Stacey Harmer

Stacey Harmer

Position Title

Department of Plant Biology, College of Biological Sciences

2129 Life Sciences

Research Interests

Understanding the molecular basis of circadian rhythms in plants and how these daily rhythms affect plant physiology.

Grad Group Affiliations

  • Designated Emphasis in Biotechnology
  • Integrative Genetics and Genomics
  • Plant Biology

Specialties / Focus

  • Cell and Developmental Biology
  • Model Plants
  • Molecular Biology, Biochemistry and Genomics


  • MCB 121 Mol Bio Eukaryotic Cells, Fall
  • MCB 160L Genetics Lab, Fall


  • Harmer Lab

Honors and Awards

  • American Society of Photobiology - New Investigator Award, 2004
  • Chancellor’s Fellow, UC Davis, 2011-2016
  • College of Biological Sciences Faculty Research Award, 2017

    Professional Societies

    • American Society of Plant Biologists
    • Society for Research on Biological Rhythms


    • 1991 BA Biochemistry University of California, Berkeley
    • 1998 PhD Biochemistry University of California, San Francisco


    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 Sciences115(27): 7147-7152.  doi: 10.1073/pnas.1805524115. 

    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

    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

    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.

    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

    Atamian HS, Creux NM, Brown EA, Garner AG, Blackman BK, Harmer SL. (2016) Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits. Science, 353(6299):587-90.

    Brady SM, Burow M, Busch W, Carlborg Ö, Denby KJ, Glazebrook J, Hamilton ES, Harmer SL, Haswell ES, Maloof JN, Springer NM, Kliebenstein DJ. (2015) Reassess the t Test: Interact with All Your Data via ANOVA. The Plant Cell 27(8):2088-94.

    Atamian HS, Harmer SL. (2016) Circadian regulation of hormone signaling and plant physiology. Plant Molecular Biology 91(6):691-702.

    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. pp.00782.2015; doi:10.1104/pp.15.00782

    Vandenbrink, J.P., Brown, E.A., Harmer, S.L., and 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.

    Hsu, P.Y., Devisetty, U.K., and Harmer, S.L. (2013) Cycling activators control the evening arm of the plant clock. eLife. 2:e00473. doi: 10.7554/eLife.00473.

    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. doi: 10.1016/j.cell.2013.02.033.

    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. doi: 10.1073/pnas.1221738110

    Hsu, P.Y. and Harmer, S.L. (2012) Circadian phase has profound effects on differential expression analysis. PLoS One, 7(11):e49853. doi: 10.1371/journal.pone.0049853.

    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. doi: 10.1105/tpc.112.104828.

    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.

    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.

    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.

    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.

    Ellison ,C.T., Vandenbussche, F., Van Der Straeten, D., Harmer, S.L. (2010) XAP5 CIRCADIAN TIMEKEEPER regulates ethylene responses in aerial tissues of Arabidopsis. Plant Physiology, 155(2):988-999.

    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.

    Harmer, S.L. (2010). Plant biology in the fourth dimension. Plant Physiology, 154:467 - 470.

    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.