Google Scholar | * equal contributions | ‡ corresponding author | lab member

Genetic code expansion enables plant-directed control of bacterial activity

Zhong V*, Jones MA*, Cabales A, Gevorgyan A, Inckemann R, Johnson A, Karunadasa S, Forti AM, Xu S, Kunjapur AM‡, Brophy JAN‡

BioRxiv (2026) DOI: 10.64898/2026.05.29.728790 

Characterization of recombinase-based genetic parts and circuits using nanopore sequencing

Greco FV, Cameron SK, Joshi SH, Guiziou S,  Brophy JAN, Grierson CS, Gorochowski TE‡

BioRxiv  (2025) DOI: 10.1101/2025.05.27.656450 

Getting to the root of the pattern

Kozaeva E, Brophy JAN‡

Science (2025) DOI: 10.1126/science.aeb6058

SeedSeg: Image-based transgenic seed counting for segregation analysis of T-DNA loci

Hernandez S*, Zhong V*,  Brophy JAN‡

Plant Methods (2025) [pdf]

Roots of synthetic ecology: microbes that foster plant resilience in the changing climate

Kozaeva E, Aziz Eida A, Gunady EF, Dangl JL‡, Conway JM‡,  Brophy JAN‡

Current Opinion in Biotechnology (2024) 88;103172  [pdf]

Policy makers, genetic engineers, and an engaged public can work together to create climate-resilient plants

Archibald BN*, Zhong V*,  Brophy JAN‡ 

PLOS Biology (2023) 21(7):e3002208  [pdf]

Transcriptional and post-transcriptional controls for tuning gene expression in plants

Zhong V*, Archibald BN*, Brophy JAN‡

Current Opinion in Plant Biology (2023) 71; 102315 [pdf]

Forging a path toward a more sustainable laboratory

Leak LB*, Tamborski J*, Commissaris A, Brophy JAN‡

Trends in Biochemical Sciences (2023) 48(1): 5-8 [pdf]

Synthetic genetic circuits as a means of reprogramming of plant roots 

Brophy JAN‡, Magallon KJ, Duan L, Zhong V, Ramachandran P, Kniazev K, Dinneny JR‡ 

Science (2022) 377(6607): 747-751 [pdf] [supplement]

News & Views: Alamos S & Shih P, Science | Yang EJY & Nemhausser JL, GEN Biotechnology | Inckemann R, Synthetic Biology | Kubota T, Stanford Report | U.S. Department of Energy | Thompson J, Quanta Magazine | Krieger LM, Mercury News

First Plant Cell Atlas symposium report

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

Plant Direct (2022) 6:e406 [pdf]

Toward synthetic plant development

Brophy JAN‡

Plant Physiology (2022) 188(2): 738-748 [pdf]

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

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 (2021) 1: 57 [pdf] [supplement]

Science Forum: Vision, challenges and opportunities for a Plant Cell Atlas

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 

eLife (2021) e66877 [pdf]

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

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 (2021) 12: 5438 [pdf] [supplement]

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

Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD, Voigt CA‡

Nature Microbiology (2018) 3(9) 1043-1053 [pdf] [supplement]

News & Views: Libby EA & Silver PA, Nature Microbiology | U.S. Army Research Laboratory | Cover 

Understanding and engineering plant form

Brophy JAN*, LaRue T*, Dinneny JR‡

Seminars in Cell & Developmental Biology (2018) 79, 68-77 [pdf]

Antisense transcription as a tool to tune gene expression

Brophy JAN & Voigt CA‡

Molecular Systems Biology (2016) 12(1) 854 [pdf] [supplement]

Principles of genetic circuit design

Brophy JAN & Voigt CA‡

Nature Methods (2014) 11(5) 508-520 [pdf]

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

Chen Y-J, Liu P, Nielsen AAK, Brophy JAN, Clancy K, Peterson T, Voigt CA‡

Nature Methods (2013) 10(7) 659-664 [pdf] [supplement]

2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts

Leguia M, Brophy JAN, Densmore D, Asante A, Anderson JC‡ 

Journal of Biological Engineering (2013) 7(1): 1-16 [pdf] 

Automated assembly of standard biological parts

Leguia M, Brophy JAN, Densmore D, Anderson JC‡

Methods in Enzymology (2011) 498, 363-397 [pdf]

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

Fu D, Brophy JAN, Chan CTY, Atmore KA, Begley U, Paules RS, Dedon PC, Begley TJ, Samson LD‡

Molecular and Cellular Biology (2010) 30(10), 2449-2459 [pdf]