Difference between revisions of "Publications"

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==Articles==
 
==Articles==
  
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* Apollo: a sequence annotation editor. <ref name=PMID:12537571/> [[Media:Gb-2002-3-12-research0082.pdf|PDF]]‎  
+
* [[Apollo]]: a sequence annotation editor. <ref name=PMID:12537571/> [[Media:Gb-2002-3-12-research0082.pdf|PDF]]‎  
−
* The generic genome browser: a building block for a model organism system database. <ref name=PMID:12368253/> [[Media:1599-1.pdf|PDF]]‎
+
* The [[GBrowse|generic genome browser]]: a building block for a model organism system database. <ref name=PMID:12368253/> [[Media:1599-1.pdf|PDF]]‎
−
* ATIDB: Arabidopsis thaliana insertion database. <ref name=PMID:12582244/> [[Media:Gkg222.pdf|PDF]]‎
+
* [http://www.atidb.org/ ATIDB]: Arabidopsis thaliana insertion database. <ref name=PMID:12582244/> [[Media:Gkg222.pdf|PDF]]‎
−
* DroSpeGe: rapid access database for new Drosophila species genomes. <ref name=PMID:17202166/> [[Media:D480.pdf|PDF]]‎  
+
* [http://insects.eugenes.org/DroSpeGe/ DroSpeGe]: rapid access database for new Drosophila species genomes. <ref name=PMID:17202166/> [[Media:D480.pdf|PDF]]‎  
−
* ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. <ref name=PMID:17142227/> [[Media:Gkl777.pdf|PDF]]‎
+
* [http://paramecium.cgm.cnrs-gif.fr/ ParameciumDB]: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. <ref name=PMID:17142227/> [[Media:Gkl777.pdf|PDF]]‎
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* wFleaBase: the Daphnia genome database. <ref name=PMID:15752432/> [[Media:1471-2105-6-45.pdf|PDF]]‎
+
* [http://wfleabase.org/ wFleaBase]: the Daphnia genome database. <ref name=PMID:15752432/> [[Media:1471-2105-6-45.pdf|PDF]]‎
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* BeetleBase: the model organism database for Tribolium castaneum. <ref name=PMID:17090595/> [[Media:Gkl776.pdf|PDF]]
+
* [http://bioinformatics.ksu.edu/BeetleBase/ BeetleBase]: the model organism database for Tribolium castaneum. <ref name=PMID:17090595/> [[Media:Gkl776.pdf|PDF]]
−
* AphidBase: a database for aphid genomic resources. <ref name=PMID:17237053/>
+
* [http://www.aphidbase.com/ AphidBase]: a database for aphid genomic resources. <ref name=PMID:17237053/>
−
* KISS: the kinetoplastid RNA editing sequence search tool. <ref name=PMID:17123956/>
+
* [http://rna.bmb.uga.edu/kiss/ KISS]: the kinetoplastid RNA editing sequence search tool. <ref name=PMID:17123956/>
−
* Xanthusbase: adapting wikipedia principles to a model organism database.  <ref name=PMID:17090585/>
+
* [http://xanthusbase.org/ Xanthusbase]: adapting wikipedia principles to a model organism database.  <ref name=PMID:17090585/>
−
* OryGenesDB: a database for rice reverse genetics. <ref name=PMID:16381969/>
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* [http://orygenesdb.cirad.fr/ OryGenesDB]: a database for rice reverse genetics. <ref name=PMID:16381969/>
−
* SynBrowse: a [[Synteny|synteny]] browser for comparative sequence analysis. <ref name=PMID:15994196/> [[Media:3461.pdf|PDF]]‎  
+
* [[SynBrowse]]: a [[Synteny|synteny]] browser for comparative sequence analysis. <ref name=PMID:15994196/> [[Media:3461.pdf|PDF]]‎  
−
* FPC Web tools for rice, maize, and distribution. <ref name=PMID:15888684/>
+
* [http://www.genome.arizona.edu/ FPC Web tools] for rice, maize, and distribution. <ref name=PMID:15888684/>
 
* Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. <ref name=PMID:15805491/>
 
* Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. <ref name=PMID:15805491/>
−
* The Legume Information System (LIS): an integrated information resource for comparative legume biology. <ref name=PMID:15608283/>
+
* [http://www.comparative-legumes.org/ The Legume Information System (LIS)]: an integrated information resource for comparative legume biology. <ref name=PMID:15608283/>
 
* Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. <ref name=PMID:17389913/>
 
* Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. <ref name=PMID:17389913/>
 
* The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. <ref name=PMID:17287974/>
 
* The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. <ref name=PMID:17287974/>
−
* T1DBase: integration and presentation of complex data for type 1 diabetes research. <ref name=PMID:17169983/>
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* [http://t1dbase.org T1DBase]: integration and presentation of complex data for type 1 diabetes research. <ref name=PMID:17169983/>
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* Gbrowse Moby: a Web-based browser for BioMoby Services. <ref name=PMID:17147784/>
+
* Gbrowse Moby: a Web-based browser for [http://biomoby.open-bio.org/ BioMoby] Services. <ref name=PMID:17147784/>
 
* Expanded protein information at SGD: new pages and proteome browser. <ref name=PMID:17142221/>
 
* Expanded protein information at SGD: new pages and proteome browser. <ref name=PMID:17142221/>
−
* SwissRegulon: a database of genome-wide annotations of regulatory sites. <ref name=PMID:17130146/>
+
* [http://www.swissregulon.unibas.ch/ SwissRegulon]: a database of genome-wide annotations of regulatory sites. <ref name=PMID:17130146/>
−
* SynView: a GBrowse-compatible approach to visualizing comparative genome data. <ref name=PMID:16844709/>
+
* [[SynView]]: a [[GBrowse]]-compatible approach to visualizing comparative genome data. <ref name=PMID:16844709/>
−
* Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. <ref name=PMID:15608211/>
+
* [http://www.pseudomonas.com/ Pseudomonas aeruginosa Genome Database] and [http://www.cmdr.ubc.ca/bobh/PAAP.html PseudoCAP]: facilitating community-based, continually updated, genome annotation. <ref name=PMID:15608211/>
 
* Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. <ref name=PMID:15601538/>
 
* Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. <ref name=PMID:15601538/>
−
* A Chado case study: an ontology-based modular schema for representing genome-associated biological information. <ref name=PMID:17646315/>
+
* A [[Chado]] case study: an ontology-based modular schema for representing genome-associated biological information. <ref name=PMID:17646315/>
 
* Celsius: a community resource for Affymetrix microarray data <ref name=PMID:17570842/> [[Media:Gb-2007-8-6-r112.pdf|PDF]]
 
* Celsius: a community resource for Affymetrix microarray data <ref name=PMID:17570842/> [[Media:Gb-2007-8-6-r112.pdf|PDF]]
  

Revision as of 23:48, 2 January 2008

The following is a partial listing of publications/references describing GMOD components or databases and applications built using GMOD components. For a list of databases see GMOD Users.

Articles

  • Apollo: a sequence annotation editor. [1] PDF‎
  • The generic genome browser: a building block for a model organism system database. [2] PDF‎
  • ATIDB: Arabidopsis thaliana insertion database. [3] PDF‎
  • DroSpeGe: rapid access database for new Drosophila species genomes. [4] PDF‎
  • ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. [5] PDF‎
  • wFleaBase: the Daphnia genome database. [6] PDF‎
  • BeetleBase: the model organism database for Tribolium castaneum. [7] PDF
  • AphidBase: a database for aphid genomic resources. [8]
  • KISS: the kinetoplastid RNA editing sequence search tool. [9]
  • Xanthusbase: adapting wikipedia principles to a model organism database. [10]
  • OryGenesDB: a database for rice reverse genetics. [11]
  • SynBrowse: a synteny browser for comparative sequence analysis. [12] PDF‎
  • FPC Web tools for rice, maize, and distribution. [13]
  • Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. [14]
  • The Legume Information System (LIS): an integrated information resource for comparative legume biology. [15]
  • Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. [16]
  • The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. [17]
  • T1DBase: integration and presentation of complex data for type 1 diabetes research. [18]
  • Gbrowse Moby: a Web-based browser for BioMoby Services. [19]
  • Expanded protein information at SGD: new pages and proteome browser. [20]
  • SwissRegulon: a database of genome-wide annotations of regulatory sites. [21]
  • SynView: a GBrowse-compatible approach to visualizing comparative genome data. [22]
  • Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. [23]
  • Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. [24]
  • A Chado case study: an ontology-based modular schema for representing genome-associated biological information. [25]
  • Celsius: a community resource for Affymetrix microarray data [26] PDF

Bibliography

  1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12537571
  2. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12368253
  3. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12582244
  4. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17202166
  5. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17142227
  6. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15752432
  7. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17090595
  8. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17237053
  9. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17123956
  10. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17090585
  11. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:16381969
  12. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15994196
  13. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15888684
  14. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15805491
  15. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15608283
  16. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17389913
  17. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17287974
  18. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17169983
  19. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17147784
  20. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17142221
  21. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17130146
  22. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:16844709
  23. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15608211
  24. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15601538
  25. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17646315
  26. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17570842


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