Research Projects
A major challenge in the biological sciences is to understand how the myriad molecular components in cells work together to create living organisms. In recent years, complete lists of many types of cellular components have become available, global profiling has been used to determine their relative abundances in different cells under varying conditions, and high-throughput techniques have identified many kinds of molecular interactions. This information can often be organized into a network structure, where nodes represent molecular components and edges represent interactions between components, such as the influence of a transcription factor on the production of a gene transcript. These recent advances have brought us to a critical scientific moment: it is now possible, and necessary, to perform quantitative studies of the dynamics of molecular networks in a variety of contexts.
The central research theme of the CSB is the study of network dynamics across various time scales, including temporal changes in both network state and structure. Currently, we support six projects that exemplify the type of multi-disciplinary, multi-investigator collaborative research that the CSB considers exciting. These six projects are organized within three areas: cell cycle, development, and network evolution. Over time, some of these projects will mature and find separate funding to become self-supporting. New projects with a similar flavor will then be selected for the CSB support on the basis of internal and external reviews. In this way, the CSB serves as an incubator for an ever-changing portfolio of promising projects.
These projects are focused on four biological systems: budding yeast, sea urchins, Arabidopsis, and human cell lines. Data from the yeast cell cycle, one of the best-characterized biological processes, is being used as a testbed for many of our modeling approaches. We are using human cell lines to generate data on a critical switching event, entry into the cell cycle. The already sophisticated models of early embryogenesis in the sea urchin are being used as a foundation for characterizing the dynamics of cell differentiation. In the Arabidopsis root, continuous development and lack of cell movement simplifies the temporal aspect of development; cell-specific expression and DNA binding data are being used to identify the network states within each of the discrete stages of root development. Network function and robustness over evolutionary time are being addressed by investigating the variation among individuals in wild sea urchin populations and among a wide panel of budding yeast strains.
As the CSB community grows through hiring and attracting additional investigators from Duke and other Research Triangle institutions, we will add other projects and other model organisms.