- Written by Dimitar Kirkovski
Plant Metabolomics
Metabolites play a central role not only for plant growth and the response of plants to environmental stresses, but have a particularly important role also for formation of flavour, taste and texture, i.e. features highly relevant for vegetable crops and their performance on the market. The department focuses on unravelling the metabolic profiles and primary/secondary metabolite pathways (and their regulatory control) in harvestable organs (e.g., fruits) of vegetable crops by employing cutting-edge mass spectrometry methods.
Head of Department: | ||
Prof. Dr. Alisdair Fernie | fernie@mpimp-golm.mpg.de | |
Members: | ||
Dr. Dimitre Ivanov | d.ivanov@cpsbb.eu |
Publications:
2024
2023
Alseekh S., Fernie A.R. (2023) Expanding our coverage: Strategies to detect a greater range of metabolites. Current Opinion in Plant Biology. 73: 102335. (IF 9.396)
Balparda M., Schmitz J., Duemmel M., Wuthenow I.C., Schmidt M., Alseekh S., Fernie A.R., Lercher M.J., Maurino V.G. (2023) Viridiplantae-specific GLXI and GLXII isoforms co-evolved and detoxify glucosone in planta. Plant Physiology. 191(2): 1214-1233. (IF 8.005)
Bulut M., Alseekh S., Fernie A.R. (2023) Natural variation of respiration-related traits in plants. Plant Physiology. 191(4): 2120-2132. (IF 8.005)
Chen Y., Wang Y., Liang X., Zhang Y., Fernie A.R. (2023) Mass spectrometric exploration of phytohormone profiles and signaling networks. Trends in Plant Science. 28(4): 399-414. (IF 22.012)
Dahmani I., Qin K., Zhang Y., Fernie A.R. (2023) The Formation and Function of Plant Metabolons. Plant Journal. 114(5): 1080-1092. (IF 7.091)
Hayashi K., Alseekh S., Fernie A.R. (2023) Genetic and epigenetic control of the plant metabolome. Proteomics. 13: e2200104. (IF 5.911)
Jia ZC., Das D., Zhang Y., Fernie A.R., Liu Y.G., Chen M., Zhang J. (2023) Plant serine/arginine-rich proteins: versatile players in RNA processing. Planta. 257(6): 109. (IF 4.54)
Li X., Tieman D., Alseekh S., Fernie A.R., Klee H.J. (2023) Natural variations in the Sl-AKR9 aldo/keto reductase gene impact fruit flavor volatile and sugar contents. The Plant Journal. DOI: doi: 10.1111/tpj.16310. (IF 7.091)
Natale R., Coppola M., D’Agostino N., Zhang Y., Fernie A.R., Castaldi V., Rao R. (2023) In silico and in vitro approaches allow the identification of the Prosystemin molecular network. Computational and Structural Biotechnology Journal. 21: 212-223. (IF 7.271)
Poplawski P., Alseekh S., Jankowska U., Skupien-Rabian B., Iwanicka-Nowicka R., Kossowska H., Fogtman A., Rybicka B., Bogusławska J., Adamiok-Ostrowska A., Hanusek K., Hanusek J., Koblowska M., Fernie A.R., Piekiełko-Witkowska A. (2023) Coordinated reprogramming of renal cancer transcriptome, metabolome and secretome associates with immune tumor infiltration. Cancer Cell International. 23(1): 2. (IF 6.07)
Salem M.A., El-Shiekh R.A, Aborehab N.M., Al-Karmalawy A.A., Ezzat S.M., Alseekh S., Fernie A.R. (2023) Metabolomics driven analysis of Nigella sativa seeds identifies the impact of roasting on the chemical composition and immunomodulatory activity. Food Chemistry. 398: 133906 (IF 9.231)
Schlossarek D., Zhang Y., Sokolowska E.M., Fernie A.R., Luzarowski M., Skirycz A. (2023) Don’t let go: co-fractionation mass spectrometry for untargeted mapping of protein-metabolite interactomes. Plant Journal. 113(5): 904-914. (IF 7.091)
Sun Y., Alseekh S., Fernie A.R. (2023) Plant secondary metabolic responses to global climate change: A meta-analysis in medicinal and aromatic plants. Global Change Biology. 29(2): 477-504. (IF 13.211)
Zhang Y., Chen M., Liu T., Qin K., Fernie A.R. (2023) TECHNICAL ADVANCE: Investigating the dynamics of protein-protein interactions in plants. Plant Journal. DOI: doi: 10.1111/tpj.16182. (IF 7.091)
Zhang Y., Jaime M.S., Bulut M., Graf A., Fernie A.R. (2023) The conditional mitochondrial protein complexes of Arabidopsis thaliana: differences between tissue-type and environmental conditions. Plant Communications. (accepted)
Zhu F., Sun Y., Jadhav S.S., Cheng Y., Alseekh S., Fernie A.R. (2023) The Plant Metabolic Changes and the Physiological and Signaling Functions in the Responses to Abiotic Stress. Methods in Molecular Biology. 2642: 129-150.
Zhu F., Wen W., Cheng Y., Alseekh S., Fernie A.R. (2023) Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways. aBIOTECH. 4(1): 47-56.
2022
Amanda D., Frey F.P., Neumann U., Przybyl M., Šimura J., Zhang Y., Chen Z., Gallavotti A., Fernie A.R., Ljung K., Acosta I.F. (2022) Auxin boosts energy generation pathways to fuel pollen maturation in barley. Current Biology. 32(8): 1798-1811. (IF 10.834)
Bovdilova. A., Alexandre B.M., Höppner. A., Luís I.M., AlvarezC.E., Bickel D., Gohlke H., Decker C., Nagel-Steger L., Alseekh S., Fernie A.R., DrincovichM.F., Abreu I.A., Maurino V.G. (2022) Corrigendum to: posttranslational modification of the NADP-malic enzyme Involved in C4 photosynthesis modulates the enzymatic activity during the day. The Plant Cell. 34:(1) 698-699. (IF 11.277)
Fernie A.R., Alseekh S. (2022) Metabolomic selection-based machine learning improves fruit taste prediction. Proceedings of the National Academy of Sciences of the United States of America. 119 (9): e2201078119 (IF 12.779)
Fernie A.R., Zhang Y. (2022) The Bacillus subtilis glutamate anti-metabolon. Nature Metabolism. 4: 161–162. (IF 19.865)
Ishihara H., Alseekh S., Feil R., Perera P., George G.M., Niedźwiecki P., Arrivault S., Zeeman S.C., Fernie A.R., Lunn J.E., Smith A.M., Stitt M. (2022) Rising rates of starch degradation during daytime and trehalose 6-phosphate optimize carbon availability. Plant Physiology. 189(4): 1976–2000. (IF 8.005)
Koschmieder J., Alseekh S, Shabani M., Baltenweck R., Maurino V.G., Palme K., Fernie A.R., Hugueney P., Welsch R. (2022) Color recycling: metabolization of apocarotenoid degradation products suggests carbon regeneration via primary metabolic pathways. Plant Cell Reports. 41: 961–977 (IF 4.570)
Martínez-Rivas F.J., Blanco-Portales R., Molina-Hidalgo F.J., Caballero J.L., Perez de Souza L., Alseekh S., Fernie A.R., Muñoz-Blanco J., Rodríguez-Franco A. (2022) Azacytidine arrests ripening in cultivated strawberry (fragaria × ananassa) by repressing key genes and altering hormone contents. BMC Plant Biology. 22(1): 278. (IF 5.26)
Rocchetti. L., Gioia. T., Logozzo. G., Brezeanu. C., Pereira L.G., la Rosa L., Marzario S., Pieri A., Fernie A.R., Alseekh S., Susek K., Cook D.R., Varshney R.K., Agrawal S.K., Hamwieh A., Bitocchi, E., Papa R. (2022) Towards the development, maintenance and standardized phenotypic characterization of single-seed-descent genetic resources for chickpea. Current protocols. DOI: https://doi.org/10.1002/cpz1.371
Powell A.F., Feder A., Li J., Schmidt M.H., Courtney L., Alseekh S., Jobson E.M, Vogel A., Xu Y, Lyon D., Dumschott K., McHale M., Sulpice R., Bao K., Lal R., Duhan A., Hallab A., Denton A.K., Bolger M.E., Fernie A.R., Hind S.R., Mueller L.A., Martin G.B., Fei Z., Martin C., Giovannoni J.J., Strickler S.R., Usadel B. (2022) A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. The Plant Journal. 110(6): 1791-1810. (IF 7.091)
Salem M.A., Aborehab N.M., Al-Karmalawy A.A., Fernie A.R., Alseekh S., Ezzat S.M. (2022) Potential valorization of edible nuts by-products: exploring the immune-modulatory and antioxidants effects of selected nut shells extracts in relation to their metabolic profiles. Antioxidants. 11(3): 462. (IF 7.675)
Sayed S.M.A., Alseekh S., Siems K., Fernie A.R., Luyten W., Schmitz-Linneweber C., Saul N. (2022) Identification of a hydroxygallic acid derivative, zingibroside R1 and a sterol lipid as potential active ongredients of cuscuta chinensis extract that has neuroprotective and antioxidant effects in aged caenorhabditis elegans. Nutrients. 14(19): 4199 (IF 6.706)
Stefan T., Wu X.N., Zhang Y., Fernie A.R., Schulze W.X. (2022) Regulatory Modules of Metabolites and Protein Phosphorylation in Arabidopsis Genotypes With Altered Sucrose Allocation. Frontiers in Plant Science. DOI: doi: 10.3389/fpls.2022.891405. (IF 6.627)
Tabatabaei I., Alseekh S., Shahid M., Leniak E., Wagner M., Mahmoudi H., Thushar S., Fernie A.R., Murphy K.M., Schmockel S.M., Tester M., Mueller-Roeber B., Skirycz A., Balazadeh S. (2022) The diversity of quinoa morphological traits and seed metabolic composition. Scientific Data. 9: 323. (IF 8.501)
Vallarino J.G., Shameer S., Zhang Y, Ratcliffe G.R, Sweetlove J.L, Fernie A.R. (2022) Leaf specific overexpression of a mitochondrially-targeted glutamine synthetase in tomato increased assimilate export resulting in earlier fruiting and elevated yield. bioRxiv. DOI: https://doi.org/10.1101/2022.06.28.497938
Zhang Y., Fernie A.R. (2022) Metabolite profiling of Arabidopsis mutants of lower glycolysis. Scientific Data. 9(1): 614. (IF 8.501)
Zhang Y., Fernie A.R. (2022) Dynamically regulating metabolic fluxes with synthetic metabolons. Trends in Biotechnology. 40(9): 1019-1020 (IF 21.942)
Zhou J., Liu C., Chen Q., Liu L., Niu S., Chen R., Li K., Sun Y., Shi Y., Yang C., Shen S., Li Y., Xing J,. Yuan H., Liu X., Fang C., Fernie A.R., Luo J. (2022) Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice. Science China Life Sciences. 65: 1794–1810. (IF 10.372)
Zhu F., Alseekh S., Wen W., Cheng Y., Fernie A.R. (2022) Genome-wide association studies of arabidopsis dark-induced senescence reveals signatures of autophagy in metabolic reprogramming. Autophagy. 18: 457-458. (IF 13.391)
Alseekh S., Aharoni A., Brotman Y., Contrepois K., D’Auria J., Ewald C.J., Ewald J., Fraser P.D., Giavalisco P., Hall R.D., Heinemann M., Link H., Luo J., Neumann S., Nielsen J., Leonardo Souza P., Saito K., Sauer U., Schroeder C.F., Schuster, S., Siuzdak, G., Skirycz A., Sumner W.L., Snyder P.M., Tang H., Tohge T., Wang Y., Wen W., Wu S., Xu G., Nicola Zamboni N., R. Fernie A.R. (2021). Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Nature Methods. 18: 747–756 (IF 28.547)
Alseekh S. and Fernie A.R. (2021) Using Metabolomics to Assist Plant Breeding. Methods in Molecular Biology. 2264: 33-46.
Alseekh S., Scossa F., Wen W., Luo J., Yan J., Beleggia R., Klee H.J., Huang S., Papa R. and Fernie A.R. (2021) Domestication of Crop Metabolomes: Desired and unintended consequences. Trends in Plant Science. Trends in Plant Science. 26(6): 650-661. (IF 18.313)
Breitel D., Brett P., Alseekh S., Fernie A.R., Butelli, E., and Martin, C. (2021) Diverting tyrosine: Data from untargeted metabolic analysis of tomato fruit accumulating L-DOPA. Metabolic Engineering. 34: 106678 (IF 9.783)
Brotman Y., Llorente-Wiegand C., Oyong G., Badoni S., Misra G., Anacleto R., Parween S., Pasion E., Jr. Tiozon R.N., Anonuevo J.J., deGuzman, M.K., Alseekh, S., Mbanjo E.G.N., Boyd L.A., Fernie, A.R. and Sreenivasulu, N. (2021) The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition. The Plant Journal. DOI: https://doi.org/10.1111/tpj.15182 (IF 6.417)
Di Vittori V., Bitocchi E., Rodriguez M., Alseekh S., Bellucci E., Nanni L., Gioia T., Marzario S., Logozzo G., Rossato M., De Quattro C., Murgia M.L., Ferreira J.J., Campa A., Xu C., Fiorani F., Sampathkumar A., Fröhlich A., Attene G., Delledonne M., Usadel B., Fernie A.R., Rau D. and Papa R. (2021) Pod indehiscence in common bean is associated with the fine regulation of PvMYB26. Journal of Experimental Botany. 72: 1617-1633. (IF 6.992)
Fernie A.R., Alseekh S., Liu J., Yan J. (2021) Using precision phenotyping to inform de novo domestication. Plant Physiology. DOI: https://doi.org/10.1093/plphys/kiab160 (IF 8.340)
Gutsch A., Hendrix S., Guerriero G., Renaut J., Lutts S., Alseekh S., Fernie A.R., Hausman J.F., Vangronsveld J., Cuypers A. and Sergeant K. (2020) Long-Term Cd exposure alters the metabolite profile in stem tissue of Medicago sativa. Cells.9(12): 2707. (IF 6.600)
Jiang L., Yoshida T., Stiegert S., Jing, Y., Alseekh S., Lenhard M., Pérez-Alfocea F., and Fernie A.R. (2021) Multi-omics approach reveals the contribution of KLU to leaf longevity and drought tolerance. Plant Physiology. 185: 352-368. 185(2): 352–368
Krahmer J., Abbas A., Mengin V., Ishihara H., Romanowski A., Furniss J.J., Moraes T.A., Krohn N., Annunziata M.G., Feil R., Alseekh S., Obata T., Fernie A.R., Stitt M. and Halliday, K.J. (2021) Phytochromes control metabolic flux, and their action at the seedling stage determines adult plant biomass. Journal of Experimental Botany. 72(8): 3263–3278. (IF 6.992)
Perez de Souza L., Alseekh S., Scossa F., Fernie A.R. (2021) Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nature Methods. (accepted) (IF 28.547)
Ren Y., Li M., Guo S., Sun H., Zhao J., Zhang J., Liu G., He H., Tian S., Yu Y., Gong G., Zhang H., Zhang X., Alseekh S., Fernie A.R., Scheller H.V. and Xu Y. (2021) Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits. The Plant Cell. https://doi.org/10.1093/plcell/koab055 (IF 11.277)
Scossa F., Alseekh S. and Fernie A.R. (2021) Integrating multi-omics data for crop improvement. Journal of Plant Physiology. 257: 153352. (IF 3.549)
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. (IF 4.932)
Wu S., Alseekh S., Brotman Y., and Fernie A.R. (2021) Metabolomic analysis of natural variation in Arabidopsis. Methods in Molecular Biology. 2200: 393-411. (IF 10.71)
Zimmermann S., Benstein M.R., Flores-Tornero, Samira Blau S., Anoman A., Rosa-Téllez A.S., Gerlich C.S., Salem A.M., Alseekh S., Kopriva, S., Vera Wewer, V., Flügge U., Jacoby P.R., Fernie A.R., Giavalisco P., Roc Ros R., Krueger S. (2021) The phosphorylated pathway of serine biosynthesis links plant growth with nitrogen metabolism. Plant Physiology. https://doi.org/10.1093/plphys/kiab167 (IF 8.340)
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. 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)
Breitel D., Brett P., Alseekh S., Fernie A.R., Butelli E. and Martin C. (2020) Metabolic engineering of tomato fruit enriched in L-DOPA. Metabolic Engineering.(In press, corrected proof). (IF 7.263)
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)
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)
Fernie A.R. and Alseekh S. (2020) Tomato multiomics at aPEELing resolution. Nature Plants. 6: 1394-1395.
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)
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)
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 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)
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 MA, Ezzat SM, 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)
Staykov N.S., Angelov M., Petrov V., Minkov P., Kanojia A., Guinan K.J., Alseekh S., Fernie A.R., Neerakkal S., Gechev T.S. (2020) An Ascophyllum nodosum-derived biostimulant protects model and crop plants from oxidative stress. Metabolites. (accepted). (4.097)
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)
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)
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)
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 Y., Sampathkumar A., Kerbler S., Swart C., Seerangan K., Graf A., Alisdair R. (2020) A novel glycolytic metabolon mediate the interaction between the mitochondria and chloroplast. Nature Communication. (accepted). (IF 11.878)
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 communication. 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
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)
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.
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.
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)
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.
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)
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).