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'''CoGe in General''': [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2007.03326.x/full Eric Lyons, Michael Freeling (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences The Plant Journal 53 (4) , 661-673] | '''CoGe in General''': [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2007.03326.x/full 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''': [http://www.plantphysiol.org/content/148/4/1772.full 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] | '''[[CoGeBlast]]''': [http://www.plantphysiol.org/content/148/4/1772.full 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]]''': [http://www.springerlink.com/content/x8295245274t240l/ 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] | '''[[SynMap]]''': [http://www.springerlink.com/content/x8295245274t240l/ 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] | ||
Revision as of 14:54, 27 November 2014
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
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