PUBLICATIONS

Basic Information
>> Group Head: Zhu Xinguang
>> Research Area: Plant Systems Biology
>> Group Secretary: Wang Sisi
>> Contact Email: wangsisi0825@163.com

PUBLICATIONS

Changpeng Xin, Danny Tholen, Vincent Devloo, Xin-Guang Zhu. The benefit of photorespiratory bypass – How can they work? Plant Physiology

Saber Hamdani, Mingnan Qu, Chang-Peng Xin, Chengcai Chu, Govindjee, and Xin-Guang Zhu. Natural variations of photosynthetic activity in Chinese elite rice revealed by simultaneous measurements of chlorophyll a fluorescence induction and 820 nm transmission signal. Journal of Plant Physiology (Accepted).

Johannes A Hofberger, Aldana Ramirez, Xin-Guang Zhu, Haro Bouwmeester, Rob Schuurink, Eric Schranz. Angiosperm-wide clustering of the specialized terpenoid phenotypic module provides Insights into dynamics underlying pathway evolution in domestic crops (2014). Plant Physiology (Accepted)

Stephen P Long and Xin-Guang Zhu (2014) Photosynthesis - The final frontier in achieving the needed jump in potential yield of our major food crops (2014). Resource SI on Feeding the world in 2050: 16

Erik van den Bergh, Canan Külahoglu, Andrea Bräutigam, Julian M. Hibberd, Andreas P.M. Weber, Xin-Guang Zhu, M. Eric Schranz (2014) Gene and genome duplications and the origin of C4 photosynthesis: Birth of a trait in the Cleomaceae, Current Plant Biology, Aug ,1, 2-9

Chunyun Jiang, Danny Tholen, Jiajia Mercedes Xu, Changpeng Xin, Hui Zhang, Xinguang Zhu*, Yanxiu Zhao* (2014) Increased expression of mitochondria-localized carbonic anhydrase activity resulted in an increased biomass accumulation in Arabidopsis thaliana.Journal of Plant Biology ,57, 6, 366

Jindong Sun, Zhaozhong Feng, Andrew Leakey, Xinguang Zhu, Carl J Bernacchi, Donald R Ort (2014) Inconsistency of mesophyll conductance estimate causes the inconsistency for the estimates of maximum rate of Rubisco carboxylation among the linear, rectangular and non-rectangular hyperbola biochemical models of leaf photosynthesis - a case study of CO2 enrichment and leaf aging effects in soybean.Plant Science (Accepted)

Taiyu Chen, Xin-Guang Zhu, Yongjun Lin (2014) Major transcriptional differences between c4 and C3-C4 photosynthesis in an amphibious species Eleocharis baldwinii. Plant Molecular Biology (accepted).

Lin Wang, Angelika Czedik-Eysenberg, Rachel A. Mertz, Yaqing Si, Takayuki Tohge, Adriano Nunes-Nesi, Stephanie Arrivault, Lauren K. Dedow, Douglas W. Bryant, Wen Zhou, Jiajia Xu, Sarit Weissmann, Anthony Studer, Pinghua Li, Cankui Zhang, Therese LaRue, Ying Shao, Zehong Ding, Qi Sun, Rohan V. Patel, Robert Turgeon, Xinguang Zhu, Nicholas J. Provart, Todd C. Mockler, Alisdair R. Fernie, Mark Stitt, Peng Liu,Thomas P. Brutnell (2014) Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice Nature Biotechnology 32, 1158–1165

Yu XB, Zheng GY,Shan LL, Meng GF, Vingron M, Liu Q, Zhu X-G(2014) Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana.Front.Plant Sci. Jun 13;5:273

Chen Yi-Bo, Lu Tian-Cong, Wang Hong-Xia, Shen Jie, Bu Tian-Tian, Chao Qing, Gao Zhi-Fang, Zhu Xin-Guang, Wang Yue-Feng, and Wang Bai-Chen (2014) Post-translational modification of maize chloroplast pyruvate orthophosphate dikinase reveals the precise regulatory mechanism of its enzyme activity. Plant Physiology. Doi:10.1104/pp.113.231993

Li YY, Xu JJ, Haq NU, Zhang H, Zhu X-G(2014). Was low CO2  a driving force of C4 evolution? Arabidopsis responses to long-term low CO2  stress. Journal of Experimental Botany 65 (13): 3657-3667.

Wang Y, Long SP and Zhu X-G(2014) Elements Required for an efficient NADP-ME type C4 photosynthesis. Plant Physiology 164(4):2231-2246

Wang Y, Bräutigam A, Weber APM, Zhu X-G(2014) Three distinct biochemical subtypes of C4 photosynthesis? A modeling analysis. Journal of Experimental Botany Jul 2014; 65(13): 3567–3578.

Stitt M and Zhu X-G (2014) The large pools of metabolites involved in intercellular metabolite shuttles in C4photosynthesis provide enormous flexibility and robustness in a fluctuating light environment Plant Cell and Environment 37(9):1985-8
 
Cheng SF,Bergh EVD, Zeng P, Zhong X, Xu JJ, Liu X, Hofberger J, Bruijn SD, Bhide AS, Kuelahoglu C, Bian C, Chen J, Fan GY, Kaufmann K, Hall JC, Becker A, Bräutigam A, Weber APM, Shi CC, Zheng ZJ, Li WJ, Lv MJ, Tao YM, Wang JY, Zou HF, Quan ZW, Hibberd JM, Zhang GY, Zhu X-G , Xu X and Schranz ME(2013). The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers Plant Cell 25(8):2813-30
 
Xin CP,Yang J, Zhu X-G (2013) A model of chlorophyll a fluorescence induction kinetics with explicit description of structural constraints of individual photosystem II units. Photosynthesis Research ;117(1-3):339-54
 
Peng Y, Leung H CM, Yiu SM, Lv MJ, Zhu X-G, Chin FYL (2013) IDBA-Tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels. Bioinformatics 29: i326–i334.
 
Xu JJ, Li YY, Ma XL, Ding JF, Wang K, Wang SS, Tian Y, Zhang H, Zhu X-G(2013)Whole transcriptome analysis using next-generation sequencing of model speciesSetaria viridis to support C4 photosynthesis research. Plant Molecular Biology 83(1-2):77 .


Song QF, Zhang G and Zhu X-G (2013) Optimal crop canopy architecture to maximise canopy photosynthetic CO2  uptake under elevated CO2  – a theoretical study using a mechanistic model of canopy photosynthesis. Functional Plant Biology 40(2) 108-124.
 
Zhu X-G, Wang Y, Ort DR, Long SP (2013) e-Photosynthesis: a comprehensive dynamic mechanistic model of C3 photosynthesis: from light capture to sucrose synthesis. Plant Cell & Environment  36, 1711–1727
 
Tholen D, Boom C, Zhu X-G (2012) Opinion:prospects for improving photosynthesis by altering leaf anatomy. Plant Science 197:92-101.
 
Tholen D, Ethier G, Pepin S, Genty B, Zhu X-G (2012) Variable mesophyll conductance revisited -- theoretical background and experimental implications. Plant Cell & Environment 35:2087-103.
 
Zhu X-G, Song QF, Ort DR (2012) Elements of a dynamic systems model of canopy photosynthesis. Current Opinion in Plant Biology 15: 237-44.
 
Tholen D, Zhu X-G (2011) The mechanistic basis of internal conductance – A theoretical analysis using a 3D reaction diffusion model of mesophyll cell photosynthesis. Plant Physiology 156:90-105.
 
Zhu X-G, Zhang G, Tholen D, Wang Y, Xin C, Song Q (2011) The next generation models for crops and agro-ecosystems. Science China: Information Sciences 54:1-9.
 
Li YY, Zhang H, Zhu X-G (2011) C4 rice: are we ready for the challenge? Plant Physiology Journal 47: 1-10.
 
Xu FQ, Ma WM, Zhu X-G(2011). Introducing pyruvate oxidase into the chloroplast of Chlamydomonas reinhardtii increases oxygen consumption and promotes hydrogen production. International Journal of Hydrogen Research 36: 10648-10654
 
Wang J, Wang Y, Wang Z, Liu L, Zhu X-G* and Ma XT*(2011). Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to telo-box motif enrichment. BMC Evolutionary Biology 11:161
 
Thakur V, Wanchana S, Xu M, Bruskiewich R, Quick WP, Mosig A, Zhu X-G(2011) Characterization of parameters in plant microRNA prediction. BMC Genomics 12:108.
 
Ort DR, Zhu X-G, Melis A (2011) Optimizing antenna size to maximize photosynthetic efficiency. Plant Physiology 155:79-85.  
 
Lei HB, Wang B, Wang RQ, Zhu X-G, Chen LN, Zhang JF (2011) A parameter condition for ruling out multiple equilibria of the photosynthetic carbon metabolism. Asia Journal of Control13:611-624
 
Sage RF and Zhu XG (2011) Exploiting the engine of C4 photosynthesis to better serve humanity. Journal of Experimental Botany 62:2989-3000.
 
Zhu X-G, Shan LL, Y Wang, WP Quick (2010) C4 Rice -- an arena for systems biology research. Journal of Integrative Plant Biology 52:762-70.  
 
Zhu X-G (2010). Systems-level modeling—A new approach for engineering efficient photosynthetic machinery. Journal of Biotechnology 149:201-209.
 
Brutnell TB, Wang L, Swartwood K, Goldschmidt A, Jackson D, Zhu X-G, Kellogg E, Van Eck J (2010) Setaria viridis: a model for C4 photosynthesis. Plant Cell 22:2537-44.
 
Parry MAJ, Reynold M, Salvucci ME, Raines C, Andralojc PJ, Zhu X-G, Price D, Furbank R (2010) Raising yield potential of wheat. II. Increasing photosynthetic capacity and efficiency. Journal of Experimental Botany 62:453-67.
 
Zhu X-G, Long SP, Ort DR (2010) Improving photosynthetic efficiency for greater yield. Annual Review of Plant Biology 61: 235-261.
 
Zhu X-G (2010) Higher energy conversion efficiency through systems-level modeling of photosynthesis. Journal of Biotechnology 149: 201-209
 
Pan W, Fettig J, Sturler E, Zhu X-G(2010) Impacts of different metabolite measurement protocols on estimating parameters in complex photosynthetic carbon metabolism models. Lecture Notes in Operations Research (SI on Computational Systems Biology), 13: 373–380 
 
Yang Y, Zhang ZL, Li YX, Zhu XG*, Liu Q* (2010) Identifying cooperative transcription factors by combining ChIP-chip data and knockout data. Cell Research 20: 1276-1278 (Joint correspondence author).
 
Miguez FE, Zhu X-G, Humphries, S, Bollero G, Long SP (2009) A semimechanistic model predicting the growth and production of the bioenergy crop Miscanthus×giganteus: description, parameterization and validation. Global Change Biology – Biofuels 1: 282-296
 
Long SP and Zhu X-G (2009) Can we use evolutionary algorithms to outdo evolution? A computational approach to increasing crop photosynthetic productivity. Comparative Biochemistry and Physiology (A) 153: S223.
 
Lei HB, Wang X, Wang RQ, Zhu X-G, Chen LN, Zhang JF (2009) Analysis on steady states of photosynthetic carbon metabolic system. Proceedings of the 48th IEEE Conference on Decision and Control P5643 – 5648
 
Wang Z, *Zhu X-G, Li YY, Chang X, Chen YZ, Li YX, Liu L (2009). Though with constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for evolution of chloroplast metabolic network. Journal of Evolutionary Biology 22: 71-79 (joint correspondence author)