Sandra Helena Unêda-Trevisoli, Lynnette M.A. Dirk, Francisco Elder Carlos Bezerra Pereira, Manohar Chakrabarti, Guijie Hao, James M. Campbell, Sai Deepshikha Bassetti Nayakwadi, Sanjay Joshi, Sharyn E. Perry, Caleb Mensah, Barbara Willard, Laura de Lorenzo, Baseerat Afroza, Arthur G. Hunt, Daniel Guariz Pinheiro, A. Bruce Downie. 2024. "Dehydrin client proteins identified using phage display affinity selected libraries processed with Paired-End PhAge Sequencing (PEPA-Seq)." Submitted. Molecular & Cellular Proteomics.

Yumin Zhang, Xianbo Song, Wenli Zhang, Feijun Liu, Chunmei Wang, Ying Liu, Lynnette Dirk, Bruce Downie, Tianyong Zhao. "Maize PIMT2 repairs the damaged 3-METHYLCROTONYL COA CARBOXYLASE in mitochondria controlling seed vigor." The Plant Journal. Accepted 03.24. 

Ying Liu, Tao Li, Chunxia Zhang, Wenli Zhang, Nan Deng, Lynnette Dirk, Bruce Downie, Tianyong Zhao. 2023. "Raffinose Positively Regulates Maize Drought Tolerance by Reducing Leaf Transpiration." The Plant Journal. 114 (1): 55-67.
Lynnette M.A. Dirk, Tianyong Zhao, John May, Tao Li, Qinghui Han, Yumin Zhang, Mohammad R. Sahib, A. Bruce Downie. “Alterations in carbohydrate quantities in freeze-dried, relative to fresh or frozen maize leaf disks." Biomolecules. 13(1):148. doi:10.3390/biom13010148

Yumin Zhang, Dan Li, Lynnette M. A. Dirk, A. Bruce Downie, Tianyong Zhao. "ZmAGA1 Hydrolyzes RFOs Late during the Lag Phase of Seed Germination, Shifting Sugar Metabolism toward Seed Germination Over Seed Aging Tolerance." Journal of Agricultural and Food Chemistry. 69(39):11606-11615. doi: 10.1021/acs.jafc.1c03677

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. 2018. "An examination of Job’s rule: Protection and repair of the proteins of the translational apparatus in seeds." Seed Science Research. 28, 168–181.
Lynnette M.A. Dirk, Manoj Majee, Santosh Kumar, A. Bruce Downie. 2018. "PHYTOCHROME INTERACTING FACTOR1 interactions leading to the completion or prolongation of seed germination." Plant Signaling and Behavior. 13(10):e1525999.
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. 2018. "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. 

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 (RFOs) in Maize and Arabidopsis." Molecular Plant. 10(12):1540:1555.

Majee Manoj, Wu Shuiqin, Salaita Louai, Gingerich Derek, Dirk Lynnette M.A., Chappell Joseph, Hunt Art G., Vierstra Richard, Downie A. Bruce. "A Misannotated Locus Positively Influencing Arabidopsis Seed Germination is Deconvoluted Using Multiple Methods, Including surrogate Splicing." Plant Gene. 10: 74-85. 

Santos, Juliana F., Dirk, Lynnette M.A., Downie, A. Bruce, Sanches, Mauricio F. G. and Vieira, Roberval D. "Soluble Sugars, Storage Proteins and Reciprocal Effect of Parental Lines of Corn Hybrid Seeds." Seed Science Research. 27: 206-216. 
"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. 

Gu Lei, Zhang Y., Zhang M., Li Tao, Dirk Lynnette M.A., Downie B., Zhao T-Y. "ZmGOLS2, a Target of Transcription Factor ZmDREB2A, Offers Similar Protection Against Abiotic Stress as ZmDREB2A, When Either is Over-Expressed in Arabidopsis, While Presenting a Wild Type Growth Habit in Unstressed kConditions." Plant Molecular Biology. 90:157–170. 

Han Q, Li T, Zhang L, Dirk Lynnette M.A, Downie B, Zhao T-Y. "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. 

Barrero J.M., Downie A.B., Xu Q, Gubler F. "A Role for Barley CRYPTOCHROME1 in Light Regulation of Grain Dormancy and Germination." The Plant Cell. 26:1094-1104.  In this issue: "Cryptochromes and Seed Dormancy: The Molecular Mechanism of Blue Light Inhibition of Grain Germination." Nancy Hofmann. The Plant Cell. 2014; 26: 846.

Kushwaha R, Schäfermeyer K.R., Downie A.B. "A Protocol for Phage Display and Affinity Selection Using Recombinant Protein Baits." Journal of Visualized Experiments. 84, e50685, doi:10.3791/50685. 
Petti C., Harman-Ware A.E., Tateno M., Kushwaha R., Shearer A., Downie A.B., Crocker M., DeBolt S. "Sorghum Mutant RG Displays Antithetic Leaf Shoot Lignin Accumulation Resulting in Improved Stem Saccharification Properties." Biotechnology for Biofuels. 6: 146. 

Gu Lei, Han Z., Zhang ., Downie B., Zhao T-Y. Functional Analysis of the 5’ Regulatory Region of the Maize GALACTINOL SYNTHASE2 Gene. Plant Science. 213: 38–45. 

Nayak N., Putnam A., Chen T., Addepalli B., Lowenson J., Jankowsky E., Perry S.E., Dinkins R., Limbach P., Clarke S.G., Downie A.B. "An ATP Dependent DEAD-box RNA-helicase Loses Activity Upon isoAsp Formation but is Restored by PROTEIN ISOASPARTYL METHYLTRANSFERASE. The Plant Cell. 25:2573-2586.