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James Boedicker

Assistant Professor of Physics and Astronomy and Biological Sciences

Contact Information
E-mail: boedicke@usc.edu
Phone: (213) 740-1104
Office: SSC 211

LINKS
Boedicker Lab Webpage
 

Education

Ph.D. Physical Chemistry, University of Chicago, 2010
B.S. Chemical Engineering, Massachusetts Institute of Technology, 2004
 

Postdoctoral Training

Postdoctoral Scholar in Applied Physics, California Institute of Technology, 2010-2013  
 

Description of Research

Summary Statement of Research Interests

Research in the Boedicker Lab focuses on understanding the rules that make complex networks of microbes work. Microbial communities play an important role in our everyday lives, and our lab aims to increase their benefit to society by developing experimental and theoretical tools to control, predict, and design the functional outputs of both synthetic and natural microbial ecosystems. Towards this goal, we have been developing predictive and quantitative models of biological decision making, using the tools of synthetic biology to test and expand our understanding of gene regulation, and investigating the role of microscale spatial structure on signal exchange and interspecies gene regulation.
 

Publications

Journal Article

Boedicker, J. Q., Garcia, H. G., Johnson, S., Phillips, R. (2013). DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation. Physical Biology. Vol. 10 (6)
Boedicker, J. Q., Garcia, H. G., Phillips, R. (2013). Theoretical and Experimental Dissection of DNA Loop-Mediated Repression. Physical Review Letters. Vol. 110 (1)
Garcia, H. G., Sanchez, A., Boedicker, J. Q., Osborne, M., Gelles, J., Kondev, J., Phillips, R. (2012). Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria. Cell Reports. Vol. 2 (1), pp. 150-161.
Garcia, H. G., Lee, H. J., Boedicker, J. Q., Phillips, R. (2011). Comparison and Calibration of Different Reporters for Quantitative Analysis of Gene Expression. Biophysical Journal. Vol. 101 (3), pp. 535-544.
Boedicker, J. Q., Vincent, M. E., Ismagilov, R. F. (2009). Microfluidic Confinement of Single Cells of Bacteria in Small Volumes Initiates High-Density Behavior of Quorum Sensing and Growth and Reveals Its Variability. Angewandte Chemie-International Edition. Vol. 48 (32), pp. 5908-5911.
Boedicker, J. Q., Li, L., Kline, T. R., Ismagilov, R. F. (2008). Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics. Lab on a Chip. Vol. 8 (8), pp. 1265-1272.
Kastrup, C. J., Boedicker, J. Q., Pomerantsev, A. P., Moayeri, M., Bian, Y., Pompano, R. R., Kline, T. R., Sylvestre, P., Shen, F., Leppla, S. H., Tang, W., Ismagilov, R. F. (2008). Spatial localization of bacteria controls coagulation of human blood by 'quorum acting'. Nature Chemical Biology. Vol. 4 (12), pp. 742-750.
Kim, H. J., Boedicker, J. Q., Choi, J. W., Ismagilov, R. F. (2008). Defined spatial structure stabilizes a synthetic multispecies bacterial community. Proceedings of the National Academy of Sciences of the United States of America. Vol. 105 (47), pp. 18188-18193.
Li, L., Boedicker, J. Q., Ismagilov, R. F. (2007). Using a multijunction microfluidic device to inject substrate into an array of preformed plugs without cross-contamination: Comparing theory and experiments. Analytical Chemistry. Vol. 79 (7), pp. 2756-2761.
Wood, K. C., Boedicker, J. Q., Lynn, D. M., Hammond, P. T. (2005). Tunable drug release from hydrolytically degradable layer-by-layer thin films. Langmuir. Vol. 21 (4), pp. 1603-1609.
Santini, C. M., Johnson, M. A., Boedicker, J. Q., Hatton, T. A., Hammond, P. T. (2004). Synthesis and bulk assembly behavior of linear-dendritic rod diblock copolymers. Journal of Polymer Science Part a-Polymer Chemistry. Vol. 42 (11), pp. 2784-2814.
 
 
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