Harmer Lab:Publications

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Room 2123
Department of Plant Biology
1002 Life Sciences, One Shields Ave.
University of California Davis
Davis, CA 95616

Contact: slharmer at ucdavis.edu

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  • Shalit-Kaneh, A., Kumimoto, R.W., Filkov, V., and Harmer, S.L. (2018) Multiple feedback loops of the Arabidopsis circadian clock provide rhythmic robustness across environmental conditions. Proceedings of the National Academy of the Sciences, 115(27) 7147-7152. doi: 10.1073/pnas.1805524115 [1]
  • Harmer, S.L. and Brooks, C.J. (2017) Growth-mediated plant movements: hidden in plain sight. Current Opinion in Plant Biology. 41:89-94. doi: 10.1016/j.pbi.2017.10.003 [2]
  • Rubin, M.J., Brock, M.T., Davis, A.M., German, Z.M., Welch, S.M., Harmer, S.L., Maloof, J.N., Davis, S.J., and Weinig, C. (2017) Circadian rhythms vary over the growing season and correlate with fitness components. Molecular Ecology. 26(20):5528-5540. doi: 10.1111/mec.14287 [3]
  • Gray, J.A., Shalit-Kaneh, A., Chu, D.N., Hsu, P.Y., and Harmer, S.L. (2017) The REVEILLE clock genes inhibit growth of juvenile and adult plants by control of cell size. Plant Physiology. 173(4):2308-2322. doi: 10.1104/pp.17.00109 [4]
  • Müller-Moulé P., Nozue, K., Pytlak, M.L., Palmer, C.M., Covington, M.F., Wallace, A.D., Harmer, S.L., and Maloof, J.N. (2016) YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance. PeerJ. 4:e2574 [5]
  • Atamian, H.S., Creux, N.M., Brown, E.A., Garner, A.G., Blackman, B.K., and Harmer, S.L. (2016) Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits. Science. 353(6299):587-90. doi: 10.1126/science.aaf9793 [6]
  • Atamian, H.S. and Harmer, S.L. (2016) Circadian regulation of hormone signaling and plant physiology. Plant Mol Biol. 91(6):691-702. doi: 10.1007/s11103-016-0477-4 [7]
  • Jones, M.A., Hu, W., Litthauer, S., Lagarias, J.C. and Harmer, S.L. (2015) A constitutively active allele of phytochrome B maintains circadian robustness in the absence of light. Plant Physiology. 169(1):814-25. doi: 10.1104/pp.15.00782 [8]
  • Brady, S.M., Burow, M., Busch, W., Carlborg, O., Denby, K.J., Glazebrook, J., Hamilton, E.S., Harmer, S.L., Haswell, E.S., Maloof, J.N., Springer, N.M., Kliebenstein, D.J. (2015) Reassess the t Test: Interact with All Your Data via ANOVA. Plant Cell. 2015 Jul 28. pii: tpc.15.00238 [9]
  • Vandenbrink, J.P., Brown, E.A., Harmer, S.L., Blackman, B.K. (2014) Turning heads: the biology of solar tracking in sunflower. Plant Sci. 224:20-6. doi: 10.1016/j.plantsci.2014.04.006 [10]
  • Anver, S., Roguev, A., Zofall, M., Krogan, N.J., Grewal, S.I.S., and Harmer, S.L. (2014) Yeast X-Chromosome Associated Protein 5 (Xap5) Functions with H2A.Z to Suppress Aberrant Transcripts. EMBO reports. pii: e201438902. [11]
  • Hsu, P.Y. and Harmer, S.L. (2014) Global profiling of the circadian transcriptome using microarrays. Methods in Molecular Biology. 1158:45-56 [12]
  • Hsu, P.Y. and Harmer, S.L. (2013) Wheels within wheels: the plant circadian system. Trends in Plant Science [13]
  • Hsu, P.Y., Devisetty, U.K., and Harmer, S.L. (2013) Cycling activators control the evening arm of the plant clock. eLife. 2:e00473. [14]
  • Zemach, A., Kim, M.Y., Hsieh, P.-H., Coleman-Derr,D., Eshed-Williams, L., Thao, K, Harmer, S.L., and Zilberman, D. (2013) The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153(1):193-205 [15]
  • Hu, W., Franklin, K.A., Sharrock, R.A., Jones, M.A., Harmer, S.L., and Lagarias, J.C. (2013) Unanticipated regulatory roles for Arabidopsis phytochromes revealed by null mutant analysis. Proceedings of the National Academy of the Sciences, 110(4) 1542-1547. [16]
  • Hsu, P.Y. and Harmer, S.L. (2012) Circadian phase has profound effects on differential expression analysis. PLoS One, 7(11):e49853 [17]
  • Jones, M.A., Williams, B.A., McNicol J., Simpson, C.G., Brown, J.W., and Harmer, S.L. (2012) Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS 1 causes circadian clock defects. Plant Cell, 24(10):4066-82 [18]
  • Nozue, K., Harmer. S.L., and Maloof, J.N. (2011) Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PIF5 as a modulator of auxin signaling in Arabidopsis. Plant Physiology, 156(1): 357-372 [19]
  • Rawat, R., Takahashi, N., Hsu, P.Y., Jones, M.A., Schwartz, J., Salemi, M.R., Phinney, B.S., and Harmer, S.L. (2011) REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genetics, 7(3): e1001350. [20]
  • Kerwin, R.E., Jimenez-Gomez, J.M., Fulop, D., Harmer, S.L., Maloof, J.N., Kliebenstein, D.J. (2011) Network QTL mapping of circadian clock outputs identifies metabolic pathway to clock linkages in Arabidopsis. Plant Cell, 23(2):471-85 [21]
  • Jones, M.A., and Harmer, S.L. (2011) JMJD5 functions in concert with TOC1 in the Arabidopsis circadian system. Plant Signaling & Behavior 6(3): 1-4. [22]
  • Jones, M.A., Covington, M.F., Ditacchio, L., Vollmers, C., Panda, S., Harmer, S.L. (2010) Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proceedings of the National Academy of the Sciences 107(50): 21623-21628. [23]
  • Ellison ,C.T., Vandenbussche, F., Van Der Straeten, D., Harmer, S.L. (2011) XAP5 CIRCADIAN TIMEKEEPER regulates ethylene responses in aerial tissues of Arabidopsis. Plant Physiology, 155(2):988-999. [24]
  • Harmer, S.L. (2010). Plant biology in the fourth dimension. Plant Physiology, 154:467 - 470. [25]
  • Rawat, R., Schwartz, J., Jones, M.A., Sairanen, I., Cheng, Y., Andersson, C.R., Zhao, Y., Ljung, K., and Harmer, S.L. (2009). REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways. Proceedings of the National Academy of the Sciences 106(39) 16883-16888. [26]
  • Harmer, S.L. (2009). The circadian system in higher plants. Annual Review of Plant Biology 60: 357 – 77. [27]
  • Covington, M.F., Maloof, J.N., Straume, M., Kay, S.A., and Harmer, S.L. (2008). Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biology, 9(8):R130. [28]
  • Martin-Tryon, E.L., and Harmer, S.L. (2008). XAP5 CIRCADIAN TIMEKEEPER coordinates light signals for proper timing of photomorphogenesis and the circadian clock in Arabidopsis. Plant Cell 20(5):1244-59. [29]
  • Gong, W., He, K., Covington, M.F., Dinesh-Kumar, S.P., Snyder, M., Harmer, S.L., Zhu, X., and Deng, X.P. (2008). The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Molecular Plant, 1(1): 27 – 41. [30]
  • Covington, M.F. and Harmer, S.L (2007) The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biology, 5(8): e227 [31]
  • Nozue, K., Covington, M.F., Duek, P.D., Lorrain, S., Fankhauser, C., Harmer, S.L., and Maloof, J.N. (2007) Rhythmic growth explained by coincidence between internal and external cues. Nature, 448:358-61. [32]
  • Walley, J.W., Coughlan, S., Hudson, M.E., Covington, M.F., Kaspi, R., Banu, G., Harmer, S.L., and Dehesh, K. (2007) Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genetics, 3(10): e172. [33]
  • Oliverio, K.A., Crepy, M., Martin-Tryon, E.L., Milich, R., Harmer, S.L., Putterill, J., Yanovsky, M., Casal, J.J. (2007) GIGANTEA regulates phytochrome A-mediated photomorphogenesis independently of its role in the circadian clock. Plant Physiology 144:495-502 [34]
  • Martin-Tryon, E.L., Kreps, J.A., Harmer, S.L. (2007). GIGANTEA acts in blue light signaling and has biochemically separable roles in circadian clock and flowering time regulation. Plant Physiology 143:473-486. [35]
  • Harmer, S. L. and Kay, S. A. (2005). Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis. Plant Cell 17:1926-1940. [36]
  • Farre, E. M., Harmer, S. L., Harmon, F. G., Yanovsky, M. J., and Kay, S. A. (2005). Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Current Biology 15:47-54. [37]
  • Harmer, S. L., Covington, M. F., Bläsing, O., and Stitt, M. (2005). Circadian regulation of global gene expression and metabolism. In: Endogenous Plant Rhythms, ed. Hall, A., and McWatters, H., Blackwell Publishing, pp.133-165 [38]
  • Alabadi, D., Mas, P., Yanovsky, M., Harmer, S. L., and Kay, S. A. (2002). Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis. Current Biology 12:757-761. [39]
  • Harmer, S. L., Panda, S., and Kay, S. A. (2001). Molecular bases of circadian rhythms. Annual Review of Cell and Developmental Biology 17:215-253. [40]
  • Harmer, S. L., Hogenesch, J. B., Straume, M., Chang, H. S., Han, B., Zhu, T., Wang, X., Kreps, J. A., and Kay, S. A. (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290:2110-2113. [41]