Contact Page

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

CoGe Support: coge.genome (@) gmail.com

We will respond within 24 hrs. (usually) 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.uoa (@) gmail.com

Matt Bomhoff

• Lead CoGe Software Engineer
• Developer of
  • EPIC-CoGe Browser
  • User-Data Management System
  • RNA-seq Pipelines

Haibao Tang

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

Blake Joyce

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

Asher Baltzell

• PhD Student in the Genetics GIDP
  • ahaug (@) email.arizona.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

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, https://doi.org/10.1093/bioinformatics/btx144 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. https://doi.org/10.1002/pld3.8

How to acknowledge CoGe?

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

NSF:

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

USDA:

• 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

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

Roey Chasman

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

James Schnable

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

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

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