Integrating the sequence and map into a genome

Speaker Name: 
Jim Kent
Speaker Title: 
Research Scientist, PI, Architect of the UCSC Genome Browser
Start Time: 
Wednesday, August 5, 2015 - 2:00pm
End Time: 
Wednesday, August 5, 2015 - 3:00pm
506 Engineering 2

In this talk Jim Kent recounts his days working on the human genome project. The project initially sequenced the yeast and C. elegans genomes to develop techniques to apply to the much larger human genome, and as a service to the scientists working on these organisms. Working on C. elegans, but outside of the genome project, Jim developed mRNA/DNA alignment tools, the Intronerator browser, and later, working with David Haussler a cross species genome alignment tool that laid the foundation for his human work. David Haussler was shortly invited into the analysis group of the genome project to do gene predictions to help make sense of the sequence, but found that the sequences were still in fragments too short to be usable. Jim played initially a supporting, but eventually a leading role in producing a draft assembly that succeeded in making the sequence usable. Later he developed the UCSC Genome Browser to help integrate and visualize the diverse sets of available genomic information. Then he turned his hand to helping clean up and finish the physical map of the genome, which in turn was used to guide the selection of BACs to sequence in order to close the gaps and complete the euchromatic parts of the genome. Recently he has worked with Karen Miga to produce draft versions of the centromeres and other heterochromatic regions formerly considered impossible to assemble, motivated in part by the artifacts caused by the absence of these regions when mapping short reads.