Publications:

Longhurst ML, D Coster, PG Wolf, AM Duffy, H Lee, and T Campbell. 2016. Multi-year professional development grounded in educative curriculum focused on integrating technology with reformed science teaching principles. School Science and Mathematics 116:430-441.

Duffy AM, MC Stensvold, and DR Farrar. 2015. Independent gametophytes of Hymenophllum wrightii in North America: not as rare as we thought. American Fern Journal 105:45-55.

Sessa EB, JA Banks, MS Barker, JP Der, AM Duffy, SW Graham, M Hasebe, J Langdale, F-W Li, DB Marchant, KM Pryer, CJ Rothfels, SJ Roux, ML Salmi, EM Sigel, DE Soltis, PS Soltis, DW Stevenson, and PG Wolf. 2014. Between two fern genomes. GigaScience 3:15.

Schilling MP, PG Wolf, AM Duffy, HS Rai, CA Rowe, BA Richardson, and KE Mock. 2014. Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches. PLoS One 9:e95292.

Duffy AM, PG Wolf, J Barrow, M Longhurst, and T Campbell. 2013. Ecological investigations within an interactive plant community simulation. Science Scope 36:42-51.

Campbell T, M Longhurst, AM Duffy, PG Wolf, and BE Shelton. 2013. Science teaching orientations and technology-enhanced tools for student learning. Research in Science Education 10.1007/s11165-012-9342-x

Campbell T, M Longhurst, AM Duffy, PG Wolf, and R Nagy. 2012. Investigating human impact in the environment with faded scaffolded inquiry supported by technologies. Science Activities 49:99-107.

Liu H, M Bowman, AM Duffy, and WA Hunt. 2012. Enabling behavior reuse in development of virtual environment applications. Proceedings of the 2012 Winter Simulation Conference, C Laroque, J Himmelspach, R Pasupathy, O Rose, and AM Uhrmacher, eds.

Clark JL, MM Funke, AM Duffy, and JF Smith. 2012. Phylogeny of a Neotropical clade in the Gesneriaceae: more tales of convergent evolution. International Journal of Plant Sciences 173:894-916

Benninghoff AD, GA Orner, C Buchner, JD Hendricks, AM Duffy, and DE Williams. 2012. Promotion of hepatocarcinogenesis by perfluoroalkyl acids in rainbow trout. Toxicological Sciences 125:69-78.

Karol KG, K Arumuganathan, JL Boore, AM Duffy, KDE Everett, JD Hall, SK Hansen, JV Kuehl, DF Mandoli, BD Mischler, RG Olmstead, KS Renzaglia, and PG Wolf. 2010. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evolutionary Biology 10:321.

Wolf PG, JP Der, AM Duffy, JB Davidson, AL Grusz, and KM Pryer. 2010. The evolution of chloroplast genes and genomes in ferns. Plant Molecular Biology 76: 251-261.

Campbell T, SK Wang, HY Hsu, AM Duffy, and PG Wolf. 2010. Learning with web tools, simulations, and other technologies in science classrooms. Journal of Science Education and Technology 19:505-511.

Wolf PG, JM Roper, and AM Duffy. 2010. The evolution of chloroplast genome structure in ferns. Genome 53:731-738.

Oliver MJ, AG Murdock, BD Mishler, JV Kuehl, JL Boore, DF Mandoli, KDE Everett, PG Wolf, AM Duffy, and KG Karol. 2010. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. BMC Genomics 11:143.

Wolf PG, AM Duffy, and JM Roper. 2009. Phylogenetic use of inversions in fern chloroplast genomes. American Fern Journal 99:132-134.

Duffy AM, SA Kelchner, and PG Wolf. 2009. Conservation of selection on matK following an ancient loss of its flanking intron. Gene 438:17-25.

Presentations:

Duffy, AM, KM Mendoza, KM Reed, RA Coulombe. 2016. Poster: Candidate miRNAs involved in regulation of alpha-class glutathione S-transferases associated with susceptibility to the carcinogen aflatoxin B1. Plant & Animal Genome Conference XXIV, San Diego, CA (2016).

Duffy AM, DR Farrar, and PG Wolf. Exploring the population genetics of independent gametophytes of Crepidomanes intricatum (Farrar) Ebihara & Weakley (Hymenophyllaceae) using genotyping-by-sequencing. Botany 2014, Boise, ID (2014).

Duffy AM. Workshop: Hands-on inquiry using the Virtual Plant Community Simulation (VPCsim). Utah State University Global Academy - Science, Technology and Inquiry session, Logan, UT (2012).

Duffy AM, T Campbell, and PG Wolf. Workshop: The Virtual Population Genetics (VPG) Simulation System: An example of learning 'with' cyber-enabled technologies in science classrooms. National Science Teachers Association Research Dissemination Conference, San Francisco, CA (2011).

Campbell T, and AM Duffy. Hands-on demo: OpenSim as an example of cyber-enabled technologies for facilitating science as inquiry. Cyberlearning Tools for STEM Education Conference, Berkeley, CA (2011).

Duffy AM. Simulating fern life cycles and population genetics in a 3-dimensional virtual world. Botany 2009, Snowbird, UT and Idaho State University Practical Bioinformatics Workshop, Lava Hot Springs, ID (2009).

Duffy AM, SA Kelchner, and PG Wolf. Conservation of selection on matK in ferns following an ancient loss of the trnK intron by genome inversion. Botany 2008, Vancouver, BC and Idaho State University Practical Bioinformatics Workshop, Lava Hot Springs, ID (2008).

Duffy AM, MM Funke, JL Clark, and JF Smith. A phylogenetic analysis of the genera of tribe Episcieae (Gesneriaceae) from multiple loci. Botany 2004, Snowbird, UT and Northwest Science Association, Boise, ID (2006).

Duffy AM, MM Funke, JL Clark, and JF Smith. Poster: A phylogenetic analysis of the genera of tribe Episcieae (Gesneriaceae) from multiple loci. BSU Day at the Legislature, Idaho State Capitol, Boise ID (2005), and BSU Undergraduate Research and Scholarship Conference, Boise, ID (2005).