{"id":213,"date":"2023-08-31T09:32:46","date_gmt":"2023-08-31T16:32:46","guid":{"rendered":"https:\/\/dornsife.usc.edu\/boedickerlab\/?page_id=213"},"modified":"2025-10-16T15:55:29","modified_gmt":"2025-10-16T22:55:29","slug":"publications","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/boedickerlab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n\n \n \n\n\n\n\n\n\n\n
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2025<\/strong><\/h1>\n

Jimenez, I.L. and Boedicker J.Q., Quorum sensing increases the diversity of bacterial communities in a Lotka-Volterra model, submitted.<\/p>\n

Das, S., Haxhimali, E., and Boedicker, J.Q., Stability of quorum sensing decision states in heterogeneous bacterial communities, submitted.<\/p>\n

Wagner, J.M., Wong, J. H., Millar, J.G., Haxhimali, E., Bruckner, A., Naragon, T. H., Boedicker, J.Q., and Parker, J., Enforced specificity of an animal symbiosis, submitted.<\/p>\n

Peach, L.J., Zhang, H., Weaver, B.P., and Boedicker J.Q., Assessing spacer acquisition rates in E. coli type 1-E CRISPR arrays, Frontiers in Microbiology<\/em>, 15, 1498959. link to paper<\/a><\/p>\n

Weaver, B.P., Zhao, F., Gao, Y., Boedicker, J.Q., and Haselwandter, C.A., The Density of Braun’s Lipoprotein Determines Vesicle Production in E. coli<\/em>, PLoS One<\/em>, 20 (9), e0332156. link to paper<\/a><\/p>\n

Sun, R., Gangan, M.S., Wang, Q., Boedicker, J.Q., and Armani, A.M., Magnetically tunable hydrogel for biofilm control, ACS Applied Bio Materials, 8 (6), 5090-97. link to paper<\/a><\/p>\n

Guo, X., Lim, S., Bogdan, P., and Boedicker, J.Q., Dynamic switch in the collective behavior of a two-strain microbial community, submitted.<\/p>\n

 <\/p>\n

2024<\/strong><\/h1>\n

Ostovar, G. and Boedicker, J.Q., Phenotypic memory in quorum sensing, PLoS Computational Biology,\u00a0<\/em>20(7), e1011696, (2024). link to paper<\/a><\/p>\n

Zhao, F., Niman, C.M., Ostovar, G., Chavez, M.S., Atkinson, J.T., Bonis, B.M., Gralnick, J.A., El-Naggar, M.Y., Boedicker, J.Q., Red-light-induced genetic system for control of extracellular electron transfer, \u00a0ACS Synthetic Biology,\u00a0<\/i>13(5), 1467-1476, (2024). link to paper<\/a><\/p>\n

 <\/p>\n

\n

2023<\/strong><\/h1>\n

Gangan M.S., Naughton K.L., and Boedicker J.Q., Utilizing a divalent metal ion transporter to control biogenic nanoparticle synthesis, Journal of Industrial Microbiology and Biotechnology<\/em>, 50(1), (2023). link to paper<\/a><\/p>\n

Weaver, B.P., Haselwandter, C. A., and Boedicker J. Q., Stochastic effects in bacterial communication mediated by extracellular vesicles, Physical Review E<\/em>, 107 (2), 024409, (2023). link to paper<\/a><\/p>\n<\/div>\n

Shaska, J., Gursoy, M.C., Ross, T.D., Cheng, Y.Y., Krieger, A., Thairu, M., Venturelli, O.S., Boedicker, J., Handelsman, J., and Mitra, U., Microbes as communication & decision-making networked communities, IEEE Nanotechnology Magazine<\/em>, 17 (3), 32-41, (2023). link to paper<\/a><\/p>\n

 <\/p>\n

\n

2022<\/strong><\/h1>\n

Courcoubetis, G., Gangan, M., Lim, S., Guo, X., Haas, S., Boedicker, J.Q., Formation, collective motion, and merging of macroscopic bacterial aggregates, PLoS Computational Biology,\u00a0<\/em>18(1): e1009153, (2022).\u00a0link to paper<\/a><\/p>\n

Gangan, M.S., Vasconcelos, M.M., Mitra, U., Camara, O., Boedicker, J.Q., Intertemporal trade-off between population growth rate and carrying capacity during public good production, iScience<\/i>, 25(4), 104117, (2022).\u00a0link to paper<\/a><\/p>\n

Zhao, F., Chavez, M.S., Naughton, K.L., Niman, C.M., Atkinson, J.T., Gralnick, J.A., El-Naggar, M.Y., Boedicker, J.Q., Light-induced patterning of electroactive bacterial biofilms, ACS Synthetic Biology,\u00a0<\/i>11, 7, 2327-2338, (2022). link to paper<\/a><\/p>\n

Tran, F., Gangan, M.S., Weaver, B.P., and Boedicker J. Q., Membrane-binding biomolecules influence the rate of vesicle exchange between bacteria, Applied and Environmental Microbiology<\/em>, e0134622, (2022). link to paper<\/a><\/p>\n

 <\/p>\n<\/div>\n

\n

2021<\/strong><\/h1>\n

Boedicker, J.Q., Gangan, M., Naughton, K., Zhao, F., Gralnick, J.A., and El-Naggar, M.Y., Engineering biological electron transfer and redox pathways for nanoparticle synthesis,\u00a0Bioelectricity<\/em>, 3(2), 126-135, (2021). link to paper<\/a><\/p>\n

Naughton, K.L., Boedicker, J.Q.,\u00a0Simulations to aid in the design of microbes for synthesis of metallic nanomaterials, ACS Synthetic Biology,<\/i><\/span>\u00a010<\/span>, 12<\/span>, 3475\u20133488, (2021)<\/span>.\u00a0link to paper<\/a><\/p>\n<\/div>\n

 <\/p>\n

\n

2020<\/strong><\/h1>\n

Ostovar, G., Naughton, K., and Boedicker, J. Q., Computation in bacterial communities, Physical Biology<\/em>, 17, 061002 (2020). link to paper<\/a><\/p>\n

Boedicker, J.Q., Multispecies microbial communities and synthetic microbial ecosystems, Biomimetic Microengineering<\/em>, edited by Hyun Jung Kim, CRC Press (2020).<\/p>\n<\/div>\n

 <\/p>\n

\n

2019<\/strong><\/h1>\n

Silva, K.P.T, and Boedicker, J.Q., A neural network model predicts community-level signaling states in a diverse microbial community, PLoS Computational Biology,\u00a0<\/em>15(6): e1007166, (2019). link to paper<\/a><\/p>\n

Chellamuthu, P., Naughton, K.L., Pirbadian, S., Silva, K.P.T., Chavez, M., El-Naggar, M.Y., Boedicker, J.Q., Biogenic control of manganese doping in zinc sulfide nanomaterial using\u00a0Shewanella oneidensis<\/em>\u00a0MR-1, Frontiers in Microbiology<\/em>, 10, 938, (2019). link to paper<\/a><\/p>\n

Lim S., Guo X., and\u00a0Boedicker J.Q., Connecting single-cell properties to collective behavior in multiple wild isolates of the\u00a0Enterobacter cloacae<\/em>\u00a0complex, PLoS ONE<\/em>, 14(4): e0214719, (2019). link to paper<\/a><\/p>\n

Silva, K.P.T., Yusufaly, T.I.,\u00a0 Chellamuthu, P., and Boedicker J.Q., Disruption of microbial communication yields a 2D percolation transition, Physical Review E<\/em>, 99, 042409, (2019). link to paper<\/a><\/p>\n

Guo, X., Silva, K.P.T., and\u00a0Boedicker, J.Q., Single-cell variability of growth interactions within a two-species bacterial community, Physical Biology<\/em>, 16(3): 036001, (2019). link to paper<\/a><\/p>\n

Tran, F. and\u00a0Boedicker J.Q., Plasmid characteristics modulate the propensity of gene exchange in bacterial vesicles,\u00a0Journal of Bacteriology<\/em>, 201 (7) e00430-18, (2019). link to paper<\/a><\/p>\n

Chellamuthu, P., Tran, F.,\u00a0Silva, K.P.T., Chavez, M.S., El Naggar, M., and Boedicker J.Q., Engineering bacteria for biogenic synthesis of chalcogenide nanomaterials,\u00a0Microbial Biotechonology,\u00a0<\/em>12(1), 161\u2013172, (2019). link to paper<\/a><\/p>\n<\/div>\n

 <\/p>\n

\n

2018<\/strong><\/h1>\n

Nazarian, P., Tran, F., and Boedicker, J.Q., Modeling multispecies gene flow dynamics reveals the unique roles of different horizontal gene transfer mechanisms, Frontiers in Microbiology<\/em>,\u00a09, 2978, (2018). link to paper<\/a><\/p>\n

Balaban, V., Lim, S., Gupta, G., Boedicker, J.Q., and Bogdan, P., Quantifying emergence and self-organisation of Enterobacter cloacae<\/em> microbial communities,\u00a0Scientific Reports<\/em>, 8, Article number 12416, (2018). link to paper<\/a><\/p>\n<\/div>\n

 <\/p>\n

\n

2017<\/strong><\/h1>\n

Silva, K.P., Chellamuthu, P., and Boedicker, J. Q., Quantifying the strength of quorum sensing crosstalk within microbial communities, PLoS Computational Biology, <\/em>13(10): e1005809, <\/em>(2017).<\/em> link to paper<\/a>
\n<\/em><\/p>\n

Yusufaly, T.I. and Boedicker, J.Q.,\u00a0Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities, Physical Biology, <\/em>vol\u00a014, Number 4, (2017). link to paper<\/a><\/p>\n

Tran, F. and Boedicker J.Q.,\u00a0Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer, Scientific Reports,<\/em>\u00a07<\/span>, Article\u00a0number:\u00a08813<\/span>\u00a0(2017<\/span>). link to paper<\/a><\/p>\n

Silva, K.P., Chellamuthu, P., and Boedicker, J.Q., Signal destruction tunes the zone of activation in spatially distributed signaling networks,\u00a0Biophysical Journal, <\/em>112(5), 1037\u20131044, (2017).link to paper<\/a><\/p>\n<\/div>\n

 <\/p>\n

\n

2016<\/strong><\/h1>\n

Guo, X., and Boedicker, J.Q., The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community,\u00a0PLoS Computational Biology,\u00a0<\/em>12(9): e1005079, (2016).link to paper<\/a><\/span><\/p>\n

Yusufaly, T.I. and Boedicker, J. Q.,\u00a0Spatial dispersal of bacterial colonies induces a dynamical transition from local to global quorum sensing,\u00a0Physical Review E<\/em>,\u00a094, 62410, (2016). link to paper<\/a><\/p>\n

Michelusi, N., Boedicker, J.Q., El-Naggar, M.Y., and Mitra, U.,\u00a0Queuing models for abstracting interactions in bacterial communities,\u00a0IEEE<\/em>\u00a0Journal on selected areas in communications,\u00a0<\/em>vol. 34, no. 3, (2016). link to paper<\/a><\/p>\n<\/div>\n

 <\/p>\n

\n

2015<\/strong><\/h1>\n

Nealson, K., and Boedicker, J.Q., Microbial communication via quorum sensing,\u00a0Transactions on Molecular\u00a0Biological and Multi-scale Communications, vol. 1, no. 4,<\/em>\u00a0December (2015).\u00a0[pdf<\/a>]<\/p>\n

Kreamer, N.N., Phillips, R., Newman, D.K., and Boedicker, J.Q.,\u00a0Predicting the impact of promoter variability on regulatory outputs, Scientific Reports,\u00a0<\/em>5, 18238 (2015). [pdf<\/a>]<\/p>\n

Boedicker, J.Q., Brenner, K., and Weibel, D., Spatial structure of microbes in nature and the biophysics of cell-cell communication, The Physical Basis of Bacterial Quorum Communication<\/em>, edited by Steve Hagen, Springer (2015).<\/p>\n<\/div>\n

 <\/p>\n

\n

2014<\/strong><\/h1>\n

Razo-Mejia, M., Boedicker, J.Q., Jones, D., Deluna, A., Kinney, J.B., and Phillips, R., Comparison of the theoretical and real-world evolutionary potential of a genetic circuit,\u00a0Physical Biology<\/em>\u00a011, 026005 (2014). \u00a0[pdf<\/a>]<\/p>\n<\/div>\n

 <\/p>\n

\n

2013<\/strong><\/h1>\n

Boedicker, J.Q., Garcia, H.G., Johnson, S., and Phillips, R., DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation,\u00a0Physical Biology<\/em>\u00a010, 066005 (2013). [pdf<\/a>]<\/p>\n

Boedicker, J.Q., Garcia, H. G., and Phillips, R., Theoretical and experimental dissection of DNA loop-mediated repression,\u00a0Physical Review Letters\u00a0<\/em>110, 018101 (2013). [pdf<\/a>]<\/p>\n<\/div>\n

 <\/p>\n

\n

2012<\/strong><\/h1>\n

*Garcia, H.G., *Sanchez, A., *Boedicker, J.Q., Osborne, M., Gelles, J., Kondev, J., and Phillips, R., Operator sequence alters gene expression independently of transcription factor occupancy in bacteria.\u00a0Cell Reports<\/em>\u00a02, 150-161 (2012). (* co-first author) [pdf<\/a>]<\/p>\n<\/div>\n

 <\/p>\n

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2011<\/strong><\/h1>\n

Garcia, H. G., Lee, H. J., Boedicker, J. Q., and Phillips, R., Comparison and calibration of different reporters for quantitative analysis of gene expression.\u00a0Biophysical Journal<\/em>\u00a0101, 535-544 (2011). [pdf<\/a>]<\/p>\n<\/div>\n

 <\/p>\n

\n

2009<\/strong><\/h1>\n

Boedicker, J. Q., Vincent, M. E., & Ismagilov, R.F. Microfluidic confinement of single cells of bacteria in small volumes initiates high-density behavior of quorum sensing and growth and reveals its variability.\u00a0Angewandte Chemie International Edition<\/em>\u00a048, 5908-5911 (2009). [pdf<\/a>]<\/p>\n<\/div>\n

 <\/p>\n

\n

2008<\/strong><\/h1>\n

Boedicker, J. Q., Li, L., Kline, T. R. & Ismagilov, R. F. Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics.\u00a0Lab on a Chip<\/em>\u00a08, 1265-1272 (2008). [pdf<\/a>]<\/p>\n

*Kim, H. J., *Boedicker, J. Q., Choi, J. W. & Ismagilov, R. F. Defined spatial structure stabilizes a synthetic multispecies bacterial community.\u00a0PNAS\u00a0<\/em>105, 18188-18193 (2008). (* co-first author) [pdf<\/a>]<\/p>\n

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.J., & Ismagilov, R.F. Spatial localization of bacteria controls coagulation of human blood by ‘quorum acting’.\u00a0Nature Chemical Biology<\/em>\u00a04, 742-750 (2008). [pdf<\/a>]<\/p>\n<\/div>\n

 <\/p>\n

\n

2007<\/strong><\/h1>\n

Li, L., Boedicker, J. Q. & Ismagilov, R. F. Using a multijunction microfluidic device to inject substrate into an array of preformed plugs without cross-contamination: Comparing theory and experiments.\u00a0Analytical Chemistry<\/em>\u00a079, 2756-2761 (2007). [pdf<\/a>]<\/p>\n<\/div>\n

 <\/p>\n

\n

2005<\/strong><\/h1>\n

Wood, K. C., Boedicker, J. Q., Lynn, D. M. & Hammond, P. T. Tunable drug release from hydrolytically degradable layer-by-layer thin films.\u00a0Langmuir<\/em>\u00a021, 1603-1609 (2005). [pdf<\/a>]<\/p>\n<\/div>\n

 <\/p>\n

\n

2004<\/strong><\/h1>\n

Santini, C. M. B., Johnson, M. A., Boedicker, J. Q., Hatton, T. A. & Hammond, P. T. Synthesis and bulk assembly behavior of linear-dendritic rod diblock copolymers.\u00a0Journal of Polymer Science Part A-Polymer Chemistry<\/em>\u00a042, 2784-2814 (2004). [pdf<\/a>]<\/p>\n<\/div>\n\n\n\n<\/div>\n\n\n <\/div><\/div>\n\n\n \n \n \n\n\n\n\n\n\n\n

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\n Contact\n <\/h2>\n\n\n<\/div>\n \n \n <\/div>\n \n \n
\n\n \n
\n\n

Boedicker Lab<\/h3>\n \n \n
\n\n \n

Department of Physics
\nUniversity of Southern California<\/p>\n\n\n\n<\/div>\n \n

\n (213) 740 – 1104<\/a>\n <\/div>\n \n
\n boedicke@usc.edu<\/a>\n <\/div>\n \n <\/div>\n \n
\n\n

James Boedicker<\/h3>\n \n \n
\n\n \n
Associate Professor of\u00a0Physics and the Biological Sciences<\/address>\n
Office: SSC 223, Lab: SSC 212<\/address>\n\n\n\n<\/div>\n \n
\n (213) 740-1104<\/a>\n <\/div>\n \n
\n boedicke@usc.edu<\/a>\n <\/div>\n \n <\/div>\n \n <\/div>\n\n \n \n \n <\/div>\n\n\n <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":584,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-213","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"\nPublications - Boedicker Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/dornsife.usc.edu\/boedickerlab\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - Boedicker Lab\" \/>\n<meta property=\"og:url\" content=\"https:\/\/dornsife.usc.edu\/boedickerlab\/publications\/\" \/>\n<meta property=\"og:site_name\" content=\"Boedicker Lab\" \/>\n<meta property=\"article:modified_time\" content=\"2025-10-16T22:55:29+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/dornsife.usc.edu\/boedickerlab\/publications\/\",\"url\":\"https:\/\/dornsife.usc.edu\/boedickerlab\/publications\/\",\"name\":\"Publications - 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