User:Eric Lyons

Contact Info



 * Eric Lyons
 * UC Berkeley
 * Department of Plant and Microbial Biology
 * 111 Koshland Hall
 * Berkeley, CA 94720
 * Email me through OpenWetWare

I work in the laboratory of Michael Freeling at UC Berkeley.

Education

 * 2008, PhD, Plant biology, UC Berkeley
 * 1999, MS, Microbial Biology, UC Berkeley
 * 1997, BS, Molecular and Cell Biology (Immunology), UC Berkeley

Research interests


Comparative genomic and genome evolution, specifically in plant genome evolution I am the project manager and lead developed of the CoGe Comparative Genomics Platform. This system is designed to: CoGe allows researchers to quickly and efficiently start with a genomic feature of interest (e.g. gene accession, gene name, sequence, genomic location, organism), find syntenic regions within the same genome or among different organisms, and visualize the results in an intuitive and interactive system that permits the rapid identification and characterization of genomic patterns of evolution. Currently, CoGe has genomes for over 6,000 organisms (in various states of completion and assembly) from all domains of life. Some tools that CoGe contains are:
 * store multiple versions of multiple genomes from multiple organisms in a single system
 * find an retrieve any genomic region from any set of organisms
 * get information about those genomic regions
 * compare those genomic regions using any sequence comparison algorithm (although only a half dozen or so have been implemented thus far)
 * visualize genomic data and results of comparative analyses
 * SynMap -- compare any two genomes to identify syntenic regions and visualize the output as syntenic dot-plots. (Uses DagChainer to identify regions of synteny by finding collinear series of putatively homologous genes or sequences.)
 * CoGeBlast -- CoGe's interface to blast that allows researchers to select any set of genomes in CoGe to search their sequence(s) against
 * GEvo -- compare multiple genomic regions using a variety of sequence comparison algorithms. Sequences may be from CoGe's genomes database, NCBI, or added by a researcher
 * GenomeView -- CoGe's genome browser based on GIS technology to have an interactive system much like Google-maps.
 * FeatView -- search for genes and other genomic features by name, annotation, organisms, type, etc.



Publications

 * 1) Paper1 pmid=18836034
 * 2) Paper2 pmid=18432245
 * 3) Paper3 pmid=18269575
 * 4) Paper4 pmid=17496117
 * 5) Paper5 pmid=17301222
 * 6) Paper6 pmid=15799959
 * 7) Paper7 pmid=12517864
 * 8) Paper8 pmid=9847346

Useful links

 * CoGe: A new kind of Comparative Genomics