Publications:

2021

• Huda N.Md., Lu S., Jahan T., Ding M., Jha R., Zhang K., Zhang W., Georgiev M.I., Park S-U., Zhou M. (2021) Treasure from garden: bioactive compounds of buckwheat. Food Chemistry. 335: 127653 (IF 6.306)
• Staykov N.S., Angelov M., Petrov V., Minkov P., Kanojia A., Guinan K.J., Alseekh S., Fernie A.R., Neerakkal S., Gechev T.S. (2021) An Ascophyllum nodosum-derived biostimulant protects model and crop plants from oxidative stress. Metabolites. 11(1): 24. (4.097)
• Vasileva L.V., Savova M.S., Tews D., Wabitsch M., Georgiev M.I. (2021) Rosmarinic acid attenuates obesity and obesity-related inflammation in human adipocytes. Food and Chemical Toxicology. 149: 112202. (IF 4.679)
• Zahmanova G., Mazalovska M., Takova K., Toneva V., Minkov I., Peyret H., Lomonossoff G. (2021) Efficient production of chimeric Hepatitis B virus-like particles bearing an epitope of Hepatitis E virus capsid by transient expression in Nicotiana benthamiana. Life. 11(1): 64. (IF 2.991)
• Zhang K., He M., Fan Y., Zhao H., Gao B., Yang K., Li F., Tang Y., Gao Q., Lin T., Quinet M., Janovska D., Meglič V., Kwiatkowski J., Romanova O., Chrungoo N., Suzuki T., Luthar Z., Germ M., Woo S-H., Georgiev M.I., Zhou M. (2021) Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits. Genome Biology. 22: 23. (IF 10.806).
• Zhang Y., Sampathkumar A., Kerbler S., Swart C., Seerangan K., Graf A., Fernie A.R. (2021) A novel glycolytic metabolon mediate the interaction between the mitochondria and chloroplast. Nature Communications.(accepted). (IF 12.121)

2020

• Aksenov A.A., Laponogov I., Zhang Z., Doran S.L.F., Belluomo I., Veselkov D., Bittremieux W., Nothias L.F., Nothias-Esposito M., Maloney K.N., Misra B.B., Melnik A.V., Smirnov A., Du X., Jones II K.L., Dorrestein K., Panitchpakdi M., Ernst M., van der Hooft J.J.J., Gonzalez M., Carazzone C., Amézquita A., Callewaert C., Morton J.T., Quinn R.A., Bouslimani A., Orio A.A., Petras D., Smania A.M., Couvillion S.P., Burnet M.C., Nicora C.D., Zink E., Metz T.O., Artaev V., Humston-Fulmer E., Gregor R., Meijler M.M., Mizrahi I., Eyal S., Anderson B., Dutton R., Lugan R., Boulch P.L., Guitton Y., Prevost S., Poirier A., Dervilly G., Le Bizec B., Fait A., Persi N.S., Song C., Gashu K., Coras R., Guma M., Manasson J., Scher J.U., Barupal D.K., Alseekh S., Fernie A.R., Mirnezami R., Vasiliou V., Schmid R., Borisov R.S., Kulikova L.N., Knight R., Wang M., Hanna G.B., Dorrestein P.C., Veselkov K. (2020) Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nature Biotechnology. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0700-3 (IF 36.558)
• Alseekh S., Ofner I., Liu Z., Osorio S., Vallarino J., Last R., Zamir D., Tohge T., Fernie A. (2020) Quantitative trait loci analysis QTL of seed specialized metabolites reveals seed-specific flavonols and differential regulation of glycoalkaloid content in tomato. The Plant Journal. DOI: 10.1111/tpj.14879. (IF 6.141)
• Alseekh S., Perez de Souza L., Benina M., Fernie A. (2020) The style and substance of plant flavonoid decoration; towards defining both structure and function. Phytochemistry. 174: 112347 (IF 3.044)
• Alseekh S., Scossa F., Fernie A. (2020) Mobile transposable elements shape plant genome diversity. Trends in Plant Science. 28:S1360-1385(20)30250-8 (IF 14.416)
• Apostolova E., Gozmanova M., Nacheva L., Ivanova Z., Toneva V., Minkov I., Baev, V., Yahubyan, G. (2020) MicroRNA profiling the resurrection plant Haberlea rhodopensis unveils essential regulators of survival under severe drought. Biologia Plantarum. 64: 541-550. (IF 1.384)
• Belwal T., Singh G., Jeandet P., Pandey A., Giri L., Ramola S., Bhatt I.D., Venskutonis P.R., Georgiev M.I., Clement C., Luo Z. (2020) Anthocyanins, multi-functional natural products of industrial relevance: recent biotechnological advances. Biotechnology Advances. 43: 107600. (IF 10.744)
• Chen M., Zhang Y., Chen X., Fernie A.R., Liu Y., Zhu F. (2020) SWATH-MS based proteomics: Strategies and Applications in Plants. Trends in Biotechnology. DOI: 10.1016/j.tibtech.2020.09.002. (IF 14.343)
• Chen M., Zhu F., Gao B., Ma K., Zhang Y., Fernie A., Chen X., Ye N., Hu Q., Tian Y., Zhang D., Liu T., Zhang J., and Liu Y. (2020) Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation. Plant Physiology. 182(3): 1510-1526. (IF 6.305)
• Correa S.M., Alseekh S., Atehortúa L., Brotman Y., Ríos-Estepa R., Fernie A.R., Nikoloski Z. (2020) Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways. The Plant Journal. 104(1): 76-95. (IF 6.141)
• Correa S. M.; Fernie A.R.; Nikoloski Z.; Brotman Y. (2020) Towards model-driven characterization and manipulation of plant lipid metabolism. Progress in Lipid Research. 80: 101051. (IF 15.083)
• Faisal M., Gechev Т., Mueller-Roeber B., Dijkwel P. (2020) Putative alternative translation start site-encoding nucleotides of CPR5 regulate growth and resistance. BMC Plant Biology 20(1):295. (IF 3.497)
• Fernie A.R., Zhang Y., Sampathkumar A. (2020) Cytoskeleton architecture regulates glycolysis coupling cellular metabolism to mechanical cues trends in biochemical sciences. Trends in Biochemical Science. 45(8): 637-638. (IF 14.732)
• Gechev T., Georgiev M.I., Fernie A. (2020) PlantaSyst: Teaming-up for systems biology and biotechnology. Trends in Plant Science. 25(7): 621-624. (IF 14.416)
• Gechev T., Petrov V. (2020) Reactive oxygen species and abiotic stress in plants. International Journal of Molecular Sciences. 21: 7433. (IF 4.556)
• Grozeva S., Tringovska I., Nankar A., Todorova V., Kostova D. (2020) Assessment of fruit quality and fruit morphology in androgenic pepper lines (Capsicum annuum L.). Crop Breeding Genetics and Genomics. 2(1):e200005
• Jiao C., Sørensen I., Sun X., Sun H., Behar H., Alseekh S., Philippe G., Palacio Lopez K., Sun L., Reed R., Jeon S., Kiyonami R., Zhang S., Fernie A., Brumer H., Domozych D., Fei Z., Rose J. (2020) The penium margaritaceum genome: Hallmarks of the origins of land plants. Cell. 181: 1097-1111 (IF 38.637)
• Joshi D.C., Zhang K., Wang C., Chandora R., Khurshid M., Li J., He M., Georgiev M.I., Zhou M. (2020) Strategic enhancement of genetic gain for nutraceutical development in buckwheat: A Genomics-driven perspective. Biotechnology Advances. 39: 107479. (IF 10.744)
• Kanojia A., Gupta S., Benina M., Fernie A., Mueller-Roeber B., Gechev T., Dijkwel P. (2020) Developmentally controlled changes during Arabidopsis leaf development indicate causes for loss of stress tolerance with age. Journal of Experimental Botany. eraa347. (IF 5.908)
• Kerchev P., van der Meer T., Sujeeth S., Verlee A., Stevens C.V., Van Breusegem F., Gechev T. (2020) Molecular priming as an approach to induce tolerance against abiotic and oxidative stresses in crop plants. Biotechnology Advances. 40: 107503. (IF 10.744)
• Kuhalskaya A., Wijesingha Ahchige M., Perez de Souza L., Vallarino J., Brotman Y., Alseekh S. (2020) Network analysis provides insight into tomato lipid metabolism. Metabolites. 10(4):152 (IF 4.097)
• Li J., Meng Y., Zhang K., Li Q., Li S., Xu B., Georgiev M.I., Zhou M. (2020) Jasmonic acid-responsive RRTF1 transcription factor controls DTX18 gene expression in hydroxycinnamic acid amide secretion. Plant Physiology. DOI: 10.1093/plphys/kiaa043. (IF 6.902)
• Li Y., Chen Y., Zhou L., You S., Deng H., Chen Y., Alseekh S., Yuan Y., Fu R., Zhang Z., Su D., Fernie A., Yuan Y., Fu R., Zhang Z., Su D. (2020) Microtom metabolic network: rewiring tomato metabolic regulatory network throughout the growth cycle. Molecular Plant. 13: 1203-1218 (IF 12.084)
• Lyall R., Gechev T. (2020) Multi-omics insights into the evolution of angiosperm resurrection plants. Annual Plant Reviews Online. 3(1): 77-110.
• Lyall R., Nikoloski Z., Gechev, T. (2020) Comparative analysis of ROS network genes in extremophile eukaryotes. International Journal of Molecular Sciences. 21: 9131. (IF 4.556)
• Marchev A., Yordanova Z.P., Georgiev M.I. (2020) Green (cell) factories for advanced production of plant secondary metabolites. Critical Reviews in Biotechnology. 40(4): 443-458. (IF 8.108)
• Mardanova E.S., Takova K.H., Toneva V.T., Zahmanova G., Tsybalova L., Ravin N. (2020) A plant-based transient expression system for the rapid production of highly immunogenic Hepatitis E virus-like particles. Biotechnology Letters. 42(11):2441-2446. (IF 1.977)
• Moreno J. C., Vicente R., Bruno E. R., Gorka M., Kosmacz M., Peralta-Ariza J. S. Peralta-Ariza, Zhang Y., Saleh A., Dorothee C., Luzarowski M., Hartman M. D., Figueroa C. M., Iglesias A. A., Fernie A.R., A. Skirycz (2020) Tyr-Asp inhibits glyceraldehyde 3-phosphate dehydrogenase activity, affecting redox metabolism and boosting plant stress EMBO J (in revision).
• Nankar A.N., Scott M.P., Pratt R.C. (2020) Compositional analyses reveal relationships among components of blue maize grains. Plants. 9: 1775 (IF: 2.762)
• Nankar A.N., Tringovska I., Grozeva S., Ganeva D., Kostova D. (2020) Tomato phenotypic diversity determined by combined approaches of conventional and high-throughput Tomato Analyzer phenotyping. Plants. 9: 197. (IF: 2.762)
• Nankar A.N., Todorova V., Tringovska I., Pasev G., Radeva V., Ivanova V., Kostova D. (2020) A step towards Balkan Capsicum annuum L. core collection: Phenotypic and biochemical characterization of 180 accessions for agronomic, fruit quality, and virus resistance traits. PLoS ONE. 15(8): e0237741
(IF 2.740)
• Omidbakhshfard M.A., Sujeeth N., Gupta S., Omranian N., Guinan K.J., Brotman Y., Nikoloski Z., Fernie A., Mueller-Roeber B., Gechev T. (2020) A biostimulant obtained from the seaweed Ascophyllum nodosum protects Arabidopsis thaliana from severe oxidative stress. International Journal of Molecular Sciences. 21(2): 1–26. (IF 4.556)
• Perez De Souza L., Alseekh S., Brotman Y., Fernie A.R. (2020) Network-based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation. Expert Review of Proteomics. 17(4): 243-255. (IF 6.614)
• Salem M.A., Perez de Souza L., Serag A., Fernie A.R., Farag M.A., Ezzat S.M., Alseekh S. (2020) Metabolomics in the context of plant natural products research: From sample preparation to metabolite analysis. Metabolites. 10: E37. (IF 4.097)
• Salem, M.A., Radwan, R.A., Mostafa, E.S., Alseekh, S., Fernie, A.R. and Ezzat, S.M. (2020) Using an UPLC/MS-based untargeted metabolomics approach for assessing the antioxidant capacity and anti-aging potential of selected herbs. RSC Advances. 10: 31511-31524.(IF 3.119)
• Salem M., Yoshida T., Perez de Souza L., Alseekh S., Bajdzienko K., Fernie A., Giavalisco P. (2020) An improved extraction method enables the comprehensive analysis of lipids, proteins, metabolites and phytohormones from a single sample of leaf tissue under water-deficit stress. The Plant Journal. 103: 1614-1632. (IF 5.726)
• Sewelam N., Brilhaus D., Bräutigam A., Alseekh S., Fernie A.R., Maurino V.G. (2020) Molecular plant responses to combined abiotic stresses put a spotlight on unknown and abundant genes. Journal of Experimental Botany. 71(16): 5098-5112. (IF 5.908)
• Shapiguzov A., Nikkanen L., Fitzpatrick D., Vainonen J., Gossens R., Alseekh S., Aarabi F., Tiwari A., Blokhina O., Panzarov K., Benedikty Z., Tyystjärvi E., Fernie A., Trtílek M., Aro E., Rintamäki E., Kangasjärvi J. (2020) Dissecting the interaction of photosynthetic electron transfer with mitochondrial signalling and hypoxic response in the Arabidopsis rcd1 mutant. Philosophical Transactions of the Royal Society of London B, Biological Sciences. 375(1801):20190413. (IF 6.139)
• Shi M., Liao P., Nile S.H., Georgiev M.I., Kai G. (2020) Biotechnological exploration of transformed root culture for value-added products. Trends in Biotechnology. DOI: 10.1016/j.tibtech.2020.06.012 (IF 14.343)
• Sieniawska E., Golus J., Sawicki R., Georgiev M.I. (2020) Untargeted metabolomic exploration of Mycobacterium tuberculosis stress response to Cinnamon Essential Oil. Biomolecules. 10(3): 357. (IF 4.082)
• Sujeeth N., 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. (2020) A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana. Cellular and Molecular Life Sciences. 77: 705–718. (IF 6.496)
• Suzuki M., Wu S., Mimura M., Alseekh S., Fernie A., Hanson A., McCarty D. (2020) Construction and applications of a B vitamin genetic resource for investigation of vitamin dependent metabolism in maize. Plant Journal. 101(2), 442–454. (IF 6.141)
• Tohge T., Scossa F., Wendenburg R., Frasse P., Balbo I., Watanabe M., Alseekh S., Jadhav S., Delfin J., Lohse M., Giavalisco P., Usadel B., Zhang Y., Luo J., Bouzayen M., Fernie A.R. (2020) Exploiting the natural variation in tomato to define pathway structure and metabolic regulation of fruit polyphenolics in the lycopersicum complex. Molecular Plant. 13(7):1027-1046. (12.084)
• Toleco M.R., Naake T., Zhang Y., Heazlewood J.L., Fernie A.R. (2020) Plant mitochondrial carriers: Molecular gatekeepers that help to regulate plant central carbon metabolism. Plants (Basel). 9(1). pii: E117. (IF 2.762)
• Tong H., Küken A., Nikoloski Z. (2020) Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth. Nature Communications 11: 2410 (IF 12.121)
• Tong H.; Nikoloski Z. (2020) Machine learning approaches for crop improvement: leveraging phenotypic and genotypic big data. Journal of Plant Physiology (accepted). (IF 3.121)
• Vasileva L., Savova M., Amirova K., Balcheva-Sivenova Zh., Ferrante C., Orlando G., Wabitsch M. , Georgiev M.I. (2020) Caffeic and chlorogenic acids synergistically activate browning program in human adipocytes: Implications of AMPK and PPAR-mediated Pathways. International Journal of Molecular Sciences. 21: 9740. (IF 4.556)
• Vasileva L., Savova M., Amirova K., Dinkova-Kostova A., Georgiev M.I. (2020) Obesity and NRF2-mediated cytoprotection: Where is the missing link? Pharmacological Research. 156: 104760. (IF 5.893)
• Wen W., Alseekh S., Fernie A. (2020) Conservation and diversification of flavonoid metabolism in the plant kingdom. Current Opinion in Plant Biology. 55: 100-108 (IF 8.356)
• Wu L., Georgiev M.I., Cao H., Nahar L., El-Seedi H.R., Sarker S.D., Xiao J., Lu B. (2020) Therapeutic potential of phenylethanoid glycosides: a systematic review. Medicinal Research Reviews. 40(6): 2605-2649. (IF 9.3)
• Wu S., Alseekh S., Brotman Y., Fernie A.R. (2020) Metabolomic Analysis of Natural Variation in Arabidopsis. Methods in Molecular Biology. 2200: 393-411. (IF 10.71)
• Zahmanova G.G., Mazalovska M., Takova K.H.,Toneva, V.T., Minkov I.N., Mardanova E.S., Ravin N.V., Lomonossoff G.P. (2020) Rapid high-yield transient expression of swine Hepatitis E ORF2 capsid proteins in Nicotiana benthamiana plants and production of chimeric Hepatitis E virus-like particles bearing the M2e influenza epitope. Plants. 9(1): 29. (IF 2.762)
• Zhang W., Alseekh S., Zhu X., Zhang Q., Fernie A., Kuang H., Wen W. (2020) Dissection of the domestication-shaped genetic architecture of lettuce primary metabolism. The Plant Journal. 104(3): 613-630. (IF 5.726)
• Zhang W., Zhang Y., Qiu H., Guo Y., Wan H., Zhang X., Scossa F., Alseekh S., Zhang Q., Wang P., Xu L., Schmidt M., Jia X., Li D., Zhu A., Guo F., Chen W., Ni D., Usadel B., Fernie A., Wen W. (2020) Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. Nature Communications. 11 (1):3719. (IF 12.121)
• Zhang Y., Chen M., Toleco M.R., Jing Y., Strotmann V., Zhang J., Stahl Y., Fernie A.R. (2020) A high efficiency method for Agrobacterium tumefaciens mediated transient transformation of plants with utility for high throughput screening of protein-protein interactions. Plant Communication. 1(5): 100028.
• Zhang Y., Fernie (2020) Metabolons, Enzyme-Enzyme Assemblies that Mediate Substrate Channeling, and Their Roles in Plant Metabolism .Plant communication. 100081
• Zhang Y., Fernie A. (2020) On the detection and functional significance of the protein – protein interactions of mitochondrial transport proteins. Biomolecules. 10 (8):e1107 (IF 4.082)
• Zhang Y., Fernie A. (2020) Resolving the metabolon: is the proof in the metabolite? EMBO Reports. 21: e50774 (IF 7.497)
• Zhang Y., Fernie A. (2020) Stable and temporary enzyme complexes and metabolons involved in energy and redox metabolism. Antioxidants and Redox Signaling. DOI:10.1089/ars.2019.7981. (in press)
• Zhang Y., Krahner I., Bolze A., Gibon Y., Fernie A. (2020) Adenine nucleotide and nicotinamide adenine dinucleotide measurements in plants. Current Protocols in Plant Biology. 5(3):e20115
• Zhang A., Sampathkumar A., Swart C., Graf A., Fernie A.R. (2020) A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts. Nature Communications. 11(1): 1-15. (IF 12.121)
• Zhang Y., Skirycz A., Fernie A. (2020) An abundance and interaction encyclopedia of plant protein function. Trends in Plant Science. 25(7):627-630
• Zhang Y., Natale R., Domingues A.P. Júnior, Toleco M.R., Siemiatkowska B., Fàbregas N., Fernie A.R. (2020) Rapid identification of protein-protein interactions in plants. Current Protocols in Plant Biology. 4(4): e20099.
• Zhu J., Lau K., Puschmann R., Harmel R.K., Zhang Y., Pries V., Gaugler Ph., Broger L., Dutta A.K., Jessen H., Schaaf G., Fernie A.R., Hothorn L.A., Fiedler D., Hothorn M. (2019) Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis. Elife 2019;8:e43582.
• Zhu J., Loubéry S., Broger L., Zhang Y., Lorenzo-Orts L., Utz-Pugin A., Fernie A.R., YoungTae C. and Hothorn M. (2020) A genetically validated approach to detect inorganic polyphosphates in plants. Plant Journal. 102(3): 507-516. (IF 6.141)

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. (IF 3.775)
• Boguslawska J., Poplawski P., Alseekh S., Koblowska M., Iwanicka-Nowicka R., Rybicka B., Kedzierska H., Gluchowska K., Hanusek K., Tanski Z., Fernie A.R., Piekielko-Witkowska A., (2019) MicroRNA-mediated metabolic reprograming in renal cancer. Cancers. 11: 1825. (IF 6.162)
• 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. (IF 5.726)
• Chen C., Zhang K., Khurshid M., Li J., He M., Georgiev M.I. , Zhang X. & Zhou M. (2019) MYB Transcription repressors regulate plant secondary metabolism. Critical Reviews in Plant Sciences. 38: 159-170. (IF 4.189)
• 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. 13: 2510– 2520. (IF 1.415)
• 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. (IF 5.726). Plant Journal. 97(4): 765–778.
• Dong Y., Gupta S., Sievers R., Wargent J., Wheeler D., Putterill J., Macknight R., Gechev T., Mueller-Roeber B., Dijkwel P. (2019) Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand's high Ultraviolet B radiation environment. BMC Genomics. 20(1): 838. (IF 3.501)
• Fang C., Fernie A., Luo J. (2019) Exploring the diversity of plant metabolism. Trends in Plant Science. 24(1): 83–98. (IF 14.006)
• 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. (IF 6.305). Plant Physiology. 180(1): 109–123.
• Gupta S., Dong Y., Dijkwel P., Mueller-Roeber B., Gechev T. (2019) Genome-wide analysis of ROS antioxidant genes in resurrection species suggest an involvement of distinct ROS detoxification systems during desiccation. International Journal of Molecular Sciences. 20(12): 3101. (IF 4.183)
• 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. 99: 216-230. (IF 5.726)
• 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. 250: 1355–1369. (IF 3.060)
• Llorente C., Jimenez R., Jackie, Brotman Y., Fernie A., Sreenivasulu N. (2019) Rice grain quality benchmarking through profiling of volatiles and metabolites in grains using gas chromatography mass spectrometry. Methods in Molecular Biology. 1892: 187–199. (IF 10.71)
• Nankar A., Tringovska I., Grozeva S., Todorova V., Kostova D. (2019) Application of high-throughput phenotyping tool Tomato Analyzer to characterize Balkan Capsicum fruit diversity. Scientia Horticulturae. 260. (IF 1.961)
• 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. (IF 11.878)
• Pandey P.K., Yu J., Omranian N., Alseekh S., Vaid N, Fernie A.R., Nikoloski Z., Laitinen R.A.E. (2019) Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations. Plant Direct. 3(11): e00186. (IF 1.725)
• Perez de Souza L., Alseekh S., Naake T., Fernie A. (2019) Mass spectrometry-based untargeted plant metabolomics. Current Protocols in Plant Biology. 4: e20100.
• 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. (IF 3.167)
• Reinholdt 0., Schwab S., Zhang Y., Reichheld J., Fernie A.R., Hagemann M., Timm S. (2019) Redox-regulation of photorespiration through mitochondrial thioredoxin o1. Plant Physiology. 181(2): 442-457
• 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. 8: e43284. (IF 7.551)
• 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. (IF 3.775)
• Wang S., Alseekh S., Fernie A., Jie Luo J. (2019) The structure and function of major plant Metabolite Modifications. Molecular Plant. 12(7): 899-919. (IF 10.812).

2018

• Alseekh S., Bermudez L., de Haro L., Fernie A., Carrari F. (2018) Crop metabolomics: from diagnostics to assisted breeding. Metabolomics. 14(11): 148. (IF 3.167)
• Alseekh S., Fernie A.R. (2018) Metabolomics 20 years on: What have we learned and what hurdles remain? Plant Journal. 94(6): 933–942. (IF 5.726)
• 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. (IF 10.71)
• 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. (IF 6.305)
• 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. (IF 6.704)
• 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. (IF 6.305)
• Fernie A., Alseekh S. (2018) Defining the convergence of ethylene and auxin signaling in tomato. New Phytologist. 219(2): 479-481. (IF 7.299)
• 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. (IF 10.812)
• 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. (IF 8.228)
• Kopka J., Fernie A.R. (2018) Editorial overview: Plant synthetic and systems biology. Current Opinion in Biotechnology. 49: viii–xi. (IF 8.083)
• 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. (IF 6.305)
• Minkov G., Toneva V., Ivanova Z., Baevv V. (2018) LoopRNA – Java Module for RNA Structure Annotation. Comptes Rendus de l'Académie Bulgare des Sciences. 71(9): 1215-1221, 2018. (IF 0.23)
• 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. (IF 5.540)
• Petrov, V., Qureshi, M. K., Hille, J., Gechev, T. (2018) Occurrence, biochemistry and biological effects of host-selective plant mycotoxins. Food and Chemical Toxicology. 112: 251–264. (IF 3.775)
• 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. (IF 2.746)
• Schwahn K., Nikoloski Z. (2018) Data reduction approaches for dissecting transcriptional effects on metabolism. Frontiers in Plant Science. 9: 538. (IF 3.678)
• 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. (IF 3.775)
• 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. (IF 3.775)
• 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. (IF 5.360)
• 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. (IF 6.305)
• 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. (IF 3.824)
• 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. (IF 36.216)

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. (IF 10.198).
• 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. (IF 11.452)
• 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. (IF 3.678)
• 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. (IF 2.645)

2016

• Georgiev, M. (2016) From plants to pharmacy shelf: natural products revival. Phytochemistry Reviews. 15(4): 511–513. (IF 3.393)
• 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. (IF 3.393)
• 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. . (IF 2.334)
• 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. (IF 12.124)

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.