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Establishment of a Center of Plant Systems Biology and Biotechnology for the translation of fundamental research into sustainable bio-based technologies in Bulgaria

Deliverables

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Publications

Reactive Oxygen Species and Abiotic Stress in Plants

Author(s): Tsanko Gechev, Veselin Petrov
Published in: International Journal of Molecular Sciences, Issue 21/20, 2020, Page(s) 7433, ISSN 1422-0067
DOI: 10.3390/ijms21207433

Adenine Nucleotide and Nicotinamide Adenine Dinucleotide Measurements in Plants

Author(s): Youjun Zhang, Ina Krahnert, Antje Bolze, Yves Gibon, Alisdair R. Fernie
Published in: Current Protocols in Plant Biology, Issue 5/3, 2020, ISSN 2379-8068
DOI: 10.1002/cppb.20115

Metabolons, enzyme–enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism

Author(s): Youjun Zhang, Alisdair R. Fernie
Published in: Plant Communications, Issue 2/1, 2021, Page(s) 100081, ISSN 2590-3462
DOI: 10.1016/j.xplc.2020.100081

Anthocyanins, multi-functional natural products of industrial relevance: Recent biotechnological advances

Author(s): Tarun Belwal, Gopal Singh, Philippe Jeandet, Aseesh Pandey, Lalit Giri, Sudipta Ramola, Indra D. Bhatt, Petras Rimantas Venskutonis, Milen I. Georgiev, Christophe Clément, Zisheng Luo
Published in: Biotechnology Advances, Issue 43, 2020, Page(s) 107600, ISSN 0734-9750
DOI: 10.1016/j.biotechadv.2020.107600

Screening of pepper (Capsicum spp.) accessions for infestation by pests in open field conditions.

Author(s): 47. Yankova V., Todorova V., Markova D.
Published in: Bulgarian Journal of Agricultural Science. 26 (4), 2020, Page(s) 841-846, ISSN 1310-0351
DOI: 10.5281/zenodo.4706815

An Abundance and Interaction Encyclopedia of Plant Protein Function

Author(s): Youjun Zhang, Aleksandra Skirycz, Alisdair R. Fernie
Published in: Trends in Plant Science, Issue 25/7, 2020, Page(s) 627-630, ISSN 1360-1385
DOI: 10.1016/j.tplants.2020.04.006

On the Detection and Functional Significance of the Protein–Protein Interactions of Mitochondrial Transport Proteins

Author(s): Youjun Zhang, Alisdair R. Fernie
Published in: Biomolecules, Issue 10/8, 2020, Page(s) 1107, ISSN 2218-273X
DOI: 10.3390/biom10081107

Rapid Identification of Protein‐Protein Interactions in Plants

Author(s): Youjun Zhang, Roberto Natale, Adilson Pereira Domingues, Mitchell Rey Toleco, Beata Siemiatkowska, Norma Fàbregas, Alisdair R. Fernie
Published in: Current Protocols in Plant Biology, Issue 4/4, 2019, ISSN 2379-8068
DOI: 10.1002/cppb.20099

Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations

Author(s): Prashant K. Pandey, Jing Yu, Nooshin Omranian, Saleh Alseekh, Neha Vaid, Alisdair R. Fernie, Zoran Nikoloski, Roosa A. E. Laitinen
Published in: Plant Direct, Issue 3/11, 2019, ISSN 2475-4455
DOI: 10.1002/pld3.186

Obesity and NRF2-mediated cytoprotection: Where is the missing link?

Author(s): Liliya V. Vasileva, Martina S. Savova, Kristiana M. Amirova, Albena T. Dinkova-Kostova, Milen I. Georgiev
Published in: Pharmacological Research, Issue 156, 2020, Page(s) 104760, ISSN 1043-6618
DOI: 10.1016/j.phrs.2020.104760

Jasmonic acid-responsive RRTF1 transcription factor controls DTX18 gene expression in hydroxycinnamic acid amide secretion

Author(s): Jinbo Li, Yu Meng, Kaixuan Zhang, Qiong Li, Shijuan Li, Bingliang Xu, Milen I Georgiev, Meiliang Zhou
Published in: Plant Physiology, Issue 185/2, 2020, Page(s) 369-384, ISSN 0032-0889
DOI: 10.1093/plphys/kiaa043

Network-based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation

Author(s): Leonardo Perez De Souza, Saleh Alseekh, Yariv Brotman, Alisdair R Fernie
Published in: Expert Review of Proteomics, Issue 17/4, 2020, Page(s) 243-255, ISSN 1478-9450
DOI: 10.1080/14789450.2020.1766975

Stable and Temporary Enzyme Complexes and Metabolons Involved in Energy and Redox Metabolism

Author(s): Youjun Zhang, Alisdair R. Fernie
Published in: Antioxidants & Redox Signaling, 2020, ISSN 1523-0864
DOI: 10.1089/ars.2019.7981

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

Author(s): Mohamed A. Salem, Takuya Yoshida, Leonardo Perez de Souza, Saleh Alseekh, Krzysztof Bajdzienko, Alisdair R. Fernie, Patrick Giavalisco
Published in: The Plant Journal, Issue 103/4, 2020, Page(s) 1614-1632, ISSN 0960-7412
DOI: 10.1111/tpj.14800

Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth

Author(s): Hao Tong, Anika Küken, Zoran Nikoloski
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-16279-5

Network Analysis Provides Insight into Tomato Lipid Metabolism

Author(s): Anastasiya Kuhalskaya, Micha Wijesingha Ahchige, Leonardo Perez de Souza, José Vallarino, Yariv Brotman, Saleh Alseekh
Published in: Metabolites, Issue 10/4, 2020, Page(s) 152, ISSN 2218-1989
DOI: 10.3390/metabo10040152

A plant-based transient expression system for the rapid production of highly immunogenic Hepatitis E virus-like particles

Author(s): Eugenia S. Mardanova, Katerina H. Takova, Valentina T. Toneva, Gergana G. Zahmanova, Liudmila M. Tsybalova, Nikolai V. Ravin
Published in: Biotechnology Letters, Issue 42/11, 2020, Page(s) 2441-2446, ISSN 0141-5492
DOI: 10.1007/s10529-020-02995-x

Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes

Author(s): Rafe Lyall, Zoran Nikoloski, Tsanko Gechev
Published in: International Journal of Molecular Sciences, Issue 21/23, 2020, Page(s) 9131, ISSN 1422-0067
DOI: 10.3390/ijms21239131

A Highly Efficient Agrobacterium-Mediated Method for Transient Gene Expression and Functional Studies in Multiple Plant Species

Author(s): Youjun Zhang, Moxian Chen, Beata Siemiatkowska, Mitchell Rey Toleco, Yue Jing, Vivien Strotmann, Jianghua Zhang, Yvonne Stahl, Alisdair R. Fernie
Published in: Plant Communications, Issue 1/5, 2020, Page(s) 100028, ISSN 2590-3462
DOI: 10.1016/j.xplc.2020.100028

Biotechnological Exploration of Transformed Root Culture for Value-Added Products

Author(s): Min Shi, Pan Liao, Shivraj Hariram Nile, Milen I. Georgiev, Guoyin Kai
Published in: Trends in Biotechnology, Issue 39/2, 2021, Page(s) 137-149, ISSN 0167-7799
DOI: 10.1016/j.tibtech.2020.06.012

Plant Mitochondrial Carriers: Molecular Gatekeepers That Help to Regulate Plant Central Carbon Metabolism

Author(s): M. Toleco, Thomas Naake, Youjun Zhang, Joshua Heazlewood, Alisdair R. Fernie
Published in: Plants, Issue 9/1, 2020, Page(s) 117, ISSN 2223-7747
DOI: 10.3390/plants9010117

MicroRNA-Mediated Metabolic Reprograming in Renal Cancer

Author(s): Bogusławska, Popławski, Alseekh, Koblowska, Iwanicka-Nowicka, Rybicka, Kędzierska, Głuchowska, Hanusek, Tański, Fernie, Piekiełko-Witkowska
Published in: Cancers, Issue 11/12, 2019, Page(s) 1825, ISSN 2072-6694
DOI: 10.3390/cancers11121825

First report of tomato spotted wilt virus on lisianthus (Eustoma grandiflorum) in Bulgaria

Author(s): Gancho Pasev, Vesela Radeva-Ivanova, Rafe Lyall, Amol Nankar, Dimitrina Kostova, Massimo Turina, Marta Vallino
Published in: Journal of Plant Pathology, Issue 103/1, 2021, Page(s) 375-375, ISSN 1125-4653
DOI: 10.1007/s42161-020-00702-3

A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts

Author(s): Youjun Zhang, Arun Sampathkumar, Sandra Mae-Lin Kerber, Corné Swart, Carsten Hille, Kumar Seerangan, Alexander Graf, Lee Sweetlove, Alisdair R. Fernie
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-18234-w

Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex

Author(s): 39. 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.
Published in: Molecular Plant Volume 13, Issue 7, 2020, Page(s) 1027-1046, ISSN 1674-2052
DOI: 10.1016/j.molp.2020.04.004

Treasure from garden: Bioactive compounds of buckwheat

Author(s): Md. Nurul Huda, Shuai Lu, Tanzim Jahan, Mengqi Ding, Rintu Jha, Kaixuan Zhang, Wei Zhang, Milen I. Georgiev, Sang Un Park, Meiliang Zhou
Published in: Food Chemistry, Issue 335, 2021, Page(s) 127653, ISSN 0308-8146
DOI: 10.1016/j.foodchem.2020.127653

Developmentally controlled changes during Arabidopsis leaf development indicate causes for loss of stress tolerance with age

Author(s): Aakansha Kanojia, Saurabh Gupta, Maria Benina, Alisdair R Fernie, Bernd Mueller-Roeber, Tsanko Gechev, Paul P Dijkwel
Published in: Journal of Experimental Botany, Issue 71/20, 2020, Page(s) 6340-6354, ISSN 0022-0957
DOI: 10.1093/jxb/eraa347

Therapeutic potential of phenylethanoid glycosides: A systematic review

Author(s): Lipeng Wu, Milen I. Georgiev, Hui Cao, Lutfun Nahar, Hesham R. El‐Seedi, Satyajit D. Sarker, Jianbo Xiao, Baiyi Lu
Published in: Medicinal Research Reviews, Issue 40/6, 2020, Page(s) 2605-2649, ISSN 0198-6325
DOI: 10.1002/med.21717

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis

Author(s): Mohamed A. Salem, Leonardo Perez de Souza, Ahmed Serag, Alisdair R. Fernie, Mohamed A. Farag, Shahira M. Ezzat, Saleh Alseekh
Published in: Metabolites, Issue 10/1, 2020, Page(s) 37, ISSN 2218-1989
DOI: 10.3390/metabo10010037

Dissection of the domestication‐shaped genetic architecture of lettuce primary metabolism

Author(s): Weiyi Zhang, Saleh Alseekh, Xiang Zhu, Qinghua Zhang, Alisdair R. Fernie, Hanhui Kuang, Weiwei Wen
Published in: The Plant Journal, Issue 104/3, 2020, Page(s) 613-630, ISSN 0960-7412
DOI: 10.1111/tpj.14950

Green (cell) factories for advanced production of plant secondary metabolites

Author(s): Andrey S. Marchev, Zhenya P. Yordanova, Milen I. Georgiev
Published in: Critical Reviews in Biotechnology, Issue 40/4, 2020, Page(s) 443-458, ISSN 0738-8551
DOI: 10.1080/07388551.2020.1731414

MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle

Author(s): Yan Li, Yang Chen, Lu Zhou, Shengjie You, Heng Deng, Ya Chen, Saleh Alseekh, Yong Yuan, Rao Fu, Zixin Zhang, Dan Su, Alisdair R. Fernie, Mondher Bouzayen, Tao Ma, Mingchun Liu, Yang Zhang
Published in: Molecular Plant, Issue 13/8, 2020, Page(s) 1203-1218, ISSN 1674-2052
DOI: 10.1016/j.molp.2020.06.005

Evaluation of pepper (Capsicum annuum L.) varieties to several methods of inoculation with Verticillium dahliae Kleb. in different conditions

Author(s): Vasileva K., Todorova V.
Published in: Bulgarian Journal of Agricultural Sciences 26 (2), 2020, Page(s) 423–430, ISSN 1310-0351
DOI: 10.5281/zenodo.4707211

PlantaSyst: Teaming up for Systems Biology and Biotechnology

Author(s): Tsanko Gechev, Milen I. Georgiev, Alisdair R. Fernie
Published in: Trends in Plant Science, Issue 25/7, 2020, Page(s) 621-624, ISSN 1360-1385
DOI: 10.1016/j.tplants.2020.04.010

Assessment of Fruit Quality and Fruit Morphology in Androgenic Pepper Lines (Capsicum annuum L.)

Author(s): Grozeva S., Tringovska I., Nankar AN., Todorova V., Kostova D.
Published in: Crop Breeding, Genetics and Genomics, Issue Crop Breed Genet Genom. 2020;2(1):e200005., 2020, ISSN 2632-7309
DOI: 10.20900/cbgg20200005

Effect of incubation period and culture medium on pepper anther culture.

Author(s): Grozeva S., Nankar AN.
Published in: Effect of incubation period and culture medium on pepper anther culture. Indian Journal of Biotechnology. 19 (1), 2020, Page(s) 53-59, ISSN 0975-0967
DOI: 10.5281/zenodo.4711172

SWATH-MS-Based Proteomics: Strategies and Applications in Plants

Author(s): Mo-Xian Chen, Youjun Zhang, Alisdair R. Fernie, Ying-Gao Liu, Fu-Yuan Zhu
Published in: Trends in Biotechnology, Issue 39/5, 2021, Page(s) 433-437, ISSN 0167-7799
DOI: 10.1016/j.tibtech.2020.09.002

Quantitative trait loci analysis of seed‐specialized metabolites reveals seed‐specific flavonols and differential regulation of glycoalkaloid content in tomato

Author(s): Saleh Alseekh, Itai Ofner, Zhongyuan Liu, Sonia Osorio, Jose Vallarino, Robert L. Last, Dani Zamir, Takayuki Tohge, Alisdair R. Fernie
Published in: The Plant Journal, Issue 103/6, 2020, Page(s) 2007-2024, ISSN 0960-7412
DOI: 10.1111/tpj.14879

MicroRNA profiling the resurrection plant Haberlea rhodopensis unveils essential regulators of survival under severe drought

Author(s): E. APOSTOLOVA, M. GOZMANOVA, L. NACHEVA, Z. IVANOVA, V. TONEVA, I. MINKOV, V. BAEV, G. YAHUBYAN
Published in: Biologia plantarum, Issue 64, 2020, Page(s) 541-550, ISSN 0006-3134
DOI: 10.32615/bp.2020.062

Molecular mechanisms preventing senescence in response to prolonged darkness in a desiccation-tolerant plant

Author(s): Meriem Durgud, Saurabh Gupta, Ivan Ivanov, Amin Omidbakhshfard, Maria Benina, Saleh Alseekh, Nikola Staykov, Mareike Hauenstein, Paul Dijkwel, Stefan Hörtensteiner, Valentina Toneva, Yariv Brotman, Alisdair R. Fernie, Bernd Mueller-Roeber, Tsanko Gechev
Published in: Plant Physiology, 2018, Page(s) pp.00055.2018, ISSN 0032-0889
DOI: 10.1104/pp.18.00055

Jasmonate-responsive MYB factors spatially repress rutin biosynthesis in Fagopyrum tataricum

Author(s): Kaixuan Zhang, Maria D Logacheva, Yu Meng, Jianping Hu, Dongpu Wan, Long Li, Dagmar Janovská, Zhiyong Wang, Milen I Georgiev, Zhuo Yu, Fuyu Yang, Mingli Yan, Meiliang Zhou
Published in: Journal of Experimental Botany, Issue 69/8, 2018, Page(s) 1955-1966, ISSN 0022-0957
DOI: 10.1093/jxb/ery032

Targeting ncRNAs by plant secondary metabolites: The ncRNAs game in the balance towards malignancy inhibition

Author(s): Diana Gulei, Nikolay Mehterov, Seyed Mohammad Nabavi, Atanas Georgiev Atanasov, Ioana Berindan-Neagoe
Published in: Biotechnology Advances, 2017, ISSN 0734-9750
DOI: 10.1016/j.biotechadv.2017.11.003

Metabolomics 20 years on: what have we learned and what hurdles remain?

Author(s): Saleh Alseekh, Alisdair R. Fernie
Published in: The Plant Journal, Issue 94/6, 2018, Page(s) 933-942, ISSN 0960-7412
DOI: 10.1111/tpj.13950

The Integration of Metabolomics and Next-Generation Sequencing Data to Elucidate the Pathways of Natural Product Metabolism in Medicinal Plants

Author(s): Federico Scossa, Maria Benina, Saleh Alseekh, Youjun Zhang, Alisdair Fernie
Published in: Planta Medica, 2018, ISSN 0032-0943
DOI: 10.1055/a-0630-1899

Quantitative trait loci analysis identifies a prominent gene involved in the production of fatty-acid-derived flavor volatiles in tomato

Author(s): Karolina Garbowicz, Zhongyuan Liu, Saleh Alseekh, Denise Tieman, Mark Taylor, Anastasiya Kuhalskaya, Itai Ofner, Dani Zamir, Harry J. Klee, Alisdair R. Fernie, Yariv Brotman
Published in: Molecular Plant, 2018, ISSN 1674-2052
DOI: 10.1016/j.molp.2018.06.003

The NAC Transcription Factor SlNAP2 Regulates Leaf Senescence and Fruit Yield in Tomato

Author(s): Xuemin Ma, Youjun Zhang, Veronika Turečková, Gang-Ping Xue, Alisdair R. Fernie, Bernd Mueller-Roeber, Salma Balazadeh
Published in: Plant Physiology, Issue 177/3, 2018, Page(s) 1286-1302, ISSN 0032-0889
DOI: 10.1104/pp.18.00292

Defining the convergence of ethylene and auxin signaling in tomato

Author(s): Alisdair R. Fernie, Saleh Alseekh
Published in: New Phytologist, Issue 219/2, 2018, Page(s) 479-481, ISSN 0028-646X
DOI: 10.1111/nph.15251

Modifications of dietary flavonoids towards improved bioactivity: An update on structure–activity relationship

Author(s): Lei Chen, Hui Teng, Zhenglu Xie, Hui Cao, Wai San Cheang, Krystyna Skalicka-Woniak, Milen I. Georgiev, Jianbo Xiao
Published in: Critical Reviews in Food Science and Nutrition, Issue 58/4, 2017, Page(s) 513-527, ISSN 1040-8398
DOI: 10.1080/10408398.2016.1196334

Rewiring of the Fruit Metabolome in Tomato Breeding

Author(s): Guangtao Zhu, Shouchuang Wang, Zejun Huang, Shuaibin Zhang, Qinggang Liao, Chunzhi Zhang, Tao Lin, Mao Qin, Meng Peng, Chenkun Yang, Xue Cao, Xu Han, Xiaoxuan Wang, Esther van der Knaap, Zhonghua Zhang, Xia Cui, Harry Klee, Alisdair R. Fernie, Jie Luo, Sanwen Huang
Published in: Cell, Issue 172/1-2, 2018, Page(s) 249-261.e12, ISSN 0092-8674
DOI: 10.1016/j.cell.2017.12.019

Occurrence, biochemistry and biological effects of host-selective plant mycotoxins

Author(s): Veselin Petrov, Muhammad Kamran Qureshi, Jacques Hille, Tsanko Gechev
Published in: Food and Chemical Toxicology, Issue 112, 2018, Page(s) 251-264, ISSN 0278-6915
DOI: 10.1016/j.fct.2017.12.047

Nutrigenomics in cancer: Revisiting the effects of natural compounds

Author(s): Cornelia Braicu, Nikolay Mehterov, Boyan Vladimirov, Victoria Sarafian, Seyed Mohammad Nabavi, Atanas G. Atanasov, Ioana Berindan-Neagoe
Published in: Seminars in Cancer Biology, Issue 46, 2017, Page(s) 84-106, ISSN 1044-579X
DOI: 10.1016/j.semcancer.2017.06.011

Stoichiometric Correlation Analysis: Principles of Metabolic Functionality from Metabolomics Data

Author(s): Kevin Schwahn, Romina Beleggia, Nooshin Omranian, Zoran Nikoloski
Published in: Frontiers in Plant Science, Issue 8, 2017, ISSN 1664-462X
DOI: 10.3389/fpls.2017.02152

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation

Author(s): Saurabh Gupta, Yanni Dong, Paul P. Dijkwel, Bernd Mueller-Roeber, Tsanko S. Gechev
Published in: International Journal of Molecular Sciences, Issue 20/12, 2019, Page(s) 3101, ISSN 1422-0067
DOI: 10.3390/ijms20123101

On the role of the tricarboxylic acid cycle in plant productivity

Author(s): Youjun Zhang, Alisdair R. Fernie
Published in: Journal of Integrative Plant Biology, Issue 60/12, 2018, Page(s) 1199-1216, ISSN 1672-9072
DOI: 10.1111/jipb.12690

Inhibition of TOR Represses Nutrient Consumption, Which Improves Greening after Extended Periods of Etiolation

Author(s): Yi Zhang, Youjun Zhang, Heather E. McFarlane, Toshihiro Obata, Andreas S. Richter, Mark Lohse, Bernhard Grimm, Staffan Persson, Alisdair R. Fernie, Patrick Giavalisco
Published in: Plant Physiology, Issue 178/1, 2018, Page(s) 101-117, ISSN 0032-0889
DOI: 10.1104/pp.18.00684

First report of Peanut stunt virus on beans in Bulgaria

Author(s): G. Pasev, V. Radeva-Ivanova, Y. Manoussopoulos, M. Turina, D. Kostova
Published in: New Disease Reports, Issue 38, 2018, Page(s) 9, ISSN 2044-0588
DOI: 10.5197/j.2044-0588.2018.038.009

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

Author(s): Adriano Nunes-Nesi, Saleh Alseekh, Franklin Magnum de Oliveira Silva, Nooshin Omranian, Gabriel Lichtenstein, Mohammad Mirnezhad, Roman R. Romero González, Julia Sabio y Garcia, Mariana Conte, Kirsten A. Leiss, Peter G. L. Klinkhamer, Zoran Nikoloski, Fernando Carrari, Alisdair R. Fernie
Published in: Metabolomics, Issue 15/4, 2019, ISSN 1573-3882
DOI: 10.1007/s11306-019-1503-8

Antidepressant-like effect of salidroside and curcumin on the immunoreactivity of rats subjected to a chronic mild stress model

Author(s): Liliya V. Vasileva, Kremena E. Saracheva, Mariya V. Ivanovska, Atanaska P. Petrova, Andrey S. Marchev, Milen I. Georgiev, Mariana A. Murdjeva, Damiyanka P. Getova
Published in: Food and Chemical Toxicology, Issue 121, 2018, Page(s) 604-611, ISSN 0278-6915
DOI: 10.1016/j.fct.2018.09.065

Causes and solutions to “globesity”: The new fa(s)t alarming global epidemic

Author(s): Liliya V. Vasileva, Andrey S. Marchev, Milen I. Georgiev
Published in: Food and Chemical Toxicology, Issue 121, 2018, Page(s) 173-193, ISSN 0278-6915
DOI: 10.1016/j.fct.2018.08.071

Data Reduction Approaches for Dissecting Transcriptional Effects on Metabolism

Author(s): Kevin Schwahn, Zoran Nikoloski
Published in: Frontiers in Plant Science, Issue 9, 2018, ISSN 1664-462X
DOI: 10.3389/fpls.2018.00538

Interorganelle Communication: Peroxisomal MALATE DEHYDROGENASE2 Connects Lipid Catabolism to Photosynthesis through Redox Coupling in Chlamydomonas

Author(s): Fantao Kong, Adrien Burlacot, Yuanxue Liang, Bertrand Légeret, Saleh Alseekh, Yariv Brotman, Alisdair R. Fernie, Anja Krieger-Liszkay, Fred Beisson, Gilles Peltier, Yonghua Li-Beisson
Published in: The Plant Cell, Issue 30/8, 2018, Page(s) 1824-1847, ISSN 1040-4651
DOI: 10.1105/tpc.18.00361

Passing the Baton: Substrate Channelling in Respiratory Metabolism

Author(s): Alisdair R. Fernie, Youjun Zhang, Lee J. Sweetlove
Published in: Research, Issue 2018, 2018, Page(s) 1-16, ISSN 2639-5274
DOI: 10.1155/2018/1539325

In vivo detection of protein cysteine sulfenylation in plastids

Author(s): Barbara De Smet, Patrick Willems, Alvaro D. Fernandez‐Fernandez, Saleh Alseekh, Alisdair R. Fernie, Joris Messens, Frank Van Breusegem
Published in: The Plant Journal, Issue 97/4, 2019, Page(s) 765-778, ISSN 0960-7412
DOI: 10.1111/tpj.14146

A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population

Author(s): Yaacov Micha Brog, Sonia Osorio, Yoav Yichie, Saleh Alseekh, Elad Bensal, Andriy Kochevenko, Dani Zamir, Alisdair R. Fernie
Published in: The Plant Journal, Issue 97/2, 2019, Page(s) 391-403, ISSN 0960-7412
DOI: 10.1111/tpj.14095

Clinopodium vulgare L. (wild basil) extract and its active constituents modulate cyclooxygenase-2 expression in neutrophils

Author(s): Kristiana M. Amirova, Petya Dimitrova, Andrey S. Marchev, Ina Y. Aneva, Milen I. Georgiev
Published in: Food and Chemical Toxicology, Issue 124, 2019, Page(s) 1-9, ISSN 0278-6915
DOI: 10.1016/j.fct.2018.11.054

Crop metabolomics: from diagnostics to assisted breeding

Author(s): Saleh Alseekh, Luisa Bermudez, Luis Alejandro de Haro, Alisdair R. Fernie, Fernando Carrari
Published in: Metabolomics, Issue 14/11, 2018, ISSN 1573-3882
DOI: 10.1007/s11306-018-1446-5

Phytochemical composition and antioxidant activity of 63 Balkan pepper (Capsicum annuum L.) accessions

Author(s): Petko Denev, Velichka Todorova, Manol Ognyanov, Yordan Georgiev, Irina Yanakieva, Ivanka Tringovska, Stanislava Grozeva, Dimitrina Kostova
Published in: Journal of Food Measurement and Characterization, 2019, ISSN 2193-4126
DOI: 10.1007/s11694-019-00171-y

Immunoregulatory natural compounds in stress-induced depression: An alternative or an adjunct to conventional antidepressant therapy?

Author(s): Liliya V. Vasileva, Mariya V. Ivanovska, Marianna A. Murdjeva, Kremena E. Saracheva, Milen I. Georgiev
Published in: Food and Chemical Toxicology, Issue 127, 2019, Page(s) 81-88, ISSN 0278-6915
DOI: 10.1016/j.fct.2019.03.004

Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors

Author(s): Alexey Shapiguzov, Julia P Vainonen, Kerri Hunter, Helena Tossavainen, Arjun Tiwari, Sari Järvi, Maarit Hellman, Fayezeh Aarabi, Saleh Alseekh, Brecht Wybouw, Katrien Van Der Kelen, Lauri Nikkanen, Julia Krasensky-Wrzaczek, Nina Sipari, Markku Keinänen, Esa Tyystjärvi, Eevi Rintamäki, Bert De Rybel, Jarkko Salojärvi, Frank Van Breusegem, Alisdair R Fernie, Mikael Brosché, Perttu Permi, Eva-M
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
DOI: 10.7554/elife.43284

A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana

Author(s): Neerakkal Sujeeth, Nikolay Mehterov, Saurabh Gupta, Muhammad K. Qureshi, Axel Fischer, Sebastian Proost, M. Amin Omidbakhshfard, Toshihiro Obata, Maria Benina, Nikola Staykov, Salma Balazadeh, Dirk Walther, Alisdair R. Fernie, Bernd Mueller-Roeber, Jacques Hille, Tsanko S. Gechev
Published in: Cellular and Molecular Life Sciences, 2019, ISSN 1420-682X
DOI: 10.1007/s00018-019-03202-5

COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors

Author(s): Gita Naseri, Jessica Behrend, Lisa Rieper, Bernd Mueller-Roeber
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-10224-x

Application of high-throughput phenotyping tool Tomato Analyzer to characterize Balkan Capsicum fruit diversity

Author(s): Amol N. Nankar, Ivanka Tringovska, Stanislava Grozeva, Velichka Todorova, Dimitrina Kostova
Published in: Scientia Horticulturae, Issue 260, 2020, Page(s) 108862, ISSN 0304-4238
DOI: 10.1016/j.scienta.2019.108862

Large‐scale metabolite quantitative trait locus analysis provides new insights for high‐quality maize improvement

Author(s): Kun Li, Weiwei Wen, Saleh Alseekh, Xiaohong Yang, Huan Guo, Wenqiang Li, Luxi Wang, Qingchun Pan, Wei Zhan, Jie Liu, Yanhua Li, Xiao Wu, Yariv Brotman, Lothar Willmitzer, Jiansheng Li, Alisdair R. Fernie, Jianbing Yan
Published in: The Plant Journal, 2019, ISSN 0960-7412
DOI: 10.1111/tpj.14317

Extensive Variations in Diurnal Growth Patterns and Metabolism Among Ulva spp. Strains

Author(s): Antoine Fort, Morgane Lebrault, Margot Allaire, Alberto A. Esteves-Ferreira, Marcus McHale, Francesca Lopez, Jose M. Fariñas-Franco, Saleh Alseekh, Alisdair R. Fernie, Ronan Sulpice
Published in: Plant Physiology, Issue 180/1, 2019, Page(s) 109-123, ISSN 0032-0889
DOI: 10.1104/pp.18.01513

Exploring the Diversity of Plant Metabolism

Author(s): Chuanying Fang, Alisdair R. Fernie, Jie Luo
Published in: Trends in Plant Science, Issue 24/1, 2019, Page(s) 83-98, ISSN 1360-1385
DOI: 10.1016/j.tplants.2018.09.006

MYB Transcription Repressors Regulate Plant Secondary Metabolism

Author(s): Cheng Chen, Kaixuan Zhang, Muhammad Khurshid, Jinbo Li, Ming He, Milen I. Georgiev, Xinquan Zhang, Meiliang Zhou
Published in: Critical Reviews in Plant Sciences, Issue 38/3, 2019, Page(s) 159-170, ISSN 0735-2689
DOI: 10.1080/07352689.2019.1632542

Construction and applications of a B vitamin genetic resource for investigation of vitamin dependent metabolism in maize

Author(s): Masaharu Suzuki, Shan Wu, Manaki Mimura, Saleh Alseekh, Alisdair R. Fernie, Andrew D. Hanson, Donald R. McCarty
Published in: The Plant Journal, 2019, ISSN 0960-7412
DOI: 10.1111/tpj.14535

The Structure and Function of Major Plant Metabolite Modifications

Author(s): Shouchuang Wang, Saleh Alseekh, Alisdair R. Fernie, Jie Luo
Published in: Molecular Plant, Issue 12/7, 2019, Page(s) 899-919, ISSN 1674-2052
DOI: 10.1016/j.molp.2019.06.001

Comparative metabolite profiling of two switchgrass ecotypes reveals differences in drought stress responses and rhizosheath weight

Author(s): Tie-Yuan Liu, Mo-Xian Chen, Youjun Zhang, Fu-Yuan Zhu, Ying-Gao Liu, Yuan Tian, Alisdair R. Fernie, Nenghui Ye, Jianhua Zhang
Published in: Planta, Issue 250/4, 2019, Page(s) 1355-1369, ISSN 0032-0935
DOI: 10.1007/s00425-019-03228-w

Redox-Regulation of Photorespiration through Mitochondrial Thioredoxin o1

Author(s): Ole Reinholdt, Saskia Schwab, Youjun Zhang, Jean-Philippe Reichheld, Alisdair R. Fernie, Martin Hagemann, Stefan Timm
Published in: Plant Physiology, Issue 181/2, 2019, Page(s) 442-457, ISSN 0032-0889
DOI: 10.1104/pp.19.00559

Transposon-associated polymorphisms of stress-responsive gene promoters in natural variants of Arabidopsis thaliana

Author(s): Mladen Naydenov, Nadezhda Gospodinova, Elena Apostolova, Nikolaj Anachkov, Vesselin Baev, Mariyana Gozmanova, Ivan Minkov, Galina Yahubyan
Published in: Acta Biochimica Polonica, Issue 65/3, 2018, ISSN 0001-527X
DOI: 10.18388/abp.2017_1590

LoopRNA – Java Module for RNA Structure Annotation

Author(s): Georgi Minkov, Valentina Toneva, Zdravka Ivanova, Vesselin Baev
Published in: Comptes rendus de l’Acade'mie bulgare des Sciences, Issue Vol 71, No9, 2018, Page(s) 1215-1221, ISSN 1310-1331
DOI: 10.7546/crabs.2018.09.08

A new liquid chromatography-high resolution Orbitrap mass spectrometry-based strategy to characterize Glucuronide Oleanane-type Triterpenoid Carboxylic Acid 3, 28-O-Bidesmosides (GOTCAB) saponins.A case study of Gypsophila glomerata Pall ex M. B. (Caryophyllaceae)

Author(s): Reneta Gevrenova, Krum Bardarov, Sabine Bouguet-Bonnet, Yulian Voynikov, Vessela Balabanova, Dimitrina Zheleva-Dimitrova, Max Henry
Published in: Journal of Pharmaceutical and Biomedical Analysis, Issue 159, 2018, Page(s) 567-581, ISSN 0731-7085
DOI: 10.1016/j.jpba.2018.07.041

Evaluation of collection of pepper (Capsicum spp.) resources for resistance to Verticillium dahliae Kleb.

Author(s): Katya Vasileva, Velichka Todorova, Stojka Masheva
Published in: Bulgarian Journal of Agricultural Science, Issue 25 (No 5) 2019, 2019, Page(s) 1030-1038, ISSN 2534-983X

Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand’s high ultraviolet B radiation environment

Author(s): Yanni Dong, Saurabh Gupta, Rixta Sievers, Jason J. Wargent, David Wheeler, Joanna Putterill, Richard Macknight, Tsanko Gechev, Bernd Mueller-Roeber, Paul P. Dijkwel
Published in: BMC Genomics, Issue 20/1, 2019, ISSN 1471-2164
DOI: 10.1186/s12864-019-6084-4

Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation

Author(s): Mo-Xian Chen, Fu-Yuan Zhu, Bei Gao, Kai-Long Ma, Youjun Zhang, Alisdair R. Fernie, Xi Chen, Lei Dai, Neng-Hui Ye, Xue Zhang, Yuan Tian, Di Zhang, Shi Xiao, Jianhua Zhang, Ying-Gao Liu
Published in: Plant Physiology, 2019, Page(s) pp.00430.2019, ISSN 0032-0889
DOI: 10.1104/pp.19.00430

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

Author(s): Gergana G. Zahmanova, Milena Mazalovska, Katerina H. Takova, Valentina T. Toneva, Ivan N. Minkov, Eugenia S. Mardanova, Nikolai V. Ravin, George P. Lomonossoff
Published in: Plants, Issue 9/1, 2020, Page(s) 29, ISSN 2223-7747
DOI: 10.3390/plants9010029

Untargetted Metabolomic Exploration of the Mycobacterium tuberculosis Stress Response to Cinnamon Essential Oil

Author(s): Elwira Sieniawska, Rafał Sawicki, Joanna Golus, Milen I. Georgiev
Published in: Biomolecules, Issue 10/3, 2020, Page(s) 357, ISSN 2218-273X
DOI: 10.3390/biom10030357

A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress

Author(s): Mohammad Amin Omidbakhshfard, Neerakkal Sujeeth, Saurabh Gupta, Nooshin Omranian, Kieran J. Guinan, Yariv Brotman, Zoran Nikoloski, Alisdair R. Fernie, Bernd Mueller-Roeber, Tsanko S. Gechev
Published in: International Journal of Molecular Sciences, Issue 21/2, 2020, Page(s) 474, ISSN 1422-0067
DOI: 10.3390/ijms21020474

Tomato Phenotypic Diversity Determined by Combined Approaches of Conventional and High-Throughput Tomato Analyzer Phenotyping

Author(s): Amol N. Nankar, Ivanka Tringovska, Stanislava Grozeva, Daniela Ganeva, Dimitrina Kostova
Published in: Plants, Issue 9/2, 2020, Page(s) 197, ISSN 2223-7747
DOI: 10.3390/plants9020197

Molecular priming as an approach to induce tolerance against abiotic and oxidative stresses in crop plants

Author(s): Pavel Kerchev, Tom van der Meer, Neerakkal Sujeeth, Arno Verlee, Christian V. Stevens, Frank Van Breusegem, Tsanko Gechev
Published in: Biotechnology Advances, 2019, Page(s) 107503, ISSN 0734-9750
DOI: 10.1016/j.biotechadv.2019.107503

The style and substance of plant flavonoid decoration; towards defining both structure and function

Author(s): Saleh Alseekh, Leonardo Perez de Souza, Maria Benina, Alisdair R. Fernie
Published in: Phytochemistry, Issue 174, 2020, Page(s) 112347, ISSN 0031-9422
DOI: 10.1016/j.phytochem.2020.112347

Resolving the metabolon: is the proof in the metabolite?

Author(s): Youjun Zhang, Alisdair R Fernie
Published in: EMBO reports, Issue 21/8, 2020, ISSN 1469-221X
DOI: 10.15252/embr.202050774

Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties

Author(s): Weiyi Zhang, Youjun Zhang, Haiji Qiu, Yafei Guo, Haoliang Wan, Xiaoliang Zhang, Federico Scossa, Saleh Alseekh, Qinghua Zhang, Pu Wang, Li Xu, Maximilian H-W Schmidt, Xinxin Jia, Daili Li, Anting Zhu, Fei Guo, Wei Chen, Dejiang Ni, Björn Usadel, Alisdair R. Fernie, Weiwei Wen
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-17498-6

Compositional Analyses Reveal Relationships among Components of Blue Maize Grains

Author(s): Amol N. Nankar, M Paul Scott, Richard C. Pratt
Published in: Plants, Issue 9/12, 2020, Page(s) 1775, ISSN 2223-7747
DOI: 10.3390/plants9121775

Molecular plant responses to combined abiotic stresses put a spotlight on unknown and abundant genes

Author(s): Nasser Sewelam, Dominik Brilhaus, Andrea Bräutigam, Saleh Alseekh, Alisdair R Fernie, Veronica G Maurino
Published in: Journal of Experimental Botany, Issue 71/16, 2020, Page(s) 5098-5112, ISSN 0022-0957
DOI: 10.1093/jxb/eraa250

The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants

Author(s): Chen Jiao, Iben Sørensen, Xuepeng Sun, Honghe Sun, Hila Behar, Saleh Alseekh, Glenn Philippe, Kattia Palacio Lopez, Li Sun, Reagan Reed, Susan Jeon, Reiko Kiyonami, Sheng Zhang, Alisdair R. Fernie, Harry Brumer, David S. Domozych, Zhangjun Fei, Jocelyn K.C. Rose
Published in: Cell, Issue 181/5, 2020, Page(s) 1097-1111.e12, ISSN 0092-8674
DOI: 10.1016/j.cell.2020.04.019

Dissecting the interaction of photosynthetic electron transfer with mitochondrial signalling and hypoxic response in the Arabidopsis rcd1 mutant

Author(s): Alexey Shapiguzov, Lauri Nikkanen, Duncan Fitzpatrick, Julia P. Vainonen, Richard Gossens, Saleh Alseekh, Fayezeh Aarabi, Arjun Tiwari, Olga Blokhina, Klára Panzarová, Zuzana Benedikty, Esa Tyystjärvi, Alisdair R. Fernie, Martin Trtílek, Eva-Mari Aro, Eevi Rintamäki, Jaakko Kangasjärvi
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 375/1801, 2020, Page(s) 20190413, ISSN 0962-8436
DOI: 10.1098/rstb.2019.0413

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data

Author(s): Alexander A. Aksenov, Ivan Laponogov, Zheng Zhang, Sophie L. F. Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis Felix Nothias, Mélissa Nothias-Esposito, Katherine N. Maloney, Biswapriya B. Misra, Alexey V. Melnik, Aleksandr Smirnov, Xiuxia Du, Kenneth L. Jones, Kathleen Dorrestein, Morgan Panitchpakdi, Madeleine Ernst, Justin J. J. van der Hooft, Mabel Gonzalez, Chiara Carazzone,
Published in: Nature Biotechnology, Issue 39/2, 2021, Page(s) 169-173, ISSN 1087-0156
DOI: 10.1038/s41587-020-0700-3

Evaluation a collection of pepper (Capsicum spp.) resources for resistance to Verticillium dahliae Kleb

Author(s): 77. Vasileva K, Todorova V, Masheva S.
Published in: Bulgarian Journal of Agricultural Science 25(3), 2019, Page(s) 415-420, ISSN 1310-0351
DOI: 10.5281/zenodo.3692692

A step towards Balkan Capsicum annuum L. core collection: Phenotypic and biochemical characterization of 180 accessions for agronomic, fruit quality, and virus resistance traits

Author(s): Amol N. Nankar, Velichka Todorova, Ivanka Tringovska, Gancho Pasev, Vesela Radeva-Ivanova, Valentina Ivanova, Dimitrina Kostova
Published in: PLOS ONE, Issue 15/8, 2020, Page(s) e0237741, ISSN 1932-6203
DOI: 10.1371/journal.pone.0237741

Cytoskeleton Architecture Regulates Glycolysis Coupling Cellular Metabolism to Mechanical Cues

Author(s): Alisdair R. Fernie, Youjun Zhang, Arun Sampathkumar
Published in: Trends in Biochemical Sciences, Issue 45/8, 2020, Page(s) 637-638, ISSN 0968-0004
DOI: 10.1016/j.tibs.2020.04.003

Conservation and diversification of flavonoid metabolism in the plant kingdom

Author(s): Weiwei Wen, Saleh Alseekh, Alisdair R Fernie
Published in: Current Opinion in Plant Biology, Issue 55, 2020, Page(s) 100-108, ISSN 1369-5266
DOI: 10.1016/j.pbi.2020.04.004

Putative alternative translation start site-encoding nucleotides of CPR5 regulate growth and resistance

Author(s): Muhammad B. Faisal, Tsanko S. Gechev, Bernd Mueller-Roeber, Paul P. Dijkwel
Published in: BMC Plant Biology, Issue 20/1, 2020, ISSN 1471-2229
DOI: 10.1186/s12870-020-02485-2

Strategic enhancement of genetic gain for nutraceutical development in buckwheat: A genomics-driven perspective

Author(s): Dinesh C. Joshi, Kaixuan Zhang, Chenglong Wang, Rahul Chandora, Muhammad Khurshid, Jinbo Li, Ming He, Milen I. Georgiev, Meiliang Zhou
Published in: Biotechnology Advances, Issue 39, 2020, Page(s) 107479, ISSN 0734-9750
DOI: 10.1016/j.biotechadv.2019.107479

Annual Plant Reviews online

Author(s): 21. Lyall R., Gechev T.
Published in: Annual Plant Reviews online 2020 Volume 3, 2018
DOI: 10.1002/9781119312994.apr0730

Rice Grain Quality Benchmarking Through Profiling of Volatiles and Metabolites in Grains Using Gas Chromatography Mass Spectrometry

Author(s): Cindy Llorente, Rosario Jimenez, Jackie, Yariv Brotman, Alisdair R. Fernie, Nese Sreenivasulu
Published in: Rice Grain Quality - Methods and Protocols, Issue 1892, 2019, Page(s) 187-199
DOI: 10.1007/978-1-4939-8914-0_11

Guidelines for Sample Normalization to Minimize Batch Variation for Large-Scale Metabolic Profiling of Plant Natural Genetic Variance

Author(s): Saleh Alseekh, Si Wu, Yariv Brotman, Alisdair R. Fernie
Published in: Plant Metabolomics, Issue 1778, 2018, Page(s) 33-46
DOI: 10.1007/978-1-4939-7819-9_3

Metabolomic Analysis of Natural Variation in Arabidopsis

Author(s): Si Wu, Saleh Alseekh, Yariv Brotman, Alisdair R. Fernie
Published in: Arabidopsis Protocols, Issue 2200, 2021, Page(s) 393-411
DOI: 10.1007/978-1-0716-0880-7_19