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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » People & Locations » Ethalinda Cannon
Ethalinda Cannon
Corn Insects and Crop Genetics Research
Biologist (Computational/Bioinformatics)

Phone: (515) 294-5558
Fax:

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Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Genomes, comparative genomics and pan-genomics tools and resources at the maize genetics and genomics database (MaizeGDB) Reprint Icon - (Book / Chapter)
Woodhouse, M.R., Portwood Ii, J.L., Sen, S., Hayford, R.K., Gardiner, J.M., Cannon, E.K., Haley, O., Andorf, C.M. 2024. Genomes, comparative genomics and pan-genomics tools and resources at the maize genetics and genomics database (MaizeGDB). Cold Spring Harbor Protocols. https://doi.org/10.1101/pdb.over108430.
Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress Reprint Icon - (Peer Reviewed Journal)
Hayford, R.K., Haley, O., Cannon, E.K., Portwood Ii, J.L., Gardiner, J.M., Andorf, C.M., Woodhouse, M.H. 2024. Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress. BMC Genomics. https://doi.org/10.1186/s12864-024-10443-7.
PanEffect: a pan-genome visualization tool for variant effects in maize Reprint Icon - (Peer Reviewed Journal)
Andorf, C.M., Haley, O., Hayford, R.K., Portwood II, J.L., Harding, S.F., Sen, S., Cannon, E.K., Gardiner, J.M., Kim, H., Woodhouse, M.R. 2024. PanEffect: a pan-genome visualization tool for variant effects in maize. Bioinformatics. 40(2). Article btae073. https://doi.org/10.1093/bioinformatics/btae073.
Enhanced pan-genomic resources at the maize genetics and genomics database Reprint Icon - (Peer Reviewed Journal)
Cannon, E.K., Portwood II, J.L., Hayford, R.K., Hayley, O.C., Gardiner, J.M., Andorf, C.M., Woodhouse, M.R. 2024. Enhanced pan-genomic resources at the maize genetics and genomics database. Genetics. 227(1). https://doi.org/10.1093/genetics/iyae036.
PanEffect: A pan-genome visualization tool for variant effects in maize Reprint Icon - (Pre-print Publication)
Andorf, C.M., Haley, O., Hayford, R., Portwood Ii, J.L., Sen, S., Cannon, E.K., Gardiner, J.M., Woodhouse, M.H. 2023. PanEffect: A pan-genome visualization tool for variant effects in maize. bioRxiv. Article 09.25.559155. https://doi.org/10.1101/2023.09.25.559155.
Pan-genome data at MaizeGDB - (Abstract Only)
Cannon, E.K., Portwood II, J.L., Hayford, R., Gardiner, J., Woodhouse, M.H., Andorf, C.M. 2023. Pan-genome data at MaizeGDB. Maize Annual Meetings. 66.
MaizeGDB: Maize protein structure resources - (Abstract Only)
Andorf, C.M., Portwood II, J.L., Sen, S., Hayford, R., Cannon, E.K., Gardiner, J., Woodhouse, M.H. 2023. MaizeGDB: Maize protein structure resources. Maize Annual Meetings. 65.
Stress response functional annotation using RNA expression in maize - (Abstract Only)
Hayford, R., Woodhouse, M.H., Portwood II, J.L., Sen, S., Gardiner, J., Cannon, E.K., Andorf, C.M. 2023. Stress response functional annotation using RNA expression in maize. Maize Annual Meetings. 68.
Maize protein structure resources at the maize genetics and genomics database Reprint Icon - (Peer Reviewed Journal)
Woodhouse, M.H., Portwood II, J.L., Sen, S., Hayford, R.K., Gardiner, J.M., Cannon, E.K., Harper, L.C., Andorf, C.M. 2023. Maize protein structure resources at the maize genetics and genomics database. Genetics. 224(1).Article iyad016. https://doi.org/10.1093/genetics/iyad016.
Guidelines for standardizing gene model nomenclature and genome assembly quality metrics - (Abstract Only)
FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology Reprint Icon - (Peer Reviewed Journal)
Andorf, C.M., Sen, S., Hayford, R.K., Portwood II, J.L., Cannon, E.K., Harper, L.C., Gardiner, J.M., Sen, T.Z., Woodhouse, M.H. 2022. FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology. bioRxiv. https://doi.org/10.1101/2022.11.10.516002.
Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.) Reprint Icon - (Peer Reviewed Journal)
Otyama, P.I., Chamberlin, K., Ozias-Akins, P., Graham, M.A., Cannon, E.K.S., Cannon, S.B., MacDonald, G.E., Anglin, N.L. 2022. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). Genes, Genomes, Genetics. 12(1). Article jkab382. https://doi.org/10.1093/g3journal/jkab382.
A pan-genomic approach to genome databases using maize as a model system Reprint Icon - (Peer Reviewed Journal)
Woodhouse, M.H., Cannon, E.K., Portwood II, J.L., Harper, E.C., Gardiner, J.M., Schaeffer, M.L., Andorf, C.M. 2021. A pan-genomic approach to genome databases using maize as a model system. Biomed Central (BMC) Plant Biology. 21. Article 385. https://doi.org/10.1186/s12870-021-03173-5.
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes Reprint Icon - (Peer Reviewed Journal)
Hufford, M.B., Seetharam, A.S., Woodhouse, M.H., Chougle, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Portwood II, J.L., Cannon, E.K., Andorf, C.M., Ware, D., Dawe, K.R. et al. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science. 373(6555):655-662. https://doi.org/10.1126/science.abg5289.
Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.) Reprint Icon - (Pre-print Publication)
Otyama, P.I., Chamberlin, K., Ozias-Akins, P., Graham, M.A., Cannon, E.K.S., Cannon, S.B., MacDonald, G.E., Anglin, N.L. 2021. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in Arachis hypogaea. bioRxiv. https://doi.org/10.1101/2021.06.03.446924.
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases Reprint Icon - (Peer Reviewed Journal)
Staton, M., Cannon, E.K., Sanderson, L., Wegrzyn, J., Buehler, S., Ficklin, S., Grau, E., Guignon, V., Gunoskey, J., Jung, S., Main, D., Poelchau, M.F., Ramnath, R., Cobo, I., Richter, P., West, J., Anderson, T.K., Inderski, B., Faaberg, K.S., Lager, K.M. 2021. Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Briefings in Bioinformatics. 22(6). https://doi.org/10.1093/bib/bbab238.
The NAM genome assemblies and 2021 release of their official annotations at MaizeGDB - (Abstract Only)
Cannon, E.K., Woodhouse, M.H., Andorf, C.M., Gardiner, J., Harper, E.C., Portwood Ii, J.L., Schaeffer, M.L. 2021. The NAM genome assemblies and 2021 release of their official annotations at MaizeGDB. Maize Annual Meetings. 76.
History of the maize genome sequence assemblies - (Abstract Only)
Harper, E.C., Gardiner, J.M., Schaeffer, M.L., Cannon, E.K., Portwood Ii, J.L., Woodhouse, M.H., Andorf, C.M. 2021. History of the maize genome sequence assemblies. Maize Annual Meetings. 59.
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes Reprint Icon - (Pre-print Publication)
Hufford, M.B., Seetharam, A.S., Woodhouse, M.H., Chougie, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Portwood Ii, J.L., Cannon, E.K., Andorf, C.M., Ware, D., Dawe, K.R., et all. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. bioRxiv. https://doi.org/10.1101/2021.01.14.426684.
GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data Reprint Icon - (Peer Reviewed Journal)
Wilkey, A., Brown, A.V., Cannon, S.B., Cannon, E.K. 2020. GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data. Biomed Central (BMC) Genomics. 21. Article 822. https://doi.org/10.1186/s12864-020-07217-2.
MaizeMine: A data mining warehouse for the maize genetics and genomics database (MaizeGDB) Reprint Icon - (Peer Reviewed Journal)
Shamimuzzaman, M., Gardiner, J.M., Walsh, A.T., Triant, D.A., Le Tourneau, J.J., Tayal, A., Unni, D.R., Nguyen, H.H., Portwood Ii, J.L., Cannon, E.K., Andorf, C.M., Elsik, C.G. 2020. MaizeMine: A data mining warehouse for the maize genetics and genomics database (MaizeGDB). Frontiers in Plant Science. 11. Article 592730. https://doi.org/10.3389/fpls.2020.592730.
Genotypic characterization of the U.S. peanut core collection Reprint Icon - (Peer Reviewed Journal)
Otyama, P.I., Kulkarni, R., Chamberlin, K., Ozias-Akins, P., Chu, Y., Lincoln, L.M., MacDonald, G.E., Anglin, N.L., Dash, S., Bertioli, D.J., Fernandez-Baca, D., Graham, M.A., Cannon, S.B., Cannon, E.K.S. 2020. Genotypic characterization of the U.S. peanut core collection. G3, Genes/Genomes/Genetics. 10(11):4013-4026. https://doi.org/10.1534/g3.120.401306.
Genotypic characterization of the U.S. peanut core collection - (Abstract Only)
Otyama, P.I., Kulkarni, R., Chamberlin, K.D., Ozias-Akins, P., Chu, Y., Lincoln, L.M., Macdonald, G.E., Anglin, N.L., Dash, S., Bertoli, D., Fernandez-Baca, D., Graham, M.A., Cannon, S.B., Cannon, E.K. 2020. Genotypic characterization of the U.S. peanut core collection [abstract]. In proceedings: American Peanut Research and Education Society, July 2020. Available: https://apresinc.com/wp-content/uploads/2020/06/OtyamaPI-Abstract-2020.pdf.
MaizeGDB 2018: The maize multi-genome genetics and genomics database Reprint Icon - (Peer Reviewed Journal)
Portwood II, J.L., Woodhouse, M.R., Cannon, E.K., Gardiner, J., Harper, E.C., Schaeffer, M.L., Walsh, J., Sen, T.Z., Cho, K., Braun, B.L., Dietze, M., Dunfee, B., Elsik, C.G., Manchanda, N., Coe, E., Sachs, M.M., Stinard, P.S., Tolbert, J.P., Zimmerman, S.A., Andorf, C.M. 2018. MaizeGDB 2018: The maize multi-genome genetics and genomics database. Nucleic Acids Research. 47(D1):D1146-D1154. https://doi.org/10.1093/nar/gky1046.
MaizeGDB: How phenotype curation has co-evolved with genomic representations - (Abstract Only)
Harper, E.C., Gardiner, J., Portwood Ii, J.L., Cho, K., Woodhouse, M.R., Cannon, E.K., Lawrence-Dill, C., Freidberg, I., Andorf, C.M. 2018. MaizeGDB: How phenotype curation has co-evolved with genomic representations. Meeting Abstract. https://www.ars.usda.gov/research/publications/publication/?seqNo115=355949.
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture Reprint Icon - (Peer Reviewed Journal)
Harper, E.C., Campbell, J., Cannon, E.K., Jung, S., Main, D., Poelchau, M.F., Walls, R.L., Andorf, C.M., Arnaud, E., Berardini, T.Z., Birkett, C.L., Cannon, S.B., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C., Farmer, A., Ficklin, S., Grant, D.M., Grau, E., Hendon, N., Hu, Z., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M., Larmande, P., Lazo, G.R., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L., Sen, T.Z., Staton, M., Subramaniam, S., Karey, T., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M. 2018. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database: The Journal of Biological Databases and Curation. 2018(1):1-32. https://doi.org/10.1093/database/bay088.
The maize W22 genome provides a foundation for functional genomics and transposon biology Reprint Icon - (Peer Reviewed Journal)
Springer, N., Anderson, S., Andorf, C.M., Ahern, K., Bai, F., Barad, O., Barbazuk, W., Bass, H.W., Baruch, K., Gen-Zvi, G., Buckler IV, E.S., Bukowski, R., Campbell, M.S., Cannon, E.K., Chomet, P., Dawe, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K., Gault, C., Guan, J., Jander, G., Hunter III, C.T., Jiao, Y., Koch, K.E., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D.R., Noshay, J., Portwood II, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Shi, J., Soifer, I., Stein, J.C., Suzuki, M., Vera, D.L., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wei, X., Wimalanathan, K., Woodhouse, M.R., Xiong, W., Brutnell, T.P. 2018. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics. 50:1282-1288. https://doi.org/10.1038/s41588-018-0158-0.
Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation - (Peer Reviewed Journal)
Sen, T.Z., Braun, B., Schott, D., Portwood II, J.L., Schaeffer, M.L., Harper, E.C., Cannon, E.K., Andorf, C.M. 2017. Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bax031.