Bioinformatician Helps Biologists Find Key Genes

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Newswise Its like looking for a needle in a haystack.

Scientists searching for the gene or gene combination that affects even one plant or animal characteristic must sort through massive amounts of data, according to associate professor Xijin Ge of the mathematics and statistics department at South Dakota State University.

Biologists used to study one gene at time, but now they can look at tens of thousands of genes at once. Ge said. Just one experiment to analyze gene expression can produce one terabyte of sequence data. Thats a little beyond many biologists' comfort zone.

He leads the bioinformatics research group, which provides the expertise that SDSU plant and animal scientists need to uncover how genes and proteins affect cell functions.

Setting up the experiments Typically, scientists consult with Ge when planning their studies. After examining what they want to investigate, the researchers decide which techniques should be used to obtain data and a plan to analyze the data.

Its critical to have the statistician and biologist working together, noted plant science professor Fedora Sutton, who worked with Ge on identifying gene interactions that account for freeze resistance in winter wheat. He is able to say, based on statistical rules and regulations, this is where this has to be.

Using the same technique on one sample is not enough, Sutton pointed out. Multiple samples must be grown under the same conditions and then analyzed to have biological replicates. Ge explained that experiments must be designed to gather biological rather than technical replicates.

Once the technique to gather data is chosen and a plan of data analyses is created, Ge said, we can figure out how many replicates are needed.

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Bioinformatician Helps Biologists Find Key Genes