Monday,
December 11, 2017

Monday,
December 11, 2017

Category:

Scientist Flourishes in Eugene McDermott Graduate Fellows Program

Reena Schellenberg, Dr. Michael Q. Zhang and Peng Xie

From left: Reena Schellenberg, director of the Eugene McDermott Graduate Fellows Program, Dr. Michael Q. Zhang and his student Peng Xie, who is a member of the first cohort of the Eugene McDermott Graduate Fellows Program.

Doctoral student Peng Xie came to The University of Texas at Dallas primarily to follow his mentor, Dr. Michael Q. Zhang, and his passion, computational biology.

In the three years he has been on campus, Xie has exemplified the multitude of reasons that promising graduate students come to UT Dallas — opportunity, support and career advancement.

Xie is a member of the first cohort of the Eugene McDermott Graduate Fellows Program. In addition to a stipend, tuition and fees, and a research budget, the McDermott fellowship provides professional development and enrichment opportunities.

Armed with those opportunities and his own drive, Xie recently co-authored a paper published in Science describing a new understanding of the mechanism that pauses gene expression.

“In this study, we’re specifically interested in a regulatory DNA strand called an enhancer,” Xie said. “An enhancer doesn’t in itself express a gene, but it controls gene expression. For the first time, we’ve shown that an enhancer controls the pause and release of a gene.”

Zhang is director of the Center for Systems Biology and the Cecil H. and Ida Green Distinguished Chair of Systems Biology Science at UT Dallas. At the center, Xie analyzed large amounts of sequencing-based genomic data to study the enhancer’s behavior. In most cases — as their name suggests — enhancers activate gene expression.

“However, a factor called PAF1 negatively regulates the enhancer’s activity — it pauses the gene’s expression,” Xie said. “When we did genetic experiments removing PAF1, enhancers became more active.”

Long-term Collaboration

Zhang, also a co-author of the paper, has been pivotal in advancing Xie’s career since the pair met in 2008 at Tsinghua University in Beijing, which Zhang described as the “Chinese MIT.”

About the Program

The Eugene McDermott Graduate Fellows Program is designed to prepare outstanding doctoral students for careers in leading research enterprises.

The Eugene McDermott Graduate Fellows receive a four-year award package that includes, annually:

• 12-month stipend of $36,000.
• health insurance.
• tuition and fees.
• discretionary budget of $10,000.
• professional development and other enrichment opportunities.

Applicants to the University's research-intensive doctoral programs are automatically considered for the fellowship. For more information, visit its website.

“Peng was in a special gifted math-physics class of undergraduate students when I first met him during my visit to Tsinghua as a guest professor,” he said. “His strong analytic background and creative thinking are exactly what I had always been looking for to join my research group.”

Xie said their relationship was grounded in career-path commonalities that they discovered while Xie was a bioinformatics master’s student in China.

“I studied physics as an undergrad. Dr. Zhang’s PhD is in physics as well,” he said. “We have highly matched backgrounds, and I became interested in computational biology through him.”

When Xie weighed potential destinations for his doctoral work, Zhang’s mentoring tipped the scales to UT Dallas.

“He’s really knowledgeable, and he’s participated in a lot of world-class projects,” Xie said. “He has a broad overview of this field, and understands what’s really important.”

But Zhang’s mentoring isn’t just about subject-matter expertise. Support and good counsel play a significant role as well.

“As a student about to commit the next four or five years to something, it’s so crucial to find the right person to work with — someone willing to not only accept you as a student, but also support you research-wise,” Xie said. “Whenever we talk about ideas, he can tell me if my idea is novel enough or important enough to pursue. When you get that direction, you can develop along a faster path.”

Zhang’s influence was instrumental in Xie’s initial connection with his collaborators on the Science paper. 

In the summer of 2009, Zhang was a professor at Cold Spring Harbor Laboratory, a pre-eminent biology research facility on Long Island, New York. In 2015, Zhang recommended his doctoral student Xie for a summer course at the lab.

“Only 20 students worldwide got in,” Xie said. “There, I made the connections that got me involved in this project.”

Xie’s expertise in computational biology — rather than experimental biology — made him a valuable asset to the collaboration.

“My course instructor at Cold Spring Harbor was Dr. Ali Shilatifard from Northwestern University, and the teaching assistant was his doctoral student Fei Chen,” Xie said. “About a year later, they got some tricky data, and they thought of me.”

Shilatifard and Chen are co-authors of the Science paper.

During his fellowship, Xie has gained critical skills on his path to becoming an independent investigator, including working with collaborators and broadening his expertise, Zhang said. 

“Peng’s fellowship has given him the resources and the freedom to pursue his own research interests,” he said. “He has developed novel computational and bioinformatics methodology that can help biologists like this research team extract insight from massive molecular sequencing data. I also encouraged him to earn another MS in computer science with emphasis on modern machine learning technologies that will prepare him for his future career.”

'A Powerful Institutional-Quality Tool'

Reena Schellenberg is the director of the Eugene McDermott Graduate Fellows Program, established in 2014 as an analog to the undergraduate McDermott Scholars Program.

“Being able to bring in — and keep — exceptional graduate students like Peng means the fellowship is a powerful institutional-quality tool,” Schellenberg said. “Beyond a typical tuition-and-stipend package, the McDermott award provides resources, including generous discretionary funding, to facilitate each fellow’s independent research.”

Peng is the exemplar of what the fellows program and our institution make possible. The combination of Peng’s prodigious abilities, Dr. Zhang’s outstanding mentorship, and the fellowship’s targeted resources is tremendous.

Reena Schellenberg,
director of the Eugene McDermott Graduate Fellows Program

That institutional quality — and how the Eugene McDermott Graduate Fellows Program nourishes it — is something Xie sees signs of every day, in his UT Dallas peers and the research they are undertaking.

“There’s no doubt these are world-class journals where UT Dallas work is being published,” Xie said. “Beyond that, I’ve seen exceptional faculty joining our department in the past few years and many promising young scientists with excellent work.”

For Xie, the next landmark will be his PhD from the biological sciences department in the School of Natural Sciences and Mathematics, which he expects to earn in the spring; after that, a new destination for postdoctoral work. Through it all, his experiences and mentor at UT Dallas are helping him.

“My personal interest is still in doing scientific research,” Xie said. “I’m also thinking about my next stop, taking a postdoc position. Dr. Zhang has introduced me to some scientists doing cutting-edge work, and they are pretty interested in me.”

The relationship is symbiotic, as Xie’s work contributes to UT Dallas in return. For Schellenberg, that’s the ideal blueprint.

“Peng is the exemplar of what the fellows program and our institution make possible,” she said. “The combination of Peng’s prodigious abilities, Dr. Zhang’s outstanding mentorship, and the fellowship’s targeted resources is tremendous, as this Science publication demonstrates.”

Media Contact: Stephen Fontenot, UT Dallas, (972) 883-4405, [email protected]
or the Office of Media Relations, UT Dallas, (972) 883-2155, [email protected]


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