Publications 2021

Aarabi F., Rakpenthai A., Barahimipour R., Gorka M., Alseekh S., Zhang Y., Salem M. A., Brückner F., Omranian N., Watanabe M., Nikoloski Z., Giavalisco P., Tohge T., Graf A., Fernie A.R., Hoefgen R. (2021)
Sulfur deficiency-induced genes affect seed protein accumulation and composition under sulfate deprivation. Plant Physiology. DOI: (IF 8.340)

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., Fernie A.R. (2021)
Using metabolomics to assist plant breeding. Methods in Molecular Biology. 2264: 33-46.

Alseekh S., Kostova D., Mustafa B., Fernie A.R. (2021)
Genome-wide association studies: assessing trait characteristics in model and crop plants. Cellular and Molecular Life Sciences. 78: 5743–5754. (IF 9.261)

Alseekh S., Scossa F., Wen W., Luo J., Yan J., Beleggia R., Klee H.J., Huang S., Papa R., Fernie A.R. (2021)
Domestication of crop metabolomes: desired and unintended consequences. Trends in Plant Science. 26(6): 650-661. (IF 18.313)

Amirova K.M., Dimitrova P.A., Marchev A.S., Krustanova S., Simova S., Alipieva K., Georgiev M.I. (2021)
Biotechnologically-produced myconoside and calceolarioside E induce Nrf2-expression in neutrophils. International Journal of Molecular Sciences. 22(4): 1759. (IF 5.924)

Atanasov A.G., Zotchev S.B., Dirsch V.M., Orhan I.E., Banach M., Rollinger J.M., Barreca D., Weckwerth W., Bauer R., Bayer E.A., Majeed M., Bishayee A., Bochkov V., Bonn G.K., Braidy N., Bucar F., Cifuentes A., D’Onofrio G., Bodkin M., Diederich M., Dinkova-Kostova A.T., Efferth T., El Bairi K., Arkells N., Fan T-P., Fiebich B.L., Freissmuth M., Georgiev M.I. et al. (2021)
Natural products in drug discovery: advances and opportunities. Nature Reviews in Drug Discovery. 20: 200-216. (IF 84.694)

Baev V., Ivanova Z., Yahubyan G., Toneva V., Apostolova E., Minkov G., Minkov I. (2021)
Analysis of the complete mitochondrial genome sequence of the resurrection plant Haberlea rhodopensis. Acta Biochim Pol. 68(2) :277-286. (IF 2.149)

Bellucci E., Aguilar O.M., Alseekh S., Bett K., Brezeanu C., Cook D., De la Rosa L., Delledonne M., Dostatny D.F., Ferreira J.J., Geffroy V., Ghitarrini S., Kroc M., Kumar Agrawal S, Logozzo G., Marino M., Mary-Huard T., McClean P., Meglič V., Messer T., Muel F., Nanni L., Neumann K., Servalli F., Străjeru S., Varshney R. K., Vasconcelos M. W., Zaccardelli M., Zavarzin A., Bitocchi E., Frontoni E., Fernie A.R., Gioia T., Graner A., Guasch L., Prochnow L., Opperman M., Susek K., Tenaillon M., Papa R. (2021)
The INCREASE project: Intelligent Collections of Food-Legume Genetic Resources for European Agrofood Systems. The Plant Journal. DOI: (IF 6.417)

Breitel D., Brett P., Alseekh S., Fernie A.R., Butelli, E., 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., Sreenivasulu N. (2021)
The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition. The Plant Journal. 106(2): 507-525. (IF 6.417)

Bulut M., Fernie A.R., Alseekh S. (2021)
Large-scale Multi-omics Genome-wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization. Jove-Journal of Visualized Experiments. DOI: 10.3791/62732. (IF 1.355)

Cervela-Cardona L., Yoshida T., Zhang Y., Okada M., Fernie A.R., Mas P., (2021)
Circadian control of metabolism by the clock component TOC1. Frontiers in Plant Science. DOI: 10.3389/fpls.2021.683516. (IF 5.753)

Cortinovis G., Oppermann M., Neumann K., Graner A., Gioia T., Marsella M., Alseekh S., Fernie A.R., Papa R., Bellucci E., Bitocchi E. (2021)
Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Common Bean. Current protocols. 1(5): e133.

Ding M., Zhang K., He Y., Zuo Q., Zhao H., He M., Georgiev M.I., Park S.U., Zhou M. (2021)
FtBPM3 modulates the orchestration of FtMYB11-mediated flavonoids biosynthesis in Tartary buckwheat. Plant Biotechnology Journal. 19(7): 1285-1287. (IF 9.803)

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., 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)

Dominguez P.G., Conti G., Duffy T., Insani M., Alseekh S., Asurmendi S., Fernie A.R., Carrari F. (2021)
Multiomics analyses reveal the roles of the ASR1 transcription factor in tomato fruits. Journal of Experimental Botany. 72(18):6490–6509. (IF 6.992)

Duarte G. T., Pandey P. K., Vaid N., Alseekh S., Fernie A.R., Nikoloski Z., Laitinen. R. (2021)
Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein. Plant cell and environment. DOI: (IF 7.228)

Fadoul H.E, Martínez Rivas F.J, Neumann K., Balazadeh S., Fernie A.R., Alseekh S. (2021)
Comparative Molecular and Metabolic Profiling of Two Contrasting Wheat Cultivars under Drought Stress. International Journal of Molecular Sciences. 22(24) :13287. (IF 5.924)

Fernie A.R., Alseekh S., Liu J., Yan J. (2021)
Using precision phenotyping to inform de novo domestication. Plant Physiology. 186(3): 1397–1411. (IF 8.340)

Gechev T., Lyall R., Petrov V., Bartels D. (2021)
Systems biology of resurrection plants. Cellular and Molecular Life Sciences. 78: 6365–6394. (IF 9.261)

Georgiev M.I., Vasileva L.V., Savova M.S. (2021)
Antiobesity molecules of natural origin: Call for lead finding acceleration. Food Frontiers. 2(1): 23-24

Fernie A.R., Alseekh S. (2021)
Unravelling the molecular networks that regulate kiwifruit flavor. New Phytologist. DOI: (IF 10.151)

Grozeva S., Pasev G., Radeva-Ivanova V., Todorova V., Ivanova V., Nankar A.N. (2021)
Double Haploid Development and Assessment of Androgenic Competence of Balkan Pepper Core Collection in Bulgaria. Plants. 10(11): 2414 (IF 3.935)

Grozeva S., Todorova V., Nankar A.N. (2021)
Creation of pepper doubled haploids and morphological characterization of androgenic plants. Euphytica. 217: 113. (IF 1.895)

Gutsch A., Hendrix S., Guerriero G., Renaut J., Lutts S., Alseekh S., Fernie A.R., Hausman J.F., Vangronsveld J., Cuypers A., Sergeant K. (2020)
Long-Term Cd exposure alters the metabolite profile in stem tissue of Medicago sativa. Cells. 9(12): 2707. (IF 6.600)

He Y., Zhang K., Georgiev M.I., Zhou M. (2021)
Ubiquitin proteins and the orchestration of transcription factors activity. Critical Reviews in Plant Sciences. 40(4): 366-377. (IF 5.188)

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 7.514)

Jin C., Fang C., Zhang Y., Fernie A.R., Luo J. (2021
Plant metabolism paves the way for breeding crops with high nutritional value and stable yield. Science China-Life Sciences. DOI: (IF 6.038)

Jiang L., Yoshida T., Stiegert S., Jing, Y., Alseekh S., Lenhard M., Pérez-Alfocea F., Fernie A.R. (2021)
Multi-omics approach reveals the contribution of KLU to leaf longevity and drought tolerance. Plant Physiology. 185(2): 352–368. (IF 8.340)

John S., Jadwiga Olas, J., Mueller-Roeber B. (2021)
Regulation of alternative splicing in response to temperature variation in plants. Journal of Experimental Botany. DOI: (IF 6.992)

Jorge T. F., Ramalho J. C., Alseekh S., Pais I. P., Leitão A. E., Rodrigues A. P., Scotti-Campos P., Ribeiro-Barros A. I., Fernie A. R., António C. (2021)
Will Casuarina glauca Stress Resilience Be Maintained in the Face of Climate Change? Metabolites. 11(9): 593. (IF 4.932)

Joshi J., Hasnain G., Logue T., Lynch M., Wu S., Guan J.C., Alseekh S., Fernie A.R., Hanson A.D., McCarty D.R. (2021)
A Core Metabolome Response of Maize Leaves Subjected to Long-Duration Abiotic Stresses. Metabolites. 11(11): 797. (IF 4.932)

Kanojia A., Shrestha K.D., Dijkwel P. (2021)
Primary metabolic processes as drivers of leaf ageing. Cellular and Molecular Life Sciences. DOI: (IF 9.261)

Kerbler M. S., Natale R., Fernie A.R., Zhang Y. (2021)
From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants. International Journal of Molecular Sciences. 22(13): 7101. (IF 5.923)

Koycheva I.K., Mihaylova L.V., Todorova M.N., Balcheva-Sivenova Z.P., Alipieva K., Ferrante C., Orlando G., Georgiev M.I. (2021)
Leucosceptoside A from Devil’s Claw modulates psoriasis-like inflammation via suppression of the PI3K/AKT signaling pathway in keratinocytes. Molecules. 26: 7014. (IF 4.412)

Koycheva I.K., Vasileva L.V., Amirova K.M., Marchev A.S., Balcheva-Sivenova Z.P., Georgiev M.I. (2021) Biotechnologically-produced Lavandula angustifolia Mill. extract rich in rosmarinic acid resolves psoriasis-related inflammation through JAK/STAT signaling. Frontiers in Pharmacology. 12: 680168. (IF 5.811)

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)

Kroc M., Tomaszewska M., Czepiel K., Bitocchi E., Oppermann M., Neumann K., Guasch L., Bellucci E., Alseekh S., Graner A., Fernie A.R., Papa R., Susek K. (2021)
Towards Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Lupins. Current Protocols. 1(7): e191.

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. 185(2): 369-384. (IF 8.340)

Marchev A.S., Vasileva L.V.Amirova K.M.Savova M.S., Balcheva-Sivenova Z.P., Georgiev M.I. (2021)
Metabolomics and health: from nutritional crops and plant-based pharmaceuticals to profiling of human biofluids. Cellular and Molecular Life Sciences. 78: 6487–6503 (IF 9.261)

Marchev A.S., Vasileva L.V., Amirova K.M., Savova M.S., Koycheva I.K., Balcheva-Sivenova Z.P., Vasileva S.M., Georgiev M.I. (2021)
Rosmarinic acid – from bench to valuable applications in food industry. Trends in Food Science and Technology. 117: 182-193. (IF 12.563)

Mladenova S.G., Vasileva L.V., Savova M.S., Marchev A.S., Tews D., Wabitsch M., Ferrante C., Orlando G., Georgiev M.I. (2021)
Anti-adipogenic effect of Alchemilla monticola is mediated via PI3K/AKT signaling inhibition in human adipocytesFrontiers in Pharmacology. DOI: 10.3389/fphar.2021.707507 (IF 5.811)

Nankar A.N., Pratt R.C. (2021)
Genotyping by sequencing reveals genetic relatedness of southwestern U.S. blue maize landraces. International Journal of Molecular Sciences. 22(7): 3436. (IF 5.923)

Nankar A.N., Scott MP., Pratt RC. (2021)
Compositional analyses reveal relationships among grain components in anthocyanin pigmented blue maize grains. Plants. 9 (12): 1775. (IF 3.935)

Pereira L., Sapkota M., Alonge M., Zheng Y., Zhang Y., Razifard H., Taitano N.K., Schatz M., Lipman Z., Fernie A.R., Wang Y, Fei Z, Caicedo A.L., Tieman D.M., Knaap E., (2021)
Natural genetic diversity in tomato flavor genes. Frontiers in Plant Science. DOI: (IF 5.753)

Omidbakhshfard M. A., Sokolowska E. M., Di Vittori V., Perez de Souza L., Kuhalskaya A., Brotman Y., Alseekh S., Fernie A.R., Skirycz, A. (2021)
Multi-omics analysis of early leaf development in Arabidopsis thaliana. Patterns. 2(4): 100235.

Omranian S., Angeleska A., Nikoloski Z. (2021)
PC2P: Parameter-free network-based prediction of protein complexes. Bioinformatics.  37(1): 73–81. (IF 6.937)

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. 18: 733–746. (IF 28.547)

Qin K., Fernie A.R., Zhang Y. (2021)
The Assembly of Super-Complexes in the Plant Chloroplast. Biomolecules. 11(12) :1839. (IF 4.879)

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., Xu Y. (2021)
Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits. The Plant Cell. 33(5): 1554–1573. (IF 11.277)

Salem M. A., Zayed A., Alseekh S., Fernie A. R., Giavalisco P. (2021)
The integration of MS-based metabolomics and multivariate data analysis allows for improved quality assessment of Zingiber officinale Roscoe. Phytochemistry. 190: 112843. (IF 4.072)

Savova M.S.Vasileva L.V., Mladenova S.G., Amirova K.M., Ferrante C., Orlando G., Wabitsch M., Georgiev M.I. (2021)
Ziziphus jujuba Mill. leaf extract restrains adipogenesis by targeting PI3K/AKT signaling pathway. Biomedicine and Pharmacotherapy. 141: 111934. (IF 6.530)

Scossa F., Alseekh S., Fernie A.R. (2021)
Integrating multi-omics data for crop improvement. Journal of Plant Physiology. 257: 153352. (IF 3.549)

Scossa F., Fernie A.R. (2021)
Ancestral sequence reconstruction – An underused approach to understand the evolution of gene function in plants?Computational and Structural Biotechnology Journal. 19: 1579–1594. (IF 7.271)

Scossa F., Fernie A.R. (2021)
When a Crop Goes Back to the Wild: Feralization. Trends in Plant Science. 26(6): 543–545. (IF 18.313)

Rasul F., Gupta S., Olas J.J., Gechev T., Sujeeth N., Mueller-Roeber B. (2021)
Priming with a seaweed extract strongly improves drought tolerance in Arabidopsis. International Journal of Molecular Sciences. 22: 1469. (IF 5.923

Sieniawska E., Georgiev M.I. (2021)
Metabolomics: Towards acceleration of antibacterial plant-based leads discovery. Phytochemistry Reviews. DOI: (IF 5.374)

Sieniawska E., Sawicki R., Marchev A.S., Truszkiewicz W., Georgiev M.I. (2021)
Tanshinones from Salvia miltiorrhiza inhibit Mycobacterium tuberculosis via disruption of the cell envelope surface and oxidative stress. Food and Chemical Toxicology. 156: 112405. (IF 6.025)

Sieniawska E., Sawicki R., Truszkiewicz W., Marchev A.S., Georgiev M.I. (2021)
Usnic acid treatment changes the composition of Mycobacterium tuberculosis cell envelope and alters bacteria redox status. mSystems. 6(3): e00097-21. (IF 6.496)

Shi M., Liao P., Nile S.H., Georgiev M.I., Kai G. (2021)
Biotechnological exploration of transformed root culture for value-added products. Trends in Biotechnology. 39(2): 137-149. (IF 19.536)

Staykov N.S., Angelov M., Petrov V., Minkov P., Kanojia A., Guinan K.J., Alseekh S., Fernie A.R., Neerakkal S., Gechev T. (2021)
An Ascophyllum nodosum-derived biostimulant protects model and crop plants from oxidative stress. Metabolites. 11(1): 24. (IF 4.932)

Takova K., Koynarski T., Minkov G., Toneva V., Mardanova E., Ravin N., Lukov G.L., Zahmanova G. (2021)
Development and Optimization of an Enzyme Immunoassay to Detect Serum Antibodies against the Hepatitis E Virus in Pigs, Using Plant-Derived ORF2 Recombinant Protein. Vaccines. 9(9): 991. (IF 4.422)

Takova K., Koynarski T., Minkov I., Ivanova Z, Toneva V., Zahmanova G. (2020)
Hepatitis E Virus Seroprevalence in Domestic Pigs and Wild Boar in Bulgaria. Animals (Basel). 10(9) :1521. (IF 2.752)

Tong H., Nikoloski Z. (2021)
Machine learning approaches for crop improvement: leveraging phenotypic and genotypic big data. Journal of Plant Physiology. 257: 153354. (IF 3.549)

Tong H., Küken A., Razaghi-Moghadam Z., Nikoloski Z. (2021)
Characterization of effects of genetic variants via genome-scale metabolic modelling. Cellular and Molecular Life Sciences. 78: 5123–5138. (IF 9.261)

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 6.025)

Wu T., Kerbler M.S., Fernie A.R., Zhang Y. (2021)
Plant cell cultures as heterologous bio-factories for secondary metabolite production. Plant Communications. 2(5): 100235.

Wang J. Y., Alseekh S., Xiao T., Ablazov A., Perez de Souza L., Fiorilli V., Anggarani M., Lin P. Y., Votta C., Novero M., Jamil M., Lanfranco L., Hsing Y. C., Blilou I., Fernie A. R., Al-Babili S. (2021)
Multi-omics approaches explain the growth-promoting effect of the apocarotenoid growth regulator zaxinone in rice. Communications Biology. 4(1): 1222 (IF 6.268)

Yang C., Shen S., Zhou S., Li Y., Mao Y., Zhou J., Shi Y., An L., Zhou Q., Peng W., Lyu Y., Liu X., Chen W., Wang S., Qu L., Liu X., Fernie A.R.,  Luo, J. (2021)
Rice metabolic regulatory network spanning its entire life cycle. Molecular Plant. DOI: (IF 13.164)

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 3.817)

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 13.583)

Zhang Y., Fernie A.R. (2021)
Stable and temporary enzyme complexes and metabolons involved in energy and redox metabolism. Antioxidants and Redox Signaling. 35(10): 788-807. (IF 8.401)

Zhang Y., Giese J., Kerbler M. S., Siemiatkowska B., Souza P. L., Medeiros D., Alpers J., Hinicha K. D., Daloso M. D., Stitt M., Finkemeier I., Fernie A.R. (2021)
Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis. Molecular Plant. 14(7): 1104-1118. (IF 13.164)

Zhang Y., Scossa, F., Fernie A. R. (2021)
The genomes of Taxus species unveil novel candidates in the biosynthesis of taxoids. Molecular Plant. DOI: /j.molp.2021.08.017. (IF 13.164)

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. 186(3): 1487–1506. (IF 8.340)

Zhu F., Alseekh S., Koper K., Tong H., Nikoloski Z., Naake T., Liu H., Yan J., Brotman Y., Wen W., Maeda H., Cheng Y., Fernie A. R. (2021)
Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. The Plant Cell. DOI: (IF 11.277)