BPP Fall Seminar Series
December 3 | Dr. Jill Wegrzyn
Cyberinfrastructure for forest health and conservation
Plant health, productivity, and biogeographical response to environmental challenges have consequences beyond food and timber production: they affect the environment, spanning areas of biodiversity, carbon cycling, and planetary health. Providing access to high quality genotypic, phenotypic and environmental data in a semantically aware, geospatial-enabled, web-based platform will enable interrogation, storage, and exchange of data from large-scale association studies. I will introduce CartograTree, the first web-based application that integrates genotype and phenotype data for model and non-model plant systems with global environmental layers. This field to analysis framework connects data collection, data submission, ontology-based metadata annotation, and analytics directly to high performance computing. Our interest in open-source and reproducible software extends to tools that support the development of high quality genomic inputs needed for these population level studies. In specific, I will discuss strategies for improving genome assembly as well as structural and functional annotation for large and complex plant genomes.
Jill Wegrzyn is an Assistant Professor of Ecology and Evolutionary Biology in the Department at UConn where she leads the Plant Computational Genomics Lab. She is also the director of the Computational Biology Core within the Institute of Systems Genomics. Her work focuses on the computational analysis of genomic and transcriptomic sequences from non-model plant species. She develops approaches to examine gene finding, gene expression, transcriptome assembly, and conserved element identification, through machine learning and computational statistics. She uses these novel methods to address questions related to genome biology and population genomics in forest tree species. She also develops web-based applications that integrate data across domains to facilitate the plant geneticist or ecologist’s ability to analyze, share, and visualize their data. Such integration requires the implementation of semantic technologies and ontologies to connect genotype, phenotype, and environmental data.