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SFSU a leader in bioinformatics

October 10, 2005

A graphical representation of an Hh receiving cellEnter the phrase "hedgehog signaling pathway" into the Google or Yahoo search engines and the first reference to appear is a Web site created at SFSU by faculty and students. The hedgehog site, devoted to the functions and structure of a process of cellular responses known as "Hedgehog" or "Hh," receives an average of 5,000 hits a month.

Hh plays a vital role in embryonic cell development, disease regression and healing processes in a variety of species, including humans. Researchers believe that the functions of this pathway, named after the shape of the mutant fruitfly in which it was first discovered, may hold the secrets to finding cures for several forms of cancer.

"We now know that when the Hh pathway in humans is disrupted, we become susceptible to cancers like basil cell carcinoma, pancreatic cancer and prostate cancer to name a few, as well as some inherited diseases," said Felipe Andres Ramirez-Weber, an assistant professor of biology whose research is partly focused on the Hh pathway. Biotech and drug companies are scrambling for new information about Hh sequencing. The amount of data that researchers are producing, however, is daunting.

"Ten to twenty papers with new information about Hh are published every week, several hundred a month," Ramirez-Weber said. "I needed a way to sift through piles of information."

A meeting with Dragutin Petkovic, chair of computer science, helped solve the problem and put "bioinformatics" collaborations at SFSU on the map. Teams of SF State computer scientists and students collaborated with Ramirez-Weber and his students to code and perfect the usability of a Web site designed to clear the logjam of hedgehog data. Regularly updated information formulated and verified by Ramirez-Weber is posted along with papers by other researchers.

"When you log on to the Web site now, you are looking at only the first phase," Petkovic said. "Within months we will be adding new features for Internet collaboration. One of these will allow registered users to make annotations to posted information -- such as segments of text -- in order to share insights with other users." He adds that students will benefit as well because they will be allowed to pose questions for the scientists represented on the site.

"Imagine how much could be accomplished if, for example, the top five scientific authorities on the hedgehog signaling pathway could utilize the annotation feature to comment on the content. This information in itself will become a new, valuable layer of knowledge," Petkovic said.

The Hedgehog Web site is a project of SFSU's new Center for Computing for Life Sciences (CCLS), which provides an environment for faculty and students to integrate study and research between the life sciences and computational sciences. Researchers and students in biology, biochemistry, geosciences, computer science, mathematics and physics are currently collaborating on a number of projects including the collection/dissemination of other genomic information and visual data modeling, real-time monitoring and recording of functioning organisms.

For details about the center visit the CCLS Web site.

-- Denize Springer


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Last modified October 10, 2005 by University Communications