Kevin D. Deem

The paper re-annotates pea aphid genomes using an integrated approach to improve gene models and enable better analysis of duplication and evolution.

The paper analyzes gene duplication and sub-functionalization in the wing gene regulatory network of pea aphids, finding limited morph-biased expression and functional divergence in duplicated genes.

The paper develops a workflow for annotating regulatory sequences in insect genomes and provides a database with enhancer predictions for 33 species, validated through multiple lines of evidence.

The paper identifies and evaluates enhancer activity in Tribolium castaneum using chromatin profiling and a cross-species reporter assay system.