San Diego Center for Systems Biology (SDCSB)

Principal investigator: Alexander Hoffmann, Ph.D., University of California San Diego (UCSD)

Other investigators: Sumit Chanda, Jeff Hasty, Trey Ideker, Tracy Johnson, Steve Kay, Richard Kolodner, Gentry Patrick, Christopher Putnam, Mel Simon, Susan Taylor, Lev Tsimring, Jean Wang.

Seed investigators: Daniel Hyduke, Amy Kiger, Giovanni Paternostro, John Reed, Scott Rifkin, Andreas Till, Dieter Wolf.

San Diego Center for Systems Biology website

The San Diego Center for Systems Biology combines top down and bottom up systems biology approaches to understand the functioning of the regulatory networks that control cellular responses to stress agents such as DNA and metabolic damaging agents, and pathogens. Cellular stress responses are tailored to limit the damage and initiate repair, but when misregulated, they can cause pathology, including chronic inflammatory disease and cancer. Network-emergent properties such as dose response and dynamic control, and systems robustness, are major determinants of an appropriate and healthy cellular stress response.

Understanding network-emergent properties requires the language of math to articulate hypotheses and communicate results; systems biology benefits from the technical approaches developed in dynamical systems engineering. The construction of mathematical models requires complete parts lists and databases of interactions that make up network maps. Parameterizing models and testing of hypotheses requires dynamic data from single cells that can be obtained with the help of in vivo reporters and microfluidic devices.

The San Diego Consortium for Systems Biology (SDCSB) was founded in 2005 to promote collaborative research and interdisciplinary research training in Systems Biology on the Torrey Pines mesa and beyond. In 2010, SDCSB became an NIGMS Center for Systems Biology, to promote and safeguard the transitioning biomedical research from a phenomenon/data-driven science to a quantitative, math-based science. Now known as the San Diego Center for Systems Biology, SDCSB comprises activities in (i) scientific research, (ii) scientific outreach, and (iii) educational outreach.

Research
SDCSB supports investigator-driven research projects and research cores. The three research cores address conceptual, technological, and educational challenges, and cover three specific areas that are critical to the mission of the Center: Network Bioinformatics, Mathematical Modeling and Cellular Dynamics. The investigator-driven research projects are organized into four programs that address innate immune, inflammatory, and genotoxic responses, as well as design principles of dynamic control. A Seed Grant Program identifies promising projects for investigator cycling, thus broadening the impact of the Center’s research activities.

Scientific Outreach
SDCSB organizes workshops on diverse topics of Systems Biology, such as new technology and their applications, and bioinformatic tools or mathematical modeling approaches. Day-long workshops cater to the broad local community of academic and biotech researchers. A three-week summer school, called La Jolla Labs, is an in-residency workshop for students from the national and international systems biology community. SDCSB has organized the annual Systems-to-Synthesis Symposium since 2005, and co-hosts the SoCal Systems Biology symposium with the NIGMS Center for Biological Complexity at UCI.

Educational Outreach
SDCSB synergizes with the UCSD PhD Program in Bioinformatics and Systems Biology (http://bioinformatics.ucsd.edu/) and catalyzes the transformation of undergraduate and graduate curricula in biological, biomedical, and biochemical sciences at UCSD to include bioinformatic network analysis and mathematical modeling approaches. Outreach activities include the involvement of local and regional high schools and community colleges, some of which have high historically under-represented minority populations and could be more effective feeder schools for premier UC institutions.