Contact Page

Contact email for CoGe: coge.genome@gmail.com

Need Help? Contact us!

CoGe Team: Many thanks to many good people

Eric Lyons

• CoGe's Project Manager
• Assistant Professor
• School of Plant Sciences
• iPlant Collaborative Member
• Bio5 Institute at the University of Arizona, Tucson
  • For CoGe related inquires: elyons.coge (@) gmail.com

Matt Bomhoff

• Lead CoGe Developer
• Developer for EPIC-CoGe Browser
• Developer for CoGe's User-Data Management System

Evan Briones

• CoGe Developer
• Developer for CoGe's Job Execution Framework (JEX)

Haibao Tang

• Senior Bioinformatics Engineer @ JCVI
• Developer of BaoTools: https://github.com/tanghaibao
• Developer of SynMap
• Developer of SynFind
• Developer of Quota Align algorithm in SynMap
• Developer of the synteny finding algorithm used in SynFind

Shabari Subramaniam

• Graduate Student
• Department of Plant and Microbial Biology
• University of California, Berkeley

James Schnable

• Graduate Student
• Department of Plant and Microbial Biology
• University of California, Berkeley
  • jschnable (@) berkeley.edu

Blake Joyce

• Postdoctoral Researcher
• University of Arizona School of Plant Sciences
  • bjoyce3 (@) email.arizona.edu
• Adjunct Professor
• Pima Community College
  • jblake@pima.edu

CoGe Development Testers

Michael Freeling

• Professor, PI of the CoGe Project
• Department of Plant and Microbial Biology
• University of California, Berkeley
• freeling (@) berkeley.edu

Damon Lisch

• Principal Investigator
• Department of Plant and Microbial Biology
• University of California, Berkeley
• dlisch (@) berkeley.edu

How to cite CoGe?

CoGe in General: Eric Lyons, Michael Freeling (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences The Plant Journal 53 (4) , 661-673

CoGeBlast: Eric Lyons*, Brent Pedersen, Josh Kane, Maqsudul Alam, Ray Ming, Haibao Tang, Xiyin Wang, John Bowers, Andrew Paterson, Damon Lisch and Michael Freeling (2008) Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids Plant Physiology 2008 vol. 148 no. 4 1772-1781

SynMap: Lyons E, Pedersen B, Kane J, Freeling M (2008) The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates rosids. Tropical Plant Biol 1 (3-4) , 181-190

Syntenic Path Assembly: Lyons E, Freeling M, Kustu S, Inwood W (2011) Using Genomic Sequencing for Classical Genetics in E. coli K12. PLoS ONE 6(2): e16717. doi:10.1371/journal.pone.0016717

Who do I contact with comments, suggestions, bug reports, general questions, etc?

Eric Lyons: elyons.coge (@) gmail.com

Former Team Members

Roey Chasman

• CoGe Developer
• Developer for CoGe's internal usage monitoring
• Developer for EPIC-CoGe Browser

Brent Pedersen

• Developer of Gobe (visualization system used GEvo
• Developer of OpenGenes (navigation system used in visualization system for GenomeView)
• Much code work behind the scenes to get algorithms working quickly

Joshua Kane

• Graduate Student
• Tetrad Department
• University of California, San Francisco