2179
Next Generation Genome Annotation and Analysis

We have entered a world where individual investigators can afford to sequence new eukaryotic genomes. While large-scale sequencing is becoming routine, genome annotation and analysis is much less so. Many genome projects have stalled in the final stages of annotation and analysis, despite having in hand a sequenced and assembled genome. A central challenge for new genome projects is how to manage the genome annotation process and to integrate those annotations with downstream comparative genomics, expression and phenotype-genotype association studies. Highlighting a number of recent and successful genome annotation and analysis efforts, this session provides a practical introduction to annotating your new genome, and integrating the results with downstream analyses. This session will prove useful to anyone involved in a new eukaryotic genome project.
Date: Saturday, January 11, 2014
Time: 4:00 PM-6:10 PM
Room: Towne - Meeting House
Organizer:
Barry Moore
4:00 PM
A Fishy Tale of Two Sequenced Vertebrate Genomes: Lamprey and Coelacanth
Chris Amemiya, Benaroya Research Institute; Michael S. Campbell, University of Utah; Mark Yandell, Eccles Institute of Human Genetics, University of Utah; Jeramiah J. Smith, University of Kentucky

4:20 PM
Genome Annotation and Comparative Genomics in Fungi
Jason Stajich, University of California Riverside

4:40 PM
Genome of the Long-Living Sacred Lotus (Nelumbo nucifera Gaertn.)
Ray Ming, University of Illinois at Urbana-Champaign; Robert VanBuren, University of Illinois at Urbana-Champaign; Mei Yang, Wuhan Botanical Garden, China; Yanling Liu, Wuhan Botabical Garden, China; Michael Schatz, Cold Spring Harbor Labrotary; Mark Yandell, Eccles Institute of Human Genetics, University of Utah; Claude dePamphilis, Penn State University; Andrew H. Paterson, Plant Genome Mapping Laboratory, University of Georgia; Shaohua Li, Wuhan Botanical Garden; Jane Shen-Miller, UCLA

5:00 PM
Introns, Ancient Transposable Elements and Gene Families Revealed in the Annotation of the Loblolly Pine (Pinus taeda L.) Megagenome
Jill Wegrzyn, University of Connecticut; John Liechty, Department of Plant Sciences, University of California, Davis; Kristian Stevens, Department of Evolution and Ecology, University of California, Davis; Carol Loopstra, Texas A&M University; Hans Vasquez-Gross, University of California Davis; Brian Lin, University of California, Davis; Jacob Zieve, University of California, Davis; Pedro J Martinez-Garcia, Department of Plant Sciences University of California; Carson Holt, University of Utah; Mark Yandell, Eccles Institute of Human Genetics, University of Utah; Aleksey Zimin, Institute for Physical Science and Technology, University of Maryland; James A Yorke, University of Maryland; Marc Crepeau, Department of Evolution and Ecology, University of California, Davis; Daniela Puiu, Johns Hopkins University, School of Medicine; Steven L Salzberg, Johns Hopkins University, School of Medicine; Pieter J. deJong, Children's Hospital Oakland Research Institute; Keithanne Mockaitis, Indiana University; Dorrie Main, Washington State University; Chuck Langley, University of California, Davis; David Neale, Dept. Plant Sciences University of California Davis

5:20 PM
The Genotype Phenotype Association Toolkit (GPAT) Applications in Population Genomics
Zev Kronenberg, Eccles Institute of Human Genetics, University of Utah; Mark Yandell, Eccles Institute of Human Genetics, University of Utah

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