Qinghui Han, Kelu Chen, Dong Yan, Guanglong Hao, Junlong Qi, Chunmei Wang, Lynnette M.A. Dirk, A. Bruce Downie, Jianhua Gong, Jianhua Wang, Tianyong Zhao. "ZmDREB2A regulates ZmGH3.2 and ZmRAFS, shifting metabolism towards seed aging tolerance over seedling growth." The Plant Journal. 104:268-282. doi: 10.1111/tpj.14922  
Ran Tian, Fangfang Wang, Qiaolin Zheng, Venus M. A. G. E. Niza, A. Bruce Downie, Sharyn E. Perry. "Direct and indirect targets of the arabidopsis seed transcription factor ABSCISIC ACID INSENSITIVE3." The Plant Journal. 103:1679-1694. doi: 10.1111/tpj.14854
Lynnette M.A. Dirk, Caser Ghaafar Abdel, Imran Ahmad, Izabel Costa Silva Neta, Cristiane Carvalho Pereira, Francisco Elder Carlos Bezerra Pereira, Sandra Helena Unêda-Trevisoli, Daniel Guariz Pinheiro, Allan Bruce Downie. “LATE EMBRYOGENESIS ABUNDANT PROTEIN-CLIENT PROTEIN interactions.” Plants. 9(7):814. doi: 10.3390/plants9070814 
Tao Li, Yumin Zhang, Ying Liu, Xudong Li, Guanglong Hao, Qinghui Han, Lynnette M.A. Dirk, A. Bruce Downie, Yong-Ling Ruan, Jianmin Wang, Guoying Wang, Tianyong Zhao. "Raffinose synthase enhances drought tolerance through raffinose synthesis or galactinol hydrolysis in maize and Arabidopsis plants." Journal of Biological Chemistry. 295(23):8064-8077. doi: 10.1074/jbc.RA120.013948
Qinghui Han, Junlong Qi, Guanglong Hao, Chunxia Zhang, Chunmei Wang, Lynnette M.A. Dirk, A. Bruce Downie, Tianyong Zhao. "ZmDREB1A regulates RAFFINOSE SYNTHASE controlling raffinose accumulation and vegetative chilling stress tolerance in maize." Plant & Cell Physiology. 61(2):331-341. doi: 10.1093/pcp/pcz200

Lei Gu, Tao Jiang, Chunxia Zhang, Xudong Li, Chunmei Wang, Yumin Zhang, Tao Li, Lynnette M.A. Dirk, A. Bruce Downie, Tianyong Zhao. “Maize HSFA 2 and HSBP 2 antagonistically modulate raffinose biosynthesis and heat tolerance in Arabidopsis.” The Plant Journal. 100(1):128-142. doi: 10.1111/tpj.14434
Yumin Zhang, Qichao Sun, Chunxia Zhang, Guanglong Hao, Chunmei Wang, Lynnette M.A. Dirk, A. Bruce Downie, and Tianyong Zhao. "Maize VIVIPAROUS1 interacts with ABA INSENSITIVE5 to regulate GALACTINOL SYNTHASE2 expression controlling seed raffinose accumulation." Journal of Agricultural and Food Chemistry. 67(15):4214-4223. doi: 10.1021/acs.jafc.9b00322
Lynnette M.A. Dirk, and A. Bruce Downie. "An examination of Job’s rule: protection and repair of the proteins of the translational apparatus in seeds." Seed Science Research. 28(Special Issue 3: Seeds as Systems):168–181. doi: 10.1017/S0960258518000284
Lynnette M.A. Dirk, Manoj Majee, Santosh Kumar, A. Bruce Downie. "PHYTOCHROME INTERACTING FACTOR1 interactions leading to the completion or prolongation of seed germination." Plant Signaling & Behavior. 13(10):e1525999. doi: 10.1080/15592324.2018.1525999 
Manoj Majee, Santosh Kumar, Praveen Kumar Kathare, Shuiqin Wu, Derek Gingerich, Nihar R. Nayak, Louai Salaita, Randy Dinkins, Kathleen Martin, Michael Goodin, Lynnette M.A. Dirk, Taylor D. Lloyd, Ling Zhu, Joseph Chappell, Art G. Hunt, Richard Vierstra, Enamul Huq, and A. Bruce Downie. "KELCH F-BOX protein positively influences seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1." Proceedings of the National Academy of Science U.S.A. 115(17):E4120-E4129. doi: 10.1073/pnas.1711919115
Tao Li, Yumin Zhang, Dong Wang, Ying Liu, Lynnette M.A. Dirk, Jack Goodman, A. Bruce Downie, Jianmin Wang, Guoying Wang, Tianyong Zhao. "Regulation of seed vigor by manipulation of raffinose family oligosaccharides in Maize and Arabidopsis thaliana." Molecular Plant. 10(12):1540:1555. doi: 10.1016/j.molp.2017.10.014  
Manoj Majee, Shuiqin Wu, Louai Salaita, Derek Gingerich, Lynnette M.A. Dirk, Joseph Chappell, Art G. Hunt, Richard Vierstra, A. Bruce Downie. "A misannotated locus positively influencing Arabidopsis seed germination is deconvoluted using multiple methods, including surrogate splicing." Plant Gene. 10:74-85. doi: 10.1016/j.plgene.2017.05.012  
Juliana F. Santos, Lynnette M.A. Dirk, A. Bruce Downie, Mauricio F.G. Sanches, Roberval D.Vieira. " Reciprocal effect of parental lines on the physiological potential and seed composition of corn hybrid seeds." Seed Science Research. 27(3):206-216. doi: 10.1017/S0960258517000095  
"Findings from Sao Paulo State University Broaden Understanding of Seed Science." (Reciprocal Effect of Parental Lines on the Physiological Potential and Seed Composition of Corn Hybrid Seeds). Agriculture Week. Sep 21, 2017, p.106.

Lei Gu, Yumin Zhang, Mingshuai Zhang, Tao Li, Lynnette M.A. Dirk, Bruce Downie, Tianyong Zhao. "ZmGOLS2, a target of transcription factor ZmDREB2A, offers similar protection against abiotic stress as ZmDREB2A." Plant Molecular Biology. 90(1-2):157–170. doi:10.1007/s11103-015-0403-1 

Qinghui Han, Tao Li, Lifeng Zhang, Lynnette M.A. Dirk, Bruce Downie, Tianyong Zhao. "Functional analysis of the 5’-regulatory region of the maize ALKALINE ALPHA-GALACTOSIDASE1 gene." Plant Molecular Biology Reporter. 33:1361-1370. doi: 10.1007/s11105-014-0840-z   

Jose M. Barrero, A. Bruce Downie, Qian Xu, Frank Gubler. "A role for barley CRYPTOCHROME1 in light regulation of grain dormancy and germination." The Plant Cell. 26(3):1094-1104. doi: 10.1105/tpc.113.121830 
In Brief: "Cryptochromes and seed dormancy: the molecular mechanism of blue light inhibition of grain germination." Nancy Hofmann. The Plant Cell. 2014; 26(3):846. doi: 10.1105/tpc.114.124727 
Rekha Kushwaha, Kim R. Schäfermeyer, A. Bruce Downie. "A protocol for phage display and affinity selection using recombinant protein baits." Journal of Visualized Experiments. 84:e50685. doi: 10.3791/50685
Carloalberto Petti, Anne E. Harman-Ware, Mizuki Tateno, Rekha Kushwaha, Andrew Shearer, A. Bruce Downie, Mark Crocker, Seth DeBolt. "Sorghum mutant RG displays antithetic leaf shoot lignin accumulation resulting in improved stem saccharification properties." Biotechnology for Biofuels. 6(1):146. doi: 10.1186/1754-6834-6-146  
Lei Gu, ZhaoXue Han, Lifeng Zhang, Bruce Downie, Tianyong Zhao. “Functional analysis of the 5’ regulatory region of the maize GALACTINOL SYNTHASE2 gene.” Plant Science. 213:38–45. doi: 10.1016/j.plantsci.2013.09.002  
Nihar R. Nayak, Andrea A. Putnam, Balasubrahmanyam Addepalli, Jonathan D. Lowenson, Tingsu Chen, Eckhard Jankowsky, Sharyn E. Perry, Randy D. Dinkins, Patrick A. Limbach, Steven G. Clarke, A. Bruce Downie. "An Arabidopsis ATP-dependent, DEAD-box RNA helicase loses activity upon isoAsp formation but is restored by PROTEIN ISOASPARTYL METHYLTRANSFERASE. The Plant Cell. 25(7):2573-2586. doi: 10.1105/tpc.113.113456  
Rekha Kushwaha, Christina M. Payne, A. Bruce Downie. "Uses of phage display in agriculture: a review of food-related protein-protein interactions discovered by biopanning over diverse baits." Computational and Mathematical Methods in Medicine. 2013(Special Issue on Phage Display Informatics):653759. doi: 10.1155/2013/653759
Rekha Kushwaha, A. Bruce Downie, Christina M. Payne. "Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggests protein-nucleic acid binding functionality." Computational and Mathematical Methods in Medicine. 2013(Special Issue on Phage Display Informatics):470390. doi: 10.1155/2013/470390