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Algae

  • Du Z-Y, Bhat WW, Poliner E, Johnson S, Bertucci C, Farre EM, Hamberger B (2023). Engineering Nannochloropsis oceanica for the production of diterpenoid compounds. mLife 2(4): 428-437 (doi.org/10.1002/mlf2.12097)
  • Poliner E, Busch AWU,  Newton L, Kim YU, Clark R, Gonzalez-Martinez SC, Jeong B-R, Montgomery BL, Farre EM (2022) Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica. Plant Physiology 189(2):906-921 (doi: 10.1093/plphys/kiac052)
  • Gong Y, Kang NK, Kim YU, Wang Z, Wei L, Xin Y, Shen C, Wang Q, You W, Lim J-M, Jeong S-W, Park Y-I, Oh H-M, Pan K, Poliner E, Yang G, Li-Beisson Y, Li Y, Hu Q, Poetsch A, Farre EM, Chang Y-K, Jeong W-J, Jeong, B-R, Xu J (2020) The NanDeSyn Database for Nannochloropsis systems and synthetic biology. The Plant Journal 104(6):1736-1745 (doi.org/10.1111/tpj.15025)
  • Farre EM (2020) The brown clock: circadian rhythms in stramenopiles. Physiol Plant. 169(3):430-441. doi: 10.1111/ppl.13104
  • Poliner E, Clark E*, Cummings C,* Benning C, Farre EM (2020) A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research. https://doi.org/10.1016/j.algal.2019.101664 (*) Undergraduate researcher.
  • Zienkiewicz A, Zienkiewicz K, Poliner E, Pulman J, Du ZY, Stefano G, Tsai CH, Horn P, Feussner I, Farre EM, Childs K, Brandizzi F, Benning B (2020) Nannochloropsis metabolism during transition from quiescence to autotrophy. Plant Physiology (doi: 10.1104/pp.19.00854)
  • Poliner E, Cummings C*, Newton L, Farré EM. Identification of circadian rhythms in Nannochloropsis species using bioluminescence reporter lines. The Plant Journal 99(1):112-127. (doi: 10.1111/tpj.14314) (*) Undergraduate researcher.
  • Poliner E, Takeuchi T, Du Z-Y, Benning C, Farré EM (2018) Non-transgenic marker-free gene disruption by an episomal CRISPR system in the oleaginous microalga Nannochloropsis oceanica CCMP1779. ACS Synthetic Biology 7(4):962-968 (doi: 10.1021/acssynbio.7b00362)
  • Poliner E, Farré EM, Benning C. Advanced genetic tools enable synthetic biology in the oleaginous micoalga Nannochloropsis oceanica (2018). Plant Cell Reports 37(10):1383-1399 (doi: 10.1007/s00299-018-2270-0)
  • Poliner E, Zienkiewicz K, Pulman J, Newton L, Benning C, Farré EM (2018). A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced fatty acid production. Plant Biotechnology Journal 16(1):298-309 (doi: 10.1111/pbi.12772.)
  • Zienkiewicz K, Zienkiewicz A, Poliner E, Du ZY, Vollheyde K, Herrfurth C, Marmon S, Farré EM, Feussner I, Benning C (2017). Nannochloropsis, a rich source of diacylglycerol acyltransferases for engineering of triacylglycerol content in different hosts. Biotechnology for Biofuels 10:8 (doi:10.1186/s13068-016-0686-8)
  • Poliner E, Panchy N, Newton L, Wu G, Lapinsky A*, Bullard B, Zienkiewicz A, Benning C, Shiu S-H, Farré EM (2015) Transcriptional coordination of physiological responses in
  • Nannochloropsis oceanica CCMP1779 under light/dark cycles. The Plant Journal 83(6):1097-1113. (*) Undergraduate researcher.
  • Panchy N, Wu G, Newton L, Tsai C-H, Chen J, Benning C, Farré EM*, Shiu S-H* (2014). Prevalence, evolution and cis-regulation of diel transcription in Chlamydomonas reinhardtii. G3. 4(12):2461-71 *Co-corresponding author.

Plants

  • Hoopes GM, Zarka D, Feke A, Acheson K, Hamilton JP, Douches D, Buell CR, Farré EM (2022) Keeping time in the dark: potato diel and circadian rhythmic gene expression reveals tissue-specific circadian clocks.(doi/10.1002/pld3.425)
  • Schneider T, Bolger A, Zeier J, Preiskowski S, Benes V, Trenkamp S, Usadel B, Farré EM, Matsubara S (in press). Fluctuating Light Interacts with Time of Day and Leaf Development to Reprogram Gene Expression. Plant Physiology. [Pubmed]
  • Hardigan M, Newton L, Crisovan E, Wiegert-Rininger K, Wood J, Douches DS, Farré EM, Veilleux R, Buell DR (2017). Genome diversity of tuber bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato. PNAS 114(46):E9999-E10008 [Pubmed]
  • Liu T, Newton L, Liu MJ, Shiu SH, Farre EM. A G-box-like motif is necessary for transcriptional regulation by circadian pseudo-response regulators in Arabidopsis(2016) Plant Physiology 170(1):528-39 [Pubmed].
    ”’NOTE:”’ An updated corrected version of the manuscript has been published online (Jan. 20, 2016)
  • Horak E, Farré EM (2015)The regulation of UV-B responses by the circadian clock. Plant Signaling and Behavior 10(5):e1000164.
  • Takeuchi T, Newton L, Burkhardt A, Mason S, Farre EM (2014) Light and the circadian clock mediate time specific changes in sensitivity to UV-B stress under light/dark cycles. Journal of Experimental Botany 65(20):6003-12 [http://www.ncbi.nlm.nih.gov/pubmed/25147271 PubMed]
  • Liu T, Carlsson J, Takeuchi T, Newton L (2013) Direct regulation of abiotic responses by the Arabidopsis circadian clock component PRR7. Plant Journal.Plant J 76(1):101-14 [http://www.ncbi.nlm.nih.gov/pubmed/23808423 PubMed]
  • Farré EM, Liu T (2013) The PRR family of transcriptional regulators reflects the complexity and evolution of plant circadian clocks. Curr Opin Plant Biol 16(5):621-9 [http://www.ncbi.nlm.nih.gov/pubmed/23856081 PubMed]
  • Farré EM, Weise SE (2012) The interactions between the circadian clock and primary metabolism. Curr Opin Plant Biol 15(3):293-300. [http://www.ncbi.nlm.nih.gov/pubmed/22305520 PubMed]
  • Farre EM (2012) The regulation of plant growth by the circadian clock. Plant Biol 14(3):401-10.[http://www.ncbi.nlm.nih.gov/pubmed/22284304 PubMed]
  • Nusinow DA, Helfer A, Hamilton EE, King JJ, Imaizumi T, Schultz TF, Farré EM, Kay SA (2011)The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475:398-402.
  • Dong M, Farre EM, Thomashow MF (2011) CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis. PNAS 108(17):7241-6.
  • Farre EM and Kay SA (2007) PRR7 Protein levels are regulated by light and the circadian clock in Arabidopsis. Plant J 52 (3):548–560.
  • Para A, Farre EM, Imaizumi T, Pruneda-Paz J, Harmon FG, Kay SA (2007). PRR3 is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. Plant Cell 19:3462-3473.
  • ^Zeilinger MN, ^Farre EM, Taylor SR, Kay SA and Doyle FJ III (2006) A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9. Mol Syst Biol 2: 58. ^Equal authorship; News and Views by Ueda HR (2006) Molecular Systems Biology 2.
  • Farre EM, Harmer SL, Harmon FG, Yanovsky MJ, Kay SA. (2005) Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Curr Biol 15(1):47-54.

Potato Tuber Metabolism

  • Farre EM, Fernie AR, Willmitzer L. (2008) Analysis of subcellular metabolite levels of potato tubers (Solanum tuberosum) displaying alterations in cellular or extracellular sucrose metabolism. Metabolomics 4:161-170.
  • Farre EM, Tech S, Trethewey RN, Fernie AR, Willmitzer L. (2006) Subcellular pyrophosphate metabolism in developing tubers of potato (Solanum tuberosum). Plant Mol Biol. 62(1-2):165-79.
  • Tiessen A, Hendriks JHM, Stitt M, Branscheid A, Gibon Y, Farre EM, Geigenberger P (2002) Starch synthesis in potato tubers is regulated by post-translational redox modification of ADP-glucose pyrophosphorylase: A novel regulatory mechanism linking starch synthesis to the sucrose supply. Plant Cell (14) 2191-2213.
  • Farre EM, Tiessen A, Roessner U, Geigenberger P, Trethewey RN, Willmitzer L (2001) Analysis of the compartmentation of glycolytic intermediates, nucleotides, sugars, organic acids, amino acids, and sugar alcohols in potato tubers using a nonaqueous fractionation method. Plant Physiology 127: 685-700.
  • Farre EM, Bachmann A, Willmitzer L, Trethewey R (2001) Sprouting of potato tubers is significantly accelerated by the expression of a bacterial pyrophosphatase. Nature Biotech 19(3):268-272.
  • Farre EM, Geigenberger P, Willmitzer L and Trethewey RN (2000) A possible role for pyrophosphate in the coordination of cytososlic and plastididal carbon metabolism within the potato tuber. Plant Physiology 123: 681-688.