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Highly resolved systems biology to dissect the etioplast-to-chloroplast transition in tobacco leaves.

Armarego-Marriott T, Kowalewska ŁM, Burgos A, Fischer A, Thiele W, Erban A, Strand DD, Kahlau S, Hertle A, Kopka J, Walther D, Reich Z, Schoettler MA, Bock R.

Plant Physiol. 2019 Mar 12. pii: pp.01432.2018. doi: 10.1104/pp.18.01432. [Epub ahead of print]


Induced, Imprinted, and Primed Responses to Changing Environments: Does Metabolism Store and Process Information?

Schwachtje J, Whitcomb SJ, Firmino AAP, Zuther E, Hincha DK, Kopka J.

Front Plant Sci. 2019 Feb 13;10:106. doi: 10.3389/fpls.2019.00106. eCollection 2019.


Focus Issue Editorial: Synthetic Biology.

Hanson AD, Hibberd JM, Koffas MAG, Kopka J, Wurtzel ET.

Plant Physiol. 2019 Mar;179(3):772-774. doi: 10.1104/pp.19.00074. No abstract available.


Both cold and sub-zero acclimation induce cell wall modification and changes in the extracellular proteome in Arabidopsis thaliana.

Takahashi D, Gorka M, Erban A, Graf A, Kopka J, Zuther E, Hincha DK.

Sci Rep. 2019 Feb 19;9(1):2289. doi: 10.1038/s41598-019-38688-3.


Molecular signatures associated with increased freezing tolerance due to low temperature memory in Arabidopsis.

Zuther E, Schaarschmidt S, Fischer A, Erban A, Pagter M, Mubeen U, Giavalisco P, Kopka J, Sprenger H, Hincha DK.

Plant Cell Environ. 2019 Mar;42(3):854-873. doi: 10.1111/pce.13502. Epub 2019 Jan 28.


Oviposition by Spodoptera exigua on Solanum dulcamara Alters the Plant's Response to Herbivory and Impairs Larval Performance.

Geuss D, Lortzing T, Schwachtje J, Kopka J, Steppuhn A.

Int J Mol Sci. 2018 Dec 12;19(12). pii: E4008. doi: 10.3390/ijms19124008.


The Synechocystis sp. PCC 6803 Genome Encodes Up to Four 2-Phosphoglycolate Phosphatases.

Rai S, Lucius S, Kern R, Bauwe H, Kaplan A, Kopka J, Hagemann M.

Front Plant Sci. 2018 Nov 27;9:1718. doi: 10.3389/fpls.2018.01718. eCollection 2018.


Natural Variation in Freezing Tolerance and Cold Acclimation Response in Arabidopsis thaliana and Related Species.

Zuther E, Lee YP, Erban A, Kopka J, Hincha DK.

Adv Exp Med Biol. 2018;1081:81-98. doi: 10.1007/978-981-13-1244-1_5. Review.


Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies.

Ulaszewska MM, Weinert CH, Trimigno A, Portmann R, Andres Lacueva C, Badertscher R, Brennan L, Brunius C, Bub A, Capozzi F, Cialiè Rosso M, Cordero CE, Daniel H, Durand S, Egert B, Ferrario PG, Feskens EJM, Franceschi P, Garcia-Aloy M, Giacomoni F, Giesbertz P, González-Domínguez R, Hanhineva K, Hemeryck LY, Kopka J, Kulling SE, Llorach R, Manach C, Mattivi F, Migné C, Münger LH, Ott B, Picone G, Pimentel G, Pujos-Guillot E, Riccadonna S, Rist MJ, Rombouts C, Rubert J, Skurk T, Sri Harsha PSC, Van Meulebroek L, Vanhaecke L, Vázquez-Fresno R, Wishart D, Vergères G.

Mol Nutr Food Res. 2019 Jan;63(1):e1800384. doi: 10.1002/mnfr.201800384. Epub 2018 Oct 11. Review.


Volatiles of rhizobacteria Serratia and Stenotrophomonas alter growth and metabolite composition of Arabidopsis thaliana.

Wenke K, Kopka J, Schwachtje J, van Dongen JT, Piechulla B.

Plant Biol (Stuttg). 2019 Jan;21 Suppl 1:109-119. doi: 10.1111/plb.12878. Epub 2018 Sep 1.


Ion-dependent metabolic responses of Vicia faba L. to salt stress.

Richter JA, Behr JH, Erban A, Kopka J, Zörb C.

Plant Cell Environ. 2019 Jan;42(1):295-309. doi: 10.1111/pce.13386. Epub 2018 Aug 9.


NLR Mutations Suppressing Immune Hybrid Incompatibility and Their Effects on Disease Resistance.

Atanasov KE, Liu C, Erban A, Kopka J, Parker JE, Alcázar R.

Plant Physiol. 2018 Jul;177(3):1152-1169. doi: 10.1104/pp.18.00462. Epub 2018 May 23.


Acquisition of Volatile Compounds by Gas Chromatography-Mass Spectrometry (GC-MS).

Vallarino JG, Erban A, Fehrle I, Fernie AR, Kopka J, Osorio S.

Methods Mol Biol. 2018;1778:225-239. doi: 10.1007/978-1-4939-7819-9_16.


The iron-stress activated RNA 1 (IsaR1) coordinates osmotic acclimation and iron starvation responses in the cyanobacterium Synechocystis sp. PCC 6803.

Rübsam H, Kirsch F, Reimann V, Erban A, Kopka J, Hagemann M, Hess WR, Klähn S.

Environ Microbiol. 2018 Aug;20(8):2757-2768. doi: 10.1111/1462-2920.14079. Epub 2018 Mar 26.


Comprehensive Metabolomics Studies of Plant Developmental Senescence.

Watanabe M, Tohge T, Balazadeh S, Erban A, Giavalisco P, Kopka J, Mueller-Roeber B, Fernie AR, Hoefgen R.

Methods Mol Biol. 2018;1744:339-358. doi: 10.1007/978-1-4939-7672-0_28.


Plant Temperature Acclimation and Growth Rely on Cytosolic Ribosome Biogenesis Factor Homologs.

Beine-Golovchuk O, Firmino AAP, Dąbrowska A, Schmidt S, Erban A, Walther D, Zuther E, Hincha DK, Kopka J.

Plant Physiol. 2018 Mar;176(3):2251-2276. doi: 10.1104/pp.17.01448. Epub 2018 Jan 30.


Primed primary metabolism in systemic leaves: a functional systems analysis.

Schwachtje J, Fischer A, Erban A, Kopka J.

Sci Rep. 2018 Jan 9;8(1):216. doi: 10.1038/s41598-017-18397-5.


Characterization of the Wheat Leaf Metabolome during Grain Filling and under Varied N-Supply.

Heyneke E, Watanabe M, Erban A, Duan G, Buchner P, Walther D, Kopka J, Hawkesford MJ, Hoefgen R.

Front Plant Sci. 2017 Nov 29;8:2048. doi: 10.3389/fpls.2017.02048. eCollection 2017.


Rapid in situ 13C tracing of sucrose utilization in Arabidopsis sink and source leaves.

Dethloff F, Orf I, Kopka J.

Plant Methods. 2017 Oct 18;13:87. doi: 10.1186/s13007-017-0239-6. eCollection 2017.


Editorial overview: Plant synthetic and systems biology.

Kopka J, Fernie AR.

Curr Opin Biotechnol. 2018 Feb;49:viii-xi. doi: 10.1016/j.copbio.2017.10.001. Epub 2017 Oct 13. No abstract available.


Metabolite and transcript markers for the prediction of potato drought tolerance.

Sprenger H, Erban A, Seddig S, Rudack K, Thalhammer A, Le MQ, Walther D, Zuther E, Köhl KI, Kopka J, Hincha DK.

Plant Biotechnol J. 2018 Apr;16(4):939-950. doi: 10.1111/pbi.12840. Epub 2017 Oct 17.


Rapid transcriptional and metabolic regulation of the deacclimation process in cold acclimated Arabidopsis thaliana.

Pagter M, Alpers J, Erban A, Kopka J, Zuther E, Hincha DK.

BMC Genomics. 2017 Sep 16;18(1):731. doi: 10.1186/s12864-017-4126-3.


Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga.

Treves H, Murik O, Kedem I, Eisenstadt D, Meir S, Rogachev I, Szymanski J, Keren N, Orf I, Tiburcio AF, Alcázar R, Aharoni A, Kopka J, Kaplan A.

Curr Biol. 2017 Aug 21;27(16):2559-2567.e3. doi: 10.1016/j.cub.2017.07.014. Epub 2017 Aug 10.


Central metabolite and sterol profiling divides tobacco male gametophyte development and pollen tube growth into eight metabolic phases.

Rotsch AH, Kopka J, Feussner I, Ischebeck T.

Plant J. 2017 Oct;92(1):129-146. doi: 10.1111/tpj.13633. Epub 2017 Aug 11.


Systems analysis of ethanol production in the genetically engineered cyanobacterium Synechococcus sp. PCC 7002.

Kopka J, Schmidt S, Dethloff F, Pade N, Berendt S, Schottkowski M, Martin N, Dühring U, Kuchmina E, Enke H, Kramer D, Wilde A, Hagemann M, Friedrich A.

Biotechnol Biofuels. 2017 Mar 6;10:56. doi: 10.1186/s13068-017-0741-0. eCollection 2017.


Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles.

Glaubitz U, Li X, Schaedel S, Erban A, Sulpice R, Kopka J, Hincha DK, Zuther E.

Plant Cell Environ. 2017 Jan;40(1):121-137. doi: 10.1111/pce.12850. Epub 2016 Nov 28.


CyAbrB2 Contributes to the Transcriptional Regulation of Low CO2 Acclimation in Synechocystis sp. PCC 6803.

Orf I, Schwarz D, Kaplan A, Kopka J, Hess WR, Hagemann M, Klähn S.

Plant Cell Physiol. 2016 Oct;57(10):2232-2243. Epub 2016 Sep 16.


Macromolecular recognition directs calcium ions to coccolith mineralization sites.

Gal A, Wirth R, Kopka J, Fratzl P, Faivre D, Scheffel A.

Science. 2016 Aug 5;353(6299):590-3. doi: 10.1126/science.aaf7889.


Editorial: Metabolome Informatics and Statistics: Current State and Emerging Trends.

Carroll AJ, Salek RM, Arita M, Kopka J, Walther D.

Front Bioeng Biotechnol. 2016 Jul 19;4:63. doi: 10.3389/fbioe.2016.00063. eCollection 2016. No abstract available.


Helping Students Process a Simulated Death Experience: Integration of an NLN ACE.S Evolving Case Study and the ELNEC Curriculum.

Kopka JA, Aschenbrenner AP, Reynolds MB.

Nurs Educ Perspect. 2016 May-Jun;37(3):180-2.


The drought response of potato reference cultivars with contrasting tolerance.

Sprenger H, Kurowsky C, Horn R, Erban A, Seddig S, Rudack K, Fischer A, Walther D, Zuther E, Köhl K, Hincha DK, Kopka J.

Plant Cell Environ. 2016 Nov;39(11):2370-2389. doi: 10.1111/pce.12780. Epub 2016 Sep 6.


A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop.

Fuentes P, Zhou F, Erban A, Karcher D, Kopka J, Bock R.

Elife. 2016 Jun 14;5. pii: e13664. doi: 10.7554/eLife.13664.


Extrafloral nectar secretion from wounds of Solanum dulcamara.

Lortzing T, Calf OW, Böhlke M, Schwachtje J, Kopka J, Geuß D, Kosanke S, van Dam NM, Steppuhn A.

Nat Plants. 2016 Apr 25;2(5):16056. doi: 10.1038/nplants.2016.56.


Insights into isoprene production using the cyanobacterium Synechocystis sp. PCC 6803.

Pade N, Erdmann S, Enke H, Dethloff F, Dühring U, Georg J, Wambutt J, Kopka J, Hess WR, Zimmermann R, Kramer D, Hagemann M.

Biotechnol Biofuels. 2016 Apr 18;9:89. doi: 10.1186/s13068-016-0503-4. eCollection 2016.


Functional specialization of one copy of glutamine phosphoribosyl pyrophosphate amidotransferase in ureide production from symbiotically fixed nitrogen in Phaseolus vulgaris.

Coleto I, Trenas AT, Erban A, Kopka J, Pineda M, Alamillo JM.

Plant Cell Environ. 2016 Aug;39(8):1767-79. doi: 10.1111/pce.12743. Epub 2016 May 5.


Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles.

Orf I, Timm S, Bauwe H, Fernie AR, Hagemann M, Kopka J, Nikoloski Z.

J Exp Bot. 2016 May;67(10):2941-52. doi: 10.1093/jxb/erw068. Epub 2016 Mar 11.


Increasing abscisic acid levels by immunomodulation in barley grains induces precocious maturation without changing grain composition.

Staroske N, Conrad U, Kumlehn J, Hensel G, Radchuk R, Erban A, Kopka J, Weschke W, Weber H.

J Exp Bot. 2016 Apr;67(9):2675-87. doi: 10.1093/jxb/erw102. Epub 2016 Mar 7.


Global Metabolic Profiling of Arabidopsis Polyamine Oxidase 4 (AtPAO4) Loss-of-Function Mutants Exhibiting Delayed Dark-Induced Senescence.

Sequera-Mutiozabal MI, Erban A, Kopka J, Atanasov KE, Bastida J, Fotopoulos V, Alcázar R, Tiburcio AF.

Front Plant Sci. 2016 Feb 18;7:173. doi: 10.3389/fpls.2016.00173. eCollection 2016.


Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics.

Mumm R, Hageman JA, Calingacion MN, de Vos RCH, Jonker HH, Erban A, Kopka J, Hansen TH, Laursen KH, Schjoerring JK, Ward JL, Beale MH, Jongee S, Rauf A, Habibi F, Indrasari SD, Sakhan S, Ramli A, Romero M, Reinke RF, Ohtsubo K, Boualaphanh C, Fitzgerald MA, Hall RD.

Metabolomics. 2016;12:38. doi: 10.1007/s11306-015-0925-1. Epub 2016 Jan 23.


Polyamine oxidase 5 loss-of-function mutations in Arabidopsis thaliana trigger metabolic and transcriptional reprogramming and promote salt stress tolerance.

Zarza X, Atanasov KE, Marco F, Arbona V, Carrasco P, Kopka J, Fotopoulos V, Munnik T, Gómez-Cadenas A, Tiburcio AF, Alcázar R.

Plant Cell Environ. 2017 Apr;40(4):527-542. doi: 10.1111/pce.12714. Epub 2016 Apr 13.


Integrative "omic" analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa 'Korona'.

Koehler G, Rohloff J, Wilson RC, Kopka J, Erban A, Winge P, Bones AM, Davik J, Alsheikh MK, Randall SK.

Front Plant Sci. 2015 Oct 15;6:826. doi: 10.3389/fpls.2015.00826. eCollection 2015.


COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C.

Metabolomics. 2015;11(6):1587-1597. Epub 2015 May 26.


Symbiosis dependent accumulation of primary metabolites in arbuscule-containing cells.

Gaude N, Bortfeld S, Erban A, Kopka J, Krajinski F.

BMC Plant Biol. 2015 Sep 30;15:234. doi: 10.1186/s12870-015-0601-7.


Integrated Analysis of Engineered Carbon Limitation in a Quadruple CO2/HCO3- Uptake Mutant of Synechocystis sp. PCC 6803.

Orf I, Klähn S, Schwarz D, Frank M, Hess WR, Hagemann M, Kopka J.

Plant Physiol. 2015 Nov;169(3):1787-806. doi: 10.1104/pp.15.01289. Epub 2015 Sep 15.


Corrigendum: Gas chromatography mass spectrometry-based metabolite profiling in plants.

Lisec J, Schauer N, Kopka J, Willmitzer L, Fernie AR.

Nat Protoc. 2015 Sep;10(9):1457. doi: 10.1038/nprot0915-1457a. Epub 2015 Aug 27. No abstract available.


Priming and memory of stress responses in organisms lacking a nervous system.

Hilker M, Schwachtje J, Baier M, Balazadeh S, Bäurle I, Geiselhardt S, Hincha DK, Kunze R, Mueller-Roeber B, Rillig MC, Rolff J, Romeis T, Schmülling T, Steppuhn A, van Dongen J, Whitcomb SJ, Wurst S, Zuther E, Kopka J.

Biol Rev Camb Philos Soc. 2016 Nov;91(4):1118-1133. doi: 10.1111/brv.12215. Epub 2015 Aug 20. Review.


High night temperature strongly impacts TCA cycle, amino acid and polyamine biosynthetic pathways in rice in a sensitivity-dependent manner.

Glaubitz U, Erban A, Kopka J, Hincha DK, Zuther E.

J Exp Bot. 2015 Oct;66(20):6385-97. doi: 10.1093/jxb/erv352. Epub 2015 Jul 23.


Dissection of jasmonate functions in tomato stamen development by transcriptome and metabolome analyses.

Dobritzsch S, Weyhe M, Schubert R, Dindas J, Hause G, Kopka J, Hause B.

BMC Biol. 2015 Apr 21;13:28. doi: 10.1186/s12915-015-0135-3.


Metabolic and transcriptomic signatures of rice floral organs reveal sugar starvation as a factor in reproductive failure under heat and drought stress.

Li X, Lawas LM, Malo R, Glaubitz U, Erban A, Mauleon R, Heuer S, Zuther E, Kopka J, Hincha DK, Jagadish KS.

Plant Cell Environ. 2015 Oct;38(10):2171-92. doi: 10.1111/pce.12545. Epub 2015 May 19.


Metabolic contribution to salt stress in two maize hybrids with contrasting resistance.

Richter JA, Erban A, Kopka J, Zörb C.

Plant Sci. 2015 Apr;233:107-115. doi: 10.1016/j.plantsci.2015.01.006. Epub 2015 Jan 15.


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