Publications 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. 39: 169–173. (IF 54.908)

Alseekh S., Ofner I., Liu Z., Osorio S., Vallarino J., Last R., Zamir D., Tohge T., Fernie A.R. (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. 103(6): 2007-2024. (IF 6.417)

Alseekh S., Perez de Souza L., Benina M.Fernie A.R. (2020)
The style and substance of plant flavonoid decoration; towards defining both structure and function. Phytochemistry. 174: 112347 (IF 4.072)

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 1.747)

Beleggia R., Omranian N., Holtz Y., Gioia T., Fiorani F., Nigro F.M., Pecchioni N., De Vita P., Schurr U., David J., Nikoloski Z., Papa R. (2020)
Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation. bioRxiv. DOI:

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 14.227)

Breitel D., Brett P., Alseekh S.Fernie A.R., Butelli E., Martin C. (2020)
Metabolic engineering of tomato fruit enriched in L-DOPA. Metabolic Engineering. 65: 185-196. (IF 9.783)

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. 39(5): 433-437. (IF 19.536)

Chen M., Zhu F., Gao B., Ma K., Zhang Y.Fernie A.R., Chen X., Ye N., Hu Q., Tian Y., Zhang D., Liu T., Zhang J., Liu Y. (2020)
Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation. Plant Physiology. 182(3): 1510-1526. (IF 8.340)

Clemente-Moreno M.J., Omranian N.b, Sáez P.d, Figueroa C.M., Del-Saz, N., Elso M., Poblete L., Orf I., Cuadros-Inostroza A., Cavieres L., Bravo L., Fernie A.R., Ribas-Carbó, M., Flexas, J., Nikoloski Z., Brotman Y., Gago, J. (2020)
Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis. New Phytologist. 225(2): 754-768. (IF 10.151)

Clemente-Moreno M. J., Omranian N., Sáez P. L., Figueroa C. M., Del-Saz N., Elso M., Poblete L., Orf I., Cuadros-Inostroza A., Cavieres L. A., Bravo L., Fernie A.R., Ribas-Carbó, M. Flexas J., Nikoloski Z., Brotman, Y., Gago J. (2020)
Low-temperature tolerance of the Antarctic species Deschampsia antarctica: A complex metabolic response associated with nutrient remobilization. Plant Cell and Environment. 43(6): 1376–1393. (7.228)

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 16.195)

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 4.215)

Fernie A.R., Alseekh S. (2020)
Tomato multiomics at aPEELing resolution. Nature Plants. 6: 1394-1395. (IF 15.793)

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 13.807)

Gechev T.Georgiev M.I.Fernie A.R. (2020)
PlantaSyst: Teaming-up for systems biology and biotechnology. Trends in Plant Science. 25(7): 621-624. (IF 18.313)

Gechev T.Petrov V. (2020)
Reactive oxygen species and abiotic stress in plants. International Journal of Molecular Sciences. 21: 7433. (IF 5.923)

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.R., 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 41.582)

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 14.227)

Kanojia A., Gupta S., Benina M.Fernie A.R.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. 71: 6340–6354. (IF 6.992)

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 14.227)

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 4.932)

Li Y., Chen Y., Zhou L., You S., Deng H., Chen Y., Alseekh S., Yuan Y., Fu R., Zhang Z., Su D., Fernie A.R., 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 13.164)

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 5.923)

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 8.429)

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 2.461)

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 resistance. EMBO Journal. DOI:10.15252/embj.2020106800. (IF 11.598)

Nankar A.N., Scott M.P., Pratt R.C. (2020)
Compositional analyses reveal relationships among components of blue maize grains. Plants. 9: 1775 (IF: 3.935)

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: 3.935)

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 3.240)

Omidbakhshfard M.A., Sujeeth N., Gupta S., Omranian N., Guinan K.J., Brotman Y., Nikoloski Z.Fernie A.R.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 5.923)

Pasev G., Radeva-Ivanova V., Lyall R.Nankar A.N.Kostova D., Turina M., Vallino M. (2020)
First report of tomato spotted wilt virus on Lisianthus (Eustoma grandiflorum) in Bulgaria. Journal of Plant Pathology. 103:375. (IF: 1.729)

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 3.940)

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 4.932)

Salem, M.A., Radwan, R.A., Mostafa, E.S., Alseekh, S.Fernie, A.R., 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 3.361)

Salem M., Yoshida T., Perez de Souza L., Alseekh S., Bajdzienko K., Fernie A.R., 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 6.417)

Scossa F., Fernie A.R. (2020)
The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Computational and Structural Biotechnology Journal. 18: 482–500. IF (7.271)

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 6.992)

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.R., 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 6.237)

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 4.879)

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.(2020)
A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana. Cellular and Molecular Life Sciences. 77: 705–718. (IF 9.261)

Suzuki M., Wu S., Mimura M., Alseekh S., Fernie A.R., Hanson A., McCarty D. (2020)
Construction and applications of a B vitamin genetic resource for investigation of vitamin dependent metabolism in maize. The Plant Journal. 101(2): 442–454. (IF 6.417)

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. (13.164)

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 3.935)

Tong H., Küken A., Nikoloski Z. (2020)
Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth. Nature Communications 11: 2410 (IF 14.919)

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 (24): 9740. (IF 5.924)

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 7.658)

Wen W., Alseekh S.Fernie A.R. (2020)
Conservation and diversification of flavonoid metabolism in the plant kingdom. Current Opinion in Plant Biology. 55: 100-108 (IF 7.834)

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 12.994)

Wu S., Alseekh S., Brotman Y., Fernie A.R. (2020)
Metabolomic Analysis of Natural Variation in Arabidopsis. Methods in Molecular Biology. 2200: 393-411.

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 3.935)

Zhang W., Alseekh S., Zhu X., Zhang Q., Fernie A.R., Kuang H., Wen W. (2020)
Dissection of the domestication-shaped genetic architecture of lettuce primary metabolism. The Plant Journal. 104(3): 613-630. (IF 6.417)

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.R., Wen W. (2020)
Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. Nature Communications. 11 (1):3719. (IF 14.919)

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 A.R. (2020)
Resolving the metabolon: is the proof in the metabolite? EMBO Reports. 21: e50774 (IF 8.807)

Zhang Y., Krahner I., Bolze A., Gibon Y., Fernie A.R. (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., Fernie A.R. (2020)
A novel glycolytic metabolon mediate the interaction between the mitochondria and chloroplast. Nature Communications. 11: 4509. (IF 14.919)

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 14.919)

Zhang Y., Skirycz A., Fernie A.R. (2020)
An abundance and interaction encyclopedia of plant protein function. Trends in Plant Science. 25(7):627-630 (IF 18.313)

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. (IF 8.140)

Zhu J., Loubéry S., Broger L., Zhang Y., Lorenzo-Orts L., Utz-Pugin A., Fernie A.R., YoungTae C., Hothorn M. (2020)
A genetically validated approach to detect inorganic polyphosphates in plants. The Plant Journal. 102(3): 507-516. (IF 6.417)