Publications:

2019

• Amirova K., Dimitrova P., Marchev A.S.,Aneva I.Y., Georgiev M.I. (2019). Clinopodium vulgare L. (wild basil) extract and its active constituents modulate cyclooxygenase-2 expression in neutrophils. Food and Chemical Toxicology. 124, 1–9. https://doi.org/10.1016/j.fct.2018.11.054.
• Brog Y., Osorio S., Yichie Y., Alseekh S., Bensal E., Kochevenko A., Zamir D., Fernie A. (2019). A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population. Plant Journal. 97(2):391–403. https://doi.org/ 10.1111/tpj.14095.
• Chen M., Zhu F., Gao B., Ma K., Zhang Y., Fernie A., Cheng X., Dai L., Ye N., Zhang A., Tian Y., Zhang D., Xiaoi S., Zhang J., Liua Y. (2019). Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation. Plant physiology. (accepted).
• Denev P., Todorova V., Ognyanov M., Georgiev Y., Yanakieva I., Tringovska I., Grozeva S.,Kostova D. (2019). Phytochemical composition and antioxidant activity of 63 Balkan pepper (Capsicum annuum L.) accessions Journal of Food Measurement and Characterization.pp 1–11. https://doi.org/10.1007/s11694-019-00171-y.
• De Smet B., Willems P., Fernandez-Fernandez A., Alseekh S., Fernie A., Messens J., Van Breusegem F. (2019). In vivo detection of protein cysteine sulfenylation in plastids. Plant Journal. 97(4):765–778. https://doi.org/10.1111/tpj.14146.
• Fang C., Fernie A., Luo J. (2019). Exploring the Diversity of Plant Metabolism. Trends in Plant Science. 24(1):83–98. https://doi.org/10.1016/j.tplants.2018.09.006.
• Fort A., Lebrault M., Allaire M., Esteves-Ferreira A., McHale M., Lopez F., Farinas Franco J., Alseekh S., Fernie A., Sulpice R. (2019). Extensive variations in diurnal growth patterns and metabolism amongst Ulva spp strains. Plant physiology. 180(1) :109–123. https://doi.org/10.1104/pp.18.01513 .
• Li K., Wen W., Alseekh S., Yang X., Guo H., Li W., Wang L., Pan Q., Zhan W., Liu J., Li Y., Wu X., Brotman Y., Willmitzer L., Li J., Fernie A., Yan J. (2019). Large-scale metabolite quantitative trait locus analysis provides new insights for high-quality maize improvement. Plant Journal. 2019 March. https://doi.org/10.1111/tpj.14317.
• Liu T., Chen M., Zhang Y., Liu Y., Zhu F., Tian Y., Fernie A., Ye N., Zhang J. (2019). Comparative metabolite profiling of two switchgrass ecotype varieties reveals differences in drought stress responses and rhizosheath size.Planta. (accepted).
• Llorente C., Jimenez R., Jackie, Brotman Y., Fernie A., Sreenivasulu N. Rice Grain Quality Benchmarking Through Profiling of Volatiles and Metabolites in Grains Using Gas Chromatography Mass Spectrometry. (2019) Methods in Molecular Biology. 1892:187–199. https://doi.org/10.1007/978-1-4939-8914-0_11.
• Naseri G., Behrend J., Rieper L., Mueller-Roeber B. (2019). COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors Nature Communications . 10(1) :2615. https://doi.org/10.1038/s41467-019-10224-x.
• Neerakkal S., Mehterov N., Gupta S., Qureshi M.K., Fischer A., Proost S., Omidbakhshfard M.A., Obata T., Benina M., Staykov N., Balazadeh S., Walther D., Fernie A.R., Mueller-Roeber B., Hille J., Gechev T.S. (2019) A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana. Cellular and Molecular Life Sciences. (accepted).
• Nunes-Nesi A., Alseekh S., de Oliveira Silva F., Omranian N., Lichtenstein G., Mirnezhad M., Gonzalez R., Sabio Y Garcia J., Conte M., Leiss K., Klinkhamer P., Nikoloski Z., Carrari F., Fernie A. (2019). Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds. Metabolomics. 15(4),46. https://doi.org/10.1007/s11306-019-1503-8.
• Shapiguzov A., Vainonen J., Hunter K., Tossavainen H., Tiwari A., Jarvi S., Hellman M., Aarabi F., Alseekh S., Wybouw B., Van Der Kelen K., Nikkanen L., Krasensky-Wrzaczek J., Sipari N., Keinanen M., Tyystjarvi E., Rintamaki E., De Rybel B., Salojarvi J., Van Breusegem F., Fernie A., Brosche M., Permi P., Aro E., Wrzaczek M., Kangasjarvi J. (2019). Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. eLife 2019;8:e43284. https://doi.org/10.7554/eLife.43284.
• Suzuki M., Wu S., Mimura M., Alseekh S., Fernie A., Hanson A., McCarty D. (2019). Construction and applications of a B vitamin genetic resource for investigation of vitamin dependent metabolism in maize.The Plant Journal. (accepted).
• Vasileva L., Ivanovska M., Murdjeva M., Saracheva K., Georgiev M. (2019). Immunoregulatory natural compounds in stress-induced depression: An alternative or an adjunct to conventional antidepressant therapy? Food and Chemical Toxicology. 127, 81–88. https://doi.org/10.1016/j.fct.2019.03.004.
• Wang S., Alseekh S., Fernie A., Jie Luo J. (2019). The Structure and Function of Major Plant Metabolite Modifications.Molecular plant. (accepted).

2018

• Alseekh S., Bermudez L., de Haro L., Fernie A., Carrari F. (2018). Crop metabolomics: from diagnostics to assisted breeding. Metabolomics. 14(11),148. https://doi.org/10.1007/s11306-018-1446-5.
• Alseekh S., Fernie A.R. (2018). Metabolomics 20 years on: What have we learned and what hurdles remain?. Plant Journal. 94(6),933–942. https://doi.org/10.1111/tpj.13950.
• Alseekh S., Wu S., Brotman Y., Fernie A.R. (2018). Guidelines for sample normalization to minimize batch variation for large-scale metabolic profiling of plant natural genetic variance. Methods in Molecular Biology. 1778, 33–46. https://doi.org/10.1007/978-1-4939-7819-9_3.
• Chen J., Wang J., Chen W., Sun W., Peng M., Yuan Z., Shen S., Xie K., Jin C., Sun Y., Liu X., Fernie A., Yu S., Luo J. (2018). Metabolome Analysis of Multi-Connected Biparental Chromosome Segment Substitution Line Populations. Plant Physiology. 178(2):612–625. https://doi.org/10.1104/pp.18.00490.
• Chen, L., Teng, H., Xie, Z., Cao, H., Cheang, W. S., Skalicka-Woniak, K., Georgiev,M., Xiao, J. (2018). Modifications of dietary flavonoids towards improved bioactivity: An update on structure–activity relationship. Critical Reviews in Food Science and Nutrition. 58(4), 513–527. https://doi.org/10.1080/10408398.2016.1196334.
• Durgud M., Gupta S., Ivanov I. Omidbakhshfard A., Benina M., Alseekh A., Staykov N., Hauen-stein M., Dijkwel P.P., Hortensteiner S., Toneva V., Brotman Y., Fernie A.R., Mueller-Roeber B., Gechev T. (2018). Molecular mechanisms preventing senescence in response to prolonged darkness in a desiccation–tolerant plant. Plant Physiology. 177(3),1319–1338. https://doi.org/10.1104/pp.18.00055.
• Fernie A., Alseekh S. (2018). Defining the convergence of ethylene and auxin signaling in tomato. New Phytologist. 219(2):479-481. https://doi.org/10.1111/nph.15251.
• Garbowicz K., Liu Z., Alseekh S., Tieman D., Taylor M., Kuhalskaya A., Ofner I., Zamir D., Klee H., Fernie A., Brotman Y. (2018). Quantitative Trait Loci Analysis Identifies a Prominent Gene Involved in the Production of Fatty Acid-Derived Flavor Volatiles in Tomato. Molecular Plant. 11(9):1147–1165. https://doi.org/10.1016/j.molp.2018.06.003.
• Kong F., Burlacot A., Liang Y., Legeret B., Alseekh S., Brotman Y., Fernie A., Krieger-Liszkay A., Beisson F., Peltier G., Li-Beisson Y. (2018). Interorganelle Communication: Peroxisomal MALATE DEHYDROGENASE2 Connects Lipid Catabolism to Photosynthesis through Redox Coupling in Chlamydomonas. Plant Cell. 30(8):1824–1847. https://doi.org/10.1105/tpc.18.00361.
• Kopka J., Fernie A.R. (2018). Editorial overview: Plant synthetic and systems biology. Current Opinion in Biotechnology. 49, viii–xi. https://doi.org/10.1016/j.copbio.2017.10.001.
• Ma, X., Zhang, Y., Tureckova, V., Xue, G.-P., Fernie, A.R., Mueller-Roeber, B., Balazadeh, S.(2018) NAC transcription factor SlNAP2 in tomato regulates leaf senescence and fruit yield. Plant Physiology. 177(3),1286–1302. https://doi.org/10.1104/pp.18.00292
• Omidbakhshfard M., Fujikura U., Olas J., Xue G., Balazadeh S., Mueller-Roeber B. (2018). GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia. PLOS Genetics. 14(7):e1007484. https://doi.org/10.1371/journal.pgen.1007484 .
• Petrov, V., Qureshi, M. K., Hille, J., Gechev, T. (2018). Occurrence, biochemistry and biological effects of host-selective plant mycotoxins. Food and Chemical Toxicology : An International Journal Published for the British Industrial Biological Research Association. 112,251–264. http://doi.org/10.1016/j.fct.2017.12.047.
• Scossa F., Benina M., Alseekh S., Zhang Y. and Fernie A.R. (2018). The integration of metabolomics and next -generation sequencing data to elucidate the pathways of natural product metabolism in medicinal plants. Planta Medica 84(12/13),855–873. http://doi.org/10.1055/a-0630-1899.
• Schwahn K., Nikoloski Z. Data Reduction Approaches for Dissecting Transcriptional Effects on Metabolism. (2018). Frontiers in Plant Science. 9:538. https://doi.org/10.3389/fpls.2018.00538.
• Vasileva L., Marchev A., Georgiev M. (2018). Causes and solutions to “globesity”: The new fa(s)t alarming global epidemic. Food and Chemical Toxicology. 121,177–193. https://doi.org/10.1016/j.fct.2018.08.071.
• Vasileva L., Saracheva K., Ivanovska M.,Petrova A., Marchev A., Georgiev M., Murdjeva M., Getova D. (2018). Antidepressant-like effect of salidroside and curcumin on the immunoreactivity of rats subjected to a chronic mild stress model. Food and Chemical Toxicology. 121,604–611. hhttps://doi.org/10.1016/j.fct.2018.09.065.
• Zhang, K., Logacheva, M. D., Meng, Y., Hu, J., Wan, D., Li, L., Janovska, D., Zhiyong, W., Georgiev, M., … Zhou, M. (2018). Jasmonate-responsive MYB factors spatially repress rutin biosynthesis in Fagopyrum tataricum. Journal of Experimental Botany. 69(8),1955–1966. http://doi.org/10.1093/jxb/ery032.
• Zhang Y., Zhang Y., McFarlane H., Obata T., Richter A., Lohse M., Grimm B., Persson S., Fernie A., Giavalisco P. (2018). Inhibition of TOR Represses Nutrient Consumption, Which Improves Greening after Extended Periods of Etiolation. Plant Physiology. 178(1):101–117. https://doi.org/10.1104/pp.18.00684.
• Zhang Y., Fernie A. (2018).On the role of the tricarboxylic acid cycle in plant productivity. Journal of Integrative Plant Biology. 60(12):1199–1216. https://doi.org/10.1111/jipb.12690.
• Zhu, G., Wang, S., Huang, Z., Zhang, S., Liao, Q., Zhang, C., Lin, T., Qin, M., Peng, M., Yang, C., Cao, X., Han, X., Wang, X., Van Der Knaap, E., Zhang, Z., Cui, X., Klee, H., Fernie, A., Luo, J., Huang, S. (2018). Rewiring of the fruit metabolome in tomato breeding. Cell. 172(1),249–261. https://doi.org/10.1016/j.cell.2017.12.019.

2017

• Braicu, C., Mehterov, N., Vladimirov, B., Sarafian, V., Nabavi, S. M., Atanasov, A. G., & Berindan-Neagoe, I. (2017). Nutrigenomics in cancer: Revisiting the effects of natural compounds. Seminars in Cancer Biology. 46,84–106. https://doi.org/10.1016/j.semcancer.2017.06.011.
• Gulei, D., Mehterov, N., Nabavi, S. M., Atanasov, A. G., Berindan-Neagoe, I. (2017). Targeting ncRNAs by plant secondary metabolites: The ncRNAs game in the balance towards malignancy inhibition. Biotechnology Advances. 36(6),1779–1799. https://doi.org/10.1016/j.biotechadv.2017.11.003.
• Schwahn, K., Beleggia, R., Omranian, N., Nikoloski, Z. (2017). Stoichiometric Correlation Analysis: Principles of Metabolic Functionality from Metabolomics Data.  Frontiers in Plant Science.  8,2152. http://doi.org/10.3389/fpls.2017.02152.
• Tohge, T., Fernie A. (2017). An Overview of Compounds Derived from the Shikimate and Phenylpropanoid Pathways and Their Medicinal Importance. Mini-Reviews in Medicinal Chemistry. 17(12),1013-1027. https://doi.org/10.2174/1389557516666160624123425.

2016

• Georgiev, M., (2016). From plants to pharmacy shelf: natural products revival. Phytochemistry Reviews. 15(4),511–513. https://doi.org/10.1007/s11101-016-9465-1.
• Marchev, A., Dinkova-Kostova, A., György, Z., Mirmazloum, I., Aneva, I., Georgiev, M. (2016). Rhodiola rosea L.: from golden root to green cell factories. Phytochemistry Reviews. 15(4),515–536. https://doi.org/10.1007/s11101-016-9453-5.
• Messerschmidt, K., Hochrein, L., Dehm, D., Schulz, K., Mueller-Roeber, B. (2016). Characterizing seamless ligation cloning extract for synthetic biological applications. Analytical Biochemistry. 509, 24–32. https://doi.org/10.1016/j.ab.2016.05.029.
• Tohge, T., Wendenburg, R., Ishihara, H., Nakabayashi, R., Watanabe, M., Sulpice, R., … Fernie, A. (2016). Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae. Nature Communications. 7,1–11. https://doi.org/10.1038/ncomms12399.

Books and book chapters:

• Yordanova, Z., Georgiev, M. (2017). Cell Factories. In B. Thomas, B. G. Murray, & D. J. Murphy (Eds.). Encyclopedia of Applied Plant Sciences (Second Edition) (pp. 72–76). Oxford: Academic Press. https://doi.org/10.1016/B978-0-12-394807-6.00158-1.