Welcome new faculty: Founder Professor Jun S. Song

Siv Schwink
2/6/2014 8:00 AM

Jun Song is a theoretical biological physicist with joint appointments in the Department of Physics and the Department of Bioengineering. His research program in computational biology and biomedicine leverages the methodologies and tools of physics and mathematics to discover how transcription factors, chromatin structure and non-coding RNAs regulate gene expression. Song is particularly interested in the genomic study of cancer. His ongoing research has implications for prognosis and treatment of cancer, in particular of malignant melanoma, one of the deadliest cancers.

“In my field of research, it’s easy now to produce 40 gigabytes of data from one experiment. Using DNA sequencing techniques, it’s possible to generate several terabytes of data just for one patient. I use statistical and mathematical tools to overcome the challenge of analyzing and integrating such large data sets.”

Song looks forward to collaborating with other theorists in both biophysics and physics at Illinois—access to quantitative theorists and the University’s growing strength in bioengineering are largely what drew him to Urbana.

“I am very happy to be here,” shares Song. “Being able to teach and recruit students who are trained in physics will allow me to develop diversity in my research program. That’s very attractive to me, and I like the interactive ‘Urbana style’ approach to collaborative research.”

Prior to joining the faculty at Illinois, Song held an appointment as associate professor in the Department of Epidemiology and Biostatistics and in the Department of Bioengineering and Therapeutic Sciences at the University of California at San Francisco, where he advised students within the biomedical sciences graduate group, the biological and medical informatics graduate group, and the developmental and stem cell biology graduate group.

Song joins the faculty at Illinois as a Founder Professor. His primary laboratory is at the Institute for Genomic Biology. He brought two postdocs with him from UCSF to Illinois. Tomas Rube joined Song’s lab in 2012. He earned his doctoral degree from Stanford University studying theoretical high energy physics and switched to the study of genomics after graduating. Miraslav Hejna received his doctoral degree from Princeton University, studying high energy and theoretical condensed matter physics. He joined Song’s lab in 2013.

A third postdoc appointment followed Song to Illinois: Courtney Onodera, who earned her doctoral degree in bioinformatics at the University of California at Santa Cruz, will finish her research under Song this academic year while remaining at UCSF.

Song has already attracted students to his lab who want to engage in interdisciplinary research. Given his own background, he is very interested in helping young quantitative scientists find their way into biology. Song also puts a high priority on teaching quantitative and computational approaches to students of biology.

“I believe Illinois can lead in this area of research, because it has a very strong presence in computational physics, physics, and biological physics,” comments Song.

Song plans to develop an educational program that crosses disciplines. He intends to take advantage of a teaching release this spring to develop new cross-listed courses that will teach state-of-the-art technologies and methodologies in computational genomics and computational biology.

“I hope to bring people together from different departments and disciplines, including mathematics, physics, statistics, and biology. I plan to introduce educational research projects for graduate students and upper-level undergraduate students.”

Song received his bachelor’s degree in physics from Harvard University in 1996, graduating summa cum laude, and went on to receive a master of advanced study degree in mathematics from the University of Cambridge in 1997, graduating with distinction. He received his doctoral degree in physics from the Massachusetts Institute of Technology in 2001 under thesis adviser Gang Tian of the Department of Mathematics.

Prior to his appointment at UCSF in 2009, Song held a position as a Charles B. Morrey, Jr. Assistant Professor of Mathematics at the University of California at Berkeley (2001–2003); held an appointment as instructor and research fellow in medical physics and as research fellow in biostatistics and computation biology at Harvard University (2003–2005); and was a member of the Institute for Advanced Study’s Simons Center for Systems Biology (2007–2009).

Song is the recipient of many honors, including a National Science Foundation CAREER Award (2011) and a Sontang Foundation Distinguished Scientist Award (2011). He was also awarded a National Science Foundation Fellowship (1997).

In addition to his academic research achievements attested by a long list of invited talks and a longer-still list of publications in peer-reviewed journals, Song has shown a strong commitment to service. Song served as an expert reviewer for the US-Israel Binational Science Foundation (2010-2014) and served as a review panel member of numerous NIH study sections.

Recent News

  • Outreach

It’s up to you and your team to save the free world from evil forces plotting its destruction, and you have precisely 60 minutes to do it. You must find out what happened to Professor Schrödenberg, a University of Illinois physicist who disappeared after developing a top-secret quantum computer that can crack any digital-security encryption code in the world.  Unfortunately, the previous groups of special agents assigned to the case disappeared while investigating the very room in which you now find yourself locked up, Schrödenberg’s secret lab.

LabEscape is a new science-themed escape room now open at Lincoln Square Mall in Urbana, testing the puzzle-solving skills of groups of up to six participants at a time. Escape rooms, a new form of entertainment cropping up in cities across the U.S. and around the globe, provide in-person mystery-adventure experiences that have been compared to living out a video-game or movie script. A team of participants is presented with a storyline and locked into a room with only one hour to find and decipher a sequence of interactive puzzles that will unlock the door and complete the mission. Two escape room businesses are already in operation in the area, C-U Adventures in Time and Space in Urbana and Brainstorm Escapes in Champaign.


  • Research
  • AMO/Quantum Physics
  • Condensed Matter Physics

Topological insulators, an exciting, relatively new class of materials, are capable of carrying electricity along the edge of the surface, while the bulk of the material acts as an electrical insulator. Practical applications for these materials are still mostly a matter of theory, as scientists probe their microscopic properties to better understand the fundamental physics that govern their peculiar behavior.

Using atomic quantum-simulation, an experimental technique involving finely tuned lasers and ultracold atoms about a billion times colder than room temperature, to replicate the properties of a topological insulator, a team of researchers at the University of Illinois at Urbana-Champaign has directly observed for the first time the protected boundary state (the topological soliton state) of the topological insulator trans-polyacetylene. The transport properties of this organic polymer are typical of topological insulators and of the Su-Schrieffer-Heeger (SSH) model.

Physics graduate students Eric Meier and Fangzhao Alex An, working with Professor Bryce Gadway, developed a new experimental method, an engineered approach that allows the team to probe quantum transport phenomena.

  • Research
  • Astrophysics/Cosmology

In its search for extrasolar planets, the Kepler space telescope looks for stars whose light flux periodically dims, signaling the passing of an orbiting planet in front of the star. But the timing and duration of diminished light flux episodes Kepler detected coming from KIC 846852, known as Tabby’s star, are a mystery. These dimming events vary in magnitude and don’t occur at regular intervals, making an orbiting planet an unlikely explanation. The source of these unusual dimming events is the subject of intense speculation. Suggestions from astronomers, astrophysicists, and amateur stargazers have ranged from asteroid belts to alien activity.  

Now a team of scientists at the University of Illinois at Urbana-Champaign—physics graduate student Mohammed Sheikh, working with Professors Karin Dahmen and Richard Weaver—proffer an entirely novel solution to the Tabby’s star puzzle. They suggest the luminosity variations may be intrinsic to the star itself.

  • Research
  • Astrophysics/Cosmology

"For decades, astronomers have known that supermassive black holes and the stars in their host galaxies grow together," said co-author Joaquin Vieira of the University of Illinois at Urbana-Champaign. "Exactly why they do this is still a mystery. SPT0346-52 is interesting because we have observed an incredible burst of stars forming, and yet found no evidence for a growing supermassive black hole. We would really like to study this galaxy in greater detail and understand what triggered the star formation and how that affects the growth of the black hole."