1. Abraham Z, Iglesias-Fernández R, Martínez M, Rubio-Somoza I, Díaz I, Carbonero P, et al. A Developmental Switch of Gene Expression in the Barley Seed Mediated by HvVP1 (Viviparous-1) and HvGAMYB Interactions. Plant Physiol. American Society of Plant Biologists; 2016 Apr;170(4):2146–58.
2. Bedhomme M, Adamo M, Marchand CH, Couturier J, Rouhier N, Lemaire SD, et al. Glutathionylation of cytosolic glyceraldehyde-3-phosphate dehydrogenase from the model plant Arabidopsis thaliana is reversed by both glutaredoxins and thioredoxins in vitro. Biochemical Journal. Portland Press Limited; 2012 Aug 1;445(3):337–47.
3. Berendzen KW, Weiste C, Wanke D, Kilian J, Harter K, Droge-Laser W. Bioinformatic Cis-Element Analyses Performed in Arabidopsis and Rice Disclose bZIP- and MYB-Related Binding Sites as Potential AuxRE-Coupling Elements in Auxin-Mediated Transcription. BMC plant biology. BioMed Central Ltd; 2012;12(1):125.
4. Berke L, Snel B. The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history. BMC Evol Biol. BioMed Central; 2015 Mar 13;15(1):44.
5. Bieker S, Riester L, Stahl M, Franzaring J, Zentgraf U. Senescence-specific alteration of hydrogen peroxide levels in Arabidopsis thaliana and oilseed rape spring variety Brassica napus L. cv. Mozart. J Integr Plant Biol. Blackwell Publishing Asia; 2012 Aug;54(8):540–54.
6. Carbonero P, Iglesias-Fernández R, Vicente-Carbajosa J. The AFL subfamily of B3 transcription factors: evolution and function in angiosperm seeds. J Exp Bot. 2016 Dec 21;:erw458.
7. Crozet P, Margalha L, Butowt R, Fernandes N, Elias CA, Orosa B, et al. SUMOylation represses SnRK1 signaling in Arabidopsis. Plant J. 2016 Jan;85(1):120–33.
8. Dietrich K, Weltmeier F, Ehlert A, Weiste C, Stahl M, Harter K, et al. Heterodimers of the Arabidopsis Transcription Factors bZIP1 and bZIP53 Reprogram Amino Acid Metabolism during Low Energy Stress. Plant Cell. 2011 ed. 2011 Jan;23(1):381–95.
9. Doerfler H, Lyon D, Nägele T, Sun X, Fragner L, Hadacek F, et al. Granger causality in integrated GC-MS and LC-MS metabolomics data reveals the interface of primary and secondary metabolism. Metabolomics. Springer US; 2013 Jun;9(3):564–74.
10. Eisele JF, Fäßler F, Bürgel PF, Chaban C. A Rapid and Simple Method for Microscopy-Based Stomata Analyses. Pandey GK, editor. PloS One. 2016;11(10):e0164576.
11. Fürtauer L, Weckwerth W, Nägele T. A Benchtop Fractionation Procedure for Subcellular Analysis of the Plant Metabolome. Frontiers in plant science. Frontiers; 2016;7:1912.
12. Hartmann L, Pedrotti L, Weiste C, Fekete A, Schierstaedt J, Göttler J, et al. Crosstalk between Two bZIP Signaling Pathways Orchestrates Salt-Induced Metabolic Reprogramming in Arabidopsis Roots. Plant Cell. 2015 Aug;27(8):2244–60.
13. Haydon MJ, Hearn TJ, Bell LJ, Hannah MA, Webb AAR. Metabolic regulation of circadian clocks. Semin Cell Dev Biol. 2013 May;24(5):414–21.
14. Hoehenwarter W, Thomas M, Nukarinen E, Egelhofer V, Röhrig H, Weckwerth W, et al. Identification of novel in vivo MAP kinase substrates in Arabidopsis thaliana through use of tandem metal oxide affinity chromatography. Mol Cell Proteomics. 2013 Feb;12(2):369–80.
15. van Hooff JJE, Snel B, Seidl MF. Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication. Genome Biology and Evolution. 2014 May;6(5):1079–85.
16. Hummel M, Dobrenel T, Cordewener JJHG, Davanture M, Meyer C, Smeekens SCM, et al. Proteomic LC-MS analysis of Arabidopsis cytosolic ribosomes: Identification of ribosomal protein paralogs and re-annotation of the ribosomal protein genes. J Proteomics. 2015 Oct 14;128:436–49.
17. Iven T, König S, Singh S, Braus-Stromeyer SA, Bischoff M, Tietze LF, et al. Transcriptional activation and production of tryptophan-derived secondary metabolites in arabidopsis roots contributes to the defense against the fungal vascular pathogen Verticillium longisporum. Molecular plant. 2012 Nov;5(6):1389–402.
18. Kirchler T, Briesemeister S, Singer M, Schutze K, Keinath M, Kohlbacher O, et al. The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. European journal of cell biology. 2010 ed. 2010 Feb-Mar;89(2-3):175–83.
19. Koster MJE, Snel B, Timmers HTM. Genesis of chromatin and transcription dynamics in the origin of species. Cell. 2015 May 7;161(4):724–36.
20. Lastdrager J, Hanson J, Smeekens SCM. Sugar signals and the control of plant growth and development. J Exp Bot. 2014 Mar;65(3):799–807.
21. Latz A, Mehlmer N, Zapf S, Mueller TD, Wurzinger B, Pfister B, et al. Salt stress triggers phosphorylation of the Arabidopsis vacuolar K+ channel TPK1 by calcium-dependent protein kinases (CDPKs). Molecular plant. 2013 Jul;6(4):1274–89.
22. Mair A, Pedrotti L, Wurzinger B, Anrather D, Simeunovic A, Weiste C, et al. SnRK1-triggered switch of bZIP63 dimerization mediates the low-energy response in plants. Elife. 2015;4:e05828.
23. Mithoe SC, Boersema PJ, Berke L, Snel B, Heck AJR, Menke FLH. Targeted Quantitative Phosphoproteomics Approach for the Detection of Phospho-tyrosine Signaling in Plants. Journal of proteome research. 2012 Jan;11(1):438–48.
24. Nägele T, Fürtauer L, Nagler M, Weiszmann J, Weckwerth W. A Strategy for Functional Interpretation of Metabolomic Time Series Data in Context of Metabolic Network Information. Frontiers; 2016;3(124):6.
25. Nägele T, Weckwerth W. Mathematical modeling reveals that metabolic feedback regulation of SnRK1 and hexokinase is sufficient to control sugar homeostasis from energy depletion to full recovery. Frontiers in plant science. Frontiers; 2014;5(2):365.
26. Nägele T, Mair A, Sun X, Fragner L, Teige M, Weckwerth W. Solving the differential biochemical Jacobian from metabolomics covariance data. Kusano M, editor. PloS One. Public Library of Science; 2014;9(4):e92299.
27. Nägele T, Weckwerth W. A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana. Frontiers in plant science. Frontiers; 2013;4:541.
28. Nägele T, Weckwerth W. Mathematical modeling of plant metabolism-from reconstruction to prediction. Molecular Diversity Preservation International; 2012 Sep 6;2(3):553–66.
29. Nagler M, Nukarinen E, Weckwerth W, Nägele T. Integrative molecular profiling indicates a central role of transitory starch breakdown in establishing a stable C/N homeostasis during cold acclimation in two natural accessions of Arabidopsis thaliana. BMC plant biology. BioMed Central; 2015 Dec 1;15(1):284.
30. Perrella G, Lopez-Vernaza MA, Carr C, Sani E, Gosselé V, Verduyn C, et al. Histone deacetylase complex1 expression level titrates plant growth and abscisic acid sensitivity in Arabidopsis. Plant Cell. 2013 Sep;25(9):3491–505.
31. Roustan V, Jain A, Teige M, Ebersberger I, Weckwerth W. An evolutionary perspective of AMPK-TOR signaling in the three domains of life. J Exp Bot. Oxford University Press; 2016 Jun;67(13):3897–907.
32. Santuari L, Sanchez-Perez GF, Luijten M, Rutjens B, Terpstra I, Berke L, et al. The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots. Plant Cell. American Society of Plant Biologists; 2016 Dec;28(12):2937–51.
33. Schulz P, Jansseune K, Degenkolbe T, Méret M, Claeys H, Skirycz A, et al. Poly(ADP-ribose)polymerase activity controls plant growth by promoting leaf cell number. Araújo WL, editor. PloS One. 2014;9(2):e90322.
34. Smykowski A, Zimmermann P, Zentgraf U. CORRECTION. G-Box Binding Factor1 Reduces CATALASE2 Expression and Regulates the Onset of Leaf Senescence in Arabidopsis. Plant Physiol. American Society of Plant Biologists; 2016 Feb;170(2):1164–7.
35. Smykowski A, Fischer SM, Zentgraf U. Phosphorylation Affects DNA-Binding of the Senescence-Regulating bZIP Transcription Factor GBF1. Plants (Basel). Multidisciplinary Digital Publishing Institute; 2015 Sep 16;4(3):691–709.
36. Stael S, Rocha AG, Wimberger T, Anrather D, Vothknecht UC, Teige M. Cross-talk between calcium signalling and protein phosphorylation at the thylakoid. J Exp Bot. Oxford University Press; 2012 Feb;63(4):1725–33.
37. Tomé F, Jansseune K, Saey B, Grundy J, Vandenbroucke K, Hannah MA, et al. rosettR: protocol and software for seedling area and growth analysis. Plant Methods. BioMed Central; 2017 Mar 15;13(1):13.
38. Tomé F, Nägele T, Adamo M, Garg A, Marco Llorca C, Nukarinen E, et al. The low energy signaling network. Frontiers in plant science. 2014;5:353.
39. Veerabagu M, Kirchler T, Elgass K, Stadelhofer B, Stahl M, Harter K, et al. The Interaction of the Arabidopsis Response Regulator ARR18 with bZIP63 Mediates the Regulation of PROLINE DEHYDROGENASE Expression. Molecular plant. 2014 Oct;7(10):1560–77.
40. Walper E, Weiste C, Mueller MJ, Hamberg M, Droge-Laser W. Screen Identifying Arabidopsis Transcription Factors Involved in the Response to 9-Lipoxygenase-Derived Oxylipins. PloS One. 2016;11(4):e0153216.
41. Wang L, Nägele T, Doerfler H, Fragner L, Chaturvedi P, Nukarinen E, et al. System level analysis of cacao seed ripening reveals a sequential interplay of primary and secondary metabolism leading to polyphenol accumulation and preparation of stress resistance. Plant J. 2016 Aug;87(3):318–32.
42. Weiste C, Droge-Laser W. The Arabidopsis transcription factor bZIP11 activates auxin-mediated transcription by recruiting the histone acetylation machinery. Nat Commun. 2014;5:3883.