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

CoGe Support: coge.genome (@)

We will respond within 24 hrs. (usually) Contact us!

CoGe Team: Many thanks to many good people

Eric Lyons

Matt Bomhoff

Haibao Tang

Blake Joyce

Asher Baltzell

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

SynMap2 and SynMap3D: Asher Haug-Baltzell, Sean A. Stephens, Sean Davey, Carlos E. Scheidegger, Eric Lyons; SynMap2 and SynMap3D: web-based whole-genome synteny browsers, Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2197–2198, 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

FractBias: Blake L. Joyce, Asher Haug-Baltzell, Sean Davey, Matthew Bomhoff, James C. Schnable, and Eric Lyons FractBias: a graphical tool for assessing fractionation bias following polyploidy Bioinformatics first published online October 29, 2016 doi:10.1093/bioinformatics/btw666

LoadExp+: Grover JW, Bomhoff M, Davey S, Gregory BD, Mosher RA, Lyons E. CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and visualization. Plant Direct. 2017;00:1–7.

How to acknowledge CoGe?

If you have an acknowledgement for CoGe, please reference one (or more) of the following grant numbers:


  • IOS-339156 Years: 2014-2017
  • IOS-1444490 Years: 2015-2019


  • 2013-00984 Years: 2013-2016

Gordon and Betty Moore Foundation:

  • 3833 Years: 2012-2014

Former Team Members

Alex Frank

  • Undergraduate student worker
  • Developer of the Admin Dashboard

Shabari Subramaniam

  • Scientific Analyst

Evan Briones

Roey Chasman

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

James Schnable

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

Brian Thomas

Sara Castelletti

Dan Hembry

CoGe Development Testers

Michael Freeling

Damon Lisch