Publications

• Peng Zhang, Kainan Chen, Bing Xu, Jinghao Li, Cheng Hu, Joshua S. Yuan*, and Susie Y. Dai*

  Chem-Bio Interface Design for Rapid Conversion of CO2 to Bioplastics in an Integrated System. Chem, 2022, Accepted.

• Jinghao Li, Xiaohan Li, Yabin Da, Jiali Yu, Bin Long, Peng Zhang, Christopher Bakker, Bruce A. McCarl, Joshua S. Yuan & Susie Y. Dai*

  Sustainable environmental remediation via biomimetic multifunctional lignocellulosic nano-framework. Nature Communications, 2022, 13: 4368.

• Bin Long, Bart Fischer, Yining Zeng, Zoe Amerigian, Qiang Li, Henry Bryant, Man Li, Susie Y. Dai, Joshua S. Yuan*

  Machine learning-Informed and synthetic biology-enabled semi-continuous algal cultivation (SAC) to unleash renewable fuel productivity. Nature Communications, 2022, 13: 541.

• Man Li, Bin Long, Susie Y. Dai, James W. Golden, Xin Wang, and Joshua S. Yuan*

  Altered carbon partitioning enhances CO2 to terpene conversion in cyanobacteria. BioDesign Research, 2022, Article ID 9897425.

• Shrameeta Shinde, Sonali Singapuri, Zhenxiong Jiang, Bin Long, Danielle Wilcox, Camille Klatt, J. Andrew Jones, Joshua S. Yuan, Xin Wang

  Thermodynamics contributes to high limonene productivity in cyanobacteria. Metabolic Engineering Communications, 2022, e00193.

• Bing Xu, Qiang Li, Yuanqiao Pu, Shangxian Xie, Arthur J. Ragauskas, Jorge Arreola-Vargas, Zhi-Hua Liu, and Joshua S. Yuan*

  A unique bacterial pelletized cultivation platform in Rhodococcus opacus PD630 enhanced lipid productivity and simplified harvest for lignin bioconversion. ACS Sustainable Chemistry and Engineering, 2022, 10, 1083-1092.

• Peng Zhang, Susie Y. Dai, Joshua S. Yuan*

  Producing the “molecules of life” from carbon dioxide. Chem, 2021, 7, 3200-3202.

• Jorge Arreola-Vargas, Xianzhi Meng, Arthur J. Ragauskas, Joshua S. Yuan*

  Enhanced medium chain length-polyhydroxyalkanoate production by co-fermentation of lignin and holocellulose fractions. Green Chemistry, 2021, 23, 8226-8237.

• Zhi-Hua Liu, Naijia Hao, Yun-Yan Wang, Chang Dou, Furong Lin, Rongchun Shen, Renata Bura, David B. Hodge, Arthur J. Ragauskas, Bin Yang, Joshua S. Yuan*

  Transforming biorefinery designs with 'plug-In processes of lignin' to enable economic waste valorization. Nature Communications, 2021, 12, 3912.

• Cheng Hu, Mingzhen Zhao, Qiang Li, Zhihua Liu, Naijia Hao, Xianzhi Meng, Jinghao Li, Furong Lin, Chenxuan Li, Lei Fang, Susie Y. Dai, Arthur J. Ragauskas, Hung-Jue Sue, Joshua Yuan*

  Phototunable lignin plastics to enable recyclability. ChemSusChem, 2021, 14, 1-11.

• Bo Wang, Yao Xu, Xin Wang, Joshua S. Yuan, Carl H. Johnson, Jamey D. Young, Jianping Yu

  Comparative analysis of cyanobacteria species reveals a novel guanidine-degrading enzyme that controls genomic stability of ethylene-producing strains. Nature Communications, 2021, 12, 5150.

• Qiang Li, Cheng Hu, Mengjie Li, Phuc Truong, Jinghao Li, Hao-Sheng Lin, Mandar Naik, Sisi Xiang, Brian Jackson, Winson Chun-Hsin Kuo, Wenhao Wu, Yunqiao Pu, Arthur Ragauskas, and Joshua S Yuan*

  Enhancing multifunctional properties of renewable lignin carbon fiber via defining structure-property relationship using different biomass feedstock. Green Chemistry, 2021, 23, 3725.

• Man Li, Zhi-Hua Liu, Naijia Hao, Michelle L. Olson, Qiang Li, Samarthya Bhagia, Katy Kao, Arthur J. Ragauskas, Shangxian Xie and Joshua S Yuan*

  Co-optimization of carbohydrate and lignin processability by biomimicking biomass processing. Frontiers in Energy, 2021, 8, 194.

• Qiang Li, Cheng Hu, Mengjie Li, Phuc Truong, Mandar T Naik, Dwarkanath Prabhu, Leo Hoffmann Jr, William L Rooney, Joshua S. Yuan*

  Discovering biomass structural determinants defining the properties of plant-derived renewable carbon fiber. iScience, 2020, 23 (8), 101405.

• Zhi-Min Zhao, Zhi-Hua Liu, Yunqiao Pu, Xianzhi Meng, Jifei Xu, Joshua S. Yuan, and Arthur J. Ragauskas

  Tailoring lignin chemistry and developing fermentation process intensification to enhance biological lignin valorization. ChemSusChem, 2020, 13 (20), 5423-5432.

• Isha Kalra, Xin Wang, Marina Cvetkovska, Jooyeon Jeong, William McHargue, Ru Zhang, Norman PA Hüner, Joshua S Yuan, and Rachael M Morgan-Kiss

  Chlamydomonas sp. UWO 241 exhibits high cyclic electron flow and rewired metabolism under high salinity. Plant Physiology, 2020, 183 (2), 588-601.

• Shangxian Xie, Su Sun, Furong Lin, Muzi Li, Yunqiao Pu, Yanbing Cheng, Bing Xu, Zhihua Liu, Leonardo da Costa Sousa, Bruce E Dale, Arthur J Ragauskas, Susie Y Dai, Joshua S Yuan*

  Mechanism-guided design of highly efficient protein secretion and lipid conversion for biomanufacturing and biorefining. Advanced Science, 2019, 6(13), 1801980.

• Zhihua Liu, N Hao, Somnath Shinde, Yuqiao Pu, Xiaofeng Kang, Arthur J Ragauskas, Joshua S Yuan*

  Defining lignin nanoparticle properties through tailored lignin reactivity by sequential organosolv fragmentation approach (SOFA). Green Chemistry, 2019, 21 (2), 245-260.

• Q Li, M Li, HS Lin, C Hu, P Truong, T Zhang, HJ Sue, Y Pu, AJ Ragauskas, and Joshua S. Yuan*

  Non-solvent fractionation of lignin enhances carbon fiber performance. ChemSusChem, 2019, 12 (14), 3249-3256.

• Zhi-Hua Liu, Rosemary K Le, Matyas Kosa, Bin Yang, Joshua S. Yuan*, Arthur J Ragauskas

  Identifying and creating pathways to improve biological lignin valorization. Renewable and Sustainable Energy Reviews, 2019, 105, 349-362.

• Qiang Li, Cheng Hu, Heidi Clarke, Mengjie Li, Patrick Shamberger, Wenhao Wu, Joshua S. Yuan*

  Microstructure defines the electroconductive and mechanical performance of plant-derived renewable carbon fiber. Chemical Communications, 2019, 55 (84), 12655-12658.

• Zhi-Hua Liu, Somnath Dattatray Shinde, Shangxian Xie, Naijia Hao, Furong Lin, Man Li, Chang Geun Yoo, Arthur Ragauskas, Joshua S. Yuan*

  Cooperative valorization of lignin and residual sugar to polyhydroxyalkanoate (PHA) for enhanced yield and carbon utilization in biorefineries. Sustainable Energy and Fuels, 2019, 3 (8), 2024-2037.

• Zhi-Hua Liu, Naijia Hao, Somnath Shinde, Michelle L. Olson, Samarthya Bhagia, John R. Dunlap, Katy C. Kao, Xiaofeng Kang, Arthur J. Ragauskas, Joshua S. Yuan*

  Co-design of combinatorial organosolv pretreatment (COP) and lignin nanoparticles (LNPs) in biorefineries. ACS Sustainable Chemistry and Engineering, 2019, 7 (2), 2634-2647.

• Xiaolu Li, Yucai He, Libing Zhang, Zhangyang Xu, Haoxi Ben, Matthew J Gaffrey, Yongfu Yang, Shihui Yang, Joshua S Yuan, Wei-Jun Qian, Bin Yang

  Discovery of potential pathways for biological conversion of poplar wood into lipids by co-fermentation of Rhodococci strains. Biotechnology for Biofuels, 2019, 12 (1), 60.

• Yuqi Guo, Shangxian Xie, Joshua S. Yuan, Katy Kao

  Effects of seawater on carotenoid production and lipid content of engineered Saccharomyces cerevisiae. Fermentation, 2019, 5 (1), 6.

• Zhangyang Xu, Xiaolu Li, Naijia Hao, Chunmei Pan, Aftab Ahamed, John H Miller, Arthur J Ragauskas, Joshua S. Yuan, Bin Yang

  Kinetic understanding of nitrogen supply condition on biosynthesis of polyhydroxyalkanoate from benzoate by Pseudomonas putida KT2440. Bioresource Technology, 2019, 273, 538-544.

• Fujie Zhou, Pravat Karki, Shangxian Xie, Joshua S. Yuan, Lijun Sun, Robert Lee, Ryan Barborak

  Toward the development of performance-related specification for bio-rejuvenators. Construction and Building Materials, 2018,174, 443-455.

• Kristina M. Mahan, Rosemary K. Le, Tyrone Wells Jr., Seth Anderson, Joshua S. Yuan, Ryan J. Stoklosa, Aditya Bhalla, David B. Hodge, Arthur J. Ragauskas

  Production of single cell protein from agro-waste using Rhodococcus opacus. Journal of Industrial Microbiology & Biotechnology, 2018,1-7.

• Qiang Li, Mandar T. Naik, Hao-Sheng Lin, Cheng Hu, Wilson K. Serem, Li Liu, Pravat Karki, Fujie Zhou, Joshua S. Yuan*

  Tuning hydroxyl groups for quality carbon fiber of lignin. Carbon, 2018, 139, 500-511.

• Xujun Chen, Hao Chen, Joshua S. Yuan, Tobias G. Köllner, Yuying Chen, Yufen Guo, Xiaofeng Zhuang, Xinlu Chen, Yong-jun Zhang, Jianyu Fu, Andreas Nebenführ, Zejian Guo, and Feng Chen

  Rice terpene synthase gene OsTPS19 functions as (S)-limonene synthase in planta and its overexpression leads to enhanced resistance to the blast fungus Magnaporthe oryzae. Plant Biotechnology Journal, 2018.

• Cheng Zhao, Yong Kyoung Kim, Yining Zeng, Man Li, Xin Wang, Cheng Hu, Connor Gorman, Shiyou Ding, Joshua S. Yuan*

  Co-compartmentation of terpene biosynthesis and storage via synthetic droplet. ACS Synthetic Biology, 2018, 7, 774-781.

• Zhi-Hua Liu, Shangxian Xie, Furong Lin, Mingjie Jin, Joshua S. Yuan*

  Combinatorial pretreatment and fermentation optimization enabled a record yield on lignin bioconversion. Biotechnology for Biofuels, 2018, 11 (1), 21.

• Alei Geng, Yanbing Cheng, Yongli Wang, Daochen Zhu, Yilin Le, Jian Wu, Rongrong Xie, Joshua S. Yuan*

  Transcriptome analysis of the digestive system of a wood-feeding termite (Coptotermes formosanus) revealed effective mechanism in biomass degradation. Biotechnology for Biofuels, 2018, 11 (1), 24.

• Zhi-Hua Liu, Michelle Olson, Somnath Shinde, Xin Wang, Naijia Hao, Chang Geun Yoo, Samarthya Bhagia, John R. Dunlap, Yunqiao Pu, Katy C. Kao, Arthur J. Ragauskas, Mingjie Jin , Joshua S. Yuan*

  Synergistic maximization of carbohydrate output and lignin processibility by combinatorial pretreatment. Green Chemistry, 2017, 19, 4939-4955.

• Su Sun, Shangxian Xie, Yanbing Cheng, Hongbo Yu, Honglu Zhao, Muzi Li, Xiaotong Li, Xiaoyu Zhang, Joshua S. Yuan*, Susie Y. Dai

  Enhancement of environmental hazard degradation in the presence of lignin: a proteomics study. Scientific Reports, 2017, 7 (1), 11356.

• Qiang Li, Wilson K. Serem, Yuan Yue, Wei Dai, Mandar T. Naik, Shangxian Xie, Pravat Karki, Li Liu, Hung-Jue Sue, Hong Liang, Fujie Zhou, Joshua S. Yuan*

  Molecular weight and uniformity define the mechanical performance of lignin-based carbon fiber. Journal of Materials Chemistry A, 2017, 5 (25), 12740-12746.

• Kristina M Mahan, Rosemary K. Le, Joshua S. Yuan, Arthur J Ragauskas

  A review on the bioconversion of lignin to microbial lipid with oleaginous Rhodococcus opacus. Journal of Biotechnology & Biomaterials, 2017, 7 (02).

• Rosemary K. Le, Parthapratim Das, Kristina M. Mahan, Seth A. Anderson, Tyrone Wells, Joshua S. Yuan, Arthur J. Ragauskas

  Utilization of simultaneous saccharification and fermentation residues as feedstock for lipid accumulation in Rhodococcus opacus. AMB Express, 2017, 7 (1) 185.

• Rosemary K. Le, Parthapratim Das, Kristina M. Mahan, Seth A. Anderson, Tyrone Wells, Joshua S. Yuan, Arthur J. Ragauskas

  Utilization of simultaneous saccharification and fermentation residues as feedstock for lipid accumulation in Rhodococcus opacus. AMB Express, 2017, 7 (1) 185.

• Narangerel Altangerel, Gombojav O. Ariunbold, Connor Gorman, Masfer H. Alkahtani, Eli Borrego, Dwight Bohlmeyer, Philip Hemmer, Michael Kolomiets, Joshua S. Yuan, and Marlan O. Scully

  In vivo diagnostics of early abiotic plant stress response via Raman spectroscopy, Proceedings of National Academy of Sciences, USA, 2017, 114(13), 3393-3396.

• Qiang Li, Shangxian Xie, Wilson Serem, Mandar Naik, Li Liu and Joshua S. Yuan*

  Quality carbon fiber from fractionated lignin, Green Chemistry, 2017, 19, 1628-1634.

• Shangxian Xie, Qiang Li, Pravat Karki, Fujie Zhou, Joshua S. Yuan*

  Lignin as renewable and superior asphalt binder modifier, ACS Sustainable Chemistry & Engineering, 2017, 5 (4), 2817-2823.

• Qiang Li, Arthur J. Ragauskas, Joshua S. Yuan*

  Lignin carbon fiber: the path for quality, TAPPI Journal, 2017, 16(03), 107-108.

• Shangxian Xie; Qining Sun, Yunqiao Pu, Furong Lin, Su Sun, Xin Wang, Arthur J. Ragauskas, Joshua S. Yuan*

  Advanced chemical design for efficient lignin bioconversion, ACS Sustainable Chemistry & Engineering, 2017, 5 (3), pp 2215-2223.

• Hasan Sadeghifar, Tyrone Wells, Rosemary K. Le, Fatemeh Sadeghifar, Joshua S. Yuan, Arthur J. Ragauskas

  Fractionation of organosolv lignin using acetone: water and properties of the obtained fractions, ACS Sustainable Chemistry & Engineering, 2017, 5, 580-587.

• Clifford J Unkefer, Richard T Sayre, Jon K Magnuson, Daniel B Anderson, Ivan Baxter, Ian K Blaby, Judith K Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P Devarenne, C Meghan Downes, Susan K Dutcher, David T Fox, Ursula Goodenough, Jan Jaworski, Jonathan E Holladay, David M Kramer, Andrew T Koppisch, Mary S Lipton, Babetta L Marrone, Margaret McCormick, István Molnár, John B Mott, Kimberly L Ogden, Ellen A Panisko, Matteo Pellegrini, Juergen Polle, James W Richardson, Martin Sabarsky, Shawn R Starkenburg, Gary D Stormo, Munehiro Teshima, Scott N Twary, Pat J Unkefer, Joshua S. Yuan, José A Olivares

  Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts, Algal Research, 2017, 22, 187-215.

• Yan Shi, Qiang Li, Xin Wang, Shangxian Xie, Liyuan Cai, Joshua S. Yuan*

  Directed bioconversion of Kraft lignin to polyhydroxyalkanoate by Cupriavidus basilensis B-8 without any pretreatment, Process Biochemistry, 2017, 52, 238-242.

• Rosemary K. Le, Tyron Wells Jr., Parthapratim Das, Xianzhi Meng, Ryan Stocklosa, Adita Bhalla, David B. Hodge, Joshua S. Yuan and Arthur J. Raguaskas

  Conversion of corn stover alkaline pre-treatment waste streams into biodiesel via rhodococci, RSC Advances, 2017, 7, 4108-4115.

• Xin Wang, Changpeng Xin, Wei Liu, Yi Zheng, Runzhe Li, Susie Y. Dai, Xinguang Zhu, Peter Rentzepis, Joshua S. Yuan*

  Enhanced limonene production in cyanobacteria reveals photosynthesis limitations, Proceedings of National Academy of Sciences, USA, 2016, 113, 14225-14230.

• Gaia Pigna, Taniya Dhillon, Elizabeth M Dlugosz, Joshua S Yuan, Connor Gorman, Piero Morandini, Scott C Lenaghan, C Neal Stewart

  Methods for suspension culture, protoplast extraction, and transformation of high biomass yielding perennial grass Arundo donax, Biotechnology Journal, 2016, 11, 1657-1666.

• Runze Li, Jie Chen, Tom C. Cesario, Xin Wang, Joshua S. Yuan, Peter M. Rentzepis

  Synergistic reaction of silver nitrate, silver nanoparticles, and methylene blue against bacteria, Proceedings of the National Academy of Sciences, USA, 2016, 113, 13612-13617.

• Lu Lin, Yanbing Cheng, Yunqiao Pu, Su Sun, Xiao Li, Mingjie Jin, Elizabeth A. Pierson, Dennis Gross, Bruce E. Dale, Susie Y. Dai, Arthur J. Ragauskas, Joshua S. Yuan*

  Systems biology-guided biodesign of consolidated lignin conversion, Green Chemistry, 2016, 18, 5536-5547.

• Elise van Buskirk, Jin Su, Ian Silverman, Sager Gosai, Brian Gregory, Joshua S. Yuan, Henry Daniell

  Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signaling, Plant Biotechnology Journal, 2016, 14, 1862-1875.

• Xueyan Chen, Ugur Uzuner, Man Li, Weibing Shi, Joshua S. Yuan, Susie Y. Dai

  Phytoestrogens and Mycoestrogens Induce Signature Structure Dynamics Changes on Estrogen Receptor a, International Journal of Environmental Research and Public Health, 2016, 13, 869.

• Shangxian Xie, Authur J. Ragauskas, Joshua S. Yuan*

  Lignin conversion: opportunities and challenges for the integrated biorefinery, Industrial Biotechnology, 2016, 12, 161-167.

• Cheng Zhao, Shangxian Xie, Yunqiao Pu, Rui Zhang, Fang Huang, Arthur J. Ragausaks, Joshua S. Yuan*

  Synergistic enzymatic and microbial conversion of lignin for lipid, Green Chemistry, 2016, 18, 1306-1312.

• Juan Yu, Yixiang Zhang, Chao Di, Qunlian Zhang, Kang Zhang, Chunchao Wang, Qi You, Hong Yan, Susie Y. Dai, Joshua S. Yuan, Wenying Xu and Zhen Su

  JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis, Journal of Experimental Botany, 2016, 67: 751-762.

• Su Sun, Shangxian Xie, Hu Chen, Xin Qin, Yanbing Cheng, Yan Shi, Susie Y. Dai, Xiaoyu Zhang, Joshua S. Yuan*

  Genomic and molecular mechanisms for efficient biodegradation of aromatic dye, Journal of Hazardous Material, 2016, 9, 302:286-295.

• Donald R. Ort, Sabeeha S. Merchant, Jean Alric, Alice Barkan, Robert E. Blankenship, Ralph Bock, Roberta Croce, Maureen R. Hanson, Julian M. Hibberd, Stephen P. Long, Thomas A. Mooreo, James Moroney, Krishna K. Niyogi, Martin A. J. Parry, Pamela P. Peralta-Yahya, Roger C. Prince, Kevin E. Redding, Martin H. Spalding, Klaas J. van Wijk, Wim F. J. Vermaas, Susanne von Caemmerer, Andreas P. M. Weber, Todd O. Yeates, Joshua S. Yuan, and Xin Guang Zhu

  Redesigning photosynthesis to sustainably meet global food and bioenergy demand, Proceedings of National Academy of Sciences, USA, 2015, 112(28), 8529-8536.

• Bo Li, Shan Jianga, Xiao Yua, Cheng Cheng, Sixue Chen, Yanbing Cheng, Joshua S. Yuan, Daohong Jiang, Ping He, Libo Shan

  Phosphorylation of trihelix transcriptional repressor ASR3 by MAP KINASE4 negatively regulates Arabidopsis immunity, Plant Cell, 2015, 27(3):839-856.

• Shangxian Xie, Xing Qin, Yanbing Cheng, Weichuan Qiao, Su Sun, Scott Sattler, Zhanguo Xin, Susie Y. Dai, Katy Gao, Bin Yang, Xiaoyu Zhang, and Joshua S. Yuan*

  Simultaneous conversion of all cell wall components with oleaginous fungi without chemical pretreatment, Green Chemistry, 2015,17: 1657-1667.

• Xin Wang, Don Ort, and Joshua S. Yuan*

  Photosynthetic terpene hydrocarbon production for fuels and chemicals, Plant Biotechnology Journal, 2015, 13: 137-46.

• Aravind Ravindran, Neha Jalan, Joshua S. Yuan, Nian Wang and Dennis C. Gross

  Comparative genomics of Pseudomonas syringae pv. syringae strains B301D and HS191 and insights into intrapathovar traits associated with plant pathogenesis, MicrobiologyOpen, 2015, 4(4): 553-573.

• Shangxian Xie, Ryan D. Syrenne, Su Sun, Joshua S. Yuan*

  Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel--from systems biology to synthetic design, Current Opinion in Biotechnology, 2014, 27:195-203.

• Yixiang Zhang, Peng Gao, Zhuo Xing, Shumei Jin, Zhide Chen, Lantao Liu, Nasie Constantino, Xingwang Wang, Weibin Shi, Joshua S. Yuan*, and Susie Y. Dai

  Application of an improved proteomics method for abundant protein cleanup: molecular and genomic mechanisms study in plant defense, Molecular and Cellular Proteomics, 2013, 12(11): 3431-42.

• Wusheng Liu, Joshua S. Yuan, and C. Neal Stewart Jr.

  Advanced genetic tools for plant biotechnology, Nature Review Genetics, 2013, 14, 781-793.

• Weibing Shi, Shangxian Xie, Su Sun, Xueyan Chen, Xin Zhou, Lantao Liu, Peng Gao, Nikos C. Kyprides, En-Gyu No, Joshua S. Yuan*

  Comparative genomic analysis of the endosymbionts of herbivorous insects reveals eco-environmental adaptations: biotechnology applications. PLoS Genetics, 2013, 9(1): e1003131.

• Shangxian Xie, Su Sun, Susie Y. Dai, and Joshua S. Yuan*

  Efficient coagulation of microalgae in cultures with filamentous fungi, Algal Research, 2013, 2(1): 28-33.

• Aravind Ravindran, Neha Jalan, Joshua S. Yuan, Nian Wang and Dennis C. Gross

  Complete genome sequencing and comparative analysis of Pseudomonas syringae pv. syringae strains B301D and HS191, Phytopathology 103 (6), 119.

• Nageswara-Rao, M., C. Kwit, S. Agarwal, M.T. Patton, J.A. Skeen, J.S. Yuan, R.M. Manshardt. C.N. Stewart Jr.

  Sensitivity of a real-time PCR method for the detection of transgenes in a mixture of transgenic and non-transgenic seeds of papaya (Carica papaya L.) BMC Biotechnology, 2013, 13:69.

• Yixiang Zhang, Sanmin Liu, Susie Y. Dai, Joshua S. Yuan*

  Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses, BMC Bioinformatics, 2012, S15: S8.

• Dongxia Yao, Wenying Xu, Joshua S. Yuan, and Zhen Su

  Comparative genome analysis and network modeling of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis, BMC Bioinformatics, 2012, S15: S10.

• Weibing Shi, Ugur Uzuner, Lingxia Huang, Palmy R Jesudhasan, Suresh D Pillai, Joshua S Yuan*

  Comparative analysis of insect gut symbionts for composition-function relationships and biofuel application potential, Biofuels, 2011, 2 (5): 529-544.

• Sanmin Liu, Lantao Liu, Ugur Uzuner, Xin Zhou, Manxi Gu, Weibing Shi, Yixiang Zhang, Susie Y. Dai, and Joshua S. Yuan*

  HDX-Analyzer: A novel package for statistical analysis of protein structure dynamics, BMC Bioinformatics, 2011, 12: S1: S43.

• Joshua S Yuan*, Xinwang Wang, C. Neal Stewart

  Biomass feedstock: diversity as a solution, Biofuels, 2011, 2 (5): 491-493.

• Joshua S Yuan*, Yinbo Qu, Shizhong Li, C Neal Stewart

  US-China collaborative biofuel research: towards a global solution for petroleum replacement, Biofuels, 2011, 2 (5): 487-489.

• Yuanchun Shi, Shizhong Li, Joshua S Yuan*

  Biomass utilization toward energy independence and sustainable economic development in China, Biofuels, 2011, 2 (5): 501-502.

• Weibing Shi, Shi-you Ding, Joshua S. Yuan*

  Comparison of insect gut cellulase and xylanase activity across different insect species with distinct food sources, BioEnergy Research, 2011,4: 1-10.

• Carl E. Sams, Dilip R. Panthee, Craig S. Charron, Dean A. Kopsell, Joshua S. Yuan

  Selenium regulates gene expression for glucosinolate and carotenoid biosynthesis in Arabidopsis, Journal of the American Society for Horticultural Science, 2011, 136(1):23-34.

• Danner H, Boeckler GA, Irmisch S, Yuan JS, Chen F, Gershenzon J, Unsicker SB, Köllner TG

  Four terpene synthases produce major compounds of the gypsy moth feeding-induced volatile blend of Populus trichocarpa. Phytochemistry, 2011, 72(9):897-908.

• Ugur Uzunner, Weibing Shi, Lantao Liu, Sanmin Liu, Susie Y. Dai, Joshua S. Yuan*

  Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum, 2010, BMC Bioinformatics, 11, S6: S12.

• Chao Di, Wenying Xu, Zhen Su, Joshua S. Yuan*

  Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function, 2010, BMC Bioinformatics, 11, S6: S22.

• Yanhui Peng, Laura G. Abercrombie, Joshua S. Yuan, R.D. Sammons, Patrick J. Tranel, and C.N. Stewart Jr.

  Characterization of de novo transcriptome for a non-model plant, Conyza canadensis (horseweed), using GS-FLX 454 pyrosequencing, 2010, Pest Management Science, 66: 1053-1062.

• Weibing Shi, Jianzhong Sun, Ryan Syrenne, Joshua S. Yuan*

  Molecular approaches to study the insect gut symbiotic microbiota at the 'Omics' age, 2010, Insect Science, 17: 199-219.

• Joshua S. Yuan, Laura L.G. Abercrombie, Yongwei Cao, Matthew D. Halfhill, Xin Zhou, Yanhui Peng, Jun Hu, Murali R. Rao, Gregory R. Heck, Thomas J. Larosa5 R. Douglas Sammons, Xinwang Wang, Priya Ranja, Denita H. Johnson, Phillip A. Wadl, Brian E. Scheffler, Timothy A. Rinehart, Robert N. Trigiano, C. Neal Stewart, Jr.

  Functional genomics analysis of glyphosate resistance in Conyza canadensis (horseweed), 2010, Weed Sciences, 58: 109-117.

• Yixiang Zhang, Peng Gao, Joshua S. Yuan*

  Plant interactome and protein-protein interaction network, Current Genomics, 2010, 11: 40-46.

• Zhanyou Xu, Dandan Zhang, Jun Hu, Xin Zhou, Xia Ye, Kristen Reichel, Nathan R. Stewart, Ryan D. Syrenne, Xiaohan Yang, Peng Gao, Weibing Shi, Crissa Doeppke, Rob Sykes, Jason Burris, Joe Bozell, Max Z. Cheng, Douglas Hayes, Nikki Labbie, Mark Davis, C. Neal Stewart Jr., Joshua S. Yuan*

  Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom, BMC Bioinformatics, 2009, 10, S11: S3.

• Joshua S. Yuan, Sari J. Himanen, Jarmo K. Holopainen, Feng Chen, and C. Neal Stewart, Jr.

  Smelling global warming: changes of ecological function of plant volatile organic compounds, Trends in Ecology and Evolution, 2009, 24: 323-331.

• Xin Zhou, Zhen Su, Doug Rammons, Yanhui Peng, Patrick R. Tranel, C. Neal Stewart Jr., and Joshua S. Yuan*

  Novel software package for cross-platform transcriptome analysis (CPTRA), BMC Bioinformatics, 2009, 10, S11: S16.

• Trigiano, R.N., X.W. Wang, L.L. Good, D. Panthee, B.E. Scheffler, T.A. Rinehart, D. Johnson, P.A. Wadl, N.R. Stewart, J.S. Yuan, C.N. Stewart, Jr.

  Microsatellites from Conyza canadensis (horseweed). Molecular Ecology Resources, 2009, 9:1375-1379.

• Wayra Navia-Gine, Joshua S. Yuan, Feng Chen, and Kenneth L. Korth

  Regulation of an insect-induced E-(beta)-ocimene synthase and other terpene synthases of Medicago truncatula. Plant Physiology and Biochemistry, 2009, 47: 416-425.

• Panthee, D.R., J.J. Marois, D.L. Wright, J.S. Yuan, and C.N. Stewart Jr.

  Differential expression of genes in soybean in response to the causal agent of Asian soybean rust, (Phakopsora pachyrhizi Sydow), is soybean growth stage-specific. 2009, Theoretical and Applied Genetics, 118: 359-370.

• Joshua S. Yuan, Kelly H. Tiller, Hani Al-Ahmad, Nathan R. Stewart, C. Neal Stewart Jr.

  Plants to power: Bioenergy to fuel the future, Trends in Plant Sciences, 2008, 13:421-429.

• Joshua S. Yuan, Tobias G. Köllner, Greg Wiggins, Jerome Grant, Nan Zhao, Xiaofeng Zhuang, Jörg Degenhardt and Feng Chen

  Elucidation of the genomic basis of indirect plant defense against insects, Plant Signaling & Behavior, 2008, 3: 720 - 721.

• Jason Abercrombie, Matthew Halfhill, Priya Ranjan, Murali Rao, Arnold Saxton, Joshua S. Yuan, C. Neal Stewart Jr.

  Transcriptional profiling of Arabidopsis thaliana grown under arsenate stress reveals antioxidant activity and repression of the phosphate starvation response, BMC Plant Biology, 2008, 8:37.

• Joshua S. Yuan, Tobias G. Köllner, Greg Wiggins, Jerome Grant, Jörg Degenhardt, and Feng Chen

  Molecular and genomic basis of volatile-mediated indirect defense against insects in rice, Plant Journal, 2008, 55: 491-503.

• Joshua S. Yuan, David W. Galbraith, Susie Y. Dai, Patrick Griffin, and C. Neal Stewart Jr.

  Plant systems biology comes of age, Trends in Plant Sciences, 2008, 13: 165-171.

• Maria Cekanova, Joshua S. Yuan, Xiuoon Li, and Seung Joon Baek

  Gene alterations by PPARy agonists in human colorectal adenocarcinoma HCT-116 cells. 2008, International Journal of Oncology, 32: 809-819.

• Joshua S. Yuan*, Donglin Wang, C. Neal Stewart Jr.

  Statistical methods for efficiency adjusted real-time PCR quantification, 2008, Biotechnology Journal, 3: 112-123.

• Joshua S. Yuan, Nathan R. Stewart, Jason Burris, C Neal Stewart Jr.

  Statistical methods for transgene detection with real-time PCR, 2007, BMC Bioinformatics, 8, S7: S6.

• D.R. Panthee, Joshua S. Yuan, D.L. Wright, J.J. Marois, D. Mailhot and C.N. Stewart Jr.

  Global gene expression analysis in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow), 2007, Functional and Integrative Genomics, 7: 291.

• Joshua S. Yuan, Pat Tranel, and C. Neal Stewart Jr.

  Non-target herbicide resistance: a family business, 2007, Trends in Plant Sciences, 12: 6.

• Joshua S. Yuan, Xiaohan Yang, Jinru Lai, Hong Lin, Zong-ming Chen, Hiroyuki Nonogaki, and Feng Chen

  Comparative genomic analysis of endo-β-mannanase gene families in Arabidopsis, rice and poplar, 2007, Functional and Integrative Genomics: 7: 1.

• Yue Yang, Joshua S. Yuan, Jeannine Ross, Joseph P. Noel, Eran Pichersky and Feng Chen

  An Arabidopsis thaliana methyltransferase capable of methylating farnesoic acid, 2006, Archives of Biochemistry and Biophysics, 448:123.

• Dhar, M.S., Joshua S. Yuan, Sarah B. Elliott and Sommardahl C.

  A type IV P-type ATPase affects insulin-mediated glucose uptake in adipose tissue and skeletal muscle in mice, 2006, Journal of Nutritional Biochemistry, 17: 811.

• Joshua S. Yuan, Ann Reed, Feng Chen, and C. Neal Stewart Jr.

  Statistical analysis of real-time PCR data, 2006, BMC Bioinformatics, 7:85.