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Research Breaks Through Genetic Name Game

Faculty Profile: Hongfang Liu

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March 16, 2010 – The gene-naming process can lend itself to duplication, but clinical informatics expert Hongfang Liu has created an easier way for researchers to identify specific genes.
 
Liu developed the BioThesaurus mapping system nearly five years ago to help scientists avoid naming genes and proteins that have already been named or giving genes and proteins names already in use. Now, she’s using recent federal stimulus grants from the National Institutes of Health (NIH) and the National Science Foundation (NSF) to further enhance the Web-based system.

She plans to advance BioThesaurus by having it compare sequences and/or functions of the genes and link them according to related characteristics.

An assistant professor in the department of biostatistics, bioinformatics and biomathematics, Liu’s research is recognized as critical to storing and retrieving information about genes and proteins.

Scientists use BioThesaurus to find particular genes relevant to their research. The online resource consists of more than 2.8 million names extracted from multiple molecular biological databases.

“It’s a big mess out there,” says the professor. “A lot of people assign names to genes not realizing other people have already done that.”

For example, “Asp” refers to 14 genes across eight species, and there also may be many names associated with a single gene.

The researcher is working toward her goal with a $1.2 million two-year NIH grant and a $843,000 NSF grant, awarded this academic year as a result of the American Recovery and Reinvestment Act of 2009.

The professor admits that identifying genes and proteins with the same name or functions can be a daunting task. But there are some names she says she won’t have to worry about coming up more than once in the database -- names such as the “Pokémon” gene mutation and the “fear of intimacy” and “Smurf” gene. They provide a bit of comic relief, Liu says.

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