Professor of Informatics and Computer Science
Following a Winding Path
Yuzhen Ye looks out the window of her office at Lindley Hall, taking a break from what has been another busy, mentally taxing day. She watches the leaves and branches flutter on a nearby tree, and maybe she imagines where the breeze will take those leaves next.
More than most, she understands that no one ever knows where the wind may blow them next.
“I don’t know why I’m here,” Ye says, a smile on her face. “I wasn’t thinking about coming to the United States. I didn’t think of it at all when I was young, but somehow it just happened.”
An Associate Professor of Informatics and Computing, Ye grew up half a world away in Jingning, China with a passion for molecular biology. She had a deep desire to learn about the world around her, and the fascinating study of life at its most basic level drew her interest early in her life.
The pursuit of knowledge about molecular biology led her first to Nankai University in Tianjin, where she earned her Bachelor of Science degree in 1996. The computer revolution was roaring strong by then, and Ye enjoyed using the new tool to help pull her research forward.
“At that time, I was very interested in computational biology,” Ye says. “I enjoyed molecular biology, and I liked working with computers. So I blended the two together.”
At the time, there weren’t a lot of institutions in China offering a Ph.D. in computational biology, but the Shanghai Institute of Biochemistry (later to be renamed Institute of Biochemistry and Cell Biology) of the Chinese Academy of Sciences was one of them. Ye jumped at the opportunity to take her studies the next step. She initially focused on protein structures and protein design while studying in Shanghai, and she wrote programs to design proteins that have more stable structures or improved functions.
After receiving her Ph.D. in 2001, Ye followed a common path and headed for the United States for her post-doctorate work. It was a decision that was easy to make – her husband, Haixu Tang, who also is a professor in SoIC, was already in the U.S. – but it also meant some sacrifice.
“My family wasn’t thinking that I would be here,” Ye says. “I’m the only one in the U.S. of my entire family. I have two sisters and one brother who are all in China. I came here with my husband, and that helped the transition.”
Ye landed at the Burnham Institute for Medical Research in San Diego where she continued to tackle the study of proteins.
“I wrote software (FATCAT) for comparing protein structures or to utilize the structure formation for other purposes,” Ye says. “I also worked on graphs of protein domains and biological pathways.”
She became a research assistant professor in 2004 and filled that role until 2007 when she headed to Bloomington.
But the winds continued to blow through her career, and Ye found herself shifting her focus yet again. It wasn’t something she planned. Much like her shift to computational biology or her move to the United States, it’s just something that kind of happened.
“I was working on proteins, but now I’ve moved into genomics,” Ye says. “Again, it just happened. There were too many people working on protein structures, so I kind of switched to genomics. I work on metagenomics. It’s the genomic study of bacterial communities, the whole collection of bacteria species, whether it be on our skin or in our gut.”
Ye continues to develop software to analyze metagenomic (and metatranscriptomic) sequences and come up with new ways to analyze the data sets. She basically is working to come up not necessarily with answers for metagenomics, but rather new questions that will allow researchers to view the subject from a different angle, as reflected in her recent research on bacterial CRISPR-Cas immune systems using metagenomic sequences.
“We make new sense of the data,” Ye says. “There’s so much new data out there, and it’s underutilized. We come up with new ideas and new problems, and we also have developed software to solve those problems.”
As Ye conducts her research, it’s clear that she won’t be too entrenched in any one line of thinking. If there’s anyone in the field who is willing to go with the flow and follow wherever the data takes her, it’s Ye, even if that direction is completely unexpected.