Cattle represent an important source of human nutrition. There are more than 800 recognized breeds of cattle, some of which are bred for beef production (e.g., Angus), and some for dairy (e.g., Holstein). We will develop and evaluate computational methods to identify and characterize the patterns of genetic differences (haplotypes) between breeds. The ultimate goals are to improve the process of cattle breeding, to promote animal health and to improve human nutrition. Another focus is on plant parasites that result in substantial economic losses worldwide. The soybean cyst nematode (SCN) is the major pest of soybean, causing an estimated $1.5 billion in damage throughout the U.S. each year. In this project, we analyze microarray data to identify genes that improve resistance response in soybean to invasion by soybean cyst nematode. By analyzing the genetic properties of plants that are naturally resistant to these pests, it may be possible to increase agricultural yields while reducing dependence on pesticides.
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Analysis of LD blocks in Cattle.

The aim of this project is to provide a knowledgebase (PATOMICS) that will serve as a portal to the intellectual property world of the human genome. The PATOMICS database permits several approaches to the analysis of patents that include nucleic acid or protein sequence data: Users can search patents by title, dates, keywords, type of claim (e.g., diagnosis, therapy, genetic engineering), by scope of coverage (e.g., patents dealing with specific diseases), or by similarity to user-supplied sequences, gene name, or chromosome location. Users can visualize the patent landscape as a custom track on the UCSC Genome Browser. This integrated informatics facility provide researchers with a unique resource to probe intellectual property rights in the human genome.

Patented sequences as custom track on UCSC Genome Browser.