Research Program

My primary research focus is on the genetics of abiotic and multiple stress responses in plants.  Components of this work include genome-wide mapping of loci that control gene expression and morphological UV responses in maize and Arabidopsis, host control of phyllosphere microbial community composition using molecular diversity of the rDNA, QTL mapping method development, including recursive partitioning and Bayesian mapping methods, and testing of a candidate UV-B photoreceptor gene in Arabidopsis.  I also have a substantial program in interdisciplinary computational biology tool and infrastructure development, in collaboration with computational scientists at UNCW and a national consortium led by the University of Arizona and Cold Spring Harbor Laboratory. 

Recent Publications (student co-authors bold type)

Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan J, Buckler ES (2008) Natural Genetic Variation in Lycopene Epsilon Cyclase Tapped for Maize Biofortification. Science 319: 330-333

Blanding CR, Simmons SJ, Casati P, Walbot V, Stapleton AE (2007) Coordinated regulation of maize genes during increasing exposure to ultraviolet radiation: identification of ultraviolet-responsive genes, functional processes and associated potential promoter motifs. Plant Biotechnology Journal 5: 677-695

Casati, P., Stapleton, A., Blum, J. E., Walbot, V. (2006) Genome-wide analysis of high altitude maize and gene knockdown stocks implicates chromatin remodeling proteins in responses to UV-B, Plant Journal 46:613-627. 

Boone, Edward L., Susan J. Simmons, Keying Ye and Ann E. Stapleton (2006) Analyzing Quantitative Trait Loci for Arabidopsis thaliana using Markov Chain Monte Carlo Model Composition with Restricted and Unrestricted Model Spaces.  Statistical Methodology 3(1): 69-78.

Simmons, S. J. and Ann E. Stapleton (2006) Bayesian hierarchical models to detect quantitative trait loci.  Chance 19(3):11-14

Stapleton, A. E. and Simmons, S. J. (2006) Plant Control of Phyllosphere Diversity:  Genotype Interactions with Ultraviolet-B Radiation in Microbial Ecology of Aerial Plant Surfaces, Ed. M. Bailey.

Kunzelman, Jennifer I., Michael J. Durako, W. Judson Kenworthy, Ann E. Stapleton, and Jeffrey L.C. Wright (2005) Irradiance-induced changes in the photobiology of Halophila johnsonii Eiseman. Marine Biology 148:241-250.

Brown, Jeffrey L., Clayton S. Ferner, Thomas C. Hudson, Ann E. Stapleton, Ronald J. Vetter, Andrew Martin, Jerry Martin, Allen Rawls, William J. Shipman, Michael Wood, and Tristan Carland (2005) GridNexus:  A Grid Services Scientific Workflow System.  International Journal of Computer & Information Science (IJCIS) 6(2): 72-82.

Blum, J. E., Casati, P., Walbot, V. and Stapleton, A. E. (2004) Split-plot microarray design allows sensitive detection of expression differences after ultraviolet radiation in the inbred parental lines of a key maize mapping population. Plant Cell and Environment 27(11):1374-1386

Wrede, C. S., Blum, J. E., Brown, J. L. and Stapleton, A. E.  (2004) Comparison of transmembrane helix frequencies using whole-genome and maize expressed sequence curve fits.  Maydica 49(2):67-76.

Hudson, T., Stapleton, A., and J. Brown (2004) Codifying bioinformatics processes without programming. Drug Discovery Today: BIOSILICO 2 (4):164-169

Kadivar, H. and A. E. Stapleton (2003) Ultraviolet Radiation Alters Maize Phyllosphere Bacterial Diversity Microbial Ecology 45:353-361

Long, L. M., H. Patel, P. Cory, W. C. and A. E. Stapleton (2003) The Maize Epicuticular Wax Layer Provides UV Protection Functional Plant Biology 30:75-81

Cartwright, H. N., Baucom, C., Singh, P., Smith, K. L., and Stapleton, A. (2001) Intraspecific comparisons reveal differences in the pattern of ultraviolet radiation responses in four maize (Zea mays L.) varieties.  Journal of Photochemistry and Photobiology B: Biology 62:88-96

Synergistic Activities

Key member of iPlant and other proposals for the $50 million NSF PSCIC competition; specialty area is supervision of synthesis activities, especially training of faculty cross-disciplinary teams in conjunction with computing infrastructure development.

Panel Manager for $10 million 2006/2007 CAP Applied Genomics Program USDA CSREES.

Mentored under-represented minority student Carletha Blanding in her MS project on time course microarray statistical analysis; she graduated with her MS in Biology in 2005 and is employed as a biostatistician.  Carletha was featured as a success story in the UNCW Research magazine.

Jointly taught graduate Bioinformatics class with CS faculty member Thomas Hudson Spring 2006; both CS and Bio graduate students enrolled and worked in cross-disciplinary teams.

Nominated for 1998 UT National Alumni Association Outstanding Teacher Award.

Grant reviewer for USDA NRI Competitive Grants Programs, NSF Division of Undergraduate Education, NSF Eukaryotic Genetics, NSF Plant Genome Research, DOE Basic Biosciences Division, NSF Environmental Genomics, Israel-US Binational Science Foundation.

Served on the Committee of Visitors for the NSF Plant Genome Research program five-year review in 2001; participated in a reverse site visit for the NSF Plant Genome Program in 2002.  Panel Member, USDA Plant Genome Program 2004.  Acting Panel Manager, USDA RICECAPS panel 2004.  Panel Member, NRICGP Plants and Environmental Adaptations panel April 2005 and May 2006. 

Manuscripts reviewed for more than 20 journals including:  Plant Physiology, Plant Cell and Environment, Planta, PNAS, Plant Cell, Global Change Biology, Genetics, Bioinformatics, Microbial Ecology.