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

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

6. Maize & Arabidopsis Insertion Databases Xiaokang Pan

7. Generic Model Organism Database Scott Cain Shulamit Avraham

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

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 candidate 1 candidate 2 candidate 3 trait Maize, Barley, Sorghum, Oat, Wheat… Rice

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. Anatomy Ontology  Term: Stem

21. Trait Ontology  Term: Cum length

22. Development Ontology

23. What Ontologies Let You Ask  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.

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. Credits CSHLCornell University Ken Clark Susan McCouch Chris Mahr Pankaj Jaswal Xiaokang Pan Jun-Jian Ni Steve Schmidt Immanuel Yap Lenny Teytelman Wei Zhang Doreen Ware Peter VanBuren