Cooper was the first to apply to rice a systems biology approach for gene discovery. The approach involved measuring protein-protein interactions and determining how protein interaction networks were associated with gene expression changes influenced by environmental and developmental cues. Cooper has since used quantitative mass spectrometry to identify in organisms networks of proteins that define a phenotypic or genetic response.
Papers:
Disruptive Effects of Resveratrol on a Bacterial Pathogen of Beans (2023). Bret Cooper. Journal of Proteome Research 22, 204-214. Published on-line before print December 13, 2022. DOI: 10.1021/acs.jproteome.2c00633
The Detriment of Salicylic Acid to the Pseudomonas savastanoi pv. phaseolicola Proteome (2022). Bret Cooper. Molecular Plant-Microbe Interactions 9, 814-824. Published on-line before print May 25, 2022. DOI: 10.1094/MPMI-05-22-0104-R
The Proteomics of Resistance to Halo Blight in Common Bean (2020). Bret Cooper, Kimberly B. Campbell, Hunter Beard, Wesley M Garrett, and Marcio E. Ferreira. Molecular Plant-Microbe Interactions 33, 1161-1175. Published on-line before print July 7, 2020. DOI: 10.1094/MPMI-05-20-0112-R
Benzothiadiazole Conditions the Bean Proteome for Immunity to Bean Rust (2020). Bret Cooper, Hunter Beard, Wesley M. Garrett, and Kimberly B. Campbell. Molecular Plant-Microbe Interactions. Published on-line before print January 30, 2020. DOI: 10.1094/MPMI-09-19-0250-R
Blistering1 Modulates Penicillium expansum Virulence via Vesicle-Mediated Protein Secretion (2019). Wayne M. Jurick II, Hui Peng, Hunter S. Beard, Wesley M. Garrett, Franz J. Lichtner, Dianiris Luciano-Rosario, Otilia Macarisin, Yingjian Liu, Kari A. Peter, Verneta L. Gaskins, Tianbao Yang, Joseph Mowery, Gary Bauchan, Nancy P. Keller, and Bret Cooper. Molecular and Cellular Proteomics 19, 344-361. Published on-line before print December 23, 2019. DOI:10.1074/mcp.RA119.001831.
Quantitative Proteomics Reveals a Role for SERINE/ARGININE-Rich 45 in Regulating RNA Metabolism and Modulating Transcriptional Suppression via the ASAP Complex in Arabidopsis thaliana (2019). Samuel L. Chen, Timothy J. Rooney, Anna R. Hu, Hunter S. Beard, Wesley M. Garrett, Leann M. Mangalath, Jordan J. Powers, Bret Cooper, and Xiao-Ning Zhang. Frontiers in Plant Science 10, 1116. Published on-line September 19, 2019. DOI: 10.3389/fpls.2019.01116
Quantitative Proteomic Analysis of Staphylococcus aureus Treated with Punicalagin, a Natural Antibiotic from Pomegranate that Disrupts Iron Homeostasis and Induces SOS (2018). Bret Cooper, Nazrul Islam, Yunfeng Xu, Hunter S. Beard, Wesley M. Garrett, Ganyu Gu, and Xiangwu Nou. Proteomics 18, 1700461.
A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii (2018). Bret Cooper, Kimberly B. Campbell, Hunter Beard, Wesley M Garrett, Joseph Mowery, Gary R. Bauchan, and Patrick Elia. Molecular Plant-Microbe Interactions 31, 334-343.
Different Cellular Origins and Functions of Extracellular Proteins from Escherichia coli O157:H7 and O104:H4 as Determined by Comparative Proteomic Analysis (2016). Nazrul Islam, Attila Nagy, Wesley M. Garrett, Dan Shelton, Bret Cooper, and Xiangwu Nou. Applied and Environmental Microbiology 82, 4371-4378.
Proteomics of Nitrogen Remobilization in Poplar Bark (2015). Nazrul Islam, Gen Li, Wesley M. Garrett, Rongshuang Lin, Ganesh Sriram, Bret Cooper, and Gary D. Coleman. Journal of Proteome Research 14, 1112-1126.
Proteomic Pleiotropy of OpgGH, an Operon Necessary for Efficient Growth of Salmonella enterica serovar Typhimurium under Low-osmotic Conditions (2012). Bret Cooper, Ruiqiang Chen, Wesley M. Garrett, Charles Murphy, Caren Chang, Mark L. Tucker, and Arvind A. Bhagwat. Journal of Proteome Research, 11, 1720-1727.
Proteomic Responses in Arabidopsis thaliana Seedlings Treated with Ethylene (2011). Ruiqiang Chen, Brad M. Binder, Wesley M. Garrett, Mark L. Tucker, Caren Chang and Bret Cooper. Molecular BioSystems, 7, 2637-2650.
Nuclear Proteomic Changes Linked to Soybean Rust Resistance (2011). Bret Cooper, Kimberly B. Campbell, Jian Feng, Wesley M. Garrett and Reid Frederick. Molecular BioSystems 7, 773-783. Published on-line before print Dec. 3, 2010.
Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus (2009). Joohyun Lee, Kimberly B. Campbell, Brian E. Scheffler, Jian Feng, Daniel Q. Naiman, Wesley M. Garrett, Sandra Thibivilliers, Gary Stacey, Mark L. Tucker, M.A. Pastor-Corrales and Bret Cooper. Molecular and Cellular Proteomics 8, 19-31. Published on-line before print August 28, 2008.
Protein Accumulation in the Germinating Uromyces appendiculatus Uredospore (2007). Bret Cooper, Anil Neelam, Kimberly B. Campbell, Joohyun Lee, George Liu, Wesley M. Garrett, Brian Scheffler and Mark L. Tucker. Molecular Plant-Microbe Interactions 20, 857-866. DOI: 10.1094/MPMI-20-7-0857
Identification of Rice (Oryza sativa) Proteins Linked to the Cyclin-Mediated Regulation of the Cell Cycle (2003). Bret Cooper, Don Hutchison, Sylvia Park, Sonia Guimil, Peter Luginbühl, Cinzia Ellero, Stephen A. Goff and Jane Glazebrook. Plant Molecular Biology 53, 273-279.
A Network of Rice Genes Associated with Stress Response and Seed Development (2003). Bret Cooper, Joseph D. Clarke, Paul Budworth, Joel Kreps, Don Hutchison, Sylvia Park, Sonia Guimil, Molly Dunn, Peter Luginbühl, Cinzia Ellero, Stephen A. Goff, and Jane Glazebrook. Proc. Natl. Acad. Sci. USA 100, 4945-50; published online before print April 8 2003, 10.1073/pnas.0737574100.