The mission of the San Diego Center for Systems Biology (SDCSB; sdcsb.ucsd.edu) is to advance the discipline and application of systems biology in the greater San Diego area and to serve as a nucleus for systems biology education and training. The SDCSB brings together a community of 19 outstanding faculty, over 100 trainees and technical staff spanning four world-renowned institutions: the University of California San Diego, the Salk Institute for Biological Studies, the Sanford-Burnham Medical Research Institute and the Ludwig Institute for Cancer Research, all located on the Torrey Pines research mesa. The SDCSB has been supported as an NIGMS National Center for Systems Biology since 2010. Over the past five years our research has led to significant systems biology advances, including genome-wide studies of how stress remodels transcriptional and genetic networks, discovery of an independent metabolic clock coordinating cell growth through cycles of TOR1 activity, demonstration that much of the Gene Ontology can be inferred directly from `omics data, prediction of cancer survival time and drug response by an approach called Network Based Stratification and a series of major feats in engineering of synthetic coupled genetic circuits. We began two successful annual symposia, formal systems biology coursework, a seminar series and journal club, workshops on systems biology techniques and a faculty seed grant program that was used to recruit 10 new systems biology faculty to UCSD. We successfully trained more than 90 graduate students and postdoctoral fellows, seven who are now in independent positions. The theme of this renewal application - From Maps to Models - addresses an important challenge in systems biology: traversing between network maps and mathematical models, two very successful but so far mostly separate biological representations and modes of study. Network maps tend to be global, static, abstract and descriptive, whereas mathematical models tend to be local, dynamic, detailed and predictive. Guided by this overarching theme, four SDCSB research projects seek to develop a general library of maps and models relevant to fundamental cellular and super-cellular processes, including the spatiotemporal architecture of the genome (Project 1), protein turnover dynamics (Project 2), cell-cell communication and heterogeneity (Project 3) and environment-genome interactions (Project 4). These mapping and modeling activities are fueled by technologies advanced across three SDCSB core platforms, aspects of which serve as an exemplar for systems biology efforts nationally and internationally. This renewal application represents a tightly integrated set of research projects, cores and educational efforts. The keys to achieving this integration are four-fold: (1) A consistent theme of developing global network maps coupled to predictive models; (2) Support of an innovative systems biology core platform jointly developed and applied across all projects; (3) Cross-cutting faculty recruitment, postdoctoral and graduate programs in systems biology, from which the center recruits and staffs its projects; and (4) Outstanding symposia, retreats, journal clubs and workshops in which we all participate. The teams spearheading these efforts are comprised of investigators with diverse backgrounds and expertise, resulting in a multidisciplinary approach incorporating genomics, bioinformatics, synthetic biology and biophysics.
Systems Biology aims to systematically map the architecture of biological systems and to develop these maps into predictive mathematical and statistical models. A global and quantitative understanding of biological systems will be critical for informed interpretation of big biomedical data sets and to enable personalized medicine. Since 2010 the San Diego Center for Systems Biology has served as a nucleus for systems biology research, education and outreach in the greater San Diego area.
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