James Boedicker

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

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.

Journal Article

• Ostovar, G., Naughton, K. L., Boedicker,Ostovar, J. Q., Naughton, K. L., Boedicker, J. Q. (2020). Computation in bacterial communities. Physical biology. Vol. 17 (6), pp. 061002. PubMed Web Address
• Silva, K. P., Yusufaly, T. I., Chellamuthu, P., Boedicker,Silva, J. Q., Yusufaly, T. I., Chellamuthu, P., Boedicker, J. Q. (2019). Disruption of microbial communication yields a two-dimensional percolation transition. Physical review. E. Vol. 99 (4-1), pp. 042409. PubMed Web Address
• Silva, K. P., Boedicker,Silva, J. Q., Boedicker, J. Q. (2019). A neural network model predicts community-level signaling states in a diverse microbial community. PLoS computational biology. Vol. 15 (6), pp. e1007166. PubMed Web Address
• Tran, F., Boedicker,Tran, J. Q., Boedicker, J. Q. (2019). Plasmid Characteristics Modulate the Propensity of Gene Exchange in Bacterial Vesicles. Journal of bacteriology. Vol. 201 (7) PubMed Web Address
• Guo, X., Silva, K. P., Boedicker,Guo, J. Q., Silva, K. P., Boedicker, J. Q. (2019). Single-cell variability of growth interactions within a two-species bacterial community. Physical biology. Vol. 16 (3), pp. 036001. PubMed Web Address
• Silva, K. P., Chellamuthu, P., Boedicker,Silva, J. Q., Chellamuthu, P., Boedicker, J. Q. (2017). Quantifying the strength of quorum sensing crosstalk within microbial communities. PLoS computational biology. Vol. 13 (10), pp. e1005809. PubMed Web Address
• Tran, F., Boedicker,Tran, J. Q., Boedicker, J. Q. (2017). Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer. Scientific reports. Vol. 7 (1), pp. 8813. PubMed Web Address
• Yusufaly, T. I., Boedicker, J. Q. (2016). Spatial dispersal of bacterial colonies induces a dynamical transition from local to global quorum sensing. Physical review. E. Vol. 94 (6-1), pp. 062410. PubMed Web Address
• Guo, X., Boedicker, J. Q. (2016). The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community. PLoS computational biology. Vol. 12 (9), pp. e1005079. PubMed Web Address
• Boedicker, J. Q., Garcia, H. G., Phillips, R. (2013). Theoretical and Experimental Dissection of DNA Loop-Mediated Repression. Physical Review Letters. Vol. 110 (1)
• 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.
• 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.