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2026
Rui Y, Zaoralova M, Dwyer W, Reyes AV, Grismer TS, Abel NB, Jayachandran D, Chundawat SPS, Ott T, Kieber JJ, Dahlberg PD, Xu S-L, Dinneny JR (2026) Plant cell wall-plasma membrane attachments mediate stress resilience through cellulose synthase complexes and remorins. Cell. doi: 10.1016/j.cell.2026.05.009
Free access link. bioRxiv preprint: 10.1101/2025.08.01.664786
Wang G, Ryu KH, Dinneny A, Carlson J, Goodstein DM, Lee J, Oh D-H, Oliva M, Lister R, Dinneny JR*, Schiefelbein J*, Dassanayake M* (2026) Evolutionary diversity of cell-type-specific expression and stress response in Brassicaceae roots. Nat Commun 17:6660. doi: 10.1038/s41467-026-73270-2. bioRxiv preprint: 10.1101/2024.06.21.599952. *Co-corresponding authors
Dundas CM, Brinkman GA, Clarke T, Payne M, Alama Ureta J, Velasco I, Wallace JG, Dinneny JR (2026) Rhizobacterial Biosensors Spatially Map Natural and Engineered Sucrose Exudation. bioRxiv. doi: 10.64898/2026.04.15.718812
Dwyer WP, Torres-Martínez HH, Dinneny JR (2026) Shaping with water: linking moisture perception to development in plant roots. BMC Biol 24:36. doi: 10.1186/s12915-026-02503-z
2025
Wang G, Dinneny JR (2025) Plant biology: Soil compaction rewires gene expression across root cell types. Current Biology 35(13):R643-R645. doi: 10.1016/j.cub.2025.06.009
Scharwies JD, Clarke T, Zheng Z, Dinneny A, Birkeland S, Veltman MA, Sturrock CJ, Torres-Martinez HH, Viana WG, Khare R, Kieber J, Pandey BKK, Bennett MJ, Schnable PS, Dinneny JR (2025) Moisture-responsive root-branching pathways identified in diverse maize breeding germplasm. Science. doi: 10.1126/science.ads5999
Free access link.
bioRxiv preprint: 10.1101/2024.08.26.609741
2024
Ragland CJ, Shih KY, Dinneny JR (2024) Choreographing root architecture and rhizosphere interactions through synthetic biology. Nature Communications 15:1370. doi: 10.1038/s41467-024-45272-5
Ramachandran P, Ramirez A, Dinneny JR (2024) Rooting for survival: how plants tackle a challenging environment through a diversity of root forms and functions. Plant Physiology 197(1):kiae586. doi: 10.1093/plphys/kiae586
Vilarrasa-Blasi J, Vellosillo T, Jinkerson RE, Fauser F, Xiang T, Minkoff BB, Wang L, Kniazev K, Guzman M, Osaki J, Sussman MR, Jonikas MC, Dinneny JR (2024) Multi-omics analysis of green lineage osmotic stress pathways unveils crucial roles of different cellular compartments. Nature Communications 15:5988. doi: 10.1038/s41467-024-49844-3. bioRxiv preprint: 10.1101/2021.07.19.453009
2023
Bennett MJ, Brady SM, Dinneny JR, Helariutta Y, Sozzani R (2023) Philip N. Benfey (1953–2023). Developmental Cell 58(22):2413-2415. doi: 10.1016/j.devcel.2023.10.013
Verslues PE, Bailey-Serres J, Brodersen C, Buckley TN, Conti L, Christmann A, Dinneny JR, Grill E, Hayes S, Heckman RW, Hsu P-K, Juenger TE, Mas P, Munnik T, Nelissen H, Sack L, Schroeder JI, Testerink C, Tyerman SD, Umezawa T, Wigge PA (2023) Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress. The Plant Cell 35(1):67-108. doi: 10.1093/plcell/koac263
Hirt H, … Dinneny JR, et al. (2023) PlantACT! – how to tackle the climate crisis. Trends in Plant Science 28(5):537-543. doi: 10.1016/j.tplants.2023.01.005
2022
LaRue T, Lindner H, Srinivas A, Exposito-Alonso M, Lobet G, Dinneny JR (2022) Uncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platform. eLife 11:e76968. doi: 10.7554/eLife.76968
bioRxiv preprint: 10.1101/2021.11.13.468476
Brophy JAN, Magallon K, Duan L, Zhong V, Ramachandran P, Kniazev K, Dinneny JR (2022) Synthetic genetic circuits as a means of reprogramming plant roots. Science 377(6607):747-751. doi: 10.1126/science.abo4326
Highlighted in a Science Perspective by Alamos and Shih. Free access link. bioRxiv preprint: 10.1101/2022.02.02.478917
Fauser F, Vilarrasa-Blasi J, Onishi M, Ramundo S, Patena W, Millican M, Osaki J, Philp C, Nemeth M, Salomé PA, Li X, Wakao S, Kim RG, Kaye Y, Grossman AR, Niyogi KK, Merchant S, Cutler S, Walter P, Dinneny JR*, Jonikas MC*, Jinkerson RE* (2022) Systematic characterization of gene function in a photosynthetic organism. Nature Genetics 54:705-714. doi: 10.1038/s41588-022-01052-9
*Co-corresponding authors
Sun Y, Oh DH, Duan L, Ramachandran P, Ramirez A, Bartlett A, Dassanayake M, Dinneny JR (2022) Divergence in a stress-associated gene regulatory network underlies differential growth control. Nature Plants 8:549-560. doi: 10.1038/s41477-022-01139-5
bioRxiv preprint: 10.1101/2020.11.18.349449
Viana W, Scharwies JD, Dinneny JR (2022) Deconstructing the root system of grasses through an exploration of development, anatomy and function. Plant Cell Environ 45(3):602-619. doi: 10.1111/pce.14270
Singhvi A, Fitzpatrick A, Scharwies JD, Dinneny JR, Arbabian A. (2022) A Thermoacoustic Imaging System for Non-Invasive and Non-Destructive Root Phenotyping. IEEE Transactions on Circuits and Systems II: Express Briefs 69(6):2703-2707. doi: 10.1109/TCSII.2022.3159448
2021
Dickinson AJ, Zhang J, Luciano M, Wachsman G, Schnermann M, Dinneny JR, Benfey PN (2021) A plant lipocalin is required for retinal-mediated oscillatory lateral root initiation. Science 373(6562):eabf7461. doi: 10.1126/science.abf7461
Friesner J, Colon-Carmona A, Schnoes AM, Stepanova AN, Mason GA, MacIntosh GC, Ullah H, Baxter IR, Callis J, Sierra-Cajas K, Elliott K, Haswell ES, Zavala ME, Wildermuth M, Williams ME, Ayalew MB, Henkhaus NA, Prunet N, Lemaux PG, Yadegari R, Amasino RM, Hangarter RP, Innes RW, Brady SM, Long T, Woodford-Thomas T, May V, Sun Y, Dinneny JR (2021) Broadening the impact of plant science through innovative, integrative and inclusive outreach. Plant Direct 5(4):e00316. doi: 10.1002/pld3.316
Cuevas-Velazquez CL, Vellosillo T, Guadalupe K, Schmidt BH, Yu F, Moses D, Brophy JAN, Cosio-Acosta D, Das A, Wang L, Jones AM, Covarrubias AA, Sukenik S, Dinneny JR (2021) Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells. Nat Commun 12:5438. doi: 10.1038/s41467-021-25736-8
bioRxiv preprint: 10.1101/2021.02.17.431712
Vellosillo T*, Dinneny JR*, Somerville CR*, Ehrhardt DW* (2021) TRANVIA (TVA) facilitates cellulose synthase trafficking and delivery to the plasma membrane. PNAS 118(30):e2021790118. doi: 10.1073/pnas.2021790118
*Co-corresponding authors
2020
Duan L, Pérez-Ruiz JM, Cejudo FJ, Dinneny JR (2020) Characterization of CYCLOPHILLIN38 shows that a photosynthesis-derived systemic signal controls lateral root emergence. Plant Physiology 185(2):519-532. doi: 10.1093/plphys/kiaa032
Dinneny JR (2020) Mechanobiology: plant cells face pressure from neighbors. Curr Biol 30(8):R344-R346. doi: 10.1016/j.cub.2020.02.025
Rui Y, Dinneny JR (2020) A wall with integrity: surveillance and maintenance of the plant cell wall under stress. New Phytol 225(4):1428-1439. doi: 10.1111/nph.16166
2019
Waidmann S, Ruiz Rosquete M, Schöller M, Sarkel E, Lindner H, LaRue T, Petřík I, Dünser K, Martopawiro S, Sasidharan R, Novak O, Wabnik K, Dinneny JR, Kleine-Vehn J. (2019) Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots. Nat Commun 10:3540. doi: 10.1038/s41467-019-11483-4
Dinneny JR (2019) Developmental responses to water and salinity in root systems. Annu Rev Cell Dev Biol 35:239-257. doi: 10.1146/annurev-cellbio-100617-062949
Argueso CT, Assmann SM, Birnbaum KD, Chen S, Dinneny JR, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall-Colón A, Mason GA, O’Lexy R, Peck SC, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM. (2019) Directions for research and training in plant omics: Big Questions and Big Data. Plant Direct 3(4):e00133. doi: 10.1002/pld3.133
Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northen TR (2019) EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nat Methods 16(7):567-571. doi: 10.1038/s41592-019-0465-0
Dickinson AJ, Lehner K, Mi J, Jia KP, Mijar M, Dinneny JR, Al-Babili S, Benfey PN (2019) β-Cyclocitral is a conserved root growth regulator. Proc Natl Acad Sci USA 116(21):10563-10567. doi: 10.1073/pnas.1821445116
Magallon KJ, Dinneny JR (2019) Environmental stress: salinity ruins a plant’s day in the sun. Curr Biol 29(10):R360-R362. doi: 10.1016/j.cub.2019.04.006
Scharwies JD, Dinneny JR (2019) Water transport, perception, and response in plants. J Plant Res 132:311-324. doi: 10.1007/s10265-019-01089-8
2018
Orosa-Puente B, Leftley N, von Wangenheim D, Banda J, Srivastava AK, Hill K, Truskina J, Bhosale R, Morris E, Srivastava M, Kümpers B, Goh T, Fukaki H, Vermeer JEM, Vernoux T, Dinneny JR, French AF, Bishopp A, Sadanandom A, Bennett MJ (2018) Roots branch towards water by post-translational modification of transcription factor ARF7. Science 362(6421):1407-1410. doi: 10.1126/science.aau3956
Dinneny JR (2018) Getting it right on GMOs. Science 360(6396):1407. doi: 10.1126/science.aau3980
Cuevas-Velazquez C, Dinneny JR (2018) Organization out of disorder: liquid-liquid phase separation in plants. Current Opinion in Plant Biology 45:68-74. doi: 10.1016/j.pbi.2018.05.005
Sun Y, Dinneny JR (2018) Q&A: How do gene regulatory networks control environmental responses in plants? BMC Biol 16:38. doi: 10.1186/s12915-018-0506-7
Wu R, Duan L, Pruneda-Paz JL, Oh DH, Pound M, Kay S, Dinneny JR (2018) The 6xABRE synthetic promoter enables the spatiotemporal analysis of ABA-mediated transcriptional regulation. Plant Physiology 177(4):1650-1665. doi: 10.1104/pp.18.00401
Highlighted in Plant Physiology.
Feng W, Kita D, Peaucelle A, Cartwright HN, Doah V, Duan Q, Liu MC, Maman J, Steinhorst L, Schmitz-Thom I, Yvon R, Kudla J, Wu HM, Cheung AY, and Dinneny JR (2018) The FERONIA receptor kinase maintains cell wall integrity during salt stress through Ca2+ signaling. Current Biology 28(5):666-675. doi: 10.1016/j.cub.2018.01.023
Highlighted in a Current Biology Dispatch and by F1000.
Robbins NE II, Dinneny JR (2018) Growth is required for perception of water availability to pattern plant root branches. Proc Natl Acad Sci USA 115(4):E822-E831. doi: 10.1073/pnas.1710709115
Highlighted by F1000.
2017
Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM (2017) The next generation of training for Arabidopsis researchers: bioinformatics and quantitative biology. Plant Physiol 175(4):1499-1509. doi: 10.1104/pp.17.01490
Brophy JAN, LaRue T, Dinneny JR (2017) Understanding and engineering plant form. Seminars in Cell and Developmental Biology 83:68-77. doi: 10.1016/j.semcdb.2017.08.051
Feldman MJ, Paul RE, Banan D, Barrett JF, Sebastian J, Yee M-C, Jiang H , Lipka AE , Brutnell TP , Dinneny JR , Leakey ADB , Baxter I (2017) Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria. PLoS Genet 13(6):e1006841. doi: 10.1371/journal.pgen.1006841
Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM, Owen MR, Band LR, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ (2017) Root hydrotropism is controlled via a cortex-specific growth mechanism. Nat Plants 3:17057. doi: 10.1038/nplants.2017.57
2016
Robbins NE II, Dinneny JR (2016) A method to analyze local and systemic effects of environmental stimuli on root development in plants. Bio-protocol 6(17):e1923. doi: 10.21769/BioProtoc.1923
Feng W, Lindner H, Robbins NE II, Dinneny JR (2016) Growing Out of Stress: The Role of Cell- and Organ-scale Growth Control in Plant Water-stress Responses. The Plant Cell 28(8):1769-1782. doi: 10.1105/tpc.16.00182
Sebastian J, Yee MC, Viana WG, Rellán-Álvarez R, Feldman M, Priest H, Trontin C, Lee T, Jiang H, Baxter I, Mockler TC, Hochholdinger F, Brutnell TP and Dinneny JR (2016) Grasses suppress shoot-borne roots to conserve water during drought. Proc Natl Acad Sci USA 113(31):8861-8866. doi: 10.1073/pnas.1604021113
Highlighted by BBC News and F1000.
Rellán-Álvarez R, Lobet G, Dinneny JR (2016) Environmental control of root system biology. Annu Rev Plant Biol 67:619-642. doi: 10.1146/annurev-arplant-043015-111848
Fahlgren N, Bart R, Herrera-Estrella L, Rellán-Álvarez R, Chitwood DH, Dinneny JR (2016) Plant scientists: GM technology is safe. Science 351(6275):824. doi: 10.1126/science.351.6275.824-a
2015
Rellán-Álvarez R, Lobet G, Lindner H, Pradier P-L, Sebastian J, Yee MC, Geng Y, Trontin C, LaRue T, Schrager A, Haney C, Nieu R, Maloof J, Vogel JP, Dinneny JR (2015) GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife 4:e07597. doi: 10.7554/eLife.07597
Highlighted in Nature Methods, the eLife digest and SF Gate.
Dinneny JR (2015) A developmental biologist’s journey to rediscover the Zen of plant physiology. F1000Research 4(F1000 Faculty Rev):264. doi: 10.12688/f1000research.6167.1
Robbins NE II, Dinneny JR (2015) The divining root: moisture-driven responses of roots at the micro- and macro-scale. J Exp Bot 66(8):2145-2154. doi: 10.1093/jxb/eru496
Duan L, Sebastian J, Dinneny JR (2015) Salt-stress regulation of root system growth and architecture in Arabidopsis seedlings. Methods Mol Biol 1242:105-122. doi: 10.1007/978-1-4939-1902-4_10
Velasquez SM, Dinneny JR, Estevez JM (2015) Live imaging of root hairs. Methods Mol Biol 1242:59-66. doi: 10.1007/978-1-4939-1902-4_5
2014
Bao Y, Aggarwal P, Robbins II NE, Sturrock CJ, Thompson, MC, Tan HQ, Tham C, Rodriguez PL, Vernoux T, Mooney SJ, Bennett MJ, Dinneny JR (2014) Plant roots employ a patterning mechanism to position lateral root branches towards available water. Proc Natl Acad Sci USA 111(25):9319-9324. doi: 10.1073/pnas.1400966111
Highlighted by F1000 Prime.
Sebastian J, Wong MK, Tang E, Dinneny JR (2014) Methods to promote germination of dormant Setaria viridis seeds. PLoS One 9(4):e95109. doi: 10.1371/journal.pone.0095109
Wang PL, Bao Y, Yee MC, Barrett SP, Hogan GJ, Olsen MN, Dinneny JR, Brown PO, Salzman J (2014) Circular RNA is expressed across the eukaryotic tree of life. PLoS One 9(3):e90859. doi: 10.1371/journal.pone.0090859
Dinneny JR (2014) Traversing organizational scales in plant salt-stress responses. Curr Opin Plant Biol 23:70-75. doi: 10.1016/j.pbi.2014.10.009
Robbins NE II, Trontin C, Duan L, Dinneny JR (2014) Beyond the barrier: communication in the root through the endodermis. Plant Physiol 166(2):551-559. doi: 10.1104/pp.114.244871
Dinneny JR (2014) A gateway with a guard: how the endodermis regulates growth through hormone signaling. Plant Sci 214:14-19. doi: 10.1016/j.plantsci.2013.09.009
2013
Emami, S, Yee MC, Dinneny JR (2013) A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology. Front Plant Sci 4:339. doi: 10.3389/fpls.2013.00339
Geng Y, Wu R, Wee CW, Xie F, Wei X, Chan PMY, Tham C, Duan L, Dinneny JR (2013) A Spatio-Temporal Understanding of Growth Regulation during the Salt Stress Response in Arabidopsis. Plant Cell 25(6):2132-2154. doi: 10.1105/tpc.113.112896
Highlighted in a Trends in Plant Science Spotlight.
Duan L, Dietrich D, Ng CH, Chan PMY, Bhalerao R, Bennett MJ, Dinneny JR (2013) Endodermal ABA signaling promotes lateral root quiescence during salt stress in Arabidopsis seedlings. Plant Cell 25(1):324-341. doi: 10.1105/tpc.112.107227
Highlighted in a Trends in Plant Science Spotlight.
Dinneny JR (2013) Cell-type resolution analysis of root development and environmental responses. Roots and their soil interactions: What we can learn from genomics Chapter 4: 63-78 Wiley Publishing
2012–2009
Wee CW andDinneny JR (2010) Tools for high-spatial and temporal-resolution analysis of environmental responses in plants. Biotechnol Lett 32(10):1361-1371
Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN (2009) Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods in Molecular Biology 553:57-77
Dinneny JR (2010) Analysis of the salt-stress response at cell-type resolution. Plant Cell & Environment 33(4):543-551
2009–2007
Dinneny JR, Benfey PN (2009) Studying root development using a genomic approach. Annual Plant Reviews, Volume 37, Root Development Chapter 12: 325-351 Blackwell Publishing
Dinneny JR, Long TA, Wang JY, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein JS, Benfey PN (2008) Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320(5878):942-945. doi: 10.1126/science.1153795
Highlighted in a Science Perspective (320:880-881) and in Nature Genetics Research Highlights (9:414).
Filiault D, Wessinger C, Dinneny JR, Lutes J, Borevitz J, Weigel D, Chory J, and Maloof JN (2008) Amino acid polymorphisms in Arabidopsis Phytochrome B causes differential response to light. Proc Natl Acad Sci USA 105(8):3157-3162
Dinneny JR and Benfey PN (2008) Plant stem cell niches: standing the test of time. Cell 132(4):553-557
Brady SM, Orlando D, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318(5851):801-806
2006–1999
Dinneny JR, Weigel D, Yanofsky MF (2006) NUBBIN and JAGGED define stamen and carpel shape in Arabidopsis. Development 133:1645-1655 (cover article)
Dinneny JR, Weigel D, Yanofsky MF (2005) A genetic framework for fruit patterning in Arabidopsis. Development 132:4687-4696 (cover article)
Dinneny JR and Benfey PN, (2005) Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development. Cell 123:1180-1182
Dinneny JR and Yanofsky MF (2005) Drawing lines and borders: how the dehiscent fruit of Arabidopsis is patterned. Bioessays 27:42-49
Dinneny JR, Yadegari R, Fischer RL, Yanofsky MF, Weigel D (2004) The role of JAGGED in shaping lateral organs. Development 131:1101-1110
Highlighted in a Developmental Cell Preview (6:318-319).
Dinneny JR and Yanofsky MF (2004) Floral Development: An ABC Gene Chips in Downstream. Curr Biol 14:R840-R841
Dinneny JR and Yanofsky MF (2004) Vascular Patterning: Xylem or Phloem? Curr Biol 14:R112-R114
Wu X, Dinneny JR, Crawford KM, Rhee Y, Citovsky V, Zambryski PC, Weigel D (2003) Modes of intercellular transcription factor movement in the Arabidopsis apex. Development 130:3735-3745
Kiyosue T, Ohad N, Yadegari R, Hannon M, Dinneny JR, Wells D, Katz A, Margossian L, Harada J, Goldberg R, Fischer RL (1999) Control of fertilization-independent-endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc Natl Acad Sci USA 96:4186-4191
Dinneny lab 