Pubmed, Google Scholar


Vilarrasa-Blasi J, Fauser F, 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. 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. doi 10.1038/s41477-022-01139-5

Viana W, Scharwies JD, Dinneny JD (2022) Deconstructing the root system of grasses through an exploration of development, anatomy and function. Plant Cell Environ. 2022 Mar;45(3):602-619. doi: 10.1111/pce.14270.

Brophy JAN, Magallon K, Kniazev K, Dinneny JR (2022) Synthetic genetic circuits enable reprogramming of plant roots. bioRxiv preprint doi: 10.1101/2022.02.02.478917

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 DOI: 10.1109/TCSII.2022.3159448


LaRue T, Lindner H, Srinivas A, Exposito-Alonso M, Lobet G, Dinneny JR (2021) Uncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platform. bioRxiv preprint doi: 10.1101/2021.11.13.468476

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.DOI: 10.1126/science.abf7461

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 (2021) Identification of green lineage osmotic stress pathways bioRxivpreprint doi:

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

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.*

*BioRxiv 2021.02.17.431712; doi:

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

*Co-corresponding authors


Sun Y, Oh DH, Duan L, Ramachandran P, Ramirez A, Bartlett A, Dassanayake M, Dinneny JR (2020) Divergence in a stress-associated gene regulatory network underlies differential growth control in the Brassicaceae family. bioRxiv preprint doi:

Vilarrasa-Blasi J, Fauser F, 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* (2020) Systematic characterization of gene function in a photosynthetic organism. bioRxiv preprint doi:

*Co-corresponding authors

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

Dinneny JR. Mechanobiology: Plant Cells Face Pressure from Neighbors. Curr
Biol. 2020 Apr 20;30(8):R344-R346. doi: 10.1016/j.cub.2020.02.025. PMID:

Rui Y, Dinneny JR. A wall with integrity: surveillance and maintenance of the
plant cell wall under stress. New Phytol. 2020 Feb;225(4):1428-1439. doi:
10.1111/nph.16166. Epub 2019 Sep 27. PMID: 31486535.

Dickinson AJ, Zhang J, Luciano M, Wachsman G, Schnermann M, Dinneny JR, Benfey PN (2020) A plant lipocalin is required for retinal-mediated de novo root organogenesis. bioRxiv preprint doi:


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. 2019 Aug 6;10(1):3540. doi: 10.1038/s41467-019-11483-4. PMID: 31387989 Free PMC Article

Dinneny JR. (2019) Developmental Responses to Water and Salinity in Root Systems. Annu Rev Cell Dev Biol. 2019 Aug 5. doi: 10.1146/annurev-cellbio-100617-062949. PMID: 31382759

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. 2019 Apr 23;3(4):e00133. doi: 10.1002/pld3.133. eCollection 2019 Apr. PMID: 31245771

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. 2019 Jul;16(7):567-571. doi: 10.1038/s41592-019-0465-0. PMID: 31227812

Dickinson AJ, Lehner K, Mi J, Jia KP, Mijar M, Dinneny J, Al-Babili S, Benfey PN. (2019) Beta-Cyclocitral is a conserved root growth regulator. Proc Natl Acad Sci U S A.116(21):10563-10567.

Magallon KJ, Dinneny JR(2019) Environmental Stress: Salinity Ruins a Plant’s Day In the Sun. Curr Biol. 2019 May 20;29(10):R360-R362. doi:10.1016/j.cub.2019.04.006. PubMed PMID: 31112684.

Scharwies JD,Dinneny JR (2019) Water transport, perception, and response in plants. J Plant Res.doi: 10.1007/s10265-019-01089-8. PMID: 30747327

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


Dinneny JR (2018) Getting it right on GMOs. Science 360 (6396), 1407

Cuevas-Velazquez C, Dinneny JR (2018) Organization out of disorder: liquid-liquid phase separation in plants. Current Opinion in Plant Biology

Sun Y, Dinneny JR (2018) Q&A: How do gene regulatory networks control environmental responses in plants? BMC Biol. 2018 Apr 11;16(1):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 DOI:**

**Highlighted by 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 DOI:

**Highlighted in a Current Biology Dispatch and F1000

Robbins NE and Dinneny JR (2018) Growth Is Required for Perception of Water Availability to Pattern Plant Root Branches. Proc. Natl. Acad. Sci. U. S. A. 1710709115v1-201710709.

**Highlighted by F1000


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. 2017 Dec;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 S1084-9521(17)30382-8. 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.

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. 2017 May 8;3:17057. doi: 10.1038/nplants.2017.57.


Robbins II, N. E. and Dinneny, J. (2016). A Method to Analyze Local and Systemic Effects of Environmental Stimuli on Root Development in Plants. Bio-protocol 6(17): e1923.

Feng W, Lindner H, Robbins II N, Dinneny JR (2016) Growing Out of Stress: The Role of Cell- and Organ-scale Growth Control in Plant Water-stress Responses. The Plant Cell vol. 28 no. 8 1769-1782

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. U. S. A. doi: 10.1073/pnas.1604021113**

**Highlight in BBC News and F1000

Rellán-Álvarez R, Lobet G, Dinneny JR (2016) Environmental control of root system biology. Annu. Rev. Plant Biol. 2016. 67:20.1–20.24

Fahlgren N, Bart R, Herrera-Estrella L, Rellán-Álvarez R, Chitwood DH, Dinneny JR (2016) Plant scientists: GM technology is safe. Science 19 Feb 2016:Vol. 351, Issue 6275, pp. 824 DOI: 10.1126/science.351.6275.824-a


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 2015;10.7554/eLife.07597**

**Highlight in Nature MethodseLife digest and SF Gate

Dinneny JR. A developmental biologist’s journey to rediscover the Zen of plant physiology. F1000Research 2015:4(F1000 Faculty Rev):264 (doi: 10.12688/f1000research.6167.1)

Robbins NE 2nd, Dinneny JR. The divining root: moisture-driven responses of roots at the micro- and macro-scale. J Exp Bot. 2015 Jan 22. pii: eru496. [Epub ahead of print] Review. PubMed PMID: 25617469.

Duan L, Sebastian J, Dinneny JR. Salt-stress regulation of root system growth and architecture in Arabidopsis seedlings. Methods Mol Biol. 2015;1242:105-22. doi: 10.1007/978-1-4939-1902-4_10. PubMed PMID: 25408448.

Velasquez SM, Dinneny JR, Estevez JM. Live imaging of root hairs. Methods Mol Biol. 2015;1242:59-66. doi: 10.1007/978-1-4939-1902-4_5. PubMed PMID: 25408443.


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. Jun 24;111(25):9319-24.**

**Recommended F1000 Prime

Sebastian J, Wong MK, Tang E, Dinneny JR. (2014) Methods to Promote Germination of Dormant Setaria viridis seeds. PLoS One 18;9(4):e95109.

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. 7;9(3):e90859

Dinneny JR. Traversing organizational scales in plant salt-stress responses. Curr Opin Plant Biol. 2014 Nov 15;23C:70-75. doi: 10.1016/j.pbi.2014.10.009. [Epub ahead of print] Review. PubMed PMID: 25449729.

Robbins NE 2nd, Trontin C, Duan L, Dinneny JR. Beyond the barrier: communication in the root through the endodermis. Plant Physiol. 2014Oct;166(2):551-9. doi: 10.1104/pp.114.244871. Epub 2014 Aug 14. PubMed PMID:25125504

Dinneny JR (2014) A gateway with a guard: how the endodermis regulates growth through hormone signaling. Plant Sci. 214, 14-19


Emami, S, Yee MC, Dinneny JR (2013) A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology. Front. Plant Sci. 2;4:339

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 Jun;25(6):2132-54**

**(‘Spotlight’ in Trends in Plant Science, 10.1016/j.tplants.2013.08.009)

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 Jan;25(1):324-41**

**(‘Spotlight’ in Trends in Plant Science, 10.1016/j.tplants.2013.08.009)

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


Wee CW and Dinneny 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 1;33(4):543-51


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 May 16;320(5878):942-5**

**(‘Perspectives’ in Science 16;320:880-1, ‘Research Highlights’ in Nature Genetics 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. Feb 26;105(8):3157-62

Dinneny JR and Benfey PN (2008) Plant stem cell niches: standing the test of time. Cell Feb 22;132(4):553-7

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 Nov 2;318(5851):801-6


Dinneny JR, Weigel D, Yanofsky MF (2006) NUBBIN and JAGGED define stamen and carpel shape in Arabidopsis. Development 133, 1645-1655 (Cover issue)

Dinneny JR, Weigel D, Yanofsky MF (2005) A genetic framework for fruit patterning in Arabidopsis. Development 132, 4687-4696 (Cover issue)

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**

**(‘Previews’ in Developmental Cell 6(3), 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 J, 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. 96, 4186-4191.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s