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

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


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

News Articles & Perspectives: Science, Stanford News, GEN, Synthetic Biology, DOE

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

Brophy, J.A.N.

Toward synthetic plant development

Plant Physiology 188(2): 738-748


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.

Genetically modifying skin microbe to produce violacein and augmenting microbiome did not defend Panamanian golden frogs from disease

ISME Communications 1: 57

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

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.

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells

Nature Communications 12: 5438


Brophy, J.A.N., Triassi, A.J., Adams, B.L., Renberg, R.L., Stratis-Cullum, D.N., Grossman, A.D., & Voigt, C.A.

Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria

Nature Microbiology 3(9) 1043-1053

Brophy, J.A.N.*, LaRue T.*, & Dinneny, J.R.

Understanding and engineering plant form

Seminars in Cell & Developmental Biology 79, 68-77


Brophy, J.A.N. & Voigt, C.A.

Antisense transcription as a tool to tune gene expression

Molecular Systems Biology 12(1) 854


Brophy, J.A.N. & Voigt, C.A.

Principles of genetic circuit design

Nature Methods 11(5) 508-520


Chen, Y-J., Liu, P., Nielsen, A.A.K., Brophy, J.A.N., Clancy, K., Peterson, T., & Voigt, C.A.

Characterization of 582 natural and synthetic terminators and quantification of their design constraints

Nature Methods 10(7) 659-664

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


Leguia, M., Brophy, J.A.N., Densmore, D., & Anderson, J.C.

Automated assembly of standard biological parts

Methods in Enzymology 498, 363-397


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.

Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival

Molecular and Cellular Biology 30(10), 2449-2459