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Eric Lyons, Ph.D

Professionsal Biography


Undergraduate UC Berkeley, Molecular and Cell Biology, Immunology (1993-1997):

  • Advisers: Loy Volkman, Jan Washburn, and Eric Haas-Stapleton
  1. Characterizing the effects on pathogenicity of multiple genome copies in an insect virus. Undergrad Research Summary

Masters UC Berkeley, Microbial Biology (1997-1999):

  • Advisers: Norm Pace and Brian Thomas
  • Two years of research focusing on two projects:
  1. Biochemistry of the catalytic RNA subunit of Ribonuclease P (RNase P), the riboprotein responsible for maturing precursor tRNAs by clearving off a 5' leader sequence.
  2. Characterization of the microbial diversity of cerumen through 16S and 18S ribsomal gene sequences.

Internship Molcular Sciences Institute, Computational Biology (2000-2001):

  • Advisors: Drew Endy and Roger Brent

Designed computational systems for systems biology. Main project was the Stochastirator: a program for simulating intracellular biomolecular reaction networks using a stochastic mathematical framework

PhD UC Berkeley, Plant Biology (2006-2008):

  • Adviser: Michael Freeling

Three years of research focusing on:

  • Designing and building CoGe: A new kind of comparative genomics platform
  • Studying plant genome evolution

Postdoc 2009 UC Berkeley, Plant Bioloby:

  • Adviser: Michael Freeling and Sydney Kustu
  • Extending CoGe beyond plant genomes.
  • Analyzing the genomes of eight strains of E. coli

Work Experience

2001 Genencore International, Bioinformatics

  1. Genome assembly and annotation of fungal genomes
  2. Identification and characterization of metaloproteases from the human genome

2002-2003 Berlex Biosciences, Computational Biologist

  1. Expression data analysis of human clinical samples, cell culture samples, and animal models for drug target identification

2004 Biotique Systems, Senior Scientific Developer

  1. Designed system for visualizing pathway and expression data

2005 UC Berkeley, Programmer/Data Analyst III

  1. Freeling lab. Plant comparative genomics.

2010-2011 Senior Scientific Developer, iPlant Collaborative, University of Arizona (Tucson)

  1. Assisted the Director, Steve Goff, with day to day operations of the project.
  2. Maintained CoGe on the weekends and evennings
  3. Leveraged iPlant Cyberinfrastructure to scale CoGe (data storage, computation, user identity management)

2012 Assistant Professor, School of Plant Sciences, University of Arizona (Tuson)

  1. Develop and fund a research program studying the structure, dynamics, and evolution of genomes
  2. Continue to develop CoGe to answer above questions