History and Vision

Distinctive Features

Clinical emphasis

All of our systems biology and data science faculty are focused on applications of high biomedical importance. For example, we have a strong emphasis on clinical issues of cardiovascular disease, cancer and infectious diseases. Rather than focusing on comprehensive description of tractable model organisms such as E. coli or yeast or a specific domain such as agricultural biotechnology, our faculty focus on major diseases that are intractable without a systems viewpoint.

Integration of computational and experimental approaches

The majority of our systems biology and biomedical data science labs integrate both computational and experimental approaches. This integration provides a rich training experience and helps to keep the research programs focused on biomedical challenges.

Co-location with the School of Medicine

Our faculty have ongoing collaborations with physicians and basic scientists in the UVA School of Medicine. There are particularly well-established collaborations with the Cancer Center, Cardiovascular Research Center, Division of Infectious Diseases, and Center for Public Health Genomics.  Hiring in systems immunology is a particular area of interest, leveraging relationships with the Carter Center for Immunology.  We will continue to hire in biomedical data sciences, strengthening relationships with the Data Science Institute, the Center for Public Health Genomics, and the Department of Computer Science.

History and Vision

Systems biology seeks to build predictive mechanistic models that are reasonably accurate given partial knowledge of the underlying physiology and environment. In modern systems biology, there is no universal measurement type and no best modeling approach. Rather, systems biology consists of a suite of enabling technologies and modeling tools whose strengths and weaknesses must be weighed when tackling a biological application.

Thirteen years ago, the department made a strategic decision to focus on systems biology.  This led to a series of junior faculty hires, which included Shayn Peirce-Cottler (vascular/inflammation), Jason Papin (metabolism/infectious disease), Jeff Saucerman (cardiovascular disease), and Kevin Janes (cancer/infection).  In addition, the department was able to attract established investigators in multiscale computational modeling, when Jeff Holmes and Silvia Blemker joined the department to collaborate with systems biology specialists. Most recently, growth in this area enabled the recruitment of Eli Zunder (stem cells, mass cytometry) and Matt Lazzara (cell signaling/cancer).

In the last decade, the pace of data generation and computational capabilities has accelerated dramatically, ushering in an era of biomedical big data. Mastering this data has highlighted the need for engineering-based pragmatism, where machine learning and other data science methods are necessary to make predictions from data despite insufficient prior knowledge to develop mechanistic models.

The department (and UVA as a whole) has viewed this development as an exciting opportunity for leadership. We recruited Gustavo Rohde (modeling of signal and image data) as a joint hire with electrical engineering.  Through collaboration with the Medical School’s Center for Public Health Genomics, we recruited Mete Civelek (systems genetics), Nathan Sheffield (computational cancer genomics; secondary in BME), and Chongzi Zang (epigenetics and transcriptional regulation; secondary in BME).  The University recruited Phil Bourne, former NIH associate director for data science and an expert in systems pharmacology, to serve as director of UVA’s Data Science Institute. Bourne is professor and Stephenson Chair of Data Science in the department of biomedical engineering.

As of summer 2017, research awards for our systems biology and biomedical data science gorup totalled $18.7 million, comprising nearly half of all research activity in the department. 

In 2016, a team led by Jason Papin (with Jeff Saucerman, Kevin Janes, Shayn Peirce-Cottler, and 28 other faculty members across UVA) won a $1.43 million, five-year National Insitutes of Health Training Grant in Biomedical Data Science (T32-LM012416) that leans heavily on systems biology.  Many of the same investigators are now also closely involved with a National Science Foundation REU Program in Multiscale Systems Bioengineering with Timothy Allen as PI.  These successes help to position the department to apply for major center grants. The department is leading the proposal preparation for a multi-institutional NSF Engineering Research Center (ERC), with Kevin Janes as PI.

NIH Training Grant in Biomedical Data Science

NSF REU Program in Multiscale Systems Bioengineering

Pharmacopredictive In Silico-Cellular Engineered Systems (PISCES)