Research

Comparative genomics to facilitate gene annotation
- Fast and accurate protein-to-genome alignments to provide homology evidence for genome annotations
- Improving protein-coding genes in non-model organism genomes using orthologs and sequence conservation
- Reasonable Gene Ontology (GO) annotation to non-model organism genomes
Orthology inference and whole genome alignment (see more in Random Questions)
- Reporting orthologs and paralogs as part of eukaryotic genome annotation
- Comparative genome browsers that are flexible and scalable
- Ux and stories: what have been the most useful to users?

Developing tools to systematically detect lineage(s)-specific modifications in gene copy numbers and gene regulatory networks (GRNs), as a part of a NSF-BSF-EDGE project
Comparative genomics of Schrenkiella parvula and Eutrema salsugineum, extreme stress-adapted relatives of Arabidopsis and Brassicaceae crops (e.g. Camelina, canola, and other Brassica crops; see target species), as a part of a multi-institution DOE project
Comparative genomics of invasive and native Phragmites australis (common reed) in North America, collaboration w/ Keith Clay (Tulane) and Kurt Kowalski (USGS)
Comparative genomics of seagrass Halophila stipulacea and its freshwater relative Vallisneria americana, collaboration w/ Simon Barak and Gidon Winters (Ben Gurion U. of Negev, Israel)

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