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Comparative genomics to facilitate gene annotation
- Reasonable and reliable Gene Ontology (GO) annotation to non-model organism genomes
- Improving protein-coding gene models using sequence conservation in non-model organism genomes
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Orthology inference and whole genome alignment (see more in Random Questions)
- What are the best pipelines + how to evaluate and improve?
- Ux and stories: what have been the most useful to users?
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Contributing to comparative genomics resources development, personal wish list:
- Comparative genome browser, scalable (and useful) ortholog groups, etc.
- Resources that assist genome analysis/annotation by the user
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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{:target="_blank"}
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Comparative genomics of Schrenkiella parvula{:target="_blank"} and Eutrema salsugineum{:target="_blank"}, extreme stress-adapted relatives of Arabidopsis and Brassicaceae crops (e.g. Camelina, canola, and other Brassica crops; see target species{:target="_blank"}), as a part of a multi-institution DOE project{:target="_blank"}
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Comparative genomics of invasive and native Phragmites australis (common reed) in North America{:target="_blank"}, collaboration w/ Keith Clay (Tulane) and Kurt Kowalski (USGS)
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Comparative genomics of seagrass Halophila stipulacea{:target="_blank"} and its freshwater relative Vallisneria americana{:target="_blank"}, collaboration w/ Simon Barak and Gidon Winters (Ben Gurion U. of Negev, Israel)
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