2022

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, 18(1): e1009153, (2022). link to paper

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, 25(4), 104117, (2022). link to paper

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, 11, 7, 2327-2338, (2022). link to paper

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, e0134622, (2022). link to paper

Weaver, B.P., Haselwandter, C. A., and Boedicker J. Q., Stochastic effects in bacterial communication mediated by extracellular vesicles, submitted.

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

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, Bioelectricity, 3(2), 126-135, (2021). link to paper

Naughton, K.L., Boedicker, J.Q., Simulations to aid in the design of microbes for synthesis of metallic nanomaterials, ACS Synthetic Biology, 10, 12, 3475–3488, (2021). link to paper

2020

Ostovar, G., Naughton, K., and Boedicker, J. Q., Computation in bacterial communities, Physical Biology, 17, 061002 (2020). link to paper

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, PLoS Computational Biology, 15(6): e1007166, (2019). link to paper

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, Frontiers in Microbiology, 10, 938, (2019). link to paper

Lim S., Guo X., and Boedicker J.Q., Connecting single-cell properties to collective behavior in multiple wild isolates of the Enterobacter cloacae complex, PLoS ONE, 14(4): e0214719, (2019). link to paper

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

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

Tran, F. and Boedicker J.Q., Plasmid characteristics modulate the propensity of gene exchange in bacterial vesicles, Journal of Bacteriology, 201 (7) e00430-18, (2019). link to paper

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, Microbial Biotechonology, 12(1), 161–172, (2019). link to paper

2018

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, 9, 2978, (2018). link to paper

Balaban, V., Lim, S., Gupta, G., Boedicker, J.Q., and Bogdan, P., Quantifying emergence and self-organisation of Enterobacter cloacae microbial communities, Scientific Reports, 8, Article number 12416, (2018). link to paper

2017

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

Yusufaly, T.I. and Boedicker, J.Q., Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities, Physical Biology, vol 14, Number 4, (2017). link to paper

Tran, F. and Boedicker J.Q., Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer, Scientific Reports, 7, Article number: 8813 (2017). link to paper

Silva, K.P., Chellamuthu, P., and Boedicker, J.Q., Signal destruction tunes the zone of activation in spatially distributed signaling networks, Biophysical Journal, 112(5), 1037–1044, (2017).link to paper

2016

Guo, X., and Boedicker, J.Q., The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community, PLoS Computational Biology, 12(9): e1005079, (2016).link to paper

Yusufaly, T.I. and Boedicker, J. Q., Spatial dispersal of bacterial colonies induces a dynamical transition from local to global quorum sensing, Physical Review E, 94, 62410, (2016). link to paper

Michelusi, N., Boedicker, J.Q., El-Naggar, M.Y., and Mitra, U., Queuing models for abstracting interactions in bacterial communities, IEEE Journal on selected areas in communications, vol. 34, no. 3, (2016). link to paper

2015

Nealson, K., and Boedicker, J.Q., Microbial communication via quorum sensing, Transactions on Molecular Biological and Multi-scale Communications, vol. 1, no. 4, December (2015). [pdf]

Kreamer, N.N., Phillips, R., Newman, D.K., and Boedicker, J.Q., Predicting the impact of promoter variability on regulatory outputs, Scientific Reports, 5, 18238 (2015). [pdf]

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, Physical Biology 11, 026005 (2014).  [pdf]

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, Physical Biology 10, 066005 (2013). [pdf]

Boedicker, J.Q., Garcia, H. G., and Phillips, R., Theoretical and experimental dissection of DNA loop-mediated repression, Physical Review Letters 110, 018101 (2013). [pdf]

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. Cell Reports 2, 150-161 (2012). (* co-first author) [pdf]

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. Biophysical Journal 101, 535-544 (2011). [pdf]

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. Angewandte Chemie International Edition 48, 5908-5911 (2009). [pdf]

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. Lab on a Chip 8, 1265-1272 (2008). [pdf]

*Kim, H. J., *Boedicker, J. Q., Choi, J. W. & Ismagilov, R. F. Defined spatial structure stabilizes a synthetic multispecies bacterial community. PNAS 105, 18188-18193 (2008). (* co-first author) [pdf]

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’. Nature Chemical Biology 4, 742-750 (2008). [pdf]

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. Analytical Chemistry 79, 2756-2761 (2007). [pdf]

2005

Wood, K. C., Boedicker, J. Q., Lynn, D. M. & Hammond, P. T. Tunable drug release from hydrolytically degradable layer-by-layer thin films. Langmuir 21, 1603-1609 (2005). [pdf]

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. Journal of Polymer Science Part A-Polymer Chemistry 42, 2784-2814 (2004). [pdf]