Publications
For a complete list of publications, please visit Jenn's Google Scholar page.
2024
Kozaeva, E., Aziz Eida, A., Gunady, E.F., Dangl, J.L.^, Conway, J.M.^ Brophy, J.A.N. ^
Roots of synthetic ecology: microbes that foster plant resilience in the changing climate
Current Opinion in Biotechnology 88;103172 [pdf]
2023
Archibald, B.N.*, Zhong, V.*, Brophy, J.A.N.
PLOS Biology 21(7):e3002208 [pdf]
Zhong, V.*, Archibald, B.N.*, Brophy, J.A.N.
Transcriptional and post-transcriptional controls for tuning gene expression in plants
Current Opinion in Plant Biology 71; 102315 [pdf]
Leak, L.B.*, Tamborski, J.*, Commissaris, A., Brophy, J.A.N.
Forging a path toward a more sustainable laboratory
Trends in Biochemical Sciences 48(1): 5-8 [pdf]
2022
Brophy, J.A.N.^, Magallon, K. J., Duan, L., Zhong, V., Ramachandran, P., Kniazev, K., Dinneny, J.R.^
Synthetic genetic circuits as a means of reprogramming of plant roots
Science 377(6607): 747-751 [pdf] [supplement]
News Articles & Perspectives: [Science] [Stanford News] [GEN] [Synthetic Biology] [DOE] [Quanta]
Rice, S.L., Lazarus, E., Anderton, E., Birnbaum, K., Brophy, J.A.N., Cole, B., Dickel, D., Erhardt, D., Fahlgren, N., Frank, M., Haswell, E., Huang, S.C., Leiboff, S., Libault, M., Otegui, M.S., Provart, N., Uhrig, R.G., Rhee, S.Y., Plant Cell Atlas Consortium
First Plant Cell Atlas symposium report
Plant Direct 6:e406 [pdf]
Brophy, J.A.N.
Toward synthetic plant development
Plant Physiology 188(2): 738-748 [pdf]
2021
Becker, M.H., Brophy, J.A.N., Barrett, K., Bronikowski, E., Evans, M., Glassey, E., Klocke, B., Lassiter, E., Meyer, A.J., Kaganer, A.E., Muletz-Wolz, C.R., Fleischer, R.C., Voigt, C.A., Gratwicke, B.
ISME Communications 1: 57 [pdf] [supplement]
Jha, S.G., Borowsky, A.T., Cole, B.J., Fahlgren, N., Farmer, A., Huang, C., Karia, P., Libault, M., Provart, N.J., Rice, S.L., Saura-Sanchez, M., Agarwal, P., Ahkami, A.H., Anderton, C.R., Briggs, S.P., Brophy, J.A.N., Denolf, P., Di Costanzo, L.F., Exposito-Alonso, M., Giacomello, S., Gomez-Cano, F., Kaufmann, K., Ko, D.K., Kumar, S., Malkovskivy, A.V., Nakayama, N., Obata, T., Otegui, M.S., Palfalvi, G., Quezada-Rodriguez, E.H., Singh, R., Uhrig, R.G., Waese, J., Van Wijk, K., Wright, R.C., Ehrhardt, D.W., Birnbaum, K.D., Rhee, S.Y., Plant Cell Atlas Consortium
Science Forum: Vision, challenges and opportunities for a Plant Cell Atlas
eLife e66877 [pdf]
Cuevas-Velazquez, C.L., Vellosillo, T., Guadalupe, K., Schmidt, H.B., Yu, F., Moses, D., Brophy, J.A.N., Cosio-Acosta, D., Das, A., Wang, L., Jones, A.M., Covarrubias, A.A., Sukenik, S., Dinneny, J.R.
Nature Communications 12: 5438 [pdf] [supplement]
2018
Brophy, J.A.N., Triassi, A.J., Adams, B.L., Renberg, R.L., Stratis-Cullum, D.N., Grossman, A.D., & Voigt, C.A.
Nature Microbiology 3(9) 1043-1053 [pdf] [supplement]
Brophy, J.A.N.*, LaRue T.*, & Dinneny, J.R.
Understanding and engineering plant form
Seminars in Cell & Developmental Biology 79, 68-77 [pdf]
2016
Brophy, J.A.N. & Voigt, C.A.
Antisense transcription as a tool to tune gene expression
Molecular Systems Biology 12(1) 854 [pdf] [supplement]
2014
Brophy, J.A.N. & Voigt, C.A.
Principles of genetic circuit design
Nature Methods 11(5) 508-520 [pdf]
2013
Chen, Y-J., Liu, P., Nielsen, A.A.K., Brophy, J.A.N., Clancy, K., Peterson, T., & Voigt, C.A.
Nature Methods 10(7) 659-664 [pdf] [supplement]
Leguia, M., Brophy, J.A.N., Densmore, D., Asante, A., Anderson, J.C.
2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts
Journal of Biological Engineering 7(1): 1-16 [pdf]
2011
Leguia, M., Brophy, J.A.N., Densmore, D., & Anderson, J.C.
Automated assembly of standard biological parts
Methods in Enzymology 498, 363-397 [pdf]
2010
Fu, D., Brophy, J.A.N., Chan, C.T.Y., Atmore, K.A., Begley, U., Paules, R.S., Dedon, P.C., Begley, T.J., & Samson, L.D.
Molecular and Cellular Biology 30(10), 2449-2459 [pdf]