- Horak E, Farré EM (in press)The regulation of UV-B responses by the circadian clock. Plant Signaling and Behavior.
- 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 PubMed
- Braun R, Farré EM, Schurr U, Matsubara S (2014) Effects of light and circadian clock on growth and chlorophyll accumulation of Nannochloropsis gaditana. Journal of Phycology 50(1):515–525 
- 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 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 PubMed
- Vieler et al. (2012) Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779. Plos Genetics8(11):e1003064. Pubmed
- Farré EM, Weise SE (2012) The interactions between the circadian clock and primary metabolism. Curr Opin Plant Biol 15(3):293-300. PubMed
- Farre EM (2012) The regulation of plant growth by the circadian clock. Plant Biol 14(3):401-10.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.
- 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.