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{{main|References}} | {{main|References}} | ||
'''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] | ||
'''[[SynMap2]] and [[SynMap3D]]''': [https://academic.oup.com/bioinformatics/article/33/14/2197/3072872 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 | * '''[[SynMap2]] and [[SynMap3D]]''': [https://academic.oup.com/bioinformatics/article/33/14/2197/3072872 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]]''': [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] | ||
'''[[ | * '''[[Syntenic Path Assembly]]''': [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016717 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]]''': [http://bioinformatics.oxfordjournals.org/content/early/2016/10/26/bioinformatics.btw666.abstract 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+]]''': [http://onlinelibrary.wiley.com/doi/10.1002/pld3.8/full 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] | * '''[[LoadExp+]]''': [http://onlinelibrary.wiley.com/doi/10.1002/pld3.8/full 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?== | ==How to acknowledge CoGe?== | ||
Revision as of 21:04, 23 February 2018
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
- 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
Brian Thomas
Sara Castelletti
Dan Hembry
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