereals) • Curated data • Genetic maps • Physical maps • Protein annotation • Mutants & phenotypes • QTLs

  12. Find Candidates in a Maize Interval

  13. Add Rice Genetic & Physical Maps

  14. Zoom in on Contig

  15. Zoom to Rice Genome

  16. Examine Individual Gene

  17. Gene Prediction Details

  18. Protein Page

  19. Rice Mutant: semidwarf-1

  20. Term: Stem Anatomy Ontology

  21. Term: Cum length Trait Ontology

  22. Development Ontology

  23. Find all rice mutants in my favorite synteneic region associated with dwarfism. What genes within a starch content QTL are predicted to be involved in carbohydrate metabolism? Find protein orthologs between rice & maize whose stage-specific expression patterns have changed. What Ontologies Let You Ask

  24. Next Steps • Finished chromosomes • Rice chromosomes 1 & 4 have just been finished. • Rice chromosome 10 is in preparation. • Others finished over next year. • Produce uniform annotation of rice genome. • “Genes of Maize” project. • Panzea project: genetic variability among wild populations

  25. CSHLCornell University Ken ClarkSusan McCouch Chris MahrPankaj Jaswal Xiaokang PanJun-Jian Ni Steve SchmidtImmanuel Yap Lenny Teytelman Wei Zhang Doreen Ware Credits Peter VanBuren

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