Branching out at CSHL: adding plant genomics to statistics and math as an URP*

By Erin DeNardo

                  This past summer, I spent my time with the Ware Lab at the Cold Spring Harbor Laboratory in New York, evaluating computational tools and performing statistical analyses on genomic data, specifically in Oryza sativa.  My project involved running Interpreting Changes to Exons (ICE) on the rice genome, performing proof-of-principle testing on the WAXY gene, which is responsible for the sticky phenotype in cooked rice.  This allowed for representation of the changes across three major varietal groups in rice.  To perform initial data analysis, I produced scripts in Perl and ran them on sets of thirty and ninety individuals in the rice population, allowing me to hone my scripting skills in genetic analyses.  The results of this data analysis aligned with what would be expected based on known biological principles.

                  Turning to the world of plant genomics presented a pretty steep learning curve, as I am a mathematics and systems engineering major at Washington University in St. Louis, having pursued only research in human genetics.  Through my experience, however, both my knowledge of plants and my ability to work with computational biology tools were greatly strengthened.  I gained a great deal of experience in handling large genomic data sets, as well as a stronger understanding of population-level genetic variation.  This summer was a dream come true, and I could not have asked for a better experience!

*The Undergraduate Research Program (URP) at CSHL provides an opportunity for undergraduate scientists from around the world to conduct first-rate research.  For more information, go to https://www.cshl.edu/Education/Undergraduate-Research.html