Eric Lyons

Associate Professor - School of Plant Sciences, BIO5 Institute, Agricultural and Biosystems Engineering, CyVerse (formerly the iPlant Collaborative), College of Agriculture and Life Sciences, 307th Floor Bio5; 441F Marley

Educational Background

  • 2006-2008 PhD: University of California, Berkeley (Plant Biology)
  • 1997-1999 MS: University of California, Berkeley (Microbial Biology)
  • 1993-1997 BA: University of California, Berkeley (Immunology)

Research Interests

  • Comparative Genomics and Genome Evolution
  • Computational systems and cyberinfrastructure for biological research

Selected Publications

Complete list can be found in Google Scholar:
Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang T-H, Lan T, Welch AJ, Juárez MJA, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, et al. Architecture and evolution of a minute plant genome. Nature advance online publication. (2013).
Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li L-T, Zhang Q, Kim M-J, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, et al. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology 14: R41. (2013).
Zheng C, Chen E, Albert V, Lyons E, and Sankoff D. Ancient Eudicot Hexaploidy Meets Ancestral Eurosid Gene Order BMC Genomics Accepted (2013)
McCarthy F, and Lyons E. From Data to Function: Functional Modeling of Poultry Genomics Data. Poultry Science, Accepted. (2013).
Tang B and Lyons E. Unleashing the genome of Brassica rapa. Front. Plant Sci. 3:172. doi: 10.3389/fpls.2012.00172 (2012)
D’Hont A, et al. (Lyons E). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature doi:10.1038/nature11241 (2012)
Reneker J, Lyons E, Conant GC,Pires JC,Freeling M,Shyu CR,Korkin D. Long identical multispecies elements in plant and animal genomes. PNAS 109 (19), E1183-E1191 (2012)
Schnable JC, Freeling M, Lyons E. Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biology and Evolution doi:10.1093/gbe/evs009 (2012)
Schnable JC, Lyons E. Comparative genomics with maize and other grasses: from genes to genomes!. Maydica Maydica 56, (2011)
Zheng, C., Swenson, K., Lyons, E. & Sankoff, D. OMG! Orthologs in Multiple Genomes – Competing Graph-Theoretical Formulations. Algorithms in Bioinformatics 6833, 364-375 (2011).
Goff SA, et al. (Lyons E). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science 2 (2011)
Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. Screening Synteny Blocks in Pairwise Genome Comparisons Through Integer Programming BMC Bioinformatics 12:102 (2011)
Banks, J. A. et al. (Lyons E) The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science 332, 960-963 (2011).Zheng, C., Swenson, K.,
Lyons E, Freeling M, Kustu S, Inwood W, Using Genomic Sequencing for Classical Genetics in E. coli K12. PLoS ONE 6(2): e16717. doi:10.1371/journal.pone.0016717 (2011)
Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biol 8(6): e1000409. (2010)
Kane J, Freeling M, Lyons E. The Evolution of a High Copy Gene Array in Arabidopsis J. Mol. Evo. 70(6): 531-544 (2010)
Paterson AH, et al. (Lyons E) The Sorghum bicolor genome and the diversification of grasses. Nature. 457(7229):551-556 (2009)
Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, et al. Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids. Plant Physiol. 148(4): 1772-1781. (2008)
Lyons E, Pedersen B, Kane J, Freeling M. The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids. Tropical Plant Biology. 1(3): 181-190. (2008)
Lyons E, Freeling M. How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal 53: 661-673 (2008)
Ming, R, Shaobin H, Yun F, et al. (Lyons E). The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 45: 991-996. (2008)
Freeling M, Lyons E, Pedersen B, Alam M, Ming R, Lisch D. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18: 1924-1937(2008)
Freeling M, Rapaka L, Lyons E, Pedersen B, Thomas, BC. G-boxes, Bigfoot genes and environmental response: characterization of conserved noncoding sequences in Arabidopsis. The Plant Cell Online 19, no. 5: 1441. (2007)
Thomas BC, Rapaka L, Lyons E, Pedersen B, Freeling M. Arabidopsis intragenomic conserved noncoding sequences. Proc. Natl. Acad. Sci, 104, 3348. (2007)

Teaching Responsibilities

  • ISTA 420/520: Applied Concepts in Cyberinfrastructure
  • PLS599: Practical Computing in Life Sciences

Research Areas

  • Genetics and Epigenetics
  • Genomics, Bioinformatics, and Systems Biology