Academic Appointments

Honors & Awards

  • CAREER Award, U.S. National Science Foundation (2023 - 2028)
  • Early Career Award, U.S. Department of Energy (2023 - 2028)
  • Chan-Zuckerberg Biohub Investigator, Chan-Zuckerberg Biohub - San Francisco (2021 - 2026)
  • Robert N. Noyce Family Faculty Fellow, Stanford University (2021 - 2024)
  • Career Award at the Scientific Interface, Burroughs Wellcome Fund (2018 - 2022)
  • Graduate Women of Excellence Award, Massachusetts Institute of Technology (2015)
  • Graduate Research Fellowship, U.S. National Science Foundation (2011 - 2014)

Professional Education

  • Postdoctoral Fellow, Stanford University, Biology
  • Ph.D., Massachusetts Institute of Technology, Biological Engineering (2016)
  • B.S., University of California at Berkeley, Bioengineering (2010)

Current Research and Scholarly Interests

We develop technologies that enable the genetic engineering of plants and their associated microbes with the goal of driving innovation in agriculture for a sustainable future. Our work is focused in synthetic biology and the reprogramming of plant development for enhanced environmental stress tolerance.

Stanford Advisees

All Publications

  • Synthetic genetic circuits as a means of reprogramming plant roots. Science (New York, N.Y.) Brophy, J. A., Magallon, K. J., Duan, L., Zhong, V., Ramachandran, P., Kniazev, K., Dinneny, J. R. 2022; 377 (6607): 747-751


    The shape of a plant's root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. We developed a collection of synthetic transcriptional regulators for plants that can be compiled to create genetic circuits. These circuits control gene expression by performing Boolean logic operations and can be used to predictably alter root structure. This work demonstrates the potential of synthetic genetic circuits to control gene expression across tissues and reprogram plant growth.

    View details for DOI 10.1126/science.abo4326

    View details for PubMedID 35951698

  • First Plant Cell Atlas symposium report PLANT DIRECT Rice, S. L., Lazarus, E., Anderton, C., Birnbaum, K., Brophy, J., Cole, B., Dickel, D., Ehrhardt, D., Fahlgren, N., Frank, M., Haswell, E., Huang, S., Leiboff, S., Libault, M., Otegui, M. S., Provart, N., Uhrig, R., Rhee, S. Y., Plant Cell Atlas Consortium 2022; 6 (6)

    View details for DOI 10.1002/pld3.406

    View details for Web of Science ID 000807524600001

  • Toward synthetic plant development. Plant physiology Brophy, J. A. 1800


    The ability to engineer plant form will enable the production of novel agricultural products designed to tolerate extreme stresses, boost yield, reduce waste, and improve manufacturing practices. While historically, plants were altered through breeding to change their size or shape, advances in our understanding of plant development and our ability to genetically engineer complex eukaryotes are leading to the direct engineering of plant structure. In this review, I highlight the central role of auxin in plant development and the synthetic biology approaches that could be used to turn auxin-response regulators into powerful tools for modifying plant form. I hypothesize that recoded, gain-of-function auxin response proteins combined with synthetic regulation could be used to override endogenous auxin signaling and control plant structure. I also argue that auxin-response regulators are key to engineering development in non-model plants and that single cell-omics techniques will be essential for characterizing and modifying auxin response in these plants. Collectively, advances in synthetic biology, single cell -omics, and our understanding of the molecular mechanisms underpinning development have set the stage for a new era in the engineering of plant structure.

    View details for DOI 10.1093/plphys/kiab568

    View details for PubMedID 34904660

  • Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells. Nature communications Cuevas-Velazquez, C. L., Vellosillo, T., Guadalupe, K., Schmidt, H. B., Yu, F., Moses, D., Brophy, J. A., Cosio-Acosta, D., Das, A., Wang, L., Jones, A. M., Covarrubias, A. A., Sukenik, S., Dinneny, J. R. 2021; 12 (1): 5438


    Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.

    View details for DOI 10.1038/s41467-021-25736-8

    View details for PubMedID 34521831

  • Vision, challenges and opportunities for a Plant Cell Atlas. eLife Plant Cell Atlas Consortium, Jha, S. G., Borowsky, A. T., Cole, B. J., Fahlgren, N., Farmer, A., Huang, S. 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., Denolf, P., Di Costanzo, L. F., Exposito-Alonso, M., Giacomello, S., Gomez-Cano, F., Kaufmann, K., Ko, D. K., Kumar, S., Malkovskiy, 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., Ahmed, J., Alaba, O., Ameen, G., Arora, V., Arteaga-Vazquez, M. A., Arun, A., Bailey-Serres, J., Bartley, L. E., Bassel, G. W., Bergmann, D. C., Bertolini, E., Bhati, K. K., Blanco-Tourinan, N., Briggs, S. P., Brumos, J., Buer, B., Burlaocot, A., Cervantes-Perez, S. A., Chen, S., Contreras-Moreira, B., Corpas, F. J., Cruz-Ramirez, A., Cuevas-Velazquez, C. L., Cuperus, J. T., David, L. I., de Folter, S., Denolf, P. H., Ding, P., Dwyer, W. P., Evans, M. M., George, N., Handakumbura, P. P., Harrison, M. J., Haswell, E. S., Herath, V., Jiao, Y., Jinkerson, R. E., John, U., Joshi, S., Joshi, A., Joubert, L., Katam, R., Kaur, H., Kazachkova, Y., Raju, S. K., Khan, M. A., Khangura, R., Kumar, A., Kumar, A., Kumar, P., Kumar, P., Lavania, D., Lew, T. T., Lewsey, M. G., Lin, C., Liu, D., Liu, L., Liu, T., Lokdarshi, A., My Luong, A., Macaulay, I. C., Mahmud, S., Mahonen, A. P., Malukani, K. K., Marand, A. P., Martin, C. A., McWhite, C. D., Mehta, D., Martin, M. M., Mortimer, J. C., Nikolov, L. A., Nobori, T., Nolan, T. M., Ogden, A. J., Otegui, M. S., Ott, M., Palma, J. M., Paul, P., Rehman, A. U., Romera-Branchat, M., Romero, L. C., Roth, R., Sah, S. K., Shahan, R., Solanki, S., Song, B., Sozzani, R., Stacey, G., Stepanova, A. N., Taylor, N. L., Tello-Ruiz, M. K., Tran, T. M., Tripathi, R. K., Vadde, B. V., Varga, T., Vidovic, M., Walley, J. W., Wang, Z., Weizbauer, R. A., Whelan, J., Wijeratne, A. J., Xiang, T., Xu, S., Yadegari, R., Yu, H., Yuan, H. Y., Zanini, F., Zhao, F., Zhu, J., Zhuang, X. 2021; 10


    With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

    View details for DOI 10.7554/eLife.66877

    View details for PubMedID 34491200

  • Understanding and engineering plant form SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY Brophy, J. N., LaRue, T., Dinneny, J. R. 2018; 79: 68–77
  • Understanding and engineering plant form. Seminars in cell & developmental biology Brophy, J. A., LaRue, T. n., Dinneny, J. R. 2017


    A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.

    View details for PubMedID 28864344