Embedded Files
For a complete list of publications, please visit Jenn's Google Scholar page.
Preprints
Greco FV, Cameron SK, Joshi SH, Guiziou S, Brophy JAN, Grierson CS, Gorochowski TE
Characterization of recombinase-based genetic parts and circuits using nanopore sequencing
BioRxiv
2025
Hernandez S*, Zhong V*, Brophy JAN
SeedSeg: Image-based transgenic seed counting for segregation analysis of T-DNA loci
Plant Methods 21;87 [pdf]
2024
Kozaeva E, Aziz Eida A, Gunady EF, Dangl JL^, Conway JM^, Brophy JAN^
Roots of synthetic ecology: microbes that foster plant resilience in the changing climate
Current Opinion in Biotechnology 88;103172 [pdf]
2023
Archibald BN*, Zhong V*, Brophy JAN
PLOS Biology 21(7):e3002208 [pdf]
Zhong V*, Archibald BN*, Brophy JAN
Transcriptional and post-transcriptional controls for tuning gene expression in plants
Current Opinion in Plant Biology 71; 102315 [pdf]
Leak LB*, Tamborski J*, Commissaris A, Brophy JAN
Forging a path toward a more sustainable laboratory
Trends in Biochemical Sciences 48(1): 5-8 [pdf]
2022
Brophy JAN^, Magallon K J, Duan L, Zhong V, Ramachandran P, Kniazev K, Dinneny JR^
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 SL, Lazarus E, Anderton E, Birnbaum K, Brophy JAN, Cole B, Dickel D, Erhardt D, Fahlgren N, Frank M, Haswell E, Huang SC, Leiboff S, Libault M, Otegui MS, Provart N, Uhrig RG, Rhee SY, Plant Cell Atlas Consortium
First Plant Cell Atlas symposium report
Plant Direct 6:e406 [pdf]
Brophy JAN
Toward synthetic plant development
Plant Physiology 188(2): 738-748 [pdf]
2021
Becker MH, Brophy JAN, Barrett K, Bronikowski E, Evans M, Glassey E, Klocke B, Lassiter E, Meyer AJ, Kaganer AE, Muletz-Wolz CR, Fleischer RC, Voigt CA, Gratwicke B
ISME Communications 1: 57 [pdf] [supplement]
Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang C, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskivy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodriguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY, Plant Cell Atlas Consortium
Science Forum: Vision, challenges and opportunities for a Plant Cell Atlas
eLife e66877 [pdf]
Cuevas-Velazquez CL, Vellosillo T, Guadalupe K, Schmidt HB, Yu F, Moses D, Brophy JAN, Cosio-Acosta D, Das A, Wang L. Jones AM, Covarrubias AA, Sukenik S, Dinneny JR
Nature Communications 12: 5438 [pdf] [supplement]
2018
Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD, Voigt CA
Nature Microbiology 3(9) 1043-1053 [pdf] [supplement]
Brophy JAN*, LaRue T*, Dinneny JR
Understanding and engineering plant form
Seminars in Cell & Developmental Biology 79, 68-77 [pdf]
2016
Brophy JAN & Voigt CA
Antisense transcription as a tool to tune gene expression
Molecular Systems Biology 12(1) 854 [pdf] [supplement]
2014
Brophy JAN & Voigt CA
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]
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