Wellesley Computer Scientists Develop DNA/RNA Sequencing Tools

“Owing to advances in genome sequencing technology, the amount of DNA and RNA that is being sequenced is growing rapidly,” explained Wellesley Computer Scientist Brian Tjaden. “A major challenge in the field of genomics is extracting new biomedical insights from this torrent of genome sequencing data.”

Tjaden, who is associate professor of computer science and chair of the computer science department, designs approaches for identifying novel genes in a genome, as well as for characterizing the functions of genes and how gene products interact as part of a system that carries out important processes in a cell.

Tjaden’s Rockhopper, a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data, is being used by biologists, genome scientists, and medical researchers to understand what regions of a genome are being activated and when, and to study diseases, including cancer. The system, which generates insights using novel algorithmic methods, has been downloaded more than 7,000 times for use by others since he created it and it has an active community of thousands of users.

According to Tjaden, Rockhopper supports the management, processing, analysis, and integration of large sequencing datasets both from organisms whose genomes are known as well as from organisms whose genomes are not yet known. Using sequencing data, Rockhopper identifies new genes and then characterizes the extent to which genes, both new and previously annotated, are expressed.

Another tool from Tjaden’s lab, called TargetRNA, identifies mRNA targets of sRNA regulatory action in bacteria. “Many gene products act as regulators, turning on or off other genes. TargetRNA takes the sequence of a regulator and identifies other genes in a genome that are likely targets of regulation,” said Tjaden. “While Rockhopper aims to characterize genes and their expression, TargetRNA aims to identify the targets of those genes that act as regulators.”

A recent Wellesley Computer Science departmental newsletter described Tjaden as “always on the lookout for students interested in bioinformatics, biotechnology, and algorithms with biomedical applications.” A second iteration of the TargetRNA program, called TargetRNA-2, was developed by then-students Mary Beth Kery ’15 and Monica Starr Feldman ’14. Kery and Feldman are lead authors on a research article describing their work.

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