Difference between revisions of "Publications"

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m (Sorted publication list by date [aka PMID])
(Added about 20 new refs from PubMed and sorted existing refs by date. Added URL for GMOD article search on PubMed.)
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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]].
 
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]].
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An RSS feed is also available of [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=1jI7fDTu3O7BUlXfDmPgimJaGHQZVwWUUg1LM8d4EjNfWbEEYr new GMOD articles on PubMed].
  
 
==Articles==
 
==Articles==
  
 +
Sorted by date, most recent first.
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* AlliumMap-a comparative genomics resource for cultivated Allium vegetables. <ref name=PMID:22559261/>
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* SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. <ref name=PMID:22120661/>
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* [[Tripal]]: a construction toolkit for online genome databases. <ref name=PMID:21959868/>
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* TparvaDB: a database to support Theileria parva vaccine development. <ref name=PMID:21546359/>
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* The GMOD Drupal bioinformatic server framework. <ref name=PMID:20971988/>
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* [[ParameciumDB]] in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. <ref name=PMID:20952411/>
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* The [http://solgenomics.net Sol Genomics Network] (solgenomics.net): growing tomatoes using Perl. <ref name=PMID:20935049/>
 
* [http://database.oxfordjournals.org/cgi/content/abstract/baq007 Choosing a genome browser for a Model Organism Database: surveying the Maize community]. <ref name=PMID:20627860/> [[Media:ChoosingAGenomeBrowser.pdf|PDF]]
 
* [http://database.oxfordjournals.org/cgi/content/abstract/baq007 Choosing a genome browser for a Model Organism Database: surveying the Maize community]. <ref name=PMID:20627860/> [[Media:ChoosingAGenomeBrowser.pdf|PDF]]
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* [http://www.aphidbase.com/ AphidBase]: a centralized bioinformatic resource for annotation of the pea aphid genome. <ref name=PMID:20482635/>
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* Next generation transcriptomes for next generation genomes using est2assembly. <ref name=PMID:20034392/>
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* BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. <ref name=PMID:19820115/>
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* [[CMap]] 1.01: a comparative mapping application for the Internet. <ref name=PMID:19648141/>
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* [[Apollo]]: a community resource for genome annotation editing. <ref name=PMID:19439563/>
 
* [http://www.popgenie.org/ PopGenIE]: The Populus Genome Integrative Explorer. <ref name=PMID:19383103/>
 
* [http://www.popgenie.org/ PopGenIE]: The Populus Genome Integrative Explorer. <ref name=PMID:19383103/>
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* Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. <ref name=PMID:18845581/>
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* MODWeb: a web framework for the Generic Model Organism Database. <ref name=PMID:18570664/>
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* [[MAKER]]: an easy-to-use annotation pipeline designed for emerging model organism genomes. <ref name=PMID:18025269/>
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* SmedGD: the Schmidtea mediterranea genome database. <ref name=PMID:17881371/>
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* The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. <ref name=PMID:17712414/>
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* Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. <ref name=PMID:17668053/>
 
* 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/>
 
* [http://celsius.genomics.ctrl.ucla.edu/ Celsius]: a community resource for Affymetrix microarray data <ref name=PMID:17570842/> [[Media:Gb-2007-8-6-r112.pdf|PDF]]
 
* [http://celsius.genomics.ctrl.ucla.edu/ Celsius]: a community resource for Affymetrix microarray data <ref name=PMID:17570842/> [[Media:Gb-2007-8-6-r112.pdf|PDF]]
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==Adding Citations==
 
==Adding Citations==
  
−
Enter them into the '''Articles''' section. References are ordered by PMID, most recent (highest) PMID first; please enter your reference in the appropriate place in the list.  
+
Enter them into the '''Articles''' section. References are ordered by PMID, most recent (highest) PMID first; please enter your reference in the appropriate place in the list.
  
 
Example:
 
Example:

Revision as of 22:40, 10 July 2012

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.

An RSS feed is also available of new GMOD articles on PubMed.

Articles

Sorted by date, most recent first.

  • AlliumMap-a comparative genomics resource for cultivated Allium vegetables. [1]
  • SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. [2]
  • Tripal: a construction toolkit for online genome databases. [3]
  • TparvaDB: a database to support Theileria parva vaccine development. [4]
  • The GMOD Drupal bioinformatic server framework. [5]
  • ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. [6]
  • The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. [7]
  • Choosing a genome browser for a Model Organism Database: surveying the Maize community. [8] PDF
  • AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. [9]
  • Next generation transcriptomes for next generation genomes using est2assembly. [10]
  • BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. [11]
  • CMap 1.01: a comparative mapping application for the Internet. [12]
  • Apollo: a community resource for genome annotation editing. [13]
  • PopGenIE: The Populus Genome Integrative Explorer. [14]
  • Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. [15]
  • MODWeb: a web framework for the Generic Model Organism Database. [16]
  • MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. [17]
  • SmedGD: the Schmidtea mediterranea genome database. [18]
  • The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. [19]
  • Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. [20]
  • A Chado case study: an ontology-based modular schema for representing genome-associated biological information. [21]
  • Celsius: a community resource for Affymetrix microarray data [22] PDF
  • Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. [23] (See YSB.)
  • The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. [24]
  • AphidBase: a database for aphid genomic resources. [25]
  • DroSpeGe: rapid access database for new Drosophila species genomes. [26] PDF
  • T1DBase: integration and presentation of complex data for type 1 diabetes research. [27]
  • Gbrowse Moby: a Web-based browser for BioMoby Services. [28]
  • ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. [29] PDF
  • Expanded protein information at SGD: new pages and proteome browser. [30]
  • SwissRegulon: a database of genome-wide annotations of regulatory sites. [31]
  • KISS: the kinetoplastid RNA editing sequence search tool. [32]
  • BeetleBase: the model organism database for Tribolium castaneum. [33] PDF
  • Xanthusbase: adapting wikipedia principles to a model organism database. [34]
  • SynView: a GBrowse-compatible approach to visualizing comparative genome data. [35]
  • OryGenesDB: a database for rice reverse genetics. [36]
  • SynBrowse: a synteny browser for comparative sequence analysis. [37] PDF
  • FPC Web tools for rice, maize, and distribution. [38]
  • 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. [39]
  • wFleaBase: the Daphnia genome database. [40] PDF
  • The Legume Information System (LIS): an integrated information resource for comparative legume biology. [41]
  • Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. [42]
  • Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. [43]
  • Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. [44]
  • ATIDB: Arabidopsis thaliana insertion database. [45] PDF
  • Apollo: a sequence annotation editor. [46] PDF
  • The generic genome browser (GBrowse): a building block for a model organism system database. [47] PDF

Bibliography

  1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:22559261
  2. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:22120661
  3. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:21959868
  4. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:21546359
  5. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20971988
  6. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20952411
  7. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20935049
  8. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20627860
  9. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20482635
  10. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20034392
  11. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19820115
  12. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19648141
  13. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19439563
  14. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19383103
  15. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18845581
  16. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18570664
  17. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18025269
  18. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17881371
  19. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17712414
  20. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17668053
  21. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17646315
  22. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17570842
  23. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17389913
  24. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17287974
  25. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17237053
  26. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17202166
  27. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17169983
  28. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17147784
  29. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17142227
  30. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17142221
  31. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17130146
  32. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17123956
  33. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17090595
  34. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17090585
  35. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:16844709
  36. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:16381969
  37. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15994196
  38. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15888684
  39. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15805491
  40. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15752432
  41. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15608283
  42. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15608211
  43. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15601538
  44. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15488149
  45. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12582244
  46. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12537571
  47. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12368253


Adding Citations

Enter them into the Articles section. References are ordered by PMID, most recent (highest) PMID first; please enter your reference in the appropriate place in the list.

Example: 

   <ref name=PMID:15752432/>
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