Associate Professor in Plant Genomics and Bioinformatics
Biography: I obtained my Ph.D. in Genomics and Bioinformatics from Pennsylvania State University where I used network analysis to explore guard cell signaling and gene expression. I did my postdoc at Duke University where I developed computational tools for annotating alternative splicing isoforms, antisense transcription, and non-coding RNA in Arabidopsis roots. I joined Virginia Tech in 2014 and have been working on the application of machine learning in plant genomics and phenomics in both model species and crop species. My current favorite non-model plant is edamame and we are working on enhancing domestic production of edamame. My basic plant biology focus is on transcriptome analysis and understanding how to translate knowledge such as the regulation of gene expression from model species to crop species.
Presentation title: Application of Explainable Machine Learning Methods in Plant Genomics and Phenomics
Biography: I grew up in rural Minnesota during the 1980s farm crisis, have seen changes and challenges that farming communities face, and have worked towards envisioning a better tomorrow through science. My professional interests have focused on translating basic research into new applications to accelerate solving complex biological problems. During graduate school, I studied mechanisms of epigenetic gene regulation and developed a method for genome-wide DNA methylation profiling to better understand the impact of epigenetic inheritance on phenotypic variation. At Corteva Agriscience, I lead a discovery research team that aims to produce doubled haploid populations more efficiently. In one aspect, the work comprises enabling a reliable and reproducible paternal doubled haploid method for maize. This presentation will describe how we have collaborated with an external partner to leverage artificial intelligence methods to better understand the recalcitrance of maize microspores as an example of using a new technology to solve an old challenge.
Presentation title: Enabling Maize Microspore Embryogenesis Using Machine Learning
Senior Staff Scientist
Biography: Dr. Seung Yon (Sue) Rhee is a Senior Staff Member of Plant Biology Department at Carnegie Institution for Science. Her group strives to uncover molecular mechanisms underlying adaptive traits in the face of heat, drought, nutrient limitation, and pests. Dr. Rhee’s group studies a variety of plants including models, crops, medicinal and desert plants. Her group employs computational modeling and targeted laboratory testing to study mechanisms of adaptation, functions of novel genes, organization and function of metabolic networks, and chemical and neuronal code of plant-animal interactions. Her group is also interested in developing translational research programs involving biomass maximization under drought in bioenergy crops. More recently, Dr. Rhee has spearheaded a grassroots community building effort called the Plant Cell Atlas initiative, which strives to map all the molecular determinants of plant cells in order to understand and engineer them. Dr. Rhee received her B.A. in biology from Swarthmore College in 1992 and a Ph.D. in biology from Stanford University in 1997. She has been an investigator at Carnegie’s Plant Biology Department since 1999. Dr. Rhee’s work is done on Stanford University campus, located on the ancestral land of the Muwekma Ohlone Tribe, which was and continues to be of great importance to the Ohlone people.
Presentation title: Towards elucidating functions of all genes in plants