Eric Lyons Ph.D.

Senior Scientific Developer
Bio5 Institute/ 4th Floor


Eric is working with iPlant to integrate CoGe with iPlant’s computational cyberinfrastructure, and develop new tools and methodologies for plant genomics.

Research Expertise

  • Genome structure, dynamics, and evolution
  • Advanced visualization of genomic data
  • Computational systems for comparative genomics

Professional Experience

  • Postdoctoral Research, University of California, Berkeley, 2009-10
  • Ph.D Graduate Student Research, University of California, Berkeley, 2006-08
  • Programmer/Analyst III, University of California, Berkeley, 2005
  • Senior Scientific Developer, Biotique Systems, Inc.,  2004
  • Computational Biologist, Berlex Biosciences (Bayer), 2002-03
  • Research Bioinformatics, Genencor International, Inc., 2001
  • Computational Biology Associate, The Molecular Sciences Institute, 2000-2001

Selected Publications

  • Lyons E, Kustu S, Inwood B. Using genomic sequencing for classical genetics in E. coli K12. Journal of Bacteriology submitted. (2010)
  • Kane J, Freeling M, Lyons E. The Evolution of a High Copy Gene Array in Arabidopsis thaliana J. Mol. Evol. 70, 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, Freeling M.  How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal  53: 661-673 (2008)
  • Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M. 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)
  • 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)

Synergistic Activities

  • Comparative Genomics Workshop, Society of Invertebrate Pathology, 2010. Conducted a workshop using CoGe on virus and bacteria genomes.
  • Comparative Genomics Workshop    University of California, Davis, 2010. Conducted a workshop using CoGe for microbial and yeast genomes. 
  • Comparative Genomics Workshop    Iowa State University, 2009.
  • Computational and Systems Biology Summer Institute. Conducted a workshop using CoGe for plant comparative genomics. 
  • Development of high school education module for CoGe, 2010. Worked with an educator intern to develop a high-school level web-based teaching module using CoGe to learn comparative genomics.


  • Ph.D., UC Berkeley; Plant Biology, 2008
  • M.A., UC Berkeley; Microbial Biology, 1999
  • B.A., UC Berkeley; Molecular Biology, 1997