PUBLICATIONS

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

Stanford News Article: link

Science Perspective: Synthetic gene circuits take root

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

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.

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

2018

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

2016

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

Antisense transcription as a tool to tune gene expression

Molecular Systems Biology 12(1) 854

2014

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

Principles of genetic circuit design

Nature Methods 11(5) 508-520

2013

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

2011

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

Automated assembly of standard biological parts

Methods in Enzymology 498, 363-397

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.

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