Welcome new faculty: Founder Professor Jun S. Song

Siv Schwink
2/6/2014

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

  • Research Funding

The United States Department of Energy awards $2.2 million to the FAIR Framework for Physics-Inspired Artificial Intelligence in High Energy Physics project, spearheaded by the National Center for Supercomputing Applications’ Center for Artificial Intelligence Innovation (CAII) and the University of Illinois at Urbana-Champaign. The primary focus of this project is to advance our understanding of the relationship between data and artificial intelligence (AI) models by exploring relationships among them through the development of FAIR (Findable, Accessible, Interoperable, and Reusable) frameworks. Using High Energy Physics (HEP) as the science driver, this project will develop a FAIR framework to advance our understanding of AI, provide new insights to apply AI techniques, and provide an environment where novel approaches to AI can be explored.

This project is an interdisciplinary, multi-department, and multi-institutional effort led by Eliu Huerta, principal investigator, director of the CAII, senior research scientist at NCSA, and faculty in Physics, Astronomy, Computational Science and Engineering and the Illinois Center for Advanced Studies of the Universe at UIUC. Alongside Huerta are co-PIs from Illinois: Zhizhen Zhao, assistant professor of Electrical & Computer Engineering and Coordinated Science Laboratory; Mark Neubauer, professor of physics, member of Illinois Center for Advanced Studies of the Universe, and faculty affiliate in ECE, NCSA, and the CAII; Volodymyr Kindratenko, co-director of the CAII, senior research scientist at NCSA, and faculty at ECE and Computer Science; Daniel S. Katz, assistant director of Scientific Software and Applications at NCSA, faculty in ECE, CS, and School of Information Sciences. In addition, the team is joined by co-PIs Roger Rusack, professor of physics at the University of Minnesota; Philip Harris, assistant professor of physics at MIT; and Javier Duarte, assistant professor in physics at UC San Diego.

  • Research

This year, 31 research teams have been awarded a combined 5.87 million node hours on the Summit supercomputer, the OLCF’s 200 petaflop IBM AC922 system. The research performed through the ALCC program this year will range from the impact of jets on offshore wind farms to the structure and states of quantum materials to the behavior of plasma within fusion reactors—all computationally intensive scientific applications necessitating the power of a large-scale supercomputer like Summit.

  • In Memoriam

Jim was widely viewed as one of the best teachers in the Physics Department. He was frequently listed in the University’s roster of excellent instructors and won awards for his classroom skills. In 2012, he received the Arnold T. Nordsieck Physics Award for Teaching Excellence for his “patient, insightful, and inspiring physics teaching, one problem at a time, that encourages undergraduate students to take their understanding to a new level.”

  • Research

Now a team of theoretical physicists at the Institute for Condensed Matter Theory (ICMT) in the Department of Physics at the University of Illinois at Urbana-Champaign, led by Illinois Physics Professor Philip Phillips, has for the first time exactly solved a representative model of the cuprate problem, the 1992 Hatsugai-Kohmoto (HK) model of a doped Mott insulator.