Difference between revisions of "User:Elyons"

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Eric Lyons, Ph.D
 
Eric Lyons, Ph.D
  
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==Professionsal Bio==
 
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*Undergrad: 
 
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**1997  UC Berkeley, Molecular and Cell Biology, Immunology
 
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**Three years of research with Loy Volkman, Jan Washburn, and Eric Haas-Stapleton studying host-pathogen relationships between a virus (baculovirus [http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?oid=27625 AcMNPV (Autographa californica nucleopolyhedrovirus)]) and its lepidopteran (caterpillars) hosts helicoverpa zea (corn earworm), trichoplusia ni (cabbage looper), heliothis virescens (tobacco budworm).  AcMNPV is double stranded DNA virus, and as such, has a relatively large genome (133kb) and contains ~150 genes.  Its pathogenesis in susceptible hosts is very interesting as it will infect nearly all of the host tissues, convert ~30% of the host's biomass to viral progeny, and cause the host to liquify into a puddle of virus laden goo.  Interesting, hosts in late stages of infection will exert a virus controlled climbing behavior, and start climbing up as high as they can before succumbing to the final stage of infection:  liquefaction and release of viral progeny.  This may serve the virus and help in its dispersion, or it may help other caterpillars by making infected caterpillars more likely to be eaten by larger predators, birds.  In either case, this highlights the incredible biological interactions between hosts and pathogens.
 
  
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**My research in the lab focused on a peculiar aspect of baculoviruses.  To spread from host to host, the virus has a specific form called occlusion derived virions (ODV) where the virions are packaged in a protective protein complex in order to survive in the environment (which for a virus is a harsh, cold, dry, high UV light exposure world).  Some baculoviruses' ODV contain a single copy of their genome, and some contain multiple copies of their genome.  This trait is part of the biology of baculoviruses and is what the "M" (multiple) strands for in AcMNPV.
 
  
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**The question I was after was why would a virus spend the resource to package multiple copies of its genome in a single infectious particle? An infected cell is an infected cell, regardless if 1 or 10 viral genomes were released during the initial phase of infection.
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=Professionsal Biography=
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==Education:==
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===Undergraduate UC Berkeley, Molecular and Cell Biology, Immunology (1993-1997):=== 
 +
*Advisers:  Loy Volkman, Jan Washburn, and Eric Haas-Stapleton
 +
# 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:
 +
#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.
 +
#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==
 +
 
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===2001  Genencore International, Bioinformatics===
 +
# Genome assembly and annotation of fungal genomes
 +
# Identification and characterization of metaloproteases from the human genome
 +
 
 +
===2002-2003 Berlex Biosciences, Computational Biologist===
 +
# Expression data analysis of human clinical samples, cell culture samples, and animal models for drug target identification
 +
 
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===2004 Biotique Systems, Senior Scientific Developer===
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# Designed system for visualizing pathway and expression data
 +
 
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===2005 UC Berkeley, Programmer/Data Analyst III===
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# Freeling lab.  Plant comparative genomics.
 +
 
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===2010-2011 Senior Scientific Developer, iPlant Collaborative, University of Arizona (Tucson)===
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# Assisted the Director, Steve Goff, with day to day operations of the project.
 +
# Maintained CoGe on the weekends and evennings
 +
# Leveraged iPlant Cyberinfrastructure to scale CoGe (data storage, computation, user identity management)
 +
 
 +
===2012 Assistant Professor, School of Plant Sciences, University of Arizona (Tuson)===
 +
# Develop and fund a research program studying the structure, dynamics, and evolution of genomes
 +
# Continue to develop CoGe to answer above questions

Latest revision as of 17:18, 13 July 2012

Eric Lyons, Ph.D


Professionsal Biography

Education:

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
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