Welcome new faculty: Founder Professor Jun S. Song

Siv Schwink

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

  • Looking back
  • Astrophysics
  • Astrophysics/Cosmology
  • Astronomy
  • Numerical Relativity

Today’s historic joint announcement by the U.S.-based Laser Interferometer Gravitational-Wave Observatory (LIGO) and the Europe-based Virgo detector of the first detection of gravitational waves produced by colliding neutron stars is doubly noteworthy. It’s also the first cosmic event observed in both gravitational waves and light—some 70 ground- and space-based observatories observed the colliding neutron stars. This is arguably the biggest moment to date in “multi-messenger astronomy.”

In a press release issued by LIGO and Virgo collaborations, National Science Foundation Director France A. Córdova comments, “It is tremendously exciting to experience a rare event that transforms our understanding of the workings of the universe. This discovery realizes a long-standing goal many of us have had, that is, to simultaneously observe rare cosmic events using both traditional as well as gravitational-wave observatories. Only through NSF’s four-decade investment in gravitational-wave observatories, coupled with telescopes that observe from radio to gamma-ray wavelengths, are we able to expand our opportunities to detect new cosmic phenomena and piece together a fresh narrative of the physics of stars in their death throes.”

Well before the development of today’s innovative technologies supporting this simultaneous gravitational-wave and optical observation, early research in numerical relativity at the University of Illinois at Urbana-Champaign helped to lay the theoretical foundation for it. In fact, many features of the discovery had been predicted in the early computational simulations of Professor of Physics and Astronomy Stuart Shapiro and his group.

  • Research
  • Astrophysics
  • Astrophysics/Cosmology

A team of scientists using the Dark Energy Camera (DECam), the primary observing tool of the Dark Energy Survey (DES), was among the first to observe the fiery aftermath of a recently detected burst of gravitational waves, recording images of the first confirmed explosion from two colliding neutron stars ever seen by astronomers.

Scientists on the DES joined forces with a team of astronomers based at the Harvard-Smithsonian Center for Astrophysics (CfA) for this effort, working with observatories around the world to bolster the original data from DECam. Images taken with DECam captured the flaring-up and fading over time of a kilonova – an explosion similar to a supernova, but on a smaller scale – that occurs when collapsed stars (called neutron stars) crash into each other, creating heavy radioactive elements.

Two scientists at the University of Illinois at Urbana-Champaign are members of the DES collaboration, Professors Joaquin Vieira of the Departments of Astronomy and of Physics and Felipe Menanteau of the Department

  • New Research Center
  • Condensed Matter Physics
  • Materials Research

Innovative materials are the foundation of countless breakthrough technologies, and the Illinois Materials Research Science and Engineering Center will develop them. The new center is supported by a six-year, $15.6 million award from the National Science Foundation’s Materials Research Science and Engineering Centers program. It is led by Professor Nadya Mason of Engineering at Illinois’ Department of Physics and its Frederick Seitz Materials Research Laboratory

By building highly interdisciplinary teams of researchers and students, the Illinois Materials Research Center will focus on two types of materials. One group will study new magnetic materials, where ultra-fast magnetic variations could form the basis of smaller, more robust magnetic memory storage. The second group will design materials that can withstand bending and crumpling that typically destroys the properties of those materials and even create materials where crumpling enhances performance.

  • In the Media
  • Condensed Matter Physics
  • Biological Physics

Quanta Magazine recently spoke with Goldenfeld about collective phenomena, expanding the Modern Synthesis model of evolution, and using quantitative and theoretical tools from physics to gain insights into mysteries surrounding early life on Earth and the interactions between cyanobacteria and predatory viruses. A condensed and edited version of that conversation follows.