Dai X., Mashiguchi K., Chen Q., Kasahara H., Kamiya Y., Ojha S., DuBois J., Ballou D., and Zhao Y. (2012). The biochemical mechanism of auxin biosynthesis by an Arabidopsis YUCCA flavin-containing monooxygenase. J. Biol. Chem. , Published online on November 27, 2012

Cheng ZJ, Wang L, Sun W, Zhang Y, Zhou C, Su YH, Li W, Sun TT, Zhao XY, Li XG, Cheng Y, Zhao Y , Xie Q, Zhang XS (2012). Pattern of Auxin and Cytokinin Responses for Shoot Meristem Induction Results from Regulation of Cytokinin Biosynthesis by Auxin Response Factor 3.   Plant Physiol. 2012 Nov 2. [Epub ahead of print]

Gao Y. and Zhao Y (2012). Epigenetic Suppression of T-DNA Insertion Mutants in Arabidopsis. Molecular Plant , Advance Access published September 12, 2012

Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., Li, G., Qin, G., Wakeley, M., Terzaghi, W., Wan, J., Zhao, Y ., Xu, J., Friml, J., Deng, X. and Wang, H. (2012) A PP6-Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis. Plant Cell , First Published on June 19, 2012

Zhao Y (2012). Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants.   Mol Plant . 5(2), 334-8


Won C.,   Shen, X., Mashiguchi K., Zheng Z, Dai D., Cheng Y., Kasahara H., Yuji Kamiya Y., Chory J, and Zhao Y . (2011) Conversion of Tryptophan to Indole-3-acetic acid by TAAs and YUCs in Arabidopsis .   PNAS , 108(45):18518-23.

Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H, Natsume M, Hanada A, Yaeno T, Shirasu K, Yao H, McSteen P, Zhao Y , Hayashi K, Kamiya Y, Kasahara H (2011).   The main auxin biosynthesis pathway in Arabidopsis.   PNAS 108(45):18512-7

Hou X., Liu S, Pierri F, Dai X., Qu L., and Zhao Y. (2011) Allelic Analyses of the Arabidopsis YUC1 Locus Reveal Residues and Domains Essential for the Functions of YUC Family of Flavin Monooxygenases. Journal of Integrative Plant Biology , 53 (1) : 54-62


Li Y., Dai X., Cheng Y., and Zhao Y. (2010) NPY Genes Play an Essential Role in Root Gravitropic Responses in Arabidopsis . Mol. Plant , 4, 171-179.

Zhao Y. (2010) Auxin Biosynthesis and its Role in Plant Development. Annu Rev Plant Biol. 61: 49-64

Hou X, Li L, Peng Z, Wei B, Tang S, Ding M, Liu J, Zhang F, Zhao Y , Gu H, Qu LJ (2010). A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis. Plant J. 63(5), 880-8


Rawat R, Schwartz J, Jones MA, Sairanen I, Cheng Y, Andersson CR, Zhao Y, Ljung K, Harmer SL. (2009) REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways. PNAS 106(39):16883-8

Bernard DG, Cheng Y, Zhao Y, Balk J.(2009) An Allelic Mutant Series of ATM3 Reveals Its Key Role in the Biogenesis of Cytosolic Iron-Sulfur Proteins in Arabidopsis. Plant Physiol.151(2):590-602

Sugawara S, Hishiyama S, Jikumaru Y, Hanada A, Nishimura T, Koshiba T, Zhao Y, Kamiya Y, Kasahara H. (2009) Biochemical analyses of indole-3-acetaldoxime-dependent auxin biosynthesis in Arabidopsis. PNAS 106(13):5430-5


Cheng, Y., Qin, G., Dai, X., and Zhao, Y. (2008) NPY genes and AGC kinases define two key steps in auxin-mediated organogenesis in Arabidopsis. PNAS 105, 21017-21022

Li, L., Qin, G., Tsuge, T., Hou, X., Ding, M., Aoyama, T., Oka, A., Chen, Z., Gu, H., Zhao, Y . & Qu, L. J. (2008) SPOROCYTELESS modulates YUCCA expression to regulate the development of lateral organs in Arabidopsis New Phytologist 179, 751-764.

McSteen P and Zhao Y (2008). Plant hormones and signaling: common themes and new developments. Dev Cell 14(4):467-73.

Zhao, Y. (2008) The role of local biosynthesis of auxin and cytokinin in plant development Curr Opin Plant Biol . 11(1):16-22.

Tao Y, Ferrer JL, Ljung K, Pojer F, Hong F, Long JA, Li L, Moreno JE, Bowman ME, Ivans LJ, Cheng Y, Lim J, Zhao Y , Ballaré CL, Sandberg G, Noel JP, Chory J (2008)   Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell 133(1):164-76.

Wollers S, Heidenreich T, Zarepour M, Zachmann D, Kraft C, Zhao Y , Mendel RR, Bittner F (2008). Binding of Sulfurated Molybdenum Cofactor to the C-terminal Domain of ABA3 from Arabidopsis thaliana Provides Insight into the Mechanism of Molybdenum Cofactor Sulfuration. J Biol Chem 283(15):9642-50.

Breuer C, Stacey NJ, West CE, Zhao Y , Chory J, Tsukaya H, Azumi Y, Maxwell A, Roberts K, Sugimoto-Shirasu K (2008). BIN4, a novel component of the plant DNA topoisomerase VI complex, is required for endoreduplication in Arabidopsis. Plant Cell 19(11):3655-68.

Li L, Hou X, Tsuge T, Ding M, Aoyama T, Oka A, Gu H, Zhao Y , Qu LJ (2008). The possible action mechanisms of indole-3-acetic acid methyl ester in Arabidopsis. Plant Cell Rep 27(3):575-84


Cheng Y., Qin G., Dai X., and Zhao Y (2007).   A role for a BTB-NPH3-like protein in auxin-regulated organogenesis in Arabidopsis.   PNAS 104, 18825-18829.

Cheng Y., Dai X., and Zhao Y. (2007) Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis.   Plant Cell 19(8): 2430-9

Cheng, Y. and Zhao Y. (2007).   A role for auxin in flower development. Journal of Integrative Plant Biology   49 (1): 99-104

Moon J, Zhao Y , Dai X, Zhang W, Gray WM, Huq E, Estelle M (2007). A New CUL1 Mutant has Altered Responses to Hormones and Light in Arabidopsis.   Plant Physiol 142

Koussevitzky S, Stanne TM, Peto CA, Giap T, Sjogren LL, Zhao Y , Clarke AK, Chory J (2007). An Arabidopsis thaliana virescent mutant reveals a role for ClpR1 in plastid development.   Plant Mol Biol. 63(1): 85-96.


Bowers, A.K. and Zhao, Y. (2006) Recent Advances in Auxin Biosynthesis and Conjugation, in Recent Advances in Phytochemistry: Integrative Plant Biochemistry. J. Romeo, Ed. (2006), vol. 40, pp. 271-285.

Cheng, Y., Dai, X., and Zhao, Y. (2006) Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis. Genes Dev. 20 (13), 1790-1799. Abstract Full Text PDF Supplemental Material Science News

Li, J., Dai, X., and Zhao, Y. (2006) A Role for Auxin Response Factor 19 in Auxin and Ethylene Signaling in Arabidopsis. Plant Physiol. 140, 899-908. Abstract Full Text PDF


Qin, G., Gu, H., Zhao, Y., Ma, Z., Shi, G., Yang, Y., Pichersky, E., Chen, H., Liu, M., Chen, Z. and Qu, L. J. (2005) An indole-3-acetic acid carboxyl methyltransferase regulates Arabidopsis leaf development. Plant Cell. 17(10), 2693-2704. Abstract Full Text PDF

Dai, X., Hayashi, K., Nozaki, H., Cheng, Y., and Zhao, Y. (2005) Genetic and chemical analyses of the action mechanisms of sirtinol in Arabidopsis. PNAS. 102(8), 3129-3134. Abstract Full Text PDF

Perry, J., Dai, X., and Zhao, Y. (2005) A Mutation in the Anticodon of a Single tRNAala Is Sufficient to Confer Auxin Resistance in Arabidopsis.
Plant Physiol. 139, 1284-1290. Abstract Full Text PDF

Before 2004

Cheng, Y., Dai, X., and Zhao, Y. (2004) AtCAND1, A HEAT-Repeat Protein That Participates in Auxin Signaling in Arabidopsis. Plant Physiol. 135, 1020-1026. Abstract Full Text PDF

Perry, J. and Zhao, Y. (2003) The CW domain, a structural module shared amongst vertebrates, vertebrate-infecting parasites and higher plants. Trends Biochem. Sci. 281(11), 576-580. Abstract PDF Supplemental Material

Blackwell, H.E., and Zhao, Y. (2003) Chemical Genetic Approaches to Plant Biology. Plant Physiol. 133, 456-461. Full Text PDF

Zhao, Y., Dai, X., Blackwell, H.E., Schreiber, S.L., and Chory, J. (2003) SIR1, an upstream auxin signaling component identified by chemical genetics. Science 301, 1107-1110. Abstract PDF

Zhao, Y., Hull, A. K., Gupta, N., Goss, K.A., Alonso, J., Ecker, J. R., Normanly, J., Chory, J., and Celenza, J. L. (2002). Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes & Development 16, 3100-3112. Abstract

Ballou, D. P., Zhao, Y., Brandish, P. E., and Marletta, M.A. (2002). Revisiting the kinetics of nitric oxide binding to soluble guanylate cyclase: the simple NO-binding model is incorrect. PNAS 99, 12097-12101

Yin, Y., Cheong, H., Friedrichsen, D., Zhao, Y., Hu, J., Mora-Garcia, S., and Chory, J (2002). A crucial role for the putative Arabidopsis topoisomerase VI in plant growth and development. PNAS 99, 10191-10196. Abstract

Zhao, Y. and Chory, J (2001). A link between the light and gibberellin signaling cascades. Development Cell 1, 315-316.

Gil, P., Dewey, E., Friml, J., Zhao, Y., Snowden, K. C., Putterill, J., Palme, K., Estelle, M., and Chory, J (2001). BIG: a calossin-like protein required for polar auxin transport in Arabidopsis. Genes & Development 15, 1985-1997. Abstract

Zhao, Y., Christensen, S. K., Fankhauser, C., Cashman, J. R., Cohen, J. D., Weigel, D., and Chory, J (2001). A Role for Flavin monooxygenase-like enzymes in auxin biosynthesis. Science 291, 306-309. Abstract

Zhao, Y., Brandish, P. E., DiValentin, D., Schelvis, J.P.M., Babcock, G. T., and Marletta, M. A. (2000). Inhibition of soluble guanylate cyclase by ODQ. Biochemistry 39, 10848-10854.

Perry, J. M., Zhao, Y., and Marletta, M. A. (2000). Cu2+ and Zn2+ inhibit nitric-oxide synthase through an interaction with the reductase domain. J. Biol. Chem., 275, 14070-14076.

Denninger, J. W., Schelvis, J. M. P., Brandish, P.E., Zhao, Y., Babcock, G. T., and Marletta, M. A. (2000). Interaction of soluble guanylate cyclase with YC-1: kinetic and resonance Raman studies, Biochemistry 39, 4191-4198.

Zhao, Y., Brandish, P. E., Ballou, D. P., and Marletta, M.A. (1999). A molecular basis for nitric oxide sensing by soluble guanylate cyclase. PNAS 96, 14753-14758.

Schelvis, J. P. M., Kim, S., Zhao, Y., Marletta, M. A., and Babcock, G. T. (1999). Structural dynamics in the guanylate cyclase heme pocket after CO photolysis. J. Am. Chem Soc. 121, 7397-7400

Barker, S. L. R., Zhao, Y., Marletta, M. A., and Kopelman, R. (1999). Cellular application of a sensitive and selective fiber-optic nitric oxide biosensor based on a dye-labeled heme domain of soluble guanylate cyclase. Anal. Chem. 71, 2071-2075.

Zhao, Y., Hoganson, C., Babcock, G. T., and Marletta, M. A. (1998). Structural changes in the heme proximal pocket induced by nitric oxide binding to soluble guanylate cyclase. Biochemistry 37, 12458-12464.

Schelvis, J. P. M., Zhao, Y., Marletta, M. A., and Babcock, G. T. (1998). Resonance Raman spectroscopic characterization of the heme domain of soluble guanylate cyclase. Biochemistry 37, 16289-16297

Zhao Y., Schelvis, J. P.M., Babcock, G. T., and Marletta, M. A. (1998). Identification of Histidine 105 in ?1 subunit of soluble guanylate cyclase as the heme proximal ligand. Biochemistry 37, 4502-4509.

Perry, J. M., Moon, N., Zhao, Y., Dunham, R. W. and Marletta, M. A.(1998). The high-potential flavin and heme of nitric oxide synthase are not magnetically linked: implications for electron transfer. Chem. Biol. 5, 355-364.

Zhao, Y., and Marletta, M. A. (1997). Localization of the heme binding region in soluble guanylate cyclase. Biochemistry 36, 15983-15991.