Eric H Lyons
Advisor, CALS' Office of the Assoc Dean - Research for Cyber Initiatives in Agricultural / Life - Vet Science
Associate Professor, Agricultural-Biosystems Engineering
Associate Professor, BIO5 Institute
Associate Professor, Genetics - GIDP
Associate Professor, Plant Science
Primary Department
Department Affiliations
(520) 626-5070
Research Interest
Eric Lyons, PhD is an assistant professor at the University of Arizona School of Plant Sciences. Dr. Lyons is internationally known for his work in understanding the evolution, structure, and dynamics of genomes. Core to his research activities is the development of software systems for managing and analyzing genomic data and cyberinfrastructure for the life sciences.Dr. Lyons has published over 30 original research papers and 5 book chapters, many in collaboration with investigators from around the world. He is a frequent presenter at national and international meetings, and has been invited to teach workshops on the analysis of genomic data to plant, vertebrate, invertebrate, microbe, and health researchers.Prior to joining the faculty in the School of Plant Sciences, Dr. Lyons worked with the iPlant Collaborative developing cyberinfrastructure, and managing its scientific activities. In addition, he spent five years working in industry at biotech, pharmaceutical, and software companies. Dr. Lyons’ core software system for managing and analyzing genomic data is called CoGe, and is available for use at


Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., DePamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., Ashton, N. W., Axtell, M. J., Barker, E., Barker, M. S., Bennetzen, J. L., Bonawitz, N. D., Chapple, C., Cheng, C., Gustavo, L., , Dacre, M., et al. (2011). The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 332(6032), 960-963.
BIO5 Collaborators
Michael S Barker, Eric H Lyons

PMID: 21551031;PMCID: PMC3166216;Abstract:

Vascular plants appeared ∼410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.

Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., & others, . (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 345, 950--953.
Joyce, B. L., Haug-Baltzell, A., Davey, S., Bomhoff, M., Schnable, J. C., & Lyons, E. (2017). FractBias: A graphical tool for assessing fractionation bias following polyploidy. Bioinformatics, 33(4), 552--554.
Leung, S., Holbrook, A., King, B., Lu, H., Evans, V., Miyamoto, N., Mallari, C., Harvey, S., Davey, D., Elena, H. o., Li, W., Parkinson, J., Horuk, R., Jaroch, S., Berger, M., Skuballa, W., West, C., Pulk, R., Phillips, G., , Bryant, J., et al. (2005). Differential inhibition of inducible T cell cytokine secretion by potent iron chelators. Journal of Biomolecular Screening, 10(2), 157-167.

PMID: 15799959;Abstract:

Effector functions and proliferation of T helper (Th) cells are influenced by cytokines in the environment. Th1 cells respond to a synergistic effect of interleukin-12 (IL-12) and interleukin-18 (IL-18) to secrete interferon-gamma (IFN-γ). In contrast, Th2 cells respond to interleukin-4 (IL-4) to secrete IL-4, interleukin-13 (IL-13), interleukin-5 (IL-5), and interleukin-10 (IL-10). The authors were interested in identifying nonpeptide inhibitors of the Th1 response selective for the IL-12/IL-18-mediated secretion of IFN-γ while leaving the IL-4-mediated Th2 cytokine secretion relatively intact. The authors established a screening protocol using human peripheral blood mononuclear cells (PBMCs) and identified the hydrazino anthranilate compound 1 as a potent inhibitor of IL-12/IL-18-mediated IFN-γ secretion from CD3′ cells with an IC50 around 200 nM. The inhibitor was specific because it had virtually no effect on IL-4-mediated IL-13 release from the same population of cells. Further work established that compound 1 was a potent intracellular iron chelator that inhibited both IL-12/IL-18- and IL-4-mediated T cell proliferation. Iron chelation affects multiple cellular pathways in T cells. Thus, the IL-12/IL-18-mediated proliferation and IFN-γ secretion are very sensitive to intracellular iron concentration. However, the IL-4-mediated IL-13 secretion does not correlate with proliferation and is partially resistant to potent iron chelation. © 2005 The Society for Biomolecular Screening.

Joyce, B., Baltzell, A., McCarthy, F., Bomhoff, M., & Lyons, E. (2017). iAnimal: Cyberinfrastructure to Support Data-driven Science. Bioinformatics in Aquaculture: Principles and Methods, 527--545.