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Selected Refereed Manuscripts

Lane, T.S., C.S. Rempe, J. Davitt, M.E.Staton, Y. Peng, D.E. Soltis, M. Melkonian, M. Deyholos, J.H. Leebens-Mack, M. Chase, C.J. Rothfels, D. Stevenson, S.W Graham, J.Yu, T. Liu, J.C. Pires, P.P. Edgar, Y. Zhang, Y. Xie, Y. Zhu, E. Carpenter, G.K.-S. Wong, C.N. Stewart, Jr. 2016. Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. BMC Biotechnology 16:47.

Willis, J.D., M. Mazarei, C.N. Stewart, Jr. 2016. Transgenic plant-produced hydrolytic enzymes and the potential of insect gut-derived hydrolases for biofuels. Frontiers in Plant Science 7: 765.

Cardi, T., C.N. Stewart, Jr. 2016. Progress of targeted genome modification approaches in higher plants. Plant Cell Reports 35: 1401-1416.

Altpeter, F., N.M. Springer, L.E. Bartley, A.E. Blechl, T.P. Brutnell, V. Citovsky, L.J. Conrad, S.B. Gelvin, D.P. Jackson, A.P. Kausch, P.G. Lemaux, J.I. Medford, M.L. Orozco-Cárdenas, D.M. Tricoli, J. Van Eck,  D.F. Voytas, V. Walbot, K. Wang, Z.J. Zhang, C.N. Stewart, Jr. 2016. Advancing crop transformation in the era of genome editing.  Plant Cell 15:1510-1520 doi: http:/​/​dx.​doi.​org/​10.​1105/​tpc.​16.​00196

Liu, W., C.N. Stewart, Jr. 2016. Plant synthetic promoters and transcription factors. Current Opinion in Biotechnology 37: 36-44.

Burris, K.P., E.M Dlugosz, A.G. Collins, C.N. Stewart, Jr., S.C. Lenaghan. 2016. Development of a rapid, low-cost protoplast transfection system for switchgrass (Panicum virgatum L.). Plant Cell Reports 35: 693-704.

Millwood, R.J., H.S. Moon, C.R. Poovaiah, B. Muthukumar, J.H. Rice. J.M. Abercrombie, L.L Abercrombie, W.D. Green, C.N. Stewart, Jr. 2016. Engineered selective plant male sterility through pollen-specific expression of the EcoRI restriction endonuclease. Plant Biotechnology Journal 14: 1281-1290.

Wuddineh, W.A., M. Mazarei, J.-Y. Zhang, G. Turner, R. Sykes, S.R. Decker, M.F. Davis, M. Udvardi, C.N. Stewart, Jr. 2016. Identification and overexpression of a Knotted1-like transcription factor in switchgrass (Panicum virgatum L.) for lignocellulosic feedstock improvement. Frontiers in Plant Science 7:520.

Baxter, H.L., L.W. Alexander, M. Mazarei, E. Haynes, G.B. Turner, R.W. Sykes, S.R. Decker, M.F. Davis, R.A. Dixon, Z.-Y.Wang, C.N. Stewart, Jr.  2016. Hybridization of downregulated-COMT transgenic switchgrass lines with field selected switchgrass for improved biomass traits. Euphytica 209: 341-355.

Wuddineh, W.A., M. Mazarei, G.B. Turner, R.W. Sykes, S.R. Decker, M.F. Davis, C.N. Stewart, Jr. 2015 Identification and molecular characterization of the switchgrass AP2/ERF transcription factor superfamily, and overexpression of PvERF001 for improvement of biomass characteristics for biofuel. Frontiers in Bioengineering and Biotechnology 3: 101.

Baxter, H.L., C.R. Poovaiah, K.L. Yee, M. Mazarei, M. Rodriguez, Jr., O.A. Thompson, H. Shen, G.B. Turner, S.R. Decker, R.W. Sykes, F. Chen, M.F. Davis, J.R. Mielenz, B.H. Davison, R.A. Dixon, C.N. Stewart Jr. 2015. Field evaluation of transgenic switchgrass plants overexpressing PvMYB4 for reduced biomass recalcitrance. BioEnergy Research 8:910-921.

Joyce, B.L., V.D. Zheljazkov, R. Sykes, C.L. Cantrell, C. Hamilton, D.G.J. Mann, M. Rodriguez, J.R. Mielenz, T. Astatkie, and C.N. Stewart, Jr. 2015. Ethanol and high-value terpene co-production from lignocellulosic biomass of Cymbopogon flexuosus and Cymbopogon martinii. PLoS ONE 10(10): e0139195.

Liu, Y., Y.-X. Zhang, S.-Q. Song, J. Li, C.N. Stewart, Jr., W. Wei, Y. Zhao, W.-Q. Wang.  2015. A proteomic analysis of seeds from Bt-transgenic Brassica napus and hybrids with wild B. juncea. Scientific Reports 5: 15480.

Liu, Y., C. N. Stewart, Jr., J. Li, H.  Huang, X.  Zhang. 2015.The presence of Bt-transgenic oilseed rape in wild mustard populations affects plant growth. Transgenic Research 24: 1043-1053.

Rempe, C.S., K.P. Burris, H.L. Woo, B. Goodrich, D.K. Gosnell, T.J. Tschaplinski, C.N. Stewart, Jr. 2015. Computational ranking of yerba mate small molecules based on their predicted contribution to antibacterial activity against methicillin-resistant Staphylococcus aureus. PLOS ONE  10(5): e0123925.

Wuddineh, W.A., M. Mazarei, J. Zhang, C.R. Poovaiah, D.G.J. Mann, A. Ziebell, R.W. Sykes, M.F. Davis, M.K. Udvardi, C.N. Stewart, Jr. 2015. Identification and overexpression of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance.  Plant Biotechnology Journal 13: 636-647.

Liu, Y.-B., H. Darmency, C. N. Stewart, Jr., W. Wei, Z.-X. Tang, K.-P. Ma. 2015. The effect of Bt-transgene introgression on plant growth and reproduction in wild Brassica juncea. Transgenic Research 24: 537-547.

Liu, J., N. Nana, J.N. Grant, Z.-M. Cheng, C.N. Stewart, Jr., T. Hewezi. 2015.  Soybean kinome: functional classification and gene expression patterns. Journal of Experimental Botany 66: 1919-1934.

Cannon, S.B., M.R. McKain, A. Harkess, M.N. Nelson, S. Dash, M.K. Deyholos, Y. Peng, B. Joyce, C.N. Stewart, Jr., M. Rolf, T. Kutchan, X. Tan, C. Chen, Y. Zhang, E. Carpenter, G.K.-S. Wong, J.J. Doyle, J. Leebens-Mack. 2015. Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. Molecular Biology and Evolution 32: 193-210.

Trumbo, J.L., B. Zhang, and C.N. Stewart, Jr. 2015. Manipulating microRNAs for improved biomass and biofuels from plant feedstocks. Plant Biotechnology Journal 13: 337-354.

Burris, K.P., K.L. Higginbotham, C.N. Stewart, Jr.  2015. Aqueous extracts of yerba mate as bacteriacidal agents against methicillin-resistant Staphylococcus aureus in a microbiological medium and ground beef mixtures. Food Control 50: 748-753.

Okada, M.,  B.D. Hanson, K.J. Hembree, Y. Peng, A. Shrestha, C.N. Stewart, Jr., S.D. Wright, and M. Jasieniuk. 2015.  Evolution and spread of glyphosate resistance in Conyza bonariensis in California and a comparison with closely related Conyza canadensis. Weed Research 55:173-184.

Poovaiah, C.R., M. Mazarei, S.R. Decker, G.B. Turner, R.W. Sykes, M.F. Davis, C.N. Stewart, Jr.2015. Overexpression of switchgrass sucrose synthase (PvSUS1) increases plant biomass in transgenic switchgrass (Panicum virgatum L.). Biotechnology Journal 10: 552-563. 

Liu, W., and C.N. Stewart, Jr. Plant synthetic biology. 2015 Trends in Plant Science 20: 309-317.

Piya, S., S.K. Shrestha, B. Binder, C.N. Stewart, Jr., T. Hewezi.  2015. Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis. Frontiers in Plant Science 5: 744 (

Liu, Y. C.N. Stewart, Jr., J. Li. 2015. China: inform public on GM, don’t cheerlead. Nature 520: 295.

Alexander, L.W., E.R. Haynes, J. Burris, S. Jackson, C.N. Stewart, Jr. 2014. Cultural treatments for accelerated growth and flowering of Panicum virgatum Biofuels 5:771-780

Peng, Y., Z. Lai, T. Lane, M. Nageswara-Rao, M. Okada, M. Jasieniuk, H. O'Geen, R.W. Kim, R.D. Sammons, L. Rieseberg, C.N. Stewart, Jr. 2014. De novo genome assembly of the economically-important weed Conyza canadensis using integrated data from multiple sequencing platforms. Plant Physiology 166: 1241-1254.

Ji, H., Y. Peng, N. Meckes, S. Allen, C.N. Stewart, Jr., and M.B. Traw. 2014. ATP-dependent binding cassette transporter G family member 16 increases plant tolerance to abscisic acid and assists in basal resistance against Pseudomonas syringae DC3000. Plant Physiology 166: 878-888.

Joyce, B.L., S. Eda, J. Dunlap, and C.N. Stewart, Jr. 2014. Morphology and ploidy level determination of Pteris vittata callus during induction and regeneration. BMC Biotechnology 14:96. (

Poovaiah, C., M. Nagaswara-Rao, J.R. Soneji, H.L. Baxter, C.N. Stewart, Jr. 2014. Altered lignin biosynthesis using biotechnology to improve lignocellulosic biofuel feedstocks. Plant Biotechnology Journal 12: 1163-1173.

Peng, Y., S. Allen, R.J. Millwood, C.N. Stewart, Jr. 2014.  Building the ‘Fukusensor:’ a genetically engineered plant for reporting DNA damage in response to gamma radiation. Plant Biotechnology Journal 12:1329-1332. 

Floyd, S.K., J.G. Ryan,  S.J. Conway, E. Brenner, K.P. Burris, J.N. Burris, T. Chen, P.P. Edger, S.W. Graham, J.H. Leebens-Mack, J.C. Pires, C.J. Rothfels, E.M. Sigel, D.W. Stevenson, C.N. Stewart, Jr., G.K.-S. Wong, J.L. Bowman. 2014. Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Molecular Phylogenetics and Evolution 81: 159-173.

Chauhan, A. A. Smartt, J.Wang, S. Utturkar, A. Frank, M. Bi, J. Liu, D. Williams, T. Xu, M. Eldridge, A. Arreaza, A. Rogers, H.C. Gonzalez, A.C. Layton, H.L. Baxter, M. Mazarei, J.M. DeBruyn, C.N. Stewart, Jr., S.D. Brown, L.J. Hauser, G.S. Sayler.  2014. Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass. Genome Announcements 2:e00777-14. doi:10.1128/genomeA.00777-14.

Nageswara-Rao, M., M. Hanson, S. Agarwal, C.N. Stewart Jr. C. Kwit. 2014. Genetic diversity analysis of switchgrass (Panicum virgatum L.) populations using microsatellites and chloroplast sequences. Agroforestry Systems 88: 823-834.

Mahfouz, M.M., A. Piatek, C.N. Stewart Jr. Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. Plant Biotechnology Journal 12: 1006-1014.

Liu, W., M. Mazarei, Y. Peng, M.H. Fethe, M.R. Rudis, J. Lin, R.J. Millwood, P.R. Arelli, C.N. Stewart, Jr. 2014. Computational discovery of soybean promoter cis-regulatory elements for the construction of soybean cyst nematode-inducible synthetic promoters. Plant Biotechnology Journal 12: 1015-1026.

Baxter, H.L, M. Mazarei, N. Labbe, L. Kline, Q. Cheng, M. Windham, D.G.J. Mann, C. Fu, A. Ziebell, R. Sykes, M. Rodriguez, M. Davis, J. Mielenz, R.A. Dixon, Z.-Y. Wang, C.N. Stewart, Jr. 2014. Two-year field analysis of decreased recalcitrance transgenic switchgrass. Plant Biotechnology Journal 12: 914-924 (with accompanying journal cover).

Fethe, M.H. W. Liu, J.N. Burris, R.J. Millwood, M. Mazarei, M.R. Rudis, D.G. Yeaman, M. Dubosquielle, C.N. Stewart Jr. 2014 The performance of pathogenic bacterial phytosensing transgenic tobacco in the field. Plant Biotechnology Journal 12: 755-764.

Ali, A., J.C. Zinnert, B. Muthukumar, Y. Peng, S.-M. Chung, C.N. Stewart, Jr. 2014. Physiological and transcriptional responses of Baccharis halimifolia to the explosive ‘composition B’ (RDX/TNT) in amended soil. Environmental Science and Pollution Research 21: 8261-8270.

Cao, D., C.N. Stewart Jr, M. Zheng, Z. Guan, Z.-X. Tang, W. Wei, K.-P. Ma. 2014. Stable Bacillus thuringiensis transgene introgression from Brassica napus to wild mustard B. juncea. Plant Science 227: 45-50.

Salgotra, R.K., B.B. Gupta, C.N. Stewart, Jr. 2014. From genomics to functional markers in the era of next-generation sequencing. Biotechnology Letters 36: 417-426.

Liu, W., M.R. Rudis, Y. Peng, M. Mazarei, R.J. Millwood, J.-P. Yang, W. Yu, J.D. Chesnut,  C.N. Stewart Jr. 2014. Synthetic TAL effectors for targeted enhancement of transgene expression in plants. Plant Biotechnology Journal 12: 436-446 (with accompanying journal cover).

Shen H., M. Mazarei, H. Hisano, F. Hardin, L.L. Escamilla-Treviño, C. Fu, Y. Pu, M.R. Rudis, Y. Tang, X. Xiao, L. Jackson, G. Li, T. Hernandez, F. Chen, A.J. Ragauskas, C.N. Stewart Jr., Z.-Y. Wang, and R.A. Dixon. 2013. A genomics approach to deciphering lignin biosynthesis in switchgrass (Panicum virgatum L.).  Plant Cell 25: 4342-4361.

Xie, F., C.N. Stewart, Jr., F. Taten, Q. He, H. Liu, B. Zhang. 2014. High throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress for biofuel production. Plant Biotechnology Journal12: 354-366.

Gressel, J., C.N Stewart, Jr., L.V. Giddings, A.J. Fischer, J.C. Streibig, N.R. Burgos, A. Trewavas, A. Merotto, Jr., C.J. Leaver, K. Ammann, V. Moses, A. Lawton-Rauh. 2014. Overexpression of epsps transgene in weedy rice: insufficient evidence to support multiple conclusions about biosafety.  New Phytologist 202:360-362.

Resnick, D.B., and C.N. Stewart, Jr. 2014. Expanding the scope of responsible conduct in research instruction. Accountability in Research 21:321-327.

Higginbotham, K.L., K.P. Burris, S. Zivanovic, P.M. Davidson, C.N. Stewart, Jr. 2014.
Antimicrobial activity of Hibiscus sabdariffa aqueousextracts against Escherichia coli O157:H7 and Staphylococcus aureus in a microbiological medium and milk of varying fat concentrations. Journal of Food Protection 77: 362-368.

Higginbotham, K.L., K.P. Burris, S. Zivanovic, P.M. Davidson, C.N. Stewart, Jr. 2014. Aqueous extracts of Hibiscus sabdariffa calyces as an antimicrobial rinse on hot dogs against Listeria monocytogenes and methicillin-resistant Staphylococcus aureus. Food Control 40: 274-277.

Lin, J. M. Mazarei, N. Zhao, J.J. Zhu, X Zhaung, W. Liu., V.R. Pantalone, P.R. Arelli, C. N. Stewart, Jr.,  F. Chen. 2013. Overexpression of a soybean salicyclic acid methlyltransferase confers resistance to soybean cyst nematode. Plant Biotechnology Journal 11: 1135-1145.

Ellstrand, N.C., P. Meirmans, J. Rong, D. Bartsch, A. Ghosh, T.J. de Jong, P. Haccou, B.-R. Lu, A.A. Snow, C.N. Stewart, Jr., J.L. Strasburg, P.H. van Tienderen, K. Vrieling, D. Hooftman. 2013. Introgression of crop alleles into wild or weedy populations. Annual Review of Ecology, Evolution, and Systematics, 44: 325-345.

Baxter, H.L. and C.N. Stewart, Jr. 2013. Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress.  Biofuels 4: 635-650. 

Liu, W., J.S. Yuan and C.N. Stewart, Jr. 2013. Advanced genetic tools for plant biotechnology. Nature Reviews Genetics 14: 781-793.      Supplement.

Rice, J.H., R.E. Mundell, R.J. Millwood, O.D. Chambers, L.G. Abercrombie, H.M. Davies, and C.N. Stewart. Jr. 2013.  An orange fluorescent protein tagging system for real-time pollen tracking. BMC Research Notes 6:383.

Muthukumar, B., B.L. Joyce, M.P.  Elless, C.N. Stewart Jr. 2013. Biolistics- and Agrobacterium tumefaciens-mediated stable transformation of Pteris vittta (Chinese brake fern) and Ceratopteris thalictroides (C-fern) spores. Plant Physiology 163: 648-658.

Nagaswara-Rao, M., J. Soneji, C. Kwit, C.N. Stewart, Jr. 2013. Advances in biotechnology and genomics of switchgrass. Biotechnology for Biofuels 6:77.

Rice, J.H., R.E. Mundell, R.J. Millwood, O.D. Chambers, C.N. Stewart. Jr. and H.M. Davies, 2013.  Assessing the bioconfinement potential of a Nicotiana hybrid platform for use in plant molecular farming applications. BMC Biotechnology 13:63.

Nageswara-Rao, M., C. Kwit, S. Agarwal, M.T. Patton, J.A. Skeen, J.S. Yuan, R.M. Manshardt. C.N. Stewart Jr. 2013. 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 13:69.

Burris, K.P., T-C. Wu, M. Vasudev, M.A. Stroscio, R.J. Millwood, and C.N. Stewart, Jr., 2013. Mega-nano detection of foodborne pathogens and transgenes using molecular beacon and semiconductor quantum dot technologies.  IEEE Transactions in NanoBioscience 12: 233-238.

Okada, M.,  B.D. Hanson, K.J. Hembree, W.T. Lanini, Y. Peng, A. Shrestha, C.N. Stewart, Jr., S.D. Wright, and M. Jasieniuk. 2013 Evolution and spread of glyphosate resistance in Conyza canadensis in California. Evolutionary Applications 6: 761-777.

Lenaghan, S., J.N. Burris,  K. Chourey, Y. Huang, L. Xia, B. Lady, R. Sharma, C. Pan, Z. LeJeune, S. Foister, R.L. Hettich,  C.N. Stewart, Jr. and M. Zhang. 2013.  Identification of the chemical nature of nanoparticles secreted by English ivy (Hedera helix). Journal of the Royal Society Interface 10 (87): 20130392.

Hardin, C.F. C. Fu, H. Hisano, X. Xaio, H. Shen, C.N. Stewart, Jr., W. Parrott, R.A. Dixon, Z-Y. Wang. 2013. Standardization of switchgrass sample collection for cell wall and biomass trait analysis. BioEnergy Research  6: 755-762.

Huang, Y., S.C. Lenaghan, L. Xia, Z. Xu, J.N. Burris, C.N. Stewart Jr., M.J. Zhang. 2013. Characterization of physicochemical properties of ivy nanoparticles for cosmetic applications. Journal of Nanobiotechnology 11:3.

Shen, H., C. R. Poovaiah, A. Ziebell, T.J. Tschaplinski, S. Pattathil,  E. Gjersing, N. Engle,  R. Katahira, Y. Pu, R. Sykes, F. Chen, A.J. Ragauskas, J.R. Mielenz, M.G. Hahn, M. Davis, C.N. Stewart, Jr., R.A. Dixon. 2013 Enhanced characteristics of genetically modified switchgrass(Panicum virgatum L.) for high biofuel production. Biotechnology for Biofuels 6:71.

Sang, Y., R.J. Millwood, C.N. Stewart Jr. 2013 Gene use restriction technologies for transgenic plant bioconfinement. Plant Biotechnology Journal 11:649-658.

Nagaswara-Rao, M., J. Soneji, C. Kwit, C.N. Stewart, Jr. 2013. Advances in biotechnology and genomics of switchgrass. Biotechnology for Biofuels 6:77.

Liu, W., M. Mazarei, M.R. Rudis, M.H. Fethe, Y. Peng, R.J. Millwood, G. Schoene, J.N. Burris and C.N. Stewart, Jr. 2013. Bacterial pathogen phytosensing in transgenic tobacco and Arabidopsis plants. Plant Biotechnology Journal 11:43-52.

Burris, J.N., S. Lenaghan, M.J. Zhang., C.N. Stewart, Jr. 2012.  Nanoparticle biofabrication using English ivy (Hedera helix).  Journal of Nanobiotechnology10:41.

Yau, Y.Y. and C.N. Stewart, Jr. 2013. Less is more: strategies to remove marker genes from transgenic plants. BMC Biotechnology 13:36.

Nageswara-Rao, M., C.N. Stewart, Jr., C. Kwit. 2013. Genetic diversity and structure of natural and agronomic switchgrass (Panicum virgatum L.) populations. Genetic Resources and Crop Evolution 60: 1057-1068.

Johnson, MTJ, Z Tian, EJ Carpenter, R Bruskiewich, JN Burris, CT Carrigan, MW Chase, ND Clarke, S Covshoff, CW dePamphilis, PP Edger, F Goh, S Graham, S Greiner, JM Hibberd, I Jordon-Thaden, TM Kutchan, J Leebens-Mack, M Melkonian, N Miles, H Myburg, JC Pires, M Rolf, RF Sage, D Soltis, P Soltis, D Stevenson, CN Stewart, Jr, B.Surek, CJM Thomsen, JC Villarreal, X Wu, Y Zhang, MK Deyholos & GK-S Wong. 2012. Evaluating methods of isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 11:e50226.

Nageswara Rao M, Stewart Jr. CN, Kwit C. 2012. Genetic diversity and structure of natural and cultivated switchgrass (Panicum virgatum L.) populations. Genetic Resources and Crop Evolution (DOI 10.1007/s10722-012-9903-x; Most Downloaded Article).

Nageswara-Rao M, Kwit C, Stewart Jr. CN, 2012. Grass to solve global fuel crisis, 30th August 2012, BioSpectrum Asia (Most Read Article

Salgotra, R.K. B.B. Gupta, R.J. Millwood, M. Balasubramaniam, and C.N Stewart, Jr. 2012. Introgression of bacterial leaf blight resistance and aroma genes using functional marker-assisted selection in rice (Oryza sativa L.). Euphytica 187: 313-323.

Fu, C., R. Sunkar, C. Zhou, H. Shen, J. Zhang, J. Wolf, Y. Tang, D. G.J. Mann, C. N. Stewart, Jr., M. Udvardi, R. A. Dixon, and Z.-Y. Wang. 2012. Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production. Plant Biotechnology Journal 10:443-452.

Zhao, N., J.-L. Ferrer, H.S. Moon, J. Kapteyn, X. Zhuang, M. Hasebe, C.N. Stewart Jr., D.R. Gang, and F. Chen. 2012. A SABATH methyltransferase from the moss Physcomitrella patens catalyzes S-methylation of thiols and has a role in detoxification. Phytochemistry 81: 31-41.

Joyce, B. and C.N. Stewart, Jr. 2012. Designing the perfect plant feedstock for biofuel production: using the whole buffalo to diversify fuel and products. Biotechnology Advances 30: 1011-1022.

Liu, Y., Z. Tang, H. Darmency, C. N. Stewart, Jr.,, K. Di, W. Wei, K. Ma.  2012. The effects of seed size on hybrids formed between oilseed rape (Brassica napus) and wild brown mustard (Brassica juncea). PLoS ONE  7(6) e39705

Mann, D.G.J., L.L. Abercrombie, M.R. Rudis, R.J. Millwood, J.R. Dunlap, C.N. Stewart, Jr. 2012. Very bright orange fluorescent plants: endoplasmic reticulum targeting of orange fluorescent proteins as visual reporters in transgenic plants. BMC Biotechnology 12:17 doi:10.1186/1472-6750-12-17

Burris, K.P., P.M Davidson, C.N. Stewart, Jr., S. Zivanovic, F.M. Harte. 2012. Aqueous extracts of Yerbe Mate (Ilex paraguariensis) as a natural antimicrobial agent against Escherichia coli O157:H7 in a microbiological medium and pH 6 apple juice. Journal of Food Protection 75: 753-757.

Sun, G., C.N. Stewart, Jr., P. Xiao, B. Zhang. 2012. MicroRNA expression analysis in the cellulosic biofuel crop switchgrass (Panicum virgatum) under abiotic stress. PLoS ONE 7(3): e32017.  doi:10.1371/journal.pone.0032017

Kwit, C. and C.N. Stewart, Jr. 2012. Gene flow matters in switchgrass (Panicum virgatum L.), a potential widespread biofuel feedstock. Ecological Applications 22: 3-7.

Liu, W., M Mazarei, M.R. Rudis, M.H. Fethe, and C.N. Stewart, Jr. 2011. Rapid in vivo analysis of synthetic promoters for pathogen phytosensing. BMC Biotechnology, 11:108

Mann, D.G.J., P.R. LaFayette, L. L. Abercrombie, Z.R. King, M. Mazarei, M.C. Halter, C.R. Poovaiah, H. Baxter, H. Shen, R.A. Dixon, W.A. Parrott, C.N. Stewart, Jr. 2012. Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.) and other monocot species.  Plant Biotechnology Journal 10:226-236.

Shen, H., X. He, C.R. Poovaiah, W.A. Wuddineh, J. Ma, D.G.J. Mann, H. Wang, L. Jackson, Y. Tang, C.N. Stewart, Jr., F. Chen, and R.A. Dixon. 2012 Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks. New Phytologist 193: 121-136.

Mazarei, M. W. Liu, H. Al-Ahmad, P.R. Arelli, V.R. Pantalone, C.N. Stewart, Jr. 2011. Gene expression profiling of resistant and susceptible soybean lines infected with soybean cyst nematode. Theoretical and Applied Genetics 12: 1193-1206.

Mazarei, M., H. Al-Ahmad, M.R. Rudis, B. L. Joyce, C.N. Stewart, Jr. 2011.  
Switchgrass (Panicum virgatum L.) cell suspension cultures: establishment, characterization, and application. Plant Science 6: 712-715.

Mann, D.J.G., Z. King, W. Liu, B.L. Joyce, R.J. Percifield, J.S. Hawkins, P.R. LaFayette,  B.J. Artelt, J.N. Burris, M. Mazarei, J.L. Bennetzen, W.A. Parrott, C.N. Stewart, Jr. 2011. Switchgrass (Panicum virgatum L.) polyubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation. BMC Biotechnology 11:74 .

Vasudev, M., T.-C. Wu, M. Datta, M.A. Stroscio, S. Guthrie, M. Reed, K.P. Burris, C. N. Stewart, Jr. 2011. Optoelectric signatures of DNA-based hybrid nanostructures. IEEE Transactions on Nanotechnology 10: 35-43.

Xia L., S.C. Lenaghan, M.  Zhang, Y.Wu, X. Zhao, J. N. Burris, C. N. Stewart, Jr. 2011. Characterization of English ivy (Hedera helix) adhesion force and imaging using atomic force microscopy. Journal of Nanoparticle Research 13:1029-1037.

Salgotra, R.K., R. J. Millwood, S. Agarwal , C. N. Stewart, Jr, 2011. High-throughput functional marker assay for detection of Xa/xa and fgr genes in rice (Oryza sativa L.). Electrophoresis 32: 2216-2222.

Kwit, C. H.S. Moon, S.I. Warwick, C.N. Stewart, Jr. 2011. Transgene introgression in crop relatives: molecular evidence and mitigation strategies. Trends in Biotechnology 29: 284-293.

Moon, H.S., L.L. Abercrombie, S. Eda, R. Blanvillain, J.G. Thomson, D.W. Ow, C.N. Stewart, Jr. 2011. Transgene excision in pollen using a codon optimized serine resolvase CinH-RS2 site-specific recombination system. Plant Molecular Biology 75:621-631.

Jiang, H., W. Wei, X. Song, C.N. Stewart, Jr., G. Zhou, Z. Jiang. Q Zhu, S. Yu, S. Peng, 2011. Hyperspectral studies of  transgenic oilseed rape. International Journal of Remote Sensing 32: 1095-1103.

Leckie, B.L., C.N. Stewart, Jr. 2011. Agroinfiltration as a technique for rapid assays for expressing candidate insect resistance transgenes in plants. Plant Cell Reports 30:325-334.

Mann, D.G.J, P.R. LaFayette, L.G Abercrombie, W.A. Parrott, C.N. Stewart, Jr. 2011.
pANIC:  A versatile set of Gateway-compatible vectors for gene overexpression and RNAi-mediated down-regulation in monocots. Pp. 161-168 In: Stewart, C.N., Jr., A. Touraev, V. Citovsky, T. Tzfira (Eds). 2011. Plant Transformation Technologies. Wiley-Blackwell Scientific Publishing, Ames Iowa.

Moon, H.S., S. Eda, A.M. Saxton, D. Ow, C.N. Stewart, Jr. 2011. An efficient and rapid transgenic pollen screening and detection method using flow cytometry. Biotechnology Journal 6:118-123.

Himanen,S.J., A.-M. Nerg, G.M. Poppy C.N. Stewart, Jr., J.K. Holopainen. 2010. Abiotic stress and transgenics: implications for reproductive success and crop-wild gene flow in Brassicas. Basic and Applied Ecology 11: 513-521.

Moon, H.S., J.M. Abercrombie, A.P. Kausch, C.N Stewart, Jr. 2010. Sustainable use of biotechnology for bioenergy feedstocks. Environmental Management  46:531-538.

Riggins, C.W., Y. Peng, C. N. Stewart, Jr., and P. J. Tranel. 2010. Characterization of de novo waterhemp (Amaranthus tuberculatus) transcriptome using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest Management Science 66: 1042-1052.

Peng, Y., L.L.G. Abercrombie, J.S. Yuan, C.W. Riggins, R.D. Sammons, P.J. Tranel, and C.N. Stewart, Jr. 2010.  Characterization of the horseweed Conyza canadensis transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide-resistance genes. Pest Management Science 66: 1053-1062.

Rao, M.R., H.S. Moon, T.M.H. Schenk, D. Becker, M. Mazarei and C.N. Stewart Jr. 2010. FLP/FRT recombination from yeast: application of a two gene cassette scheme as an inducible system in plants. Sensors 10: 8526-8535; doi:10.3390/s100908526. 

Kang, B-g., X. Ye, L.D. Osburn, C.N. Stewart, Jr., Z-M. Cheng. 2010. Transgenic hybrid aspen overexpressing the Atwbc19 gene encoding an ATP binding cassette transporter confers resistance to four aminoglycoside antibiotics. Plant Cell Reports 29:643-650.

Yuan, J.S., L.G. Abercrombie, Y. Cao, M.D. Halfhill, X. Zhou, Y. Peng, J. Hu, M.R. Rao, G.R. Heck, T.J. Larosa, R. D. Sammons, R. N. Trigiano, X. Wang, P. Ranjan, D. H. Johnson, P. A. Wadl, B.E. Scheffler, T.A Rinehart, R.N. Trigiano, C. N. Stewart, Jr. 2010. Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance. Weed Science. 58: 109-117.

Kausch, A.P., J. Hague, M. Oliver, Y. Li. H. Daniell, P. Maschia, L.S. Watrud, and C.N. Stewart, Jr. 2010. Transgenic biofuel feedstocks and strategies for bioconfinement. Biofuels

Millwood, Reginald J., H. S. Moon, and C. N. Stewart Jr. 2010. Fluorescent proteins in Transgenic plants.

Moon, H.S., Y. Li., C.N. Stewart, Jr. 2010. Keeping the genie in the bottle: transgene biocontainment by excision in pollen. Trends in Biotechnology, 28: 3-8.bullet(with accompanying journal cover)

Stewart, C.N., Jr., L. Shugart, G.-S. Liu, J. Zhuang, Y. Ma, G.A. Tuskan, R. Meilan, R.W. Gentry, G.S. Sayler. 2010. China-U.S. workshop on biotechnology of bioenergy plants.  Ecotoxicology 19: 1-3.

Mann, D.J.G., N. Labbé, R. Sykes, K. Reichel, L. Kline, I.M. Swamidoss, J.N. Burris, M. Davis, C.N. Stewart, Jr. 2009. Rapid assessment of lignin content and structure in switchgrass (Panicum virgatum L.) grown under different environmental conditions. BioEnergy Research 2: 246-256.

Burris, J.N., D.J.G. Mann, B.L. Joyce, C.N. Stewart, Jr. 2009. An improved tissue culture system for embyrogenic callus production and plant regeneration in switchgrass (Panicum virgatum L.). BioEnergy Research 2: 267-274.

Rose, C.W., R.J. Millwood, H.S. Moon, M.R. Rao, M.D. Halfhill, P.L. Raymer, S.I. Warwick, H. Al-Ahmad, J. Gressel, and C.N. Stewart, Jr. 2009. Genetic load and transgenic mitigating genes in transgenic Brassica rapa (field mustard) × Brassica napus (oilseed rape) hybrid populations. BMC Biotechnology 9: 93

Chen, F., H. Al-Ahmad, B. Joyce, N. Zhao, T. G. Köllner,  J. Degenhardt, C. N. Stewart, Jr. 2009. Within-plant distribution and emission of sesquiterpenes from Copaifera officinalis. Plant Physiology and Biochemistry, 47: 1017-1023.

Zhou, X., Z. Su, R.D. Sammons, Y. Peng, P.J. Tranel, C.N. Stewart, Jr., J.S. Yuan. 2009. Novel software package for cross-platform transcriptome analysis (CPTRA). BMC Bioinformatics 10 (Suppl 11): S16

Xu, Z, D. Zhang, J. Hu, X. Zhou, X. Ye, K.L. Reichel, N.R. Stewart, R.D. Syrenne, X. Yang, P. Gao, W. Shi, C. Doeppke, R. W. Sykes, J.N. Burris, J. Bozell, Max Z.-M.. Cheng, D.G. Hayes, N. Labbe, M. Davis, C.N. Stewart, Jr., J.S. Yuan. 2009. Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom. BMC Bioinformatics  10 (Suppl 11): S3

Stewart, C.N., Jr., P.J. Tranel, D.P. Horvath, J.V. Anderson, L.H. Rieseberg, J.H. Westwood, C.A. Mallory-Smith, M.L. Zapiola, K.M. Dlugosch. 2009. Evolution of weediness and invasiveness: charting the course for weed genomics. Weed Science 57: 451-462.

Rao, M.R., M.D. Halfhill, L.G Abercrombie, P. Ranjan, J.M. Abercrombie, J.S. Gouffon, A.M. Saxton, and C.N. Stewart, Jr. 2009. Phytoremediation and phytosensing of chemical
contaminants, RDX and TNT: identification of the required target genes
. Functional and Integrative Genomics 9:537-547.

Di, K., C.N. Stewart, Jr.,W. Wei, B. Shen, Z.-X. Tang, K.-P. Ma.  2009. Fitness and maternal effects in hybrids formed between transgenic oilseed rape (Brassica napus L.) and wild brown mustard [B. juncea (L.) Czern et. Coss.] in the field. Pest Management Science 65:753-760.

Yuan, J.S., S. Himanen, J.K. Holopainen, F. Chen, and C.N. Stewart, Jr.  2009. Smelling climate change: plant volatile organic compounds in changing environments.  Trends in Ecology and Evolution 24: 323-331.

Himanen, S., A.-M. Nerg A. Nissinen, D. M. Pinto, C.N. Stewart, Jr., G.M. Poppy, and J.K. Holopainen, 2009. Effects of elevated carbon dioxide and ozone on volatile terpenoid emissions and multitrophic communication of transgenic insecticidal oilseed rape (Brassica napus).  New Phytologist 181: 174-186.

Panthee, D.R.., J.J. Marois, D.L. Wright,  D. Narváez, J.S. Yuan, and C.N. Stewart Jr. 2009. Differential expression of genes in soybean in response to the causal agent of Asian soybean rust, (Phakopsora pachyrhizi Sydow), is soybean growth stage-specific. Theoretical and Applied Genetics 118: 359-370

Himanen S.J., A.M. Nerg, A. Nissinen, C.N. Stewart, Jr., G.M. Poppy and J.K. Holopainen. 2009. Elevated atmospheric ozone increases concentration of insecticidal Bacillus thuringiensis (Bt) Cry1Ac protein concentrations in Bt Brassica napus and reduces feeding of a Bt target herbivore on the non-transgenic parent. Environmental Pollution 157:181-185.

Himanen, S., A. Nissinen, W.-X. Dong, A.-M. Nerg, C.N. Stewart, Jr., G.M. Poppy, and J.K. Holopainen. 2008. Interactions of elevated carbon dioxide and temperature with aphid feeding on transgenic oilseed rape: Are Bacillus thuringiensis (Bt) plants more susceptible to nontarget herbivores in future climate? Global Change Biology 14: 1437-1454.
Stewart, C.N., Jr. 2008. Pharming in crop communities. Nature Biotechnology 26:1222-1223.

Abercrombie, J.M., M.D. Halfhill, P. Ranjan, M.R. Rao, A. Saxton, J.S. Yuan, and C.N. Stewart, Jr. 2008. Transcriptional responses of Arabidopsis thaliana to As(V) stress. BMC Plant Biology 8:87 ( ).

Yuan, J.S., K.H. Tiller, H. Al-Ahmad, N.R. Stewart, C.N. Stewart, Jr. 2008. Plants to power: bioenergy to fuel the future. Trends in Plant Science 13: 421-429.

Stewart, C.N., Jr. (Ed.) 2008. Plant Biotechnology and Genetics: Principles, Techniques and Applications, Wiley and Sons, New York, 400 pp. June 2008.

Yuan, J.S., D. W. Galbraith, S. Y. Dai, P. Griffin and C.N. Stewart, Jr. 2008. Plant systems biology comes of age. Trends in Plant Science. 13:165-171

Mazarei, M.H., I. Teplova, M. R. Hajimorad and C.N. Stewart, Jr. 2008. Pathogen phytosensing: plants to report plant pathogens. Sensors. 8:2628-2641.

Mazarei, M.H., H. Al-Ahmad, M. R. Rudis and C.N. Stewart, Jr. 2008. Protoplast isolation and transient gene expression in switchgrass, Panicum virgatum L. Biotechnology Journal. 3:354-359.

Burris, K.A., A. Mentewab, S. Ripp, and C.N. Stewart, Jr. 2008. An Arabidopsis thaliana ABC transporter that confers kanamycin resistance in transgenic plants does not endow resistance to Escherichia coli. Microbial Biotechnology. 1:191-195.

Stewart, C.N., Jr. and L. E. Edwards. 2008. How to teach research ethics. The Scientist. 22:27.

Yuan, J., D. Wang. and C. N. Stewart, Jr. 2008. Statistical methods for efficiency adjusted real-time PCR analysis. Biotechnology Journal. 3:112-123.

Yancey, A. and C. N. Stewart, Jr. 2007. Are university researchers at risk for patent infringement? Nature Biotechnology. 25:1225-1228.

Yuan, J.S., J. Burris, N. R. Stewart, A. Mentewab and C. N. Stewart, Jr. 2007. Statistical tools for transgene copy number estimation based on real-time PCR. BMC Bioinformatics. 8(Suppl 2): S6 doi:10.1186/1471-2105-8-S7-S6.

Panthee, D.R., J. Yuan, D.L. Wright, J.J. Marois, D. Mailhot and C. N. Stewart, Jr. 2007. Gene expression analysis in soybean in response tothe casual agent of Asian soybean rust Phakospora pachyrhizi Sydow) in an early growth stage. Functional and Integrative Genomics. 7:291-301. Appels Figure

Moon, H.S., M.D. Halfhill, L. L. Good, P. L. Raymer and C. N. Stewart, Jr. 2007. Characterization of directly transformed weedy Brassica rapa and introgressed B. rapa with Bt crylAc and gfp genes. Plant Cell Reports. 26:1001-1010.

Luo, K., H. Duan, D. Zhao, X. Zheng, W. Deng, Y. Chen, C. N. Stewart, Jr., R. McAvoy, X. Jiang, Y. Wu, A. He, Y. Pei and Y. Li. 2007. 'GM-gene-deletor': fused loxP-FRT recognition sequences dramatically improve the efficiency of FLP or CRE recombinase on transgene excision from pollen and seed of tobacco plants. Plant Biotechnology Journal. 5:263-274.

Stewart, C.N., Jr. 2007. Biofuels and biocontainment. Nature Biotechnology. 25:283-284.

Halfhill, M.D., L.L. Good, C. Basu, J. Burris, C.L.Main, T.C. Mueller, and C.N. Stewart, Jr. 2007. Transformation and segregation of GFP fluorescence and glyphosate resistance in horseweed (Conyza canadensis) hybrids. Plant Cell Reports. 26:303-311.

  • Halfhill, M.D., R. J. Millwood, and C. N. Stewart, Jr. 2004. GFP Quantification in whole plants. pp. 215-226. In: L. Pena (Ed). Transgenic Plants: Methods and Protocols. Methods in Molecular Biology. Humana Press, Totawa, NJ.

  • Hudson, L.C., M.D. Halfhill, and C. N. Stewart, Jr. 2004. Transgene dispersal through pollen. pp. 365-374 In: L. Pena (Ed). Transgenic Plants: Methods and Protocols. Methods in Molecular Biology. Humana Press, Totawa, NJ.

  • Stewart, C.N., Jr. 2004. Genetically Modified Planet: Environmental Impacts of Genetically Engineered Plants. Oxford University Press, New York. 240 pp.