PUBLICATIONS

PUBLICATIONS

1. Mingnan Qu, Guangyong Zheng, Jemaa Essmine, Saber Hamdani, Qingfeng Song, Hongru Wang, Chengcai Chu, Xavier Sirault and Xin-Guang Zhu (2017). Leaf photosynthetic parameters related to biomass accumulation in a global rice diversity panel. Plant Physiology (doi: 10.1104/pp.17.00332).

2. Yi Xiao and Xin-Guang Zhu (2017) Component of mesophyll conductance and their environmental responses. Plant Cell and Environment (doi: 10.1111/pce.13040).

3. Qingfeng Song, Yu Wang, Mingnan Qu, Donald R Ort, Xin-Guang Zhu (2017). The impact of modifying antenna size of photosystem II on canopy photosynthetic efficiency – Development of a new canopy photosynthesis model scaling from metabolism to canopy level processes. Plant Cell and Environment (doi: 10.1111/pce.13041).

4. 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 (Accepted).

5. 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. doi: 10.3389/fpls.2017.00786.

6. 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

7. 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 (Accepted).

8. 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 (Accepted)..

9. Jemaa Essemine, Yi Xiao, Hualing Mi, Xin-Guang Zhu (2017). Cyclic electron flow may provide some protection against PSII photoinhbition in rice (Oryza sativa L.) leaves under heat stress. Journal of Plant Physiology (Accepted) .

10. 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. Building the new international science of the agri-food-water-environment nexus. Ecosystem Health and Sustainability (Accepted).

11. 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. DOI: 10.1111/pce.12834 .

12. 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 (Accepted).

13. Qingfeng 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 DOI: 10.1111/pce.12816.

14. Jiajia Xu, Andrea Brautigam, Andreas PM Weber, Xinguang Zhu(2016)Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomics data from greening leaves.Journal of Experimental Botany. 67(17), 5105-5117.

15. Mingnan Qu, Saber Hamdani, Wenzhen Li, Shimei Wang, Jiuyou Tang, Zhuo Chen, Qingfeng Song, Ming Li, Honglong Zhao, Tiangen Chang, Chengcai Chu and Xinguang Zhu (2016) Rapid stomatal response to fluctuating light: an under-explored mechanism to improve drought tolerance in rice.Functional plant biology. 43(8) 727-738 .

16. Jemaa Essemine, Mingnan Qu, Hualing Mi and Xinguang 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. Front Plant Sci.7:283.

17. 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.

18. Yimin Tao, Ming-Ju Amy Lyu, Xin-Guang Zhu(2016) Transcriptome comparisons shed light on the pre-condition and potential barrier for C4 photosynthesis evolution in eudicots. Plant Mol Biol. 91(1-2):193-209.

19. Qingfeng Song, Chengcai Chu, Martin A.J.Parry and XinGuang 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. 5(1):18-25.

20. Qingfeng 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.

21. Ray Ming, Robert Van Buren, et al, Xin-Guang Zhu, Andrew Smith, John C. Cushman, Robert E. Paull, Qingyi Yu. The pineapple genome and evolution of CAM photosynthesis. Nature Genetics 47(12):1435-1442.

22. 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(5):1049-1057.

23. 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.

24. Donald R. Ort, Sabeeha S. Merchant, Jean Alric, Alice Barkan, Robert E. Blankenship, 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.Redesigning photosynthesis to sustainably meet global food and bioenergy demand.PNAS.112(28):8529-36.

25. Stephen P. Long, Amy Marshall-Colonand Xin-Guang Zhu (2015) Meeting the Global Food Demand of the Future by Engineering Crop Photosynthesis and Yield Potential.Cell.161: 56-66.

26. Fang Yuan, Ming-Ju Lv, Bingying Leng, Guangyong Zheng, Zhongtao Feng, Pinghua Li, Xin-Guang Zhu, Baoshan Wang (2015) Comparative transcriptome analysis of developmental stages of the Limonium bicolor leaf generates insights into salt gland differentiation.Plant Cell and Environment .38(8):1637-57.

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

28. 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.

29. 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.

30. Erik van den Bergh, Canan Kulahoglu, 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.

31. Chunyun Jiang, Jiajia Mercedes Xu, Changpeng Xin, Danny Tholen, Hui Zhang, Xin-Guang 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: 366-374.

32. 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 .86: 93-110.

33. 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.

34. 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.5:373.

35. Yi-Bo Chen, Tian-Cong Lu, Hong-Xia Wang, Jie Shen, Tian-Tian Bu, Qing Chao, Zhi-Fang Gao, Xin-Guang Zhu, Yue-Feng Wang, Bai-Chen Wang (2014) Post-translational modification of maize chloroplast pyruvate orthophosphate dikinase reveals the precise regulatory mechanism of its enzyme activity .Plant Physiology .165:534-549.

36. 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.

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

38. 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.

39. Mark Stitt andXin-Guang Zhu (2014) The large pools of metabolites involved in intercellular metabolite shuttles in C-4 photosynthesis provide enormous flexibility and robustness in a fluctuating light environment. Plant Cell and Environment.37:1985-8.

40. Shifeng Cheng, Erik van den Bergh, Peng Zeng, Xiao Zhong, Jiajia Xu, Xin Liu, Johannes Hofberger, Suzanne de Bruijn, Amey S. Bhide, Chao Bian, Jing Chen, Guangyi Fan, Kerstin Kaufmann, Jocelyn C. Hall, Annette Becker, Chengcheng Shi, Zhijun Zheng,Wujiao Li,Mingju Lv, Yimin Tao, Xun Xu, Junyi Wang, Hongfeng Zou, Zhiwu Quan, Julian M. Hibberd,Boon Leong Lim, Xin-Guang Zhu, Gengyun Zhang, M. Eric Schranz (2013) The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers.Plant Cell.25: 2813-2830.

41. 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.

42. 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.

43. 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.

44. 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.

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

46. 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.

47. 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.

48. Fu-Qiao Xu, Wei-Min Ma, Xin-Guang Zhu (2011) Introducing pyruvate oxidase into the chloroplast of Chlamydomonas reinhardtiiincreases oxygen consumption and promotes hydrogen production.International Journal of Hydrogen Research .36: 10648-10654

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

50. 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.

51. 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.

52. 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.

53. 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.

54. 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.

55. 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.

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

57. Xin-Guang Zhu (2010) Systems-level modeling-A new approach for engineering efficient photosynthetic machinery.Journal of Biotechnology .149: 201-208.

58. 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.

59. 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 conditions.Nonlinear Analysis.3:1490-1499.

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

61. 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.

62. Stephen P Long, Xin-Guang Zhu, Shawna Naidu, Donald R Ort (2006) Can improvement in photosynthesis increase crop yields? Plant Cell and Environment.29: 315-330.

63. 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.

64. 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.

65. 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.