代表论著：(#Co-first author, *corresponding author)
1.Youjun Zhang, Katherine FM Beard, Corné Swart, Susan Bergmann, Ina Krahnert, Zoran Nikoloski, Alexander Graf, R. George Ratcliffe, Lee J. Sweetlove, Alisdair R. Fernie*, Toshihiro Obata. (2017) Protein-protein interactions and metabolite channeling in the plant tricarboxylic acid cycle Nature Communications 8 (1), 1-11
2.Youjun Zhang*, Arun Sampathkumar, Sandra Mae-Lin Kerbler, Corné Swart, Kumar Seerangan, Alexander Graf, Alisdair R. Fernie*. (2020) A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts Nature Communications 11 (1), 1-15
3.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*. (2020) Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties Nature Communications 11 (1), 1-12
4.
Youjun Zhang*, Jonas Giese, Sandra Mae-Lin Kerbler, Beata Siemiatkowska, Leonardo Perez de Souza, David Barbosa Medeiros, Jessica Alpers, Dirk K. Hincha, Danilo M. Daloso, Mark Stitt, Iris Finkemeier* and Alisdair R. Fernie*. (2021)
Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in ArabidopsisMolecular plant 14 (7), 1104-1118
6.Qiu, Haiji#, Zhang, Xiaoliang
#,
Zhang, Youjun#, Jiang, Xiaohui, Ren, Yujia, Gao, Dawei, Zhu, Xiang, Usadel, Björn, Fernie, Alisdair, Wen, Weiwei (2023) Depicting the genetic and metabolic panorama of chemical diversity in the tea plant.
Plant Biotechnology Journal pp. 1–16
7.Chang Su, Andrzej Kokosza, Xiaonan Xie, Aleš Pěnčík, Youjun Zhang, Pasi Raumonen, Xueping Shi, Sampo Muranen, Melis Kucukoglu Topcu, Juha Immanen, Risto Hagqvist, Omid Safronov, Juan Alonso-Serra, Gugan Eswaran, Mirko Pavicic Venegas, Karin Ljung, Sally Ward, Ari Pekka Mähönen, Kristiina Himanen, Jarkko Salojärvi, Alisdair R. Fernie, Ondrej Novak, Ottoline Leyser, Wojtek Palubicki, Ykä Helariutta, Kaisa Nieminen (2023) Tree architecture: Strigolactone-deficient mutant reveals connection between branching order and auxin gradient along tree stem Proc. Natl. Acad. Sci. Nov 28;120(48):e2308587120.
8.Alisdair R. Fernie, Youjun Zhang (2023) Observations and implication of thermal tolerance in the Arabidopsis proteome, Cell Systems, 14, 10, p819-821,
9.Nan Shan#, Youjun Zhang#, Yicong Guo, Wenna Zhang, Jing Nie, Alisdair R Fernie, Xiaolei Sui, (2023) Cucumber malate decarboxylase, CsNADP-ME2, functions in the balance of carbon and amino acid metabolism in fruit, Horticulture Research, 10(12), uhad216
10.Ji-Qin Xie, Xiang Zhou, Zi-Chang Jia, Chang-Feng Su, Youjun Zhang, Alisdair R. Fernie, Jianhua Zhang, Zhi-Yan Du, and Mo-Xian Chen (2023) Alternative Splicing, An Overlooked Defense Frontier of Plants with Respect to Bacterial Infection. Journal of Agricultural and Food Chemistry 71, 45, 16883–16901
11.Giese, Jonas, Eirich, Jürgen, Walther, Dirk, Youjun Zhang, Lassowskat, Ines, Fernie, Alisdair, Elsässer, Marlene, Maurino, Veronica, Schwarzländer, Markus, Finkemeier, Iris* (2023) The interplay of posttranslational protein modifications in Arabidopsis leaves during photosynthesis induction The plant journal 2023 Nov,116(4):1172-1193.
12.João Antonio Siqueira, Youjun Zhang, Adriano Nunes-Nesi, Alisdair R. Fernie, Wagner L. Araújo* (2023) Beyond photorespiration: significance of glycine and serine in leaf metabolism Trends in plant science 2023.06.12
13.Hongjian Wan#, Youjun Zhang#, Limin Wu, Guozhi Zhou, Luzhao Pan, Alisdair R Ferine* and Yong-Ling Ruan* (2023). Evolution and diversification of cytosolic and organelle invertases empowered the colonization and subsequent thriving of land plants Plant Physiology kiad401
14.Yu-Chen Song, Debatosh Das, Youjun Zhang, Moxian Chen,*, Fernie R. Alisdair R. Fernie*, Fu-Yuan Zhu,*, Fu-Liang Cao* (2023). Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants Trends in Biotechnology 2023.05.010
16.Giese, J., Eirich, J., Walther, D., Youjun Zhang, Lassowskat, I., Fernie, A.R., Elsässer, M., Maurino, V.G., Schwarzländer, M. and Finkemeier, I. (2023), The interplay of post-translational protein modifications in Arabidopsis leaves during photosynthesis induction. Plant Journal, 116: 1172-1193.
18.Zi-Chang Jia, Debatosh Das, Youjun Zhang, Alisdair R. Fernie, Ying-Gao Liu, Moxian Chen and Jianhua Zhang (2023). Plant serine/arginine-rich proteins: versatile players in RNA processing. Planta 257, 109.
19.Youjun Zhang*, Alisdair R. Fernie* (2023) Leveraging Glycoside-Targeted Metabolomics to Gain Insight into Biological Function Trends in plant science S1360-1385(23)00130-9
20.Ishmail Dahmani, Kezhen Qin, Youjun Zhang*, Alisdair Fernie* (2023) The Formation and Function of Plant Metabolons The plant journal 114: 1080-1092
21.Fu-Yuan Zhu, Yun-Jing Bao, Mo-Xian Chen, Youjun Zhang, Alisdair R. Fernie, Jianhua Zhang, Bao-Xing Huang, Fu-Liang Cao. (2023) Emerging role of jasmonic acid in woody plant development Authorea DOI: 10.22541/au.167420536.65415896/v1.
22.Youjun Zhang*, Moxian Chen, Tieyuan Liu, Kezhen Qin and Alisdair R. Fernie* (2023) TECHNICAL ADVANCE: Investigating the dynamics of protein-protein interactions in plants The plant journal 114: 965-983
23.Dennis Schlossarek, Youjun Zhang, Ewelina, Sokolowska, Alisdair Fernie, Marcin Luzarowski, Aleksandra Skirycz (2023) Don’t let go – co-fractionation mass spectrometry for untargeted mapping of protein-metabolite interactomes The plant journal 113(5):904-914
24.Yanmei Chen*, Yi Wang, Xinlin Liang, Youjun Zhang and Alisdair R.Fernie (2023). Mass spectrometric exploration of phytohormone profiles and signaling networks Trends in Plant Science 1360-1385(22)00327-2
25.Roberto Natale, Mariangela Coppola, Nunzio D’Agostino, Youjun Zhang, Alisdair R. Fernie, Valeria Castaldi* (2023) In Silico and In Vitro Approaches Allow the Identification of the Prosystemin Molecular Network Computational and Structural Biotechnology Journal 21,212-223
27.Dorrell RG, Liang Y, Gueguen N, Nonoyama T, Zhang Youjun, Croteau D, Penot M, Adiba S, Bailleul B, Gros V, Karlusich JJP, Zweig N, Fernie AR, Jouhet J, Maréchal E, Bowler C. A Plastidial Glycolytic-Gluconeogenic Switch of Mitochondrial Origin Enables Diatom Adaptations to High Latitudes. bioRxiv, 2022.
28.José G. Vallarino, Sanu Shameer, Youjun Zhang, R. George Ratcliffe, Lee J. Sweetlove, Alisdair R. Fernie* (2022) Leaf specific overexpression of a mitochondrially-targeted glutamine synthetase in tomato increased assimilate export resulting in earlier fruiting and elevated yield bioRxiv 2022.06.28.497938
29.Stefan Timm*, Nicole Klaas, Janice Niemann, Kathrin Jahnke, Saleh Alseekh, Youjun Zhang, PauloV.L. Souza, LiangYu Hou, Peter Geigenberger, DaniloM. Daloso, AlisdairR. Fernie, Martin Hagemann. (2022). Simultaneous adjustments of major mitochondrial pathways through redox regulation of dihydrolipoamide dehydrogenase (mtLPD1) bioRxiv 2022. 486831
30.Youjun Zhang*, Alisdair R. Fernie*. (2022) Dynamically regulating metabolic fluxes with synthetic metabolons Trends in Biotechnology 2022.06.005
31.Thorsten Stefan*, Xu Na Wu, Youjun Zhang, Alisdair Fernie and Waltraud X. Schulze. (2022) Regulatory modules of metabolites and protein phosphorylation in Arabidopsis genotypes with altered sucrose allocation Frontiers in Plant Science 13, 891405
32.Dhika Amanda, Felix P. Frey, Ulla Neumann, Marine Przybyl, Jan Šimura, Youjun Zhang, Zongliang Chen, Andrea Gallavotti, Alisdair R. Fernie, Karin Ljung, Iván F. Acosta*. (2022) Auxin boosts energy generation pathways to fuel pollen maturation in barley, Current Biology 21, 32022
33.Alisdair R. Fernie*, Youjun Zhang. (2022) The Bacillus subtilis glutamate anti-metabolon Nature Metabolism 4, 161-162
34.Kezhen Qin, Alisdair R. Fernie*, Youjun Zhang*. (2021) The Assembly of Super-Complexes in the Plant Chloroplast Biomolecules 11 (12), 1839
35.Youjun Zhang, Federico Scossa, and Alisdair R. Fernie*. (2021) The genomes of Taxus species unveil novel candidates in the biosynthesis of toxoids Molecular Plant 14(11):1773-1775
36.Tong Wu, Sandra M. Kerbler, Alisdair R. Fernie and Youjun Zhang*. (2021) Plant cell cultures as heterologous bio-factories for secondary metabolite production Plant Communications 2 (5), 1-12
37.Sandra M. Kerbler, Roberto Natale, Alisdair R. Fernie and Youjun Zhang*. (2021) Affinity purification Mass Spectrometry Methods to Study Biomolecular Complexes in plant International Journal of Molecular Sciences 22 (13), 7101
38.Fayezeh Aarabi*, Apidet Rakpenthai , Rouhollah Barahimipour , Michal Gorka, Youjun Zhang, Mohamed A. Salem, Nooshin Omranian, Franziska Brückner, Zoran Nikoloski, Patrick Giavalisco, Alexander Graf, Takayuki Tohge, Alisdair R. Fernie, Rainer Hoefgen*. (2021) Sulfur deficiency-induced genes affect seed protein accumulation and composition under sulfate deprivation Plant Physiology 187 (4), 2419-2434
39.Luis M. Cervela-Cardona, Takuya Yoshida, Youjun Zhang, Masaaki Okada, Alisdair
Fernie and Paloma Mas* (2021) Circadian control of metabolism by the clock component TOC1 Frontiers in Plant Science 12, 1126
40.Lara Pereira, Manoj Sapkota, Michael Alonge, Yi Zheng, Youjun Zhang, Hamid Razifard, Nathan K. Taitano, Michael Schatz, Zachary Lippman, Alisdair R. Fernie, Ying Wang, Zhangjun Fei, Ana L. Caicedo, Denise M. Tieman, Esther van der Knaap* (2021) Natural genetic diversity in tomato flavor genes Frontiers in Plant Science 12, 914
41.Juan C. Moreno, Rubén Vicente, Bruno E. Rojas, Michal Gorka, Monika Kosmacz, Juan S. Peralta-Ariza, Youjun Zhang, Saleh Alseekh, Dorothee Childs, Marcin Luzarowski, Matías D. Hartman, Carlos M. Figueroa, Alberto A. Iglesias, Alisdair R. Fernie, Aleksandra Skirycz*. (2021) Tyr‐Asp inhibition of glyceraldehyde 3‐phosphate dehydrogenase affects plant redox metabolism EMBO Journal 40,e106800
42.Youjun Zhang*, Alisdair R. Fernie*. (2020) On the detection and functional significance of the protein-protein interactions of mitochondrial carriers Biomolecules 10(8),1107
43.Youjun Zhang Alisdair R. Fernie*. (2020) Resolving the metabolon: is the proof in the metabolite? EMBO reports 21(8),e50774
44.Youjun Zhang*, Ina Krahnert, Antje Bolze , Yves Gibon, Alisdair R. Fernie. (2020) Adenine nucleotide and nicotinamide adenine dinucleotide measurements in plants Current Protocols in Plant Biology 5 (3), e20115
45.Youjun Zhang*, Alisdair R. Fernie*. (2020) Metabolons, Enzyme-Enzyme Assemblies that Mediate Substrate Channeling, and Their Roles in Plant Metabolism Plant Communications 2 (1), 100081
46.Youjun Zhang, Alisdair R. Fernie*. (2020) Stable and temporary enzyme complexes and metabolons involved in energy and redox metabolism Antioxidants & Redox Signaling 35 (10), 788-807
47.Youjun Zhang, AleksandraSkirycz, Alisdair R.Fernie*. (2020) An Abundance and Interaction Encyclopedia of Plant Protein Function Trends in Plant Science 25 (7), 627-630
48.Youjun Zhang*, Moxian Chen, Mitchell Rey Toleco, Jing, Yue, Vivien Strotmann, Jianghua Zhang, Yvonne Stahl, and Alisdair R.Fernie*. (2020) A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species Plant Communications 1 (5), 100028
49.Mo-Xian Chen, Youjun Zhang, Alisdair R, Fernie, Ying-Gao Liu*, Fu-Yuan Zhu*. (2020) SWATH-MS based proteomics: Strategies and Applications in Plants Trends in Biotechnology 39 (5), 433-437
50.Alisdair R. Fernie*, Youjun Zhang, Arun Sampathkumar. (2020) Cytoskeleton Architecture Regulates Glycolysis Coupling Cellular Metabolism to Mechanical Cues Trends in Biochemical Sciences 45 (8), 637-638
51.Takayuki Tohge, Federico Scossa, Regina Wendenburg, Pierre Frasse, Ilse Balbo, Mutsumi Watanabe, Saleh Alseekh, Sagar Sudam Jadhav, Jay C Delfin, Marc Lohse, Patrick Giavalisco, Bjoern Usadel, Youjun Zhang, Jie Luo, Mondher Bouzayen, Alisdair R Fernie*. (2020). Exploiting natural variation in tomato to define pathway structure and metabolic regulation of fruit polyphenolics in the lycopersicum complex Molecular plant 13 (7), 1027-1046
52.M. Rey Toleco, Thomas Naake, Youjun Zhang, Joshua L. Heazlewood and Alisdair R. Fernie*. (2020) Plant Mitochondrial Carriers: Molecular Gatekeepers that Help to Regulate Plant Central Carbon Metabolism Plants 9(1), 117
53.Moxian Chen, Fu-yuan Zhu, Bei Gao, Kai-Long Ma, Youjun Zhang, Alisdair Fernie, Xi Chen, Neng-Hui Ye, Qi-Juan Hu, Yuan Tian, Di Zhang, Tieyuan Liu, Jianhua Zhang, and Ying-Gao Liu*. (2020) Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation Plant Physiology 182 (3), 1510-1526
54.Jinsheng Zhu, Sylvain Loubéry, Larissa Broger, Youjun Zhang, Laura Lorenzo‐Orts, Anne Utz‐Pugin, Alisdair R Fernie, Chang Young‐Tae, Michael Hothorn*. (2020), A genetically validated approach to detect inorganic polyphosphates in plants The Plant Journal 102 (3), 507-516
55.Youjun Zhang*, Roberto Natale, Adilson Pereira Domingues Junior, Mitchell Rey Toleco, Beata Siemiatkowska, Norma Fàbregas, Alisdair R. Fernie. (2019) Rapid identification of protein‐protein interactions in plants Current Protocols in Plant Biology 4 (4), e20099
56.Jinsheng Zhu, Kelvin Lau, Robert Puschmann, Robert K. Harmel, Youjun Zhang, Verena Pries, Philipp Gaugler, Larissa Broger, Amit K. Dutta, Henning Jessen, Gabriel Schaaf, Alisdair R. Fernie3, Ludwig A. Hothorn, Dorothea Fiedler, Michael Hothorn*. (2019) Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis Elife 8, e43582
57.Ole Reinholdt, Saskia Schwab, Youjun Zhang, Jean-Philippe Reichheld, Alisdair R. Fernie, Martin Hagemann, Stefan Timm*. (2019) Redox-regulation of photorespiration through mitochondrial thioredoxin o1 Plant Physiology 181 (2), 442-457
58.Youjun Zhang, Alisdair Fernie*. (2018) On the role of the Tricarboxylic Acid Cycle in Plant Productivity. Journal of Integrative Plant Biology 60 (12), 1199-1216
59.Alisdair R. Fernie*, Youjun Zhang and Lee J. Sweetlove*. (2018). Passing the baton: substrate channelling in respiratory metabolism Research 1,1539325
60.Tie-Yuan Liu, Mo-Xian Chen, Youjun Zhang, Ying-Gao Liu, Fu-Yuan Zhu, Yuan Tian, Alisdair R Fernie, Nenghui Ye, Jianhua Zhang*. (2018) Comparative metabolite profiling of two switchgrass ecotype varieties reveals differences in drought stress responses and rhizosheath size Planta 250 (4), 1355-1369
61.Yi Zhang, Youjun Zhang, Heather E. McFarlane, Toshihiro Obata, Andreas Richter, Mark Lohse7, Bernhard Grimm, Staffan Persson, Alisdair R. Fernie, Patrick Giavalisco*. (2018) Inhibition of TOR represses nutrient consumption, which improves greening after extended periods of etiolation Plant Physiology 178 (1), 101-117
62.Federico Scossa, Maria Benina, Saleh Alseekh, Youjun Zhang and Alisdair R. Fernie*. (2018) The integration of metabolomics and next-generation sequencing data to elucidate the pathways of natural product metabolism in medicinal plants Planta Medica 84 (12/13), 855-873
63.Yuling Zhang, Rita Giuliani, Youjun Zhang, Yang Zhang, Wagner Luiz Araujo, Baichen Wang, Peng Liu, Qi Sun, Asaph Cousins, Gerald Edwards, Alisdair Fernie, Thomas P Brutnell, Pinghua Li*. (2018) Characterization of maize leaf pyruvate orthophosphate dikinase using high throughput sequencing Journal of Integrative Plant Biology 60 (8), 670-690
64.Xuemin Ma, Youjun Zhang, Veronika Turečková, Gang-Ping Xue, Alisdair R Fernie, Bernd Mueller-Roeber, Salma Balazadeh. (2018) The NAC transcription factor SlNAP2 regulates leaf senescence and fruit yield in tomato Plant Physiology 177 (3), 1286-1302
65.Mariette Andersson, Helle Turesson, Stéphanie Arrivault, Youjun Zhang, Ann-Sofie Fält, Alisdair R Fernie, Per Hofvander*. (2018). Inhibition of plastid PPase and NTT leads to major changes in starch and tuber formation in potato Journal of Experimental Botany 69(8): 1913-1924.
66.Semidán Robaina-Estévez, Danilo M Daloso, Youjun Zhang, Alisdair R Fernie, Zoran Nikoloski*. (2017) Resolving the central metabolism of Arabidopsis guard cells Scientific Reports 7 (1), 1-13
67.Fu-Yuan Zhu, Mo-Xian Chen, Lu Shi, Neng-Hui Ye, Jing-Fang Yang, Yun-Ying Cao, Youjun Zhang, Takuya Yoshida, Alisdair R. Fernie, Lin Su, Tie-Yuan Liu, Tao Fan, Ge-Fei Hao, Shi Xiao, Ying-Gao Liu, Jianhua Zhang*. (2017) Proteogenomic analysis reveals alternative splicing and alternative translation elements of the abscisic acid response in Arabidopsis seedlings The Plant Journal 91 (3), 518-533
68.Youjun Zhang, Corné Swart, Saleh Alseekh, Liang Jiang, Toshihiro Obata, Alexander Graf, Alisdair R. Fernie*. (2017) The extra-pathway interactome of the TCA cycle: expected and unexpected metabolic interactions Plant Physiology 177 (3), 966-979
69.Zengyu Liu, Rene Schneider, Youjun Zhang, Yi Zhang, Michaela Eder, Alisdair Fernie, Staffan Persson*. (2016) Cellulose-microtubule uncoupling proteins prevent lateral displacement of microtubules during cellulose synthesis in Arabidopsis Development Cell, 38(3),305-315.
70.Chao Liang, Shifeng Cheng, Youjun Zhang, Yuzhe Sun, Alisdair R. Fernie, Kang Kang, Gianni Panagiotou, Clive Lo and, Boon Leong Lim*. (2016) Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination BMC Plant Biology16 (1), 1-17
71.Chao Liang, Youjun Zhang, Shifeng Cheng, Sonia Osorio, Yuzhe Sun, Alisdair R. Fernie, C. Y. M. Cheung, and Boon L. Lim*. (2015) Impacts of high ATP supply from chloroplasts and mitochondria on the leaf metabolism of Arabidopsis thaliana Frontiers in Plant Science 6, 922
72.Phuong Anh Pham, Vanessa Wahl, Takayuki Tohge, Laise Rosado de Souza, Youjun Zhang, Phuc Thi Do, Justyna J. Olas, Mark Stitt, Wagner L. Araújo, Alisdair R. Fernie*. (2015) Analysis of knockout mutants reveals non-redundant functions of poly(ADP-ribose) polymerase isoforms in Arabidopsis Plant Molecular Biology 89 (4), 319-338
73.Youjun Zhang, Feng Sun, Joerg Fettke, Mark Aurel Schöttler, Lawrence Ramsden, Alisdair R. Fernie*, Boon Leong Lim*. (2014) Heterologous expression of AtPAP2 in transgenic potato influences carbon metabolism and tuber development FEBS letters 588 (20), 3726-3731
74.Feng Sun, Pui Kit Suen, Youjun Zhang, Chao Liang, Chris Carrie, James Whelan, Jane L. Ward, Nathaniel D. Hawkins, Liwen Jiang, Boon Leong Lim*. (2012) A dual-targeted purple acid phosphatase in Arabidopsis thaliana moderates carbon metabolism and its overexpression leads to faster plant growth and higher seed yield New Phytologist 194 (1), 206-219
75.Youjun Zhang, Laura Yu, Ka-Fu Yung, Dennis YC Leung, Sun Feng, Boon Leong Lim*. (2012). Over-expression of AtPAP2 in Camelina sativa leads to faster plant growth and higher seed yield Biotechnology for Biofuels 5 (1), 1-10
