EASEL (Efficient, Accurate, Scalable Eukaryotic modeLs), a Tool for Improvement of Eukaryotic Genome Annotation
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• Benchmarking of existing annotation across diverse plant genomes (multiexonic vs. monoexonic genes and BUSCO completeness)
• Optimizing AUGUSTUS and training (with RNA/EST hints) to improve gene prediction for non-model organisms
• Scaling the framework for organisms with larger genome sizes
Expression Analysis of Needle Abscission in Easetern North American Firs
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• Assemble RNA-Seq transcript data of three gymnosperm species (Abies balsamea, Abies fraseri and Abies balsamea phanerolepis) using Oyster River Protocol
• Identify genes expressed at the extremes of needle abscission retention (good vs bad)
Complete Genome Assembly of Inga vera
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• Estimate genome size in GenomeScope
Comparative Transcriptomic Analysis of Juvenile and Adult Leaf Morphologies in Conifers
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• Evaluate differences in anatomy and gene expression patterns of juvenile and adult conifer leaves from two independent lineages (Juniperus flaccida and Pinus cembroides) known to exhibit heteroblastic development
• Perform de novo RNA-Seq analysis on twelve libraries sequenced on Illumina with HiSeq 2500 (100bp PE)
• Identify differentially expressed genes in each species using DESeq2 and categorize them by biological functional via network analysis with GeneMANIA
• Functionally classify Gene Ontology (GO) terms and run OrthoFinder to identify gene families