2025
Jimenez, I.L. and Boedicker J.Q., Quorum sensing increases the diversity of bacterial communities in a Lotka-Volterra model, submitted.
Das, S., Haxhimali, E., and Boedicker, J.Q., Stability of quorum sensing decision states in heterogeneous bacterial communities, submitted.
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.
Peach, L.J., Zhang, H., Weaver, B.P., and Boedicker J.Q., Assessing spacer acquisition rates in E. coli type 1-E CRISPR arrays [LINK], Frontiers in Microbiology, 15, 1498959.
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 [LINK], PLoS One, 20 (9), e0332156.
Sun, R., Gangan, M.S., Wang, Q., Boedicker, J.Q., and Armani, A.M., Magnetically tunable hydrogel for biofilm control, ACS Applied Bio Materials [LINK], 8 (6), 5090-97.
Guo, X., Lim, S., Bogdan, P., and Boedicker, J.Q., Dynamic switch in the collective behavior of a two-strain microbial community, submitted.
2024
Ostovar, G. and Boedicker, J.Q., Phenotypic memory in quorum sensing [LINK], PLoS Computational Biology, 20(7), e1011696, (2024).
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 [LINK], ACS Synthetic Biology, 13(5), 1467-1476, (2024).
2023
Gangan M.S., Naughton K.L., and Boedicker J.Q., Utilizing a divalent metal ion transporter to control biogenic nanoparticle synthesis [LINK], Journal of Industrial Microbiology and Biotechnology, 50(1), (2023).
Weaver, B.P., Haselwandter, C. A., and Boedicker J. Q., Stochastic effects in bacterial communication mediated by extracellular vesicles [LINK], Physical Review E, 107 (2), 024409, (2023).
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 [LINK], IEEE Nanotechnology Magazine, 17 (3), 32-41, (2023).
2022
Courcoubetis, G., Gangan, M., Lim, S., Guo, X., Haas, S., Boedicker, J.Q., Formation, collective motion, and merging of macroscopic bacterial aggregates [LINK], PLoS Computational Biology, 18(1): e1009153, (2022).
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 [LINK], iScience, 25(4), 104117, (2022).
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 [LINK], ACS Synthetic Biology, 11, 7, 2327-2338, (2022).
Tran, F., Gangan, M.S., Weaver, B.P., and Boedicker J. Q., Membrane-binding biomolecules influence the rate of vesicle exchange between bacteria [LINK], Applied and Environmental Microbiology, e0134622, (2022).
2021
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 [LINK], Bioelectricity, 3(2), 126-135, (2021).
Naughton, K.L., Boedicker, J.Q., Simulations to aid in the design of microbes for synthesis of metallic nanomaterials [LINK], ACS Synthetic Biology, 10, 12, 3475–3488, (2021).
2020
Ostovar, G., Naughton, K., and Boedicker, J. Q., Computation in bacterial communities [LINK], Physical Biology, 17, 061002 (2020).
Boedicker, J.Q., Multispecies microbial communities and synthetic microbial ecosystems, Biomimetic Microengineering, edited by Hyun Jung Kim, CRC Press (2020).
2019
Silva, K.P.T, and Boedicker, J.Q., A neural network model predicts community-level signaling states in a diverse microbial community [LINK], PLoS Computational Biology, 15(6): e1007166, (2019).
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 Shewanella oneidensis MR-1 [LINK], Frontiers in Microbiology, 10, 938, (2019).
Lim S., Guo X., and Boedicker J.Q., Connecting single-cell properties to collective behavior in multiple wild isolates of the Enterobacter cloacae complex [LINK], PLoS ONE, 14(4): e0214719, (2019).
Silva, K.P.T., Yusufaly, T.I., Chellamuthu, P., and Boedicker J.Q., Disruption of microbial communication yields a 2D percolation transition [LINK], Physical Review E, 99, 042409, (2019).
Guo, X., Silva, K.P.T., and Boedicker, J.Q., Single-cell variability of growth interactions within a two-species bacterial community [LINK], Physical Biology, 16(3): 036001, (2019).
Tran, F. and Boedicker J.Q., Plasmid characteristics modulate the propensity of gene exchange in bacterial vesicles [LINK], Journal of Bacteriology, 201 (7) e00430-18, (2019).
Chellamuthu, P., Tran, F., Silva, K.P.T., Chavez, M.S., El Naggar, M., and Boedicker J.Q., Engineering bacteria for biogenic synthesis of chalcogenide nanomaterials [LINK], Microbial Biotechonology, 12(1), 161–172, (2019).
2018
Nazarian, P., Tran, F., and Boedicker, J.Q., Modeling multispecies gene flow dynamics reveals the unique roles of different horizontal gene transfer mechanisms [LINK], Frontiers in Microbiology, 9, 2978, (2018).
Balaban, V., Lim, S., Gupta, G., Boedicker, J.Q., and Bogdan, P., Quantifying emergence and self-organisation of Enterobacter cloacae microbial communities [LINK], Scientific Reports, 8, Article number 12416, (2018).
2017
Silva, K.P., Chellamuthu, P., and Boedicker, J. Q., Quantifying the strength of quorum sensing crosstalk within microbial communities [LINK], PLoS Computational Biology, 13(10): e1005809, (2017).
Yusufaly, T.I. and Boedicker, J.Q., Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities [LINK], Physical Biology, vol 14, Number 4, (2017).
Tran, F. and Boedicker J.Q., Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer [LINK], Scientific Reports, 7, Article number: 8813 (2017).
Silva, K.P., Chellamuthu, P., and Boedicker, J.Q., Signal destruction tunes the zone of activation in spatially distributed signaling networks [LINK], Biophysical Journal, 112(5), 1037–1044, (2017).
2016
Guo, X., and Boedicker, J.Q., The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community [LINK], PLoS Computational Biology, 12(9): e1005079, (2016).
Yusufaly, T.I. and Boedicker, J. Q., Spatial dispersal of bacterial colonies induces a dynamical transition from local to global quorum sensing [LINK], Physical Review E, 94, 62410, (2016).
Michelusi, N., Boedicker, J.Q., El-Naggar, M.Y., and Mitra, U., Queuing models for abstracting interactions in bacterial communities [LINK], IEEE Journal on selected areas in communications, vol. 34, no. 3, (2016).
2015
Nealson, K., and Boedicker, J.Q., Microbial communication via quorum sensing [LINK], Transactions on Molecular Biological and Multi-scale Communications, vol. 1, no. 4, December (2015).
Kreamer, N.N., Phillips, R., Newman, D.K., and Boedicker, J.Q., Predicting the impact of promoter variability on regulatory outputs [LINK], Scientific Reports, 5, 18238 (2015).
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, edited by Steve Hagen, Springer (2015).
2014
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 [LINK], Physical Biology 11, 026005 (2014).
2013
Boedicker, J.Q., Garcia, H.G., Johnson, S., and Phillips, R., DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation [LINK], Physical Biology 10, 066005 (2013).
Boedicker, J.Q., Garcia, H. G., and Phillips, R., Theoretical and experimental dissection of DNA loop-mediated repression [LINK], Physical Review Letters 110, 018101 (2013).
2012
*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 [LINK]. Cell Reports 2, 150-161 (2012). (* co-first author)
2011
Garcia, H. G., Lee, H. J., Boedicker, J. Q., and Phillips, R., Comparison and calibration of different reporters for quantitative analysis of gene expression [LINK]. Biophysical Journal 101, 535-544 (2011).
2009
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 [LINK]. Angewandte Chemie International Edition 48, 5908-5911 (2009).
2008
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 [LINK]. Lab on a Chip 8, 1265-1272 (2008).
*Kim, H. J., *Boedicker, J. Q., Choi, J. W. & Ismagilov, R. F. Defined spatial structure stabilizes a synthetic multispecies bacterial community [LINK]. PNAS 105, 18188-18193 (2008). (* co-first author).
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’ [LINK]. Nature Chemical Biology 4, 742-750 (2008).
2007
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 [LINK]. Analytical Chemistry 79, 2756-2761 (2007).
2005
Wood, K. C., Boedicker, J. Q., Lynn, D. M. & Hammond, P. T. Tunable drug release from hydrolytically degradable layer-by-layer thin films [LINK]. Langmuir 21, 1603-1609 (2005).
2004
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 [LINK]. Journal of Polymer Science Part A-Polymer Chemistry 42, 2784-2814 (2004).