Selected Publications

Link to all of Dr. Chory’s publications on PubMed here.

Conn A, Pedmale UV, J. Chory, Navlakha S. High-Resolution Laser Scanning Reveals Plant Architectures that Reflect Universal Network Design Principles. Cell Syst. 2017 Jul 26;5(1):53-62.

Conn A, Pedmale UV, J. Chory, Stevens CF, Navlakha S. A Statistical Description of Plant Shoot Architecture. Curr Biol. 2017 Jul 24;27(14).

Vermeer JEM, van Wijk R, Goedhart J, Geldner N, J. Chory, Gadella TWJ Jr, Munnik T. In Vivo Imaging of Diacylglycerol at the Cytoplasmic Leaflet of Plant Membranes. Plant Cell Physiol. 2017 Jul 1;58(7):1196-1207

Seluzicki A, Burko Y, J. Chory. Dancing in the dark: darkness as a signal in plants. Plant Cell Environ. 2017 Jan 3. doi: 10.1111/pce.12900. Review.

Hetzel J, Duttke SH, Benner C, J. Chory. Nascent RNA sequencing reveals distinct features in plant transcription. Proc Natl Acad Sci U S A. 2016 Oct 25;113(43). Free PMC Article

Procko C, Burko Y, Jaillais Y, Ljung K, Long JA, J. Chory. Corrigendum: The epidermis coordinates auxin-induced stem growth in response to shade. Genes Dev. 2016 Sep 1;30(17). Free PMC Article

de Saint Germain A, Clavé G, Badet-Denisot MA, Pillot JP, Cornu D, Le Caer JP, Burger M, Pelissier F, Retailleau P, Turnbull C, Bonhomme S, J. Chory, Rameau C, Boyer FD. An histidine covalent receptor and butenolide complex mediates strigolactone perception. Nat Chem Biol. 2016 Oct;12(10):787-794. Free PMC Article

Bjornson M, Dandekar AM, J. Chory, Dehesh K. Brassinosteroid’s multi-modular interaction with the general stress network customizes stimulus-specific responses in Arabidopsis. Plant Sci. 2016 Sep;250:165-177.

Procko C, Burko Y, Jaillais Y, Ljung K, Long JA, J. Chory. The epidermis coordinates auxin-induced stem growth in response to shade. Genes Dev. 2016 Jul 1;30(13):1529-41. Free PMC Article

Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SS, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroeder JI, J. Chory, LaBaer J, Vidal M, Braun P, Ecker JR. Mapping transcription factor interactome networks using HaloTag protein arrays. Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4238-47. Free PMC Article

Zheng Z, Guo Y, Novák O, Chen W, Ljung K, Noel JP, J. Chory. Local auxin metabolism regulates environment-induced hypocotyl elongation. Nat Plants. 2016 Mar 21;2:16025. Free PMC Article

Pedmale UV, Huang SS, Zander M, Cole BJ, Hetzel J, Ljung K, Reis PA, Sridevi P, Nito K, Nery JR, Ecker JR, J. Chory. Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light. Cell. 2016 Jan 14;164(1-2):233-45. Free PMC Article

Kaiserli E, Páldi K, O’Donnell L, Batalov O, Pedmale UV, Nusinow DA, Kay SA, J. Chory. Integration of Light and Photoperiodic Signaling in Transcriptional Nuclear Foci. Dev Cell. 2015 Nov 9;35(3):311-21. Free PMC Article

Willige BC, J. Chory. A current perspective on the role of AGCVIII kinases in PIN-mediated apical hook development. Front Plant Sci. 2015 Oct 6;6:767. Free PMC Article

Woodson JD, Joens MS, Sinson AB, Gilkerson J, Salomé PA, Weigel D, Fitzpatrick JA, J. Chory. Ubiquitin facilitates a quality-control pathway that removes damaged chloroplasts. Science. 2015 Oct 23;350(6259):450-4. Free PMC Article

Yu J, Qiu H, Liu X, Wang M, Gao Y, J. Chory, Tao Y. Characterization of tub4(P287L) , a ?-tubulin mutant, revealed new aspects of microtubule regulation in shade. J Integr Plant Biol. 2015 Sep;57(9):757-69. Free PMC Article

Wudick MM, Li X, Valentini V, Geldner N, J. Chory, Lin J, Maurel C, Luu DT. Subcellular Redistribution of Root Aquaporins Induced by Hydrogen Peroxide. Mol Plant. 2015 Jul;8(7):1103-14. Cell Press Open Access

Zorzatto C, Machado JP, Lopes KV, Nascimento KJ, Pereira WA, Brustolini OJ, Reis PA, Calil IP, Deguchi M, Sachetto-Martins G, Gouveia BC, Loriato VA, Silva MA, Silva FF, Santos AA, J. Chory, Fontes EP. NIK1-mediated translation suppression functions as a plant antiviral immunity mechanism. Nature. 2015 Apr 30;520(7549):679-82. Free PMC Article

Brustolini OJB, Machado JPB, Condori-Apfata JA, Coco D, Deguchi M, Loriato VAP, Pereira WA, Alfenas-Zerbini P, Zerbini FM, Inoue-Nagata AK, Santos AA, J. Chory, Silva FF, Fontes EPB. Sustained NIK-mediated antiviral signalling confers broad-spectrum tolerance to begomoviruses in cultivated plants. Plant Biotechnol J. 2015 Dec;13(9):1300-1311. Free PMC Article

Martins S, Dohmann EM, Cayrel A, Johnson A, Fischer W, Pojer F, Satiat-Jeunemaître B, Jaillais Y, J. Chory, Geldner N, Vert G. Internalization and vacuolar targeting of the brassinosteroid hormone receptor BRI1 are regulated by ubiquitination. Nat Commun. 2015 Jan 21;6:6151. Free PMC Article

J. Chory. Interview with Joanne Chory. Trends Biochem Sci. 2014 Oct;39(10):435-6. Cell Press Access

Belkhadir Y, Yang L, Hetzel J, Dangl JL, J. Chory. The growth-defense pivot: crisis management in plants mediated by LRR-RK surface receptors. Trends Biochem Sci. 2014 Oct;39(10):447-56. Free PMC Article

Krzymuski M, Cerdán PD, Zhu L, Vinh A, J. Chory, Huq E, Casal JJ. Phytochrome A antagonizes PHYTOCHROME INTERACTING FACTOR 1 to prevent over-activation of photomorphogenesis. Mol Plant. 2014 Sep;7(9):1415-28. Cell Press Open Access

Li L, Zhang Q, Pedmale UV, Nito K, Fu W, Lin L, Hazen SP, J. Chory. PIL1 participates in a negative feedback loop that regulates its own gene expression in response to shade. Mol Plant. 2014 Oct;7(10):1582-5. Free PMC Article

Procko C, Crenshaw CM, Ljung K, Noel JP, J. Chory. Cotyledon-Generated Auxin Is Required for Shade-Induced Hypocotyl Growth in Brassica rapa. Plant Physiol. 2014 Jul;165(3):1285-1301. Free PMC Article

Zhong X, Du J, Hale CJ, Gallego-Bartolome J, Feng S, Vashisht AA, J. Chory, Wohlschlegel JA, Patel DJ, Jacobsen SE. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell. 2014 May 22;157(5):1050-60. Free PMC Article

Fitz Gerald JN, Carlson AL, Smith E, Maloof JN, Weigel D, J. Chory, Borevitz JO, Swanson RJ. New Arabidopsis advanced intercross recombinant inbred lines reveal female control of nonrandom mating. Plant Physiol. 2014 May;165(1):175-85. Free PMC Article

Zheng Z, Germain Ade S, J. Chory. Unfolding the mysteries of strigolactone signaling. Mol Plant. 2014 Jun;7(6):934-6. Free PMC Article

Simon ML, Platre MP, Assil S, van Wijk R, Chen WY, J. Chory, Dreux M, Munnik T, Jaillais Y. A multi-colour/multi-affinity marker set to visualize phosphoinositide dynamics in Arabidopsis. Plant J. 2014 Jan;77(2):322-37. Free PMC Article

Jung HS, Crisp PA, Estavillo GM, Cole B, Hong F, Mockler TC, Pogson B. J. Chory J. Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light. Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14474-9. Free PMC Article

Nito K, Wong CC, Yates JR 3rd, J. Chory. Tyrosine phosphorylation regulates the activity of phytochrome photoreceptors. Cell Rep. 2013 Jun 27;3(6):1970-9. Free PMC Article

Zhong SH, Liu JZ, Jin H, Lin L, Li Q, Chen Y, Yuan YX, Wang ZY, Huang H, Qi YJ, Chen XY, Vaucheret H, J. Chory, Li J, He ZH. Warm temperatures induce transgenerational epigenetic release of RNA silencing by inhibiting siRNA biogenesis in Arabidopsis. Proc Natl Acad Sci U S A. 2013 May 28;110(22):9171-6. Free PMC Article

Guo Y, Zheng Z, La Clair JJ, J. Chory, Noel JP. Smoke-derived karrikin perception by the ?/?-hydrolase KAI2 from Arabidopsis. Proc Natl Acad Sci U S A. 2013 May 14;110(20):8284-9. Free PMC Article

Shani E, Weinstain R, Zhang Y, Castillejo C, Kaiserli E, J. Chory, Tsien RY, Estelle M. Gibberellins accumulate in the elongating endodermal cells of Arabidopsis root. Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4834-9. Free PMC Article

Zheng Z, Guo Y, Novák O, Dai X, Zhao Y, Ljung K, Noel JP, J. Chory. Coordination of auxin and ethylene biosynthesis by the aminotransferase VAS1. Nat Chem Biol. 2013 Apr;9(4):244-6. Free PMC Article

Iñigo S, Giraldez AN, J. Chory, Cerdán PD. Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription. Plant Physiol. 2012 Nov;160(3):1662-73. Free PMC Article

Woodson JD, J. Chory. Organelle signaling: how stressed chloroplasts communicate with the nucleus. Curr Biol. 2012 Sep 11;22(17):R690-2. Free PMC Article

Woodson JD, Perez-Ruiz JM, Schmitz RJ, Ecker JR, J. Chory. Sigma factor-mediated plastid retrograde signals control nuclear gene expression. Plant J. 2013 Jan;73(1):1-13. Free PMC Article

Cole BJ, J. Chory. Image-based analysis of light-grown seedling hypocotyls in Arabidopsis. Methods Mol Biol. 2012;918:1-7.

Gilkerson J, Perez-Ruiz JM, J. Chory, Callis J. The plastid-localized pfkB-type carbohydrate kinases FRUCTOKINASE-LIKE 1 and 2 are essential for growth and development of Arabidopsis thaliana. BMC Plant Biol. 2012 Jul 8;12:102. Free PMC Article

Li, L., K. Ljung, G. Breton, R.J. Schmitz, J. Pruneda-Paz, C. Cowing-Vitron, B.J. Cole, U. Pedmale, H.-S. Jung, L.J. Ivans, J.R. Ecker, S.A. Kay, and J. Chory. (2012). Linking photoreceptor excitation to changes in plant architecture. Genes Dev. 26: 785-790. Free PMC Article

Lu YJ, Schornack S, Spallek T, Geldner N, Chory J, Schellmann S, Schumacher K, Kamoun S, Robatzek S. Patterns of plant subcellular responses to successful oomycete infections reveal differences in host cell reprogramming and endocytic trafficking. Cell Microbiol. 2012 May;14(5):682-97. Free PMC Article

Belkhadir, Y., Y. Jaillais, P. Epple, E. Balsemao-Pires, J.L. Dangl, and J. Chory. (2012). Brassinsteroids modulate the efficiency of plant immune responses to microbe-associated molecular patterns. Proc. Natl. Acad. Sci. 109: 297-302. Epub 2011 Nov15. Free PMC Article

Won, C., SX. Shen, K. Mashiguchi, Z. Zheng, X. Dai, Y. Cheng, H. Kasahara, Y Kamiya, J. Chory, and Y. Zhao. (2011). Conversion of tryptophan to indole-3-acetic acid by TAAs and YUCs in Arabidopsis. Proc. Natl. Acad. Sci. Epub 2011Oct 24. Free PMC Article

Hothorn, M., T. Dabi, and J. Chory. (2011). Structural basis for cytokinin recognition by Arabidopsis thaliana histidine kinase 4. Nature Chem Bio. 7: 766-768. Free PMC Article

Hothorn, M., Y. Belkhadir, M. Dreux, T. Dabi, J.P. Noel, I.A. Wilson, and J. Chory. (2011). Structural basis of steroid hormone perception by a membrane receptor kinase BRI1. Nature, 474: 467-471. Free PMC Article

Woodson, J.D., J.M. Perez-Ruiz, and J. Chory. (2011). Heme synthesis by plastid ferrochelatase I regulates nuclear gene expression in plants. Curr. Biol. 24: 897-903. Free PMC Article

Jaillais, Y.*, Y. Belkhadir*, E. Balsemao-Pires, J.L. Dangl, and J. Chory. (2011). Extracellular leucine-rich-repeats as a platform for receptor-co-receptor complex formation. Proc. Natl. Acad. Sci. 108:8503-8507. Free PMC Article

Keller, M.M., Y. Jaillais, U.V. Pedmale, J.E. Moreno, J. Chory, and C.L. Ballaré. (2011). Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially-independent hormonal cascades. Plant J. 67: 195-207. Free PMC Article

Jaillais, Y.*, M. Hothorn*, Y. Belkhadir, T. Dabi, Z.L. Nimchuk, E.M. Meyerowitz, and J. Chory. (2011). Tyrosine phosphorylation controls brassinosteroid receptor activation by triggering membrance release of its kinase inhibitor. Genes Dev. 25: 232-237. Free PMC Article

Cole, B., S.A. Kay, and J. Chory (2011). Automated analysis of hypocotyl growth dynamics during shade avoidance in Arabidopsis. Plant J., 65: 991-1000. Free PMC Article

Todesco, M., S. Balasubramanian, T. Hu, P. Epple, C. Kuhns, S. Sureshkumar, C. Schwartz, M.B. Traw, C. Lanz, R.A.E. Laitinen, J. Chory, V. Lipka, J.O. Borevitz, J. Bergelson, J.L. Dangl, M. Nordborg, and D. Weigel. (2010). Natural allelic variation underlying a major fitness trade off in Arabidopsis thaliana. Nature. 465: 632-636. Free PMC Article

Atwell, S., Y. Huang, B. Vilhjalmsson, G. Willems, M. Horton, Y. Li, D. Meng, A. Platt, A. Tarone, T. Hu, R.Jiang, W. Muliyati, X. Zhang, M.A. Amer, I. Baxter, B. Brachi, J. Chory, C. Dean, M. Debieu, J. de Meaux, J. Ecker, N. Faure, J. Kriskern, J.D.G. Jones, T. Michael, A. Nemri, F. Roux, D. Salt, C. Tang, M.B. Traw, D. Weigel, J. Borevitz, J. Bergelson, and M. Nordborg. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 465: 627-631. Free PMC Article

Ibanes, M., N. Fabregas, J. Chory* and A. Cano-Delgado*. (2009). Brassinosteroid signaling and auxin transport are required to establish the periodic pattern of Arabidopsis shoot vascular bundles. Proc. Natl. Acad. Sci. 106:13630-13635. (*co-corresponding authors). Free PMC Article

Sellaro, R., U. Hoecker, M. Yanovsky, J. Chory, JJ Casal. (2009). Synergism of red and blue light in the control of Arabidopsis gene expression and development. Curr. Biol. 19: 1216-1220. Free PMC Article

Loudet, O., T.P. Michael, B. Burger, C. Le Mette, T.C. Mockler, D. Weigel, and J. Chory. (2008). A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana. Proc. Natl. Acad. Sci. 105:17193-17198. Free PMC Article

Moreno, J., Y. Tao, J. Chory*, and C.L. Ballaré*. (2009). Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity. Proc. Natl. Acad. Sci. 106:4935-4940. (*Co-corresponding authors). Free PMC Article

Geldner, N., V. Dénervaud-Tendon, U. Mayer, Y.D. Stierhof, D.L. Hyman, and J. Chory. (2009). Rapid, combinatorial analysis of membrane compartments in intact plants with a multi-color marker set. Plant J. 59: 169-178. Free PMC Article

Balasubramanian, S., C. Schwartz, A. Singh, N. Warthmann, M.C. Kim, J. Maloof, O. Loudet, G.T. Trainer, T. Dabi, J. Borevitz, J. Chory, and D. Weigel. (2009). QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines. PLoS One 4: e4318. Free PMC Article . Li, X. Yu, A. Thompson, M. Guo, S. Yoshida, T. Asami, J. Chory, and Y. Yin. (2008). The Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J. Apr;58(2):275-86. Free PMC Article

Savaldi-Goldstein, S., F. Pojer, T.J. Baiga, T. Dabi, C. Butterfield, N. Dharmasiri, G. Parry, A. Santner, Y. Tao, M. Estelle, J.P. Noel, and J. Chory. (2008). New auxin analogs with growth promoting effects in intact plants reveal a chemical strategy to improve hormone delivery. Proc. Natl. Acad. Sci. 105:15190-15195. Free PMC Article

Michael, T.P., G. Breton, S.P. Hazen, T.C. Mockler, S.A. Kay, and J. Chory. (2008) A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biol. 6: e255. 2008 September 16. Free PMC Article

Vert, G., C. Walcher, J. Chory, and J. Nemhauser. (2008). Integration of auxin and brassinosteroid pathways by auxin response factor 2. Proc. Natl. Acad. Sci. 105: 9829-9834. Free PMC Article

Yu, X., L. Li, L. Li, J. Chory, and Y. Yin. (2008). Modulation of brassinosteroid regulated gene expression by jumonji domain-containing proteins ELF6 and REF6. Proc. Natl. Acad. Sci. 105:7618-7623. Free PMC Article

Tao, Y., K. Ljung, J-L. Ferrer, F. Pojer, F. Hong, J. Long, L. Li, J. Moreno, M. Bowman, L. Ivans, Y. Chen, J. Lim, Y. Zhao, C. Ballare, G. Sandberg, J. Noel, and J. Chory. (2008). Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell. 133: 164-176. Free PMC Article

Mockler, T.C., T.P. Michael, H.D. Priest, R. Shen, C.M. Sullivan, S.A. Givan, C. McEntee, S.A. Kay, and J. Chory. (2007). The DIURNAL PROJECT: Diurnal and circadian expression profiling, model-based pattern matching and promoter analysis. Cold Spring Harbor Symp. 72: 353-363. CSHL Access

Borevitz, J.O., S. Hazen. T.P. Michael, G. Morris, I. Baxter, T. Hu, H. Chen, J. Werner, M. Nordborg, D. Salt, S. Kay, J. Chory, D. Weigel, J. Jones, and J. Ecker. (2007). Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc. Natl. Acad. Sci. 104: 12057-12062. Free PMC Article

Geldner, N., X. Wang, K. Schumacher, and J. Chory. (2007). Endosomal signaling of plant steroid receptor kinase BRI1. Genes Dev. 21: 1598-1602. Free PMC Article

Koussevitzky, S*., A. Nott*, T.C. Mockler, F. Hong, G. Sacheto-Martins, M. Surpin, J. Lim, R. Mittler, and J. Chory. (2007). Signals from chloroplasts converge to regulate nuclear gene expression. (Article). Science. 316: 715-719. (Accompanying Perspectives) (*co-first authors). Free Article

Savaldi-Goldstein, S., C. Peto, and J. Chory. (2007). The epidermis both drives and restricts plant shoot growth. Nature. 446:199-202. (Accompanying News and Views).