2025
Yan, H., Mendieta, J. P., Zhang, X., Luo, Z., Marand, A. P., Liang, Y., Minow, M. A. A., Zhong, Y., Jin, Y., Jang, H., Li, X., Zhang, X., Roulé, T., Wagner, D., Tu, X., Wang, Y., Jiang, D., Zhong, S., Huang, L., Wessler, S. R., … Schmitz, R. J. (2025). A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution. Nature plants, 11(10), 2050–2071.
Zhu, K., Chen, J., Zhao, L., Lu, F., Deng, J., Lin, X., He, C., Wagner, D., & Xiao, J. (2025). Dynamic control of H2A.Zub and H3K27me3 by ambient temperature during cell fate determination in Arabidopsis. Developmental cell, 60(16), 2192–2208.e5.
2024
Yan, H., Mendieta, J. P., Zhang, X., Marand, A. P., Liang, Y., Luo, Z., Roulé, T., Wagner, D., Tu, X., Wang, Y., Zhong, S., Wessler, S. R. & Schmitz, R. J. (2024). Evolution of cell-type-specific accessible chromatin regions and the cis-regulatory elements that drive lineage-specific innovation. bioRxiv, 2024-01.
2023
Huang, T., Guillotin, B., Rahni, R., Birnbaum, K. D., & Wagner, D. (2023). A rapid and sensitive, multiplex, whole mount RNA fluorescence in situ hybridization and immunohistochemistry protocol. Plant Methods, 19(1), 131.
2022
Lee, U. S., Bieluszewski, T., Xiao, J., Yamaguchi, A., & Wagner, D. (2022). H2A. Z contributes to trithorax activity at the AGAMOUS locus. Molecular Plant, 15(2), 207-210.
Klasfeld, S., & Wagner, D. (2022). Greenscreen decreases type I errors and increases true peak detection in genomic datasets including ChIP-seq. bioRxiv, 2022-02.
Klasfeld, S., Roulé, T., & Wagner, D. (2022). Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data. The Plant Cell, 34(12), 4795-4815.
2021
Bieluszewski, T., Xiao, J., Yang, Y., & Wagner, D. (2021). PRC2 activity, recruitment, and silencing: a comparative perspective. Trends in Plant Science, 26(11), 1186-1198.
Zhu, Y., Klasfeld, S., & Wagner, D. (2021). Molecular regulation of plant developmental transitions and plant architecture via PEPB family proteins: an update on mechanism of action. Journal of experimental botany, 72(7), 2301-2311.
2020
Zhu, Y., Klasfeld, S., Jeong, C. W., Jin, R., Goto, K., Yamaguchi, N., & Wagner, D. (2020). TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T. Nature communications, 11(1), 5118.
Zhu, Y., & Wagner, D. (2020). Plant inflorescence architecture: The formation, activity, and fate of axillary meristems. Cold Spring Harbor perspectives in biology, 12(1), a034652.
2019
Sun, B., Zhou, Y., Cai, J., Shang, E., Yamaguchi, N., Xiao, J., Looi, L.S., Wee, W.Y., Gao, X., Wagner, D. & Ito, T. (2019). Integration of transcriptional repression and Polycomb-mediated silencing of WUSCHEL in floral meristems. The Plant Cell, 31(7), 1488-1505.
Chung, Y., Zhu, Y., Wu, M., Simoni, S., Kuhn, A., Armenta-Medine, A., Jin, R., Østergaard, L., Gillmor, C.S., Wagner, D. (2019). Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS. Nature communications, 10(1), 886.
2017
Xiao, J., Jin, R., Yu, X., Shen, M., Wagner, J. D., Pai, A., Song, C., Zhuang, M., Klasfeld, S., He, C., Santos, A. M., Helliwell, C., Pruneda-Paz, J. L., Kay, S. A., Lin, X., Cui, S., Garzia, M. F., Clarenz, O., Goodrich, J., Zhang, X., Austin, R., Bonasio, R., & Wagner, D. (2017). Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature genetics, 49(10), 1546-1552.
Bossi, F., Fan, J., Xiao, J., Chandra, L., Shen, M., Dorone, Y., Wagner, D., & Rhee, S. Y. (2017). Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. BMC genomics, 18(1), 1-20.
Xiao, J., Jin, R., & Wagner, D. (2017). Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome biology, 18(1), 1-14.
Wagner, D. (2017). Key developmental transitions during flower morphogenesis and their regulation. Current opinion in genetics & development, 45, 44-50.
2016
Xiao, J., Lee, U. S., & Wagner, D. (2016). Tug of war: adding and removing histone lysine methylation in Arabidopsis. Current opinion in plant biology, 34, 41-53.
Wagner, D. (2016). Making flowers at the right time. Developmental Cell, 37(3), 208-210.
Yamaguchi, N., Jeong, C. W., Nole-Wilson, S., Krizek, B. A., & Wagner, D. (2016). AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 induce LEAFY expression in response to auxin to promote the onset of flower formation in Arabidopsis. Plant Physiology, 170(1), 283-293.
Weijers, D., & Wagner, D. (2016). Transcriptional responses to the auxin hormone. Annual review of plant biology, 67, 539-574.
Provart, N. J., Alonso, J., Assmann, S. M., Bergmann, D., Brady, S. M., Brkljacic, J., Browse, J., Chapple, C., Colot, V., Cutler. S., Dangl, J., Ehrhardt, D., Friesner, J. D., Frommer, W. B., Grotewold, E., Meyerowitz, E., Nemhauser, J., Nordborg, M., Pikaard, C., Shanklin, J., Somerville, C., Stitt, M., Torii, K. U., Waese, J., Wagner, D., & McCourt, P. (2016). 50 years of Arabidopsis research: highlights and future directions. New Phytologist, 209(3), 921-944.
Peirats-Llobet, M., Han, S. K., Gonzalez-Guzman, M., Jeong, C. W., Rodriguez, L., Belda-Palazon, B., Wagner, D., & Rodriguez, P. L. (2016). A direct link between abscisic acid sensing and the chromatin-remodeling ATPase BRAHMA via core ABA signaling pathway components. Molecular Plant, 9(1), 136-147.
2015
Xiao, J., & Wagner, D. (2015). Polycomb repression in the regulation of growth and development in Arabidopsis. Current opinion in plant biology, 23, 15-24.
Amtmann, A., Ma, H., & Wagner, D. (2015). Chromatin and epigenetics. Plant physiology, 168(4), 1185-1188.
Wu, M. F., Yamaguchi, N., Xiao, J., Bargmann, B., Estelle, M., Sang, Y., & Wagner, D. (2015). Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. elife, 4, e09269.
Yamaguchi, N., Winter, C. M., Wellmer, F., & Wagner, D. (2015). Identification of direct targets of plant transcription factors using the GR fusion technique. Plant Functional Genomics: Methods and Protocols, 123-138.
2014
Yamaguchi, N., Winter, C. M., Wu, M. F., Kanno, Y., Yamaguchi, A., Seo, M., & Wagner, D. (2014). Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis. Science, 344(6184), 638-641.
Vercruyssen, L., Verkest, A., Gonzalez, N., Heyndrickx, K. S., Eeckhout, D., Han, S. K., Jégu, T., Archacki, R., Van Leene, J., Andriankaja, M., De Bodt, S., Abeel, T., Coppens, F., Dhondt, S., De Milde, L., Vermeersch, M., Maleux, K., Gevaert, K., Jerzmanowski, A., Benhamed, M., Wagner, D., Vandepoele, K., De Jaeger, G., & Inzé, D. (2014). ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. The Plant Cell, 26(1), 210-229.
De Rybel, B., Adibi, M., Breda, A. S., Wendrich, J. R., Smit, M. E., Novak, O., Yamaguchi, N., Yoshida, S., Van Isterdael, G., Palovaara, J., Nijsse, B., Boekschoten, M. V., Hooiveld, G., Beeckman, T., Wagner, D., Ljung, K., Fleck, C., & Weijers, D. (2014). Integration of growth and patterning during vascular tissue formation in Arabidopsis. Science, 345(6197), 1255215.
Yamaguchi, N., Wu, M. F., Winter, C. M., & Wagner, D. (2014). LEAFY and polar auxin transport coordinately regulate Arabidopsis flower development. Plants, 3(2), 251-265.
Xiao, J., Xu, S., Li, C., Xu, Y., Xing, L., Niu, Y., Huan, Q., Tang, Y., Zhao, C., Wagner, D., Gao, C., & Chong, K. (2014). O-GlcNAc-mediated interaction between VER2 and TaGRP2 elicits TaVRN1 mRNA accumulation during vernalization in winter wheat. Nature communications, 5(1), 4572.
Yamaguchi, N., Winter, C. M., Wu, M. F., Kwon, C. S., William, D. A., & Wagner, D. (2014). PROTOCOLS: Chromatin immunoprecipitation from Arabidopsis tissues. The Arabidopsis book/American Society of Plant Biologists, 12.
Han, S. K., & Wagner, D. (2014). Role of chromatin in water stress responses in plants. Journal of experimental botany, 65(10), 2785-2799.
2013
Efroni, I., Han, S. K., Kim, H. J., Wu, M. F., Steiner, E., Birnbaum, K. D., Hong, J. C., Eshed, Y., & Wagner, D. (2013). Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Developmental cell, 24(4), 438-445.
Yamaguchi, N., Wu, M. F., Winter, C. M., Berns, M. C., Nole-Wilson, S., Yamaguchi, A., Coupland, G., Krizek, B. A., & Wagner, D. (2013). A molecular framework for auxin-mediated initiation of flower primordia. Developmental cell, 24(3), 271-282.
2012
Sang, Y., Silva-Ortega, C. O., Wu, S., Yamaguchi, N., Wu, M. F., Pfluger, J., Gillmor, C. S., Gallagher, K. L., & Wagner, D. (2012). Mutations in two non‐canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects. The plant journal, 72(6), 1000-1014.
Yamaguchi, N., Yamaguchi, A., Abe, M., Wagner, D., & Komeda, Y. (2012). LEAFY controls Arabidopsis pedicel length and orientation by affecting adaxial–abaxial cell fate. The Plant Journal, 69(5), 844-856.
Wu, M. F., Sang, Y., Bezhani, S., Yamaguchi, N., Han, S. K., Li, Z., Su, Y., Slewinski, T. L., & Wagner, D. (2012). SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors. Proceedings of the National Academy of Sciences, 109(9), 3576-3581.
Han, S. K., Sang, Y., Rodrigues, A., BIOL425 F2010, Wu, M. F., Rodriguez, P. L., & Wagner, D. (2012). The SWI2/SNF2 chromatin remodeling ATPase BRAHMA represses abscisic acid responses in the absence of the stress stimulus in Arabidopsis. The Plant Cell, 24(12), 4892-4906.
EPIC Planning Committee. (2012). Reading the second code: Mapping epigenomes to understand plant growth, development, and adaptation to the environment. The Plant Cell, 24(6), 2257-2261.
Wu, M. F., & Wagner, D. (2012). RNA in situ hybridization in Arabidopsis. RNA Abundance Analysis: Methods and Protocols, 75-86.
2011
Pastore, J. J., Limpuangthip, A., Yamaguchi, N., Wu, M. F., Sang, Y., Han, S. K., Malaspina, L., Chavdaroff, N., Yamaguchi, A., & Wagner, D. (2011). LATE MERISTEM IDENTITY2 acts together with LEAFY to activate APETALA1. Development, 138(15), 3189-3198.
Winter, C. M., Austin, R. S., Blanvillain-Baufume, S., Reback, M. A., Monniaux, M., Wu, M. F., Sang, Y., Yamaguchi, A., Yamaguchi, N., Parker, J. E., Parcy, F., Jensen, S. T., Li, H., & Wagner, D. (2011). LEAFY target genes reveal floral regulatory logic, cis motifs, and a link to biotic stimulus response. Developmental cell, 20(4), 430-443.
Wagner, D., & Meyerowitz, E. M. (2011). Switching on flowers: transient LEAFY induction reveals novel aspects of the regulation of reproductive development in Arabidopsis. Frontiers in plant science, 2, 60.
2009
Wagner, D. (2009). Flower morphogenesis: timing is key. Developmental Cell, 16(5), 621-622.
Sang, Y., Wu, M. F., & Wagner, D. (2009). The stem cell—chromatin connection. In Seminars in cell & developmental biology (Vol. 20, No. 9, pp. 1143-1148). Academic Press.
Yamaguchi, A., Wu, M. F., Yang, L., Wu, G., Poethig, R. S., & Wagner, D. (2009). The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Developmental cell, 17(2), 268-278.
Moyroud, E., Tichtinsky, G., & Parcy, F. (2009). The LEAFY floral regulators in angiosperms: conserved proteins with diverse roles. Journal of Plant Biology, 52, 177-185.
2007
Bezhani, S., Winter, C., Hershman, S., Wagner, J. D., Kennedy, J. F., Kwon, C. S., Pfluger, J., Su, Y., & Wagner, D. (2007). Unique, shared, and redundant roles for the Arabidopsis SWI/SNF chromatin remodeling ATPases BRAHMA and SPLAYED. The Plant Cell, 19(2), 403-416.
Pfluger, J., & Wagner, D. (2007). Histone modifications and dynamic regulation of genome accessibility in plants. Current opinion in plant biology, 10(6), 645-652.
Kwon, C. S., & Wagner, D. (2007). Unwinding chromatin for development and growth: a few genes at a time. Trends in Genetics, 23(8), 403-412.
2006
Su, Y., Kwon, C. S., Bezhani, S., Huvermann, B., Chen, C., Peragine, A., Kennedy, J. F., & Wagner, D. (2006). The N‐terminal ATPase AT‐hook‐containing region of the Arabidopsis chromatin‐remodeling protein SPLAYED is sufficient for biological activity. The Plant Journal, 46(4), 685-699.
Saddic, L. A., Huvermann, B., Bezhani, S., Su, Y., Winter, C. M., Kwon, C. S., Collum, R. P., & Wagner, D. (2006). The LEAFY target LMI1 is a meristem identity regulator and acts together with LEAFY to regulate expression of CAULIFLOWER. Development, 133 (9): 1673–1682.
Kwon, C. S., Hibara, K. I., Pfluger, J., Bezhani, S., Metha, H., Aida, M., Tasaka, M., & Wagner, D. (2006). A role for chromatin remodeling in regulation of CUC gene expression in the Arabidopsis cotyledon boundary. Development, 133 (16): 3223–3230.
Wang, L. S., Wagner, D., Kwon, C. S., Su, Y., & Kim, J. (2006). Transcriptional target prediction using qualitative reasoning. In 2006 International Conference of the IEEE Engineering in Medicine and Biology Society (pp. 3138-3141). IEEE.
2005
Kwon, C. S., Chen, C., & Wagner, D. (2005). WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis. Genes & development, 19(8), 992-1003.
2004
Wagner, D., Wellmer, F., Dilks, K., William, D., Smith, M. R., Kumar, P. P., Riechmann, J. L., Greenland, A. J., & Meyerowitz, E. M. (2004). Floral induction in tissue culture: a system for the analysis of LEAFY‐dependent gene regulation. The Plant Journal, 39(2), 273-282.
William, D. A., Su, Y., Smith, M. R., Lu, M., Baldwin, D. A., & Wagner, D. (2004). Genomic identification of direct target genes of LEAFY. Proceedings of the National Academy of Sciences, 101(6), 1775-1780.
2003
Wagner, D. (2003). Chromatin regulation of plant development. Current opinion in plant biology, 6(1), 20-28.
Wagner, D., Saddic, L. A., Lu, M., Kim, F., Su, Y., William, D., & Kwon, C. S. (2003). Meristem identity in Arabidopsis thaliana. Flowering Newsletter. 36. 25-35.
2002
Wagner, D., & Meyerowitz, E. M. (2002). SPLAYED, a novel SWI/SNF ATPase homolog, controls reproductive development in Arabidopsis. Current Biology, 12(2), 85-94.
Wagner, D. & Sablowski, R. W. (2002). Glucocorticoid fusions for transcription factors. Arabidopsis: A Laboratory Manual, 296-299.
1999
Wagner, D., Sablowski, R. W., & Meyerowitz, E. M. (1999). Transcriptional activation of APETALA1 by LEAFY. Science, 285(5427), 582-584.
1997
Wagner, D., Hoecker, U., & Quail, P. H. (1997). RED1 is necessary for phytochrome B-mediated red light-specific signal transduction in Arabidopsis. The Plant Cell, 9(5), 731-743.
1996
Wagner, D., Koloszvari, M., & Quail, P. H. (1996). Two small spatially distinct regions of phytochrome B are required for efficient signaling rates. The Plant Cell, 8(5), 859-871.
Wagner, D., Fairchild, C. D., Kuhn, R. M., & Quail, P. H. (1996). Chromophore-bearing NH2-terminal domains of phytochromes A and B determine their photosensory specificity and differential light lability. Proceedings of the National Academy of Sciences, 93(9), 4011-4015.
1995
Wagner, D., & Quail, P. H. (1995). Mutational analysis of phytochrome B identifies a small COOH-terminal-domain region critical for regulatory activity. Proceedings of the National Academy of Sciences, 92(19), 8596-8600.
Quail, P. H., Boylan, M. T., Parks, B. M., Short, T. W., Xu, Y., & Wagner, D. (1995). Phytochromes: photosensory perception and signal transduction. Science, 268(5211), 675-680.
Bagnall, D. J., King, R. W., Whitelam, G. C., Boylan, M. T., Wagner, D., & Quail, P. H. (1995). Flowering responses to altered expression of phytochrome in mutants and transgenic lines of Arabidopsis thaliana (L.) Heynh. Plant Physiology, 108(4), 1495-1503.
1992
Deng, X. W., Matsui, M., Wei, N., Wagner, D., Chu, A. M., Feldmann, K. A., & Quail, P. H. (1992). COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a Gβ homologous domain. Cell, 71(5), 791-801.
1991
Wagner, D., Tepperman, J. M., & Quail, P. H. (1991). Overexpression of phytochrome B induces a short hypocotyl phenotype in transgenic Arabidopsis. The Plant Cell, 3(12), 1275-1288.
1989
Bush, D. S., Sticher, L., Van Huystee, R., Wagner, D., & Jones, R. L. (1989). The calcium requirement for stability and enzymatic activity of two isoforms of barley aleurone α-amylase. Journal of Biological Chemistry, 264(32), 19392-19398.