植物系统生物学研究组

朱新广 研究员(植物系统生物学研究组)


研究兴趣:

    提高光能利用效率是进一步大幅度提高产量的关键途径。当前作物光能利用效率一般小于1%,远远低于C3C4植物的光能利用效率的理论最大值。长期以来,研究组致力于探索提高光能利用效率的新途径。主要从两个方面开展工作:1)系统模型指导下的C3C4光合改良。其核心是利用系统生物学方法,构建从代谢、细胞、叶片以至于冠层光合作用机理模型,用于鉴定控制光能利用效率的限制因子;进一步结合全基因组关联分析及遗传调控网络构建,鉴定控制光能转化效率的关键基因;最终利用转基因手段,创建高光效作物,确定高光效作物育种新靶点;(2C4改造。其核心是鉴定C3代谢进化为C4代谢的关键步骤,进而结合传统分子生物学手段及系统生物学手段,鉴定控制该转换的分子控制元件,进而以此为基础,在C3植物中创建C4光合原型。


现有成员:

工作人员:陈根云、宋青峰、曲明南、常天根、刘欣雨

博士后:吕明菊、赵洪龙、Shanhaz Praveen、Jemma Essamine

学生:陈法铭、辛端凤、赵永耀、王燕杰、苗芬芬、唐启鸣、黄榆慧、坚乃提(联培)、倪晓祥、毛林雄、杨健钊、谭晓雪(联培)

近年来代表性论文:

 

Xin-Guang Zhu and Jian-Kang Zhu (2021) Precision genome editing heralds rapid de novo domestication for new crops. Cell (in press).

Henry Daniell, Shuangxia Jin, Xin-Guang Zhu, Matthew A. Gitzendanner, Douglas E. Soltis and Pamela S. Soltis (2021) Green giant – a tiny organellar genome with mighty power to produce high-value proteins and reduce global warming. Plant Biotechnology Journal (in press). doi: 10.1111/pbi.13556

Yi Xiao; Jennifer Sloan; Christopher Hepworth, Colin Osborne, Andrew Fleming, Xinyuan Chen, Xin-Guang Zhu (2021) Estimating uncertainty: a Bayesian approach to modelling photosynthesis in C3 leaves. Plant Cell and Environment. doi.org/10.1111/pce.13995

Govindjee Govindjee, Yun-Kang Shen, Xin-Guang Zhu, Hualing Mi, Teruo Ogawa (2021) Honoring Bacon Ke at 100: A legend amongst the many luminaries and a highly collaborative scientist in photosynthesis research. Photosynthesis Research. doi: 10.1007/s11120-021-00820-8

Faming Chen, Guangyong Zheng, Mingnan Qu, Yanjie Wang, Ming-ju Amy Lyu, and Xin-Guang Zhu*(2020) Knocking out a negative regulator of photosynthesis 1 (NRP1) increases rice leaf photosynthesis and biomass production in the field. Journal of Experimental Botany, eraa566, https://doi.org/10.1093/jxb/eraa566.

Honglong Zhao, Qiming Tang, Tiangen Chang, Yi Xiao, Xin-Guang Zhu (2020) Why an increase in activity of an enzyme in the Calvin Benson Cycle does not always lead to an increased photosynthetic CO2 uptake rate? – A theoretical analysis. In silico Plants, diaa009, https://doi.org/10.1093/insilicoplants/diaa009.

Alexandrina Stirbet; Lars Bjorn, Dmitry Shevela, Suleyman Allakhverdiev, Arthur Nonomura, Xin-Guang Zhu, Dusan Lazar, Ashwani Pareek, Gyozo Garab and Julian Eaton-Rye (2020) Celebrating the contributions of Govindjee after his retirement: 1999–2020. New Zealand Journal of Botany (Accepted).

Naveed Khana, Jemaa Essemine, Saber Hamdani, Mingnan Qu, Ming-Ju Amy Lyu, Shahnaz Parveen, Alexandrina Stirbet, Govindjee Govindjeed and Xin-GuangZhu*(2020). Natural variation in the fast phase of chlorophyll a fluorescence induction curve (OJIP) in a global rice minicore panel. Photosynthesis Research https://doi.org/10.1007/s11120-020-00794-z.

Mingnan Qu, Jemaa Essemine, Jianlong Xu, Ablat, Guljannat Ablat, Shahnaz Perveen, Hongru Wang, Kai Chen, Yang Zhao, Genyun Chen, Chengcai Chu,Xin-Guang Zhu(2020) Alterations in stomatal response to fluctuating light increase biomass and yield of rice under drought conditions.Plant Journal, 104:1334–1347, https://doi.org/10.1111/tpj.15004.

Shuoqi Chang, Tiangen Chang, Qingfeng Song, Jun Wu, Yi Luo, Xiaolong Chen, Xin-Guang Zhu*, Qiyun Deng* (2020) Architectural and physiological features to gain high yield in an elite rice line YLY1. Rice, 13:60, https://doi.org/10.1186/s12284-020-00419-y.

Jemaa Essemine, Mingnan Qu, Ming-Ju Amy Lyu; Qingfeng Song; Naveed Khan; Genyun Chen, Peng Wang, Xin-Guang Zhu (2020) Photosynthetic and transcriptomic responses of two C4 grass species with different NaCl tolerance. Plant Physiology Journal. 253:153244, https://doi.org/10.1016/j.jplph.2020.153244.

Mingnan Qu, Jemaa Essemine, Shuoqi Chang, Ming Li, Tiangen Chang, Gen-Yun Chen and Xin-Guang Zhu* (2020) Genome-wide association study unravels LRK1 as a dark respiration regulator in rice (Oryza sativa L.). International Journal of Molecular Sciences, 21(14):4930, https://doi.org/10.3390/ijms21144930.

Tiangen Chang, Qingfeng Song, Changpeng Xin, Xin-Guang Zhu (2020) An in situ approach to characterizing photosynthetic gas exchange of rice panicle. Plant Method, 16:92, https://doi.org/10.1186/s13007-020-00633-1.

Jemaa EssemineMing-Ju Amy LyuMingnan Qu, Shahnaz Perveen, Naveed KhanQingfeng Song, Genyun Chen and Xin-Guang Zhu* (2020) Contrasting responses of plastid terminal oxidase activity under salt stress in two C4species with different salt tolerance. Frontiers in Plant Physiology, 11:1009, https://doi.org/10.3389/fpls.2020.01009.

Ming-Ju Amy Lyu, Yaling Wang, Jianjun Jiang, Xinyu Liu, Genyun Chen, and Xin-Guang Zhu* (2020) Evolutionary changes of phosphoenolpyruvate transporter (PPT) during the emergence of C4 photosynthesis. Frontiers in Plant Physiology, 11:935, https://doi.org/10.3389/fpls.2020.00935.

Zai Shi, Tiangen Chang, Faming Chen, Honglong Zhao, Qingfeng Song, Mengyao Wang, Yanjie Wang, Zhiwei Zhou, Chongrong Wang, Shao-chuan Zhou, Baoshan Wang, Genyun Chen, Xin-Guang Zhu* (2020) Factors contributing to stronger early vigor in the rice cultivar 9311 as compared to Huanghuazhan. Scientific Reports, 10:14813, https://doi.org/10.1038/s41598-020-71913-y.

Shahnaz Perveen, Mingnan Qu, Faming Chen, Jemaa Essemine, Naveed khan, Mingju Lv, Tiangen Chang, Qingfeng Song, Gen-Yun Chen, Xin-Guang Zhu* (2020) Over-expression of Maize transcription factor mEmBP-1 increases photosynthesis, biomass and yield in rice. Journal of Experimental Botany, 71(16):4944-4957, https://doi.org/10.1093/jxb/eraa248.  

Daquan Xu, Xin-Guang Zhu (2020) Maize-Rice, Plant Physiology Journal,  56(7):1313-1320, https://doi.org/10.13592/j.cnki.ppj.2020.0044.

Xin-Guang Zhu, Tiangen Chang, Qingfeng Song, Shuoqi Chang, Chongrong Wang, Guoqing Zhang, Ya Guo, Shaochuan Zhou (2020) ePlant: scientific connotations, bottlenecks, and development strategies. Synthetic Biology, 1(3):285-297, https://doi.org/10.12211/2096-8280.2020-018.

Xin-Guang Zhu*, Donald R Ort, Martin A.J. Parry and Susanne von Caemmerer* (2020) A wish list for synthetic biology in photosynthesis research, Journal of Experimental Botany. 71(7): 2219-2225, https://doi.org/10.1093/jxb/eraa075.  

Qingfeng Song,Venkatraman Srinivasan, Stephen P Long, Xin-Guang Zhu (2019) Decomposition analysis on soybean productivity increase under elevated CO2 using 3D canopy model reveals synergistic effects of CO2 and light in photosynthesis. Annals of Botany, https://doi.org/10.1093/aob/mcz163.

Zhana Duren, Yaling Wang, Jiguang Wang, Xing-Ming Zhao, Le Lv, Xiaobo Li, Jingdong Liu*, Xin-Guang Zhu*, Luonan Chen*, and Yong Wang* (2019) Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana.NPJ Systems Biology and Applications, 5:28, https://doi.org/10.1038/s41540-019-0106-3.  0

Zai Shi#, Tiangen Chang#, Genyun Chen, Qingfeng Song, Yanjie Wang, Zhiwei Zhou, Mengyao Wang, Baoshan Wang* and Xin-Guang Zhu*(2019) Dissection of mechanisms for high yield in two elite rice cultivars. Field Crop Research, 241:107563, https://doi.org/10.1016/j.fcr.2019.107563.

Youfa Liu, Shuoqi Chang, Tiangen Chang, Yang Ouyang, Qiyun Deng, Shitou Xia*, Xin-Guang Zhu*(2020) QTL mapping of cold tolerance and analysis of heterosis of super hybrid rice Y Liangyou II. Molecular Plant Breeding. 2020, 18(07):2233-2243. https://doi.org/10.13271/j.mpb.018.002233.

Saber Hamdani#, Hongru Wang, Guangyong Zheng, Shahnaz Perveen, Mingnan Qu, Naveed Khan, Waqasuddin Khan, Jianjun Jiang, Ming Li, Xinyu Liu, Xiaocen Zhu, Govindjee, Chengcai Chu* and Xin-Guang Zhu*(2019), Genome-wide association study identifies variation of glucosidase being linked to natural variation of the maximal quantum yield of photosystem II, Physiologia Plantarum, 166: 105–119, https://doi.org/10.1111/ppl.12957.

Pan Li, Shuoqi Chang, Tiangen Chang, Xiang Ouyang, Jun Wu, Qiyun Deng, Shitou Xia, Xin-Guang Zhu*(2020). QTL Mapping of leaf chlorophyll content in the recombinant inbred lines population of a super hybrid rice Y Liang You 2. Molecular Plant Breeding, 18(12):3944-3951, https://doi.org/10.13271/j.mpb.018.003944.

Xin-Guang Zhu (2019) Developing the nuts, bolts, theoretical frameworks and community infrastructures to support global plant systems biology research. In silico Plants, https://doi.org/10.1093/insilicoplants/diz002.

Tiangen Chang, Shuoqi Chang, Qingfeng Song, Shahnaz Perveen and Xin-Guang Zhu (2019) Systems models, phenomics and genomics: three pillars for developing High-Yielding Photosynthetically Efficient Crops (HYPEC). In silico Plants, 1(1):diy003, https://doi.org/10.1093/insilicoplants/diy003.

Tian-Gen Chang, Honglong Zhao, Ning Wang, Qingfeng Song, Xiaojuan Fan, Yi Xiao, andXin-Guang Zhu(2019) A three-dimensional canopy photosynthesis model in rice with a complete description of the canopy architecture, leaf physiology, and mechanical properties.Journal of Experimental Botany,70(9): 2479–2490,https://doi.org/10.1093/jxb/ery430.

Changsong Zou, Leiting Li, Daisuke Miki, Delin Li, Qiming Tang, Lihong Xiao, Santosh Rajput, Ping Deng, Li Peng, Wei Jia, Ru Huang, Meiling Zhang, Yidan Sun, Jiamin Hu, Xing Fu, Patrick Schnable, Yuxiao Chang, Feng Li, Hui Zhang, Baili Feng, Xinguang Zhu, Renyi Liu, James Schnable, Jian-Kang Zhu, and Heng Zhang (2019) The genome of broomcorn millet. Nature Communication. 10: 436, https://doi.org/10.1038/s41467-019-08409-5.

Xin-Guang Zhu, Yan Xiong, Meihua Ruan, Xiao Liu, Jian Xu and Chao Zhong (2018) Research status and future development strategies of synthetic biology in photosynthesis. Bulletin of Chinese Academy of Sciences 33, 1239-1248.

Pan Li, Tiangen Chang, Shuoqi Chang, Xiang Ouyang, Mingnan Qu, Qingfeng Song, Langtao Xiao, Shitou Xia, Qiyun Deng,Xin-Guang Zhu(2018) Systems model guided rice yield improvements based on genes controlling source, sink and flow.Journal of Integrative Plant Biology,60, 1154-1180.https://doi.org/10.1111/jipb.12738.

Jisen Zhang, Xingtan Zhang, Haibao Tang, Qing Zhang, et al. (2018) Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics, 50 ,1565-1573. https://doi.org/10.1038/s41588-018-0237-2.

Saber Hamdani, Naveed Khan, Shahnaz Perveen, Mingnan Qu, Jianjun Jiang, Govindjee and Xin-Guang Zhu (2018) Changes in the photosynthesis properties and photoprotection capacity in rice (Oryza sativa) grown under red, blue or white light. Photosynthesis Research 139, 207-121. https://doi.org/10.1007/s11120-018-0589-6.

Tiangen Chang, Xin-Guang Zhu (2018) Systematic Optimization of Whole Plant Carbon Nitrogen Interaction (WACNI) to Support Crop Design for Greater Yield. BioRxiv. https://doi.org/10.1101/286112.

Ming-Ju Amy Lyu, Udo Gowik, Peter Westhoff, Yimin Tao, Steve Kelly, Sarah Covshoff, Harmony Clayton, Julian M. Hibberd, Rowan F. Sage, Martha Ludwig, Gane Ka-Shu Wong, Xin-Guang Zhu (2018) The Coordination and Jumps along C4 Photosynthesis Evolution in the Genus Flaveria. BioRxiv. https://doi.org/10.1101/460287.

Qingfeng Song, Mingnan Qu, Jianlong Xu, Xin-Guang Zhu (2018) Theory, molecular approach and perspectives on canopy light use efficiency. Life Sciences, 33(11). https://doi.org/10.16418/j.issn.1000-3045.

Mingnan Qu, Guangyong Zheng, Jemaa Essmine, Saber Hamdani, Qingfeng Song, Hongru Wang, Chengcai Chu, Xavier Sirault and Xin-Guang Zhu. Leaf photosynthetic parameters related to biomass accumulation in a global rice diversity panel. Plant Physiology, 75:248-258, https://doi.org/10.1104/pp.17.00332.

Yi Xiao and Xin-Guang Zhu (2017) Component of mesophyll resistance and their environmental responses. Plant Cell and Environment 40:2729-2742. https://doi.org/10.1111/pce.13040.  

Qingfeng Song, Yu Wang, Mingnan Qu, Donald R Ort,Xin-Guang Zhu. The impact of modifying photosystem antenna size on canopy photosynthetic efficiency. Plant Cell and Environment40:2946-2957.https://doi.org/10.1111/pce.13041.

Yi Xiao, Tiangen Chang, Qingfeng Song, Shuyue Wang, Danny Tholen, Yu Wang, Changpeng Xin, Guangyong Zheng, Honglong Zhao, Xin-Guang Zhu (2017) ePlant for quantitative and predictive plant science research in the big data era. Quantitative Biology. 5(2):260-271, https://doi.org/10.1007/s40484-017-0110-9.   

Amy Marshall-Colon, Stephen P. Long, Douglas K. Allen, Gabrielle Allen, Daniel A. Beard, Bedrich Benes, Susanne von Caemmerer, AJ Christensen, Donna J. Cox, John C. Hart, Peter M. Hirst, Kavya Kannan, Daniel S. Katz, Jonathan P. Lynch, Andrew J. Millar, Balaji Panneerselvam, Nathan D. Price, Przemyslaw Prusinkiewicz, David Raila, Rachel G. Shekar, Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Eberhard O. Voit, Yu Wang, Xinyou Yin, Xin-Guang Zhu (2017) Crops in silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform.  Frontiers in Plant Science doi: 8:786. https://doi.org/10.3389/fpls.2017.00786.  

Rebecca A Slattery, Andy VanLoocke, Carl J Bernacchi, Xin-Guang Zhu, Donald R Ort (2017) Photosynthesis, light use efficiency, and yield of reduced-chlorophyll soybean mutants in field conditions. Frontiers in Plant Science, 8:549, https://doi.org/10.3389/fpls.2017.00549.

Yu Wang, Qingfeng Song, Deepak Jaiswal, de Souza Amanda, Stephen P Long,Xin-Guang Zhu(2017) Development of a three-dimensional ray-tracing model of sugarcane canopy photosynthesis and its application in assessing impacts of varied row spacing.BioEnery Research,10:626-634,https://doi.org/10.1007/s12155-017-9823-x.

Tian-Gen Chang and Xin-Guang Zhu (2017) Source sink interaction: a century old concept under the light of modern molecular systems biology. Journal of Experimental Botany, 66(16):4417-4431, https://doi.org/10.1093/jxb/erx002.  

Jemaa Essemine, Yi Xiao, Hualing Mi, Xin-Guang Zhu (2017) Cyclic electron flow may provide some protection against PSII photoinhibition in rice (Oryza sativa L.) leaves under heat stress. Journal of Plant Physiology 211: 138-146. https://doi.org/10.1016/j.jplph.2017.01.007.

Jiajia Xu, Yuanyuan Li, Yaling Wang, Xinyu Liu, Xin-Guang Zhu (2017). Altered expression profiles of microRNA families during de-etiolation of maize and rice leaves. BMC Research Notes, 10:108, https://doi.org/10.1186/s13104-016-2367-x.

Xin Wang, Wei Liu, Changpeng Xin, Yi Zheng, Yanbing Cheng, Su Sun, Runze Li, Xin-Guang Zhu, Susie Y Dai, Peter M Rentzepis, Joshua S Yuan. Enhanced limonene production in cyanobacteria reveals photosynthesis limitations. PNAS 113:14225-14230. https://doi.org/10.1073/pnas.1613340113.

Tian-Gen Chang, Changpeng Xin, Mingnan Qu, Hong-Long Zhao, Qing-Feng Song, Xin-Guang Zhu (2017) Evaluation of protocols for measuring field-grown rice leaf photosynthetic properties. Rice Science 24:1-9. https://doi.org/10.1016/j.rsci.2016.08.007.

Xin-Guang Zhu, Martin Parry, Yonglong Lu, Matthew Heard, Guangguo Ying, Simon Vaughan, Jianbo Shen, Alan Jenkins, Yunpeng Wang, Silvia Lacorte, Tingping Ouyang, Francisco Pedrero Salcedo, Jun Niu, John Quinton, Chunling Luo, Fusuo Zhang, Gan Zhang, Achim Dobermann, William Davies, Kevin Jones, and David Tyfield (2016). Building the new international science of the agri-food-water-environment nexus. Ecosystem Health and Sustainability 2016, 2(11): e01249, https://doi.org/10.1002/ehs2.1249.

Shuyue Wang, Danny Tholen, Xin-Guang Zhu (2016) C4 photosynthesis in C3 rice: a theoretical analysis of biochemical and anatomical factors. Plant Cell and Environment 40(1): 80-94. https://doi.org/10.1111/pce.12834.

Yi Xiao, Danny Tholen, Xin-Guang Zhu (2016) The influence of leaf anatomy on the internal light environment and photosynthetic electron transport rate. Journal of Experimental Botany 67(21): 6021-6035.  https://doi.org/10.1093/jxb/erw359.

Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen, and Xin-Guang Zhu (2016) CMIP: a software package capable of reconstructing gene regulatory networks using genome-scale data with parallel computing strategy. BMC Bioinformatics 17(17): 137-144. https://doi.org/10.1186/s12859-016-1324-y.

Yi Xiao and Xin-Guang Zhu (2016) Chlorophyll fluorescence and stable isotope signals in photosynthesis. Plant Physiology Journal, 52, 1663 – 1670, https://doi.org/10.13592/j.cnki.ppj.2016.1009.

Jiajia Xu, Andrea Bra?utigam, Yuanyuan Li, Andreas P. M. Weber and Xin-Guang Zhu (2016) Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. Journal of Experimental Botany 67: 5105-5117. https://doi.org/10.1093/jxb/erw275.

Qing-Feng Song, Dairui Chen, Stephen P Long, Xin-Guang Zhu (2016) A user-friendly means to scale from the biochemistry of photosynthesis to whole crop canopies and production in time and space - development of Java WIMOVAC. Plant Cell and Environment 40: 51-55.

Zehong Ding, Yang Zhang, Yi Xiao, Fangfang Liu, Minghui Wang, Xin-Guang Zhu, Peng Liu, Qi Sun, Wenquan Wang, Ming Peng, Tom Brutnell, Pinghua Li (2016) Transcriptome response of cassava leaves under natural shade. Scientific Reports (doi: 10.1038/srep31673).

Michael Hodges, Younès Dellero, Olivier Keech, Marco Betti, Agepati S. Raghavendra, Rowan Sage, Xin-Guang Zhu, Douglas K. Allen, Andreas P.M. Weber (2016) Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network. Journal of Experimental Botany 67: 3015-3026.

Jemaa Essemine, Mingnan Qu, Hualing Mi and Xin-Guang Zhu (2016) Response of chloroplast NAD(P)H dehydrogenase-mediated cyclic electron flow to a shortage or lack in ferredoxin-quinone oxidoreductase-dependent pathway in rice following short-term heat stress. Frontiers in Plant Science 7: 383 doi: 10.3389/fpls.2016.00383.

Mingnan Qu, Saber Hamdani, Wenzhen Li, Shimei Wang, Jiuyou Tang, Zhuo Chen, Qingfeng Song, Ming Li, Honglong Zhao, Tiangen Chang, Chengcai Chu and Xin-Guang Zhu (2016) Rapid stomatal response to fluctuating light: an under-explored mechanism to improve drought tolerance in rice. Functional Plant Biology 43: 727-738.

Chensi Cao, Jiajia Xu, Guangyong Zheng, Xin-Guang Zhu (2016) Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis. BMC Genomics 17:201.

Qing-Feng Song, Han Xiao, Xianglin Xiao, Xin-Guang Zhu (2016) A new canopy photosynthesis and transpiration measurement system (CAPTS) for canopy gas exchange research. Agricultural and Forest Meteorology 217:101-107.

Qing-Feng Song, Chengcai Chu, Martin Parry, Xin-Guang Zhu (2016) Genetics based dynamic systems model of canopy photosynthesis: the key to improve light and resource use efficiencies for crops. Food and Energy Security, doi: 10.1002/fes3.74.

Yimin Tao, Mingzhu Lyv, Xin-Guang Zhu (2016) Transcriptome comparisons shed light on the pre-condition and potential barrier for C4 photosynthesis evolution in eudicots. Plant Molecular Biology 91: 193-209.

Shuoqi Chang, Tiangen Chang, Qingfeng Song,Xin-Guang Zhu*, Qiyun Deng* (2016) Photosynthetic and agronomic traits of an elite hybrid rice Y-Liang-You 900 with a record-high yield.Field Crops Research187: 49-57.

Justin McGrith, Amy M. Betzelberger, Shaowen Wang, Eric Shook, Xin-Guang Zhu, Steve P Long, Elizebeth A Ainsworth (2015) An analysis of ozone damage to historical maize and soybean yields in the United States. PNAS 112:14390-5.

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang M-L, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo H-B, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X-G, Yang X, Smith JAC, Cushman JC, Paull RE, Yu Q (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genetics 47: 1435-1442.

Xin-Guang Zhu, Jonathan P. Lynch, David S. LeBauer, Andrew J. Millar, Mark Stitt, Stephen P. Long (2015) Plants in silico: why, why now and what?--an integrative platform for plant systems biology research. Plant Cell and Environment 39:1049-1057.

Donald R. Ort, Sabeeha S. Merchant, Jean Alric, Alice Barkan, Robert E. Blankenship, Ralph Bock, Roberta Croce, Maureen R. Hanson, Julian Hibberd, Derek L. Lindstrom, Stephen P. Long, Thomas A. Moore, James Moroney, Krishna K. Niyogi, Martin Parry, Pamela Peralta-Yahya, Roger Prince, Kevin Redding, Martin Spalding, Klaas van Wijk, Wim F.J. Vermaas, Susanne von Caemmerer, Andreas Weber, Todd Yeates, Joshua Yuan,Xin-Guang Zhu(2015) Redesigning photosynthesis to sustainably meet global food and bioenergy demand.PNAS112:8529-36.

Ming-Ju Amy Lyu, Udo Gowik, Steve Kelly, Sarah Covshoff, Julia Mallmann, Peter Westhoff, Julian M. Hibberd, Matt Stata, Rowan F. Sage, Haorong Lu, Xiaofeng Wei, Gane Ka-Shu Wong, Xin-Guang Zhu (2015) RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evolutionary Biology 15:116.

Chengzhen Liang, Guangyong Zheng, Wenzhen Li, Yiqin Wang, Bin Hu, Hongru Wang, Hongkai Wu, Yangwen Qian, Xin-Guang Zhu, Duan Xian Tan, Shou-Yi Chen and Chengcai Chu (2015) Melatonin delays leaf senescence and enhances salt stress tolerance in rice. Journal of Pineal Research 59: 91-101.

Johannes Anton Hofberger, Aldana M. Ramirez, Xin-Guang Zhu, Harro J. Bouwmeester, Robertus C. Schuurink, Eric Schranz (2015) Large-scale evolutionary analysis of genes and supergene clusters from terpenoid modular pathways provides insights into metabolic diversification in flowering plants. PLOS One 10(6):e0128808. doi: 10.1371/journal.pone.0128808. 19(1):43-51.

Stephen P. Long, Amy Marshall-Colon,Xin-Guang Zhu(2015) Meeting the global food demand of the future by engineering crop photosynthesis and yield potential.Cell161: 56-66.

Jinling Zhou, Zuohuan Zheng, Xin-Guang Zhu (2015) A mathematical model of photosynthetic carbon metabolism has mulitple steady states under the same parameter condition. Acta Mathematicae Applicatae Sinica 32: 591-604.

Changpeng Xin, Danny Tholen, Xin-Guang Zhu (2015) The benefit of photorespiratory bypass – How can they work? Plant Physiology 167: 574-585.

Saber Hamdani, Mingnan Qu, Chang-Peng Xin, Chengcai Chu, Govindjee, Xin-Guang Zhu (2015) Variations between the photosynthetic properties of elite and landrace Chinese rice cultivars revealed by simultaneous measurements of 820 nm transmission signal and chlorophyll a fluorescence induction. Journal of Plant Physiology 177: 128-138.

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. Resource (SI on Feeding the world in 2050) 16.

Erik van den Bergh, Canan Külahoglu, Andrea Br?utigam, 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 1: 2-9.

Taiyu Chen, Xin-Guang Zhu, Yongjun Lin (2014) Major alterations in transcript profiles between C3–C4 and C4 photosynthesis of an amphibious species Eleocharis baldwinii. Plant Molecular Biology 86: 93-110.

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, Xin-Guang 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.

Xianbin Yu, Guangyong Zheng, Lanlan Shan, Guofeng Meng, Martin Vingron, Qi Liu, Xin-Guang Zhu (2014) Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. Frontiers in Plant Sciences. doi: 10.3389/fpls.2014.00273.

Yuanyuan Li, Jiajia Xu, Noor UI Haq, Hui Zhang, Xin-Guang Zhu (2014) Was low CO2 a driving force of C4 evolution? Arabidopsis responses to long-term low CO2 stress. Journal of Experimental Botany 65: 3657-67.

Yu Wang, Stephen P Long, Xin-Guang Zhu (2014) Elements required for an efficient NADP-Malic Enzyme type C4 photosynthesis. Plant Physiology 164: 2231-2246.

Yu Wang, Andrea Br?utigam, Andreas PM Weber, Xin-Guang Zhu (2014) Three distinct biochemical subtypes of C4 photosynthesis? A modeling analysis. Journal of Experimental Botany 65:3567-78.

Mark Stitt and Xin-Guang Zhu (2014) The large pools of metabolites involved in intercellular metabolite shuttles in C4 photosynthesis provide enormous flexibility and robustness in a fluctuating light environment. Plant Cell and Environment 37:1985-8.

Changpeng Xin, Jin Yang, Xin-Guang Zhu (2013) A model of chlorophyll a fluorescence induction kinetics with explicit description of structural constraints of individual photosystem II units. Photosynthesis Research 117: 339-354.

Yu Peng, Henry CM Leung, SM Yiu, Ming-Ju Lv, Xin-Guang Zhu, Francis YL Chin (2013) IDBA-Tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels. Bioinformatics 29: i326–i334.

Mercedes Xu,Yuanyuan Li, Hui Zhang, Sisi Wang, Ye Tian, Xin-Guang Zhu (2013) Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. Plant Molecular Biology 83: 77-87.

Qingfeng Song, Guilian Zhang, Xin-Guang Zhu (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: 108-124.

Xin-Guang Zhu, Yu Wang, Donald R Ort and Stephen P Long (2012) e-Photosynthesis: a comprehensive dynamic mechanistic model of C3 photosynthesis: from light capture to sucrose synthesis. Plant Cell & Environment 36:1711-27.

Danny Tholen, Carolina Boom, Xin-Guang Zhu (2012) Opinion: prospects for improving photosynthesis by altering leaf anatomy. Plant Science 197: 92-101.

Danny Tholen, Gilbert Ethier, Steeve Pepin, Bernard Genty, Xin-Guang Zhu (2012). Variable mesophyll conductance revisited -- theoretical background and experimental implications. Plant Cell & Environment 35: 2087-103.

Xin-Guang Zhu, Qingfeng Song, Donald R Ort (2012) Elements of a dynamic systems model of canopy photosynthesis. Current Opinion in Plant Biology 15: 237-44.

Yuanyuan Li, Hui Zhang, Xin-Guang Zhu (2011) C4 rice: are we ready for the challenge? Plant Physiology Journal 47: 1-10.

Fu-Qiao Xu, Wei-Min Ma, Xin-Guang Zhu (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.

Rowan Sage, Xin-Guang Zhu (2011) Exploiting the engine of C4 photosynthesis. Journal of Experimental Botany 62:2989-3000.

Vivek Thakur, Samart Wanchana, Mercedes Xu, Richard Bruskiewich, William Paul Quick, Axel Mosig, Xin-Guang Zhu (2011) Characterization of parameters in plant microRNA prediction. BMC Genomics 12:108.

Danny Tholen, Xin-Guang Zhu (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.

Xin-Guang Zhu, Guilian Zhang, Danny Tholen, Yu Wang, Changpeng Xin, Qingfeng Song (2011) The next generation models for crops and agro-ecosystems. Science China: Information Sciences 54(3) 1-9.

Donald R Ort, Xin-Guang Zhu, Anastasios Melis (2011) Optimizing antenna size to maximize photosynthetic efficiency. Plant Physiology 155:79-85.

Wei Pan, John Fettig, Eric de Sturler, Xin-Guang Zhu (2010) Impacts of different metabolite measurement protocols on estimating parameters in complex photosynthetic carbon metabolism models. Lecture Notes in Operations Research  13: 373–380.

Xin-Guang Zhu, Lanlan Shan, Yu Wang, William Paul Quick (2010) C4 Rice – an arena for systems biology research. Journal of Integrative Plant Biology 52:762-70.

Thomas P. Brutnell, Wang Lin, Swartwood Kerry, Goldschmidt Alexander, Jackson David, Xin-Guang Zhu, Elizabeth Kellogg and Joyce Van Eck (2010) Setaria viridis: a model for C4 photosynthesis. Plant Cell 22:2537-44.

Martin A. J. Parry, Reynolds Matthew, Michael E. Salvucci, Christine Raines, P. John Andralojc, Xin-Guang Zhu, Dean Price, Anthony G. Condon,  Robert T. Furbank. (2010) Raising yield potential of wheat. II. Increasing photosynthetic capacity and efficiency. Journal of Experimental Botany 62(2):453-67. 10.1093/jxb/erq304.

Yi Yang, Zili Zhang, YiXue Li*, Xin-Guang Zhu*, Qi Liu* (2010) Identifying cooperative transcription factors by combining ChIP-chip data and knockout data. Cell Research 20: 1276-1278.

Xin-Guang Zhu, Stephen P Long, Donald R Ort (2010) Improving photosynthetic eficiency for greater yield. Annual Review of Plant Biology 61: 235-261.

Xin-Guang Zhu (2010) Systems-level modeling—A new approach for engineering efficient photosynthetic machinery. Journal of Biotechnology 149: 201-209.

Min-Rui Fei, Yi-Juan Di, Zeng-Rong Liu, Xin-Guang Zhu (2009) Modeling and simulation of plant metabolism process. Bulletin of Chinese Computer Science Society 5(9):22-25.

Xin-Guang Zhu, Stephen P Long, Donald R Ort (2008) What is the maximum efficiency with which photosynthesis can convert solar energy into biomass? Current Opinion in Biotechnology 19: 153-159.

Xin-Guang Zhu, Eric de Sturler, Rafal Alba (2008) A simple model of the Calvin cycle has only one physiologically feasible steady state under the same external condition. Nonlinear Analysis 3:1490-1499.

Shaowen Wang, Xin-Guang Zhu (2008) Coupling Cyberinfrastructure and Geographic Information Systems to Empower Ecological and Environmental Research. Bioscience 58: 6-7.

Xin-Guang Zhu, Eric de Sturler, Stephen P Long (2007) Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: a numerical simulation using an evolutionary algorithm.  Plant Physiology 145: 513-526.

Xin-Guang Zhu, Govindjee, Neil R Baker, Eric de Sturler, Stephen P Long (2005) Chlorophyll a fluorescence induction kinetics in leaves predicted from a model describing each discrete step of excitation energy and electron transfer associated with Photosystem II.  Planta 223: 114-133.

Xin-Guang Zhu, Archie Portis, Stephen P Long (2004) Would transformation of C3 crop plants with foreign Rubisco increase productivity? A computational analysis extrapolating from kinetic properties to canopy photosynthesis. Plant Cell and Environment 27:155-165.

Xin-Guang Zhu, John Whitmarsh, Donald R Ort, Stephen P Long (2004) The slow reversibility of photosystem II thermal energy dissipation on transfer from high to low light may cause large losses in carbon gain by crop canopies: a theoretical analysis. Journal of Experimental Botany 55: 1167-1175.

Xin-Guang Zhu, Qiang Wang, Qi-De Zhang, CongMing Lu, TingYun Kuang (2002) The response of photosynthesis to salt stress in winter wheat. Plant Nutrition and Fertilizer Science 8: 177 – 180.

Xin-Guang Zhu, QiDe Zhang, Qiang Wang, CongMing Lu (2001) Effects of photoinhibition and its recovery on photosynthetic functions of winter wheat under salt stress. Acta Botanica Sinica 43: 1250-1254 (Now Journal of Integrative Plant Biology).

Xin-Guang Zhu, Qi-De Zhang, TingYun Kuang (2000) Damage to photosynthetic function of wheat by NaCl results mainly from its ionic effect. Chinese Bulletin of Botany 17(4) 360-365.

Xin-Guang Zhu, Qi-De Zhang, TingYun Kuang (1999) Effects of NaCl stress on light utilization and dissipation by PSII. Acta Biophysica Sinica 15: 787-791.

Xin-Guang Zhu, Qi-De Zhang (1999) The effects of NaCl on photosynthesis performance. Chinese Bulletin of Botany 4: 332-338.