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Difference between revisions of "Publications"

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==Articles==
 
==Articles==
  
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Sorted by PubMed ID, highest (most recent) first.
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Sorted by PubMed ID, highest (most recent) first. This listing is compatible with the [http://www.mendeley.com Mendeley web importer].
  
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* AlliumMap-a comparative genomics resource for cultivated Allium vegetables. <span
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* AlliumMap-a comparative genomics resource for cultivated Allium vegetables. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F22559261">PMID:22559261</span> <ref name=PMID:22559261/>
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  class="Z3988"  
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* SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F22120661">PMID:22120661</span> <ref name=PMID:22120661/>
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  title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft.atitle=AlliumMap-a+comparative+genomics+resource+for+cultivated+Allium+vegetables.&amp;rft_id=info%3Apmid%2F22559261">PMID:22559261</span><ref name=PMID:22559261/>
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* [[Tripal]]: a construction toolkit for online genome databases. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F21959868">PMID:21959868</span> <ref name=PMID:21959868/>
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* SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. <ref name=PMID:22120661/>
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* TparvaDB: a database to support Theileria parva vaccine development. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F21546359">PMID:21546359</span> <ref name=PMID:21546359/>
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* [[Tripal]]: a construction toolkit for online genome databases. <ref name=PMID:21959868/>
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* The GMOD Drupal bioinformatic server framework. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20971988">PMID:20971988</span> <ref name=PMID:20971988/>
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* TparvaDB: a database to support Theileria parva vaccine development. <ref name=PMID:21546359/>
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* [[ParameciumDB]] in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20952411">PMID:20952411</span> <ref name=PMID:20952411/>
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* The GMOD Drupal bioinformatic server framework. <ref name=PMID:20971988/>
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* The [http://solgenomics.net Sol Genomics Network] (solgenomics.net): growing tomatoes using Perl. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20935049">PMID:20935049</span> <ref name=PMID:20935049/>
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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/>
+
* Using the Generic Synteny Browser ([[GBrowse_syn]]) <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20836076">PMID:20836076</span> <ref name=PMID:20836076/>
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* The [http://solgenomics.net Sol Genomics Network] (solgenomics.net): growing tomatoes using Perl. <ref name=PMID:20935049/>
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* [[Galaxy]]: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20738864">PMID:20738864</span> <ref name=PMID:20738864/>
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* Using the Generic Synteny Browser ([[GBrowse_syn]]) <ref name=PMID:20836076/>
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* [http://database.oxfordjournals.org/cgi/content/abstract/baq007 Choosing a genome browser for a Model Organism Database: surveying the Maize community]. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20627860">PMID:20627860</span> <ref name=PMID:20627860/> [[Media:ChoosingAGenomeBrowser.pdf|PDF]]
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* [[Galaxy]]: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. <ref name=PMID:20738864/>
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* [http://www.aphidbase.com/ AphidBase]: a centralized bioinformatic resource for annotation of the pea aphid genome. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20482635">PMID:20482635</span> <ref name=PMID:20482635/>
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* [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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* [[Galaxy]]: a web-based genome analysis tool for experimentalists". <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20069535">PMID:20069535</span> <ref name=PMID:20069535/>
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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]]. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F20034392">PMID:20034392</span> <ref name=PMID:20034392/>
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* [[Galaxy]]: a web-based genome analysis tool for experimentalists". <ref name=PMID:20069535/>
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* Using the Generic Genome Browser ([[GBrowse]]). <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F19957275">PMID:19957275</span> <ref name=PMID:19957275/>
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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. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F19820115">PMID:19820115</span> <ref name=PMID:19820115/>
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* Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:19957275/>
+
* SNP@Evolution: a hierarchical database of positive selection on the human genome. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F19732458">PMID:19732458</span> <ref name=PMID:19732458/> ([[GBrowse]]-related)
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* BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. <ref name=PMID:19820115/>
+
* TBrowse: an integrative genomics map of Mycobacterium tuberculosis. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F19683474">PMID:19683474</span> <ref name=PMID:19683474/> ([[GBrowse]]-related)
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* SNP@Evolution: a hierarchical database of positive selection on the human genome. <ref name=PMID:19732458/> ([[GBrowse]]-related)
+
* [[CMap]] 1.01: a comparative mapping application for the Internet. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F19648141">PMID:19648141</span> <ref name=PMID:19648141/>
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* TBrowse: an integrative genomics map of Mycobacterium tuberculosis. <ref name=PMID:19683474/> ([[GBrowse]]-related)
+
* [[Apollo]]: a community resource for genome annotation editing. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F19439563">PMID:19439563</span> <ref name=PMID:19439563/>
−
* [[CMap]] 1.01: a comparative mapping application for the Internet. <ref name=PMID:19648141/>
+
* [http://www.popgenie.org/ PopGenIE]: The Populus Genome Integrative Explorer. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F19383103">PMID:19383103</span> <ref name=PMID:19383103/>
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* [[Apollo]]: a community resource for genome annotation editing. <ref name=PMID:19439563/>
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* [[Artemis]] and ACT: viewing, annotating and comparing sequences stored in a relational database. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F18845581">PMID:18845581</span> <ref name=PMID:18845581/>
−
* [http://www.popgenie.org/ PopGenIE]: The Populus Genome Integrative Explorer. <ref name=PMID:19383103/>
+
* [[GMODWeb]]: a web framework for the Generic Model Organism Database. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F18570664">PMID:18570664</span> <ref name=PMID:18570664/>
−
* [[Artemis]] and ACT: viewing, annotating and comparing sequences stored in a relational database. <ref name=PMID:18845581/>
+
* FishMap: a community resource for zebrafish genomics. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F18554176">PMID:18554176</span> <ref name=PMID:18554176/> ([[GBrowse]]-related)
−
* [[GMODWeb]]: a web framework for the Generic Model Organism Database. <ref name=PMID:18570664/>
+
* Using the Generic Genome Browser ([[GBrowse]]). <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F18428797">PMID:18428797</span> <ref name=PMID:18428797/>
−
* FishMap: a community resource for zebrafish genomics. <ref name=PMID:18554176/> ([[GBrowse]]-related)
+
* [[MAKER]]: an easy-to-use annotation pipeline designed for emerging model organism genomes. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F18025269">PMID:18025269</span> <ref name=PMID:18025269/>
−
* Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:18428797/>
+
* SmedGD: the Schmidtea mediterranea genome database. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17881371">PMID:17881371</span> <ref name=PMID:17881371/>
−
* [[MAKER]]: an easy-to-use annotation pipeline designed for emerging model organism genomes. <ref name=PMID:18025269/>
+
* The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17712414">PMID:17712414</span> <ref name=PMID:17712414/>
−
* SmedGD: the Schmidtea mediterranea genome database. <ref name=PMID:17881371/>
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* Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17668053">PMID:17668053</span> <ref name=PMID:17668053/>
−
* The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. <ref name=PMID:17712414/>
+
* A [[Chado]] case study: an ontology-based modular schema for representing genome-associated biological information. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17646315">PMID:17646315</span> <ref name=PMID:17646315/>
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* Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. <ref name=PMID:17668053/>
+
* [http://celsius.genomics.ctrl.ucla.edu/ Celsius]: a community resource for Affymetrix microarray data <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17570842">PMID:17570842</span> <ref name=PMID:17570842/> [[Media:Gb-2007-8-6-r112.pdf|PDF]]
−
* A [[Chado]] case study: an ontology-based modular schema for representing genome-associated biological information. <ref name=PMID:17646315/>
+
* Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17389913">PMID:17389913</span> <ref name=PMID:17389913/> (See [http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps/ YSB].)
−
* [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]]
+
* The development of BAC-end sequence-based microsatellite markers and placement in the [http://soybeangenome.siu.edu/ physical and genetic maps of soybean]. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17287974">PMID:17287974</span> <ref name=PMID:17287974/>
−
* Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. <ref name=PMID:17389913/> (See [http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps/ YSB].)
+
* [http://www.aphidbase.com/ AphidBase]: a database for aphid genomic resources. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17237053">PMID:17237053</span> <ref name=PMID:17237053/>
−
* The development of BAC-end sequence-based microsatellite markers and placement in the [http://soybeangenome.siu.edu/ physical and genetic maps of soybean]. <ref name=PMID:17287974/>
+
* [http://insects.eugenes.org/DroSpeGe/ DroSpeGe]: rapid access database for new Drosophila species genomes. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17202166">PMID:17202166</span> <ref name=PMID:17202166/> [[Media:D480.pdf|PDF]]
−
* [http://www.aphidbase.com/ AphidBase]: a database for aphid genomic resources. <ref name=PMID:17237053/>
+
* [http://t1dbase.org T1DBase]: integration and presentation of complex data for type 1 diabetes research. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17169983">PMID:17169983</span> <ref name=PMID:17169983/>
−
* [http://insects.eugenes.org/DroSpeGe/ DroSpeGe]: rapid access database for new Drosophila species genomes. <ref name=PMID:17202166/> [[Media:D480.pdf|PDF]]
+
* Gbrowse Moby: a Web-based browser for [http://biomoby.open-bio.org/ BioMoby] Services. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17147784">PMID:17147784</span> <ref name=PMID:17147784/>
−
* [http://t1dbase.org T1DBase]: integration and presentation of complex data for type 1 diabetes research. <ref name=PMID:17169983/>
+
* [[ParameciumDB]]: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17142227">PMID:17142227</span> <ref name=PMID:17142227/> [[Media:Gkl777.pdf|PDF]]
−
* 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. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17142221">PMID:17142221</span> <ref name=PMID:17142221/>
−
* [[ParameciumDB]]: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. <ref name=PMID:17142227/> [[Media:Gkl777.pdf|PDF]]
+
* [http://www.swissregulon.unibas.ch/ SwissRegulon]: a database of genome-wide annotations of regulatory sites. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17130146">PMID:17130146</span> <ref name=PMID:17130146/>
−
* Expanded protein information at SGD: new pages and proteome browser. <ref name=PMID:17142221/>
+
* [http://rna.bmb.uga.edu/kiss/ KISS]: the kinetoplastid RNA editing sequence search tool. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17123956">PMID:17123956</span> <ref name=PMID:17123956/>
−
* [http://www.swissregulon.unibas.ch/ SwissRegulon]: a database of genome-wide annotations of regulatory sites. <ref name=PMID:17130146/>
+
* [http://bioinformatics.ksu.edu/BeetleBase/ BeetleBase]: the model organism database for Tribolium castaneum. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17090595">PMID:17090595</span> <ref name=PMID:17090595/> [[Media:Gkl776.pdf|PDF]]
−
* [http://rna.bmb.uga.edu/kiss/ KISS]: the kinetoplastid RNA editing sequence search tool. <ref name=PMID:17123956/>
+
* [http://xanthusbase.org/ Xanthusbase]: adapting wikipedia principles to a model organism database. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F17090585">PMID:17090585</span> <ref name=PMID:17090585/>
−
* [http://bioinformatics.ksu.edu/BeetleBase/ BeetleBase]: the model organism database for Tribolium castaneum. <ref name=PMID:17090595/> [[Media:Gkl776.pdf|PDF]]
+
* [[SynView]]: a [[GBrowse]]-compatible approach to visualizing comparative genome data. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F16844709">PMID:16844709</span> <ref name=PMID:16844709/>
−
* [http://xanthusbase.org/ Xanthusbase]: adapting wikipedia principles to a model organism database. <ref name=PMID:17090585/>
+
* [http://orygenesdb.cirad.fr/ OryGenesDB]: a database for rice reverse genetics. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F16381969">PMID:16381969</span> <ref name=PMID:16381969/>
−
* [[SynView]]: a [[GBrowse]]-compatible approach to visualizing comparative genome data. <ref name=PMID:16844709/>
+
* [http://dictybase.org dictyBase], the model organism database for Dictyostelium discoideum. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F16381903">PMID:16381903</span> <ref name=PMID:16381903/>
−
* [http://orygenesdb.cirad.fr/ OryGenesDB]: a database for rice reverse genetics. <ref name=PMID:16381969/>
+
* [[Galaxy]]: a platform for interactive large-scale genome analysis. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F16169926">PMID:16169926</span> <ref name=PMID:16169926/>
−
* [http://dictybase.org dictyBase], the model organism database for Dictyostelium discoideum. <ref name=PMID:16381903/>
+
* [[SynBrowse]]: a [[Synteny|synteny]] browser for comparative sequence analysis. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F15994196">PMID:15994196</span> <ref name=PMID:15994196/> [[Media:3461.pdf|PDF]]
−
* [[Galaxy]]: a platform for interactive large-scale genome analysis. <ref name=PMID:16169926/>
+
* [http://www.genome.arizona.edu/ FPC Web tools] for rice, maize, and distribution. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F15888684">PMID:15888684</span> <ref name=PMID:15888684/>
−
* [[SynBrowse]]: a [[Synteny|synteny]] browser for comparative sequence analysis. <ref name=PMID:15994196/> [[Media:3461.pdf|PDF]]
+
* 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. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F15805491">PMID:15805491</span> <ref name=PMID:15805491/>
−
* [http://www.genome.arizona.edu/ FPC Web tools] for rice, maize, and distribution. <ref name=PMID:15888684/>
+
* [http://wfleabase.org/ wFleaBase]: the Daphnia genome database. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F15752432">PMID:15752432</span> <ref name=PMID:15752432/> [[Media:1471-2105-6-45.pdf|PDF]]
−
* 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/>
+
* [http://www.comparative-legumes.org/ The Legume Information System (LIS)]: an integrated information resource for comparative legume biology. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F15608283">PMID:15608283</span> <ref name=PMID:15608283/>
−
* [http://wfleabase.org/ wFleaBase]: the Daphnia genome database. <ref name=PMID:15752432/> [[Media:1471-2105-6-45.pdf|PDF]]
+
* [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. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F15608211">PMID:15608211</span> <ref name=PMID:15608211/>
−
* [http://www.comparative-legumes.org/ The Legume Information System (LIS)]: an integrated information resource for comparative legume biology. <ref name=PMID:15608283/>
+
* Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F15601538">PMID:15601538</span> <ref name=PMID:15601538/>
−
* [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/>
+
* [[Caryoscope]]: an Open Source Java application for viewing microarray data in a genomic context. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F15488149">PMID:15488149</span> <ref name=PMID:15488149/>
−
* Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. <ref name=PMID:15601538/>
+
* [http://www.atidb.org/ ATIDB]: Arabidopsis thaliana insertion database. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F12582244">PMID:12582244</span> <ref name=PMID:12582244/> [[Media:Gkg222.pdf|PDF]]
−
* [[Caryoscope]]: an Open Source Java application for viewing microarray data in a genomic context. <ref name=PMID:15488149/>
+
* [[Apollo]]: a sequence annotation editor. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F12537571">PMID:12537571</span> <ref name=PMID:12537571/> [[Media:Gb-2002-3-12-research0082.pdf|PDF]]
−
* [http://www.atidb.org/ ATIDB]: Arabidopsis thaliana insertion database. <ref name=PMID:12582244/> [[Media:Gkg222.pdf|PDF]]
+
* The [[GBrowse|generic genome browser (GBrowse)]]: a building block for a model organism system database. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F12368253">PMID:12368253</span> <ref name=PMID:12368253/> [[Media:1599-1.pdf|PDF]]
−
* [[Apollo]]: a sequence annotation editor. <ref name=PMID:12537571/> [[Media:Gb-2002-3-12-research0082.pdf|PDF]]
+
−
* The [[GBrowse|generic genome browser (GBrowse)]]: a building block for a model organism system database. <ref name=PMID:12368253/> [[Media:1599-1.pdf|PDF]]
+
  
 
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[[Category:Publications]]

Revision as of 16:20, 16 August 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 PubMed ID, highest (most recent) first. This listing is compatible with the Mendeley web importer.

  • AlliumMap-a comparative genomics resource for cultivated Allium vegetables. PMID:22559261 [1]
  • SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. PMID:22120661 [2]
  • Tripal: a construction toolkit for online genome databases. PMID:21959868 [3]
  • TparvaDB: a database to support Theileria parva vaccine development. PMID:21546359 [4]
  • The GMOD Drupal bioinformatic server framework. PMID:20971988 [5]
  • ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. PMID:20952411 [6]
  • The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. PMID:20935049 [7]
  • Using the Generic Synteny Browser (GBrowse_syn) PMID:20836076 [8]
  • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. PMID:20738864 [9]
  • Choosing a genome browser for a Model Organism Database: surveying the Maize community. PMID:20627860 [10] PDF
  • AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. PMID:20482635 [11]
  • Galaxy: a web-based genome analysis tool for experimentalists". PMID:20069535 [12]
  • Next generation transcriptomes for next generation genomes using est2assembly. PMID:20034392 [13]
  • Using the Generic Genome Browser (GBrowse). PMID:19957275 [14]
  • BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. PMID:19820115 [15]
  • SNP@Evolution: a hierarchical database of positive selection on the human genome. PMID:19732458 [16] (GBrowse-related)
  • TBrowse: an integrative genomics map of Mycobacterium tuberculosis. PMID:19683474 [17] (GBrowse-related)
  • CMap 1.01: a comparative mapping application for the Internet. PMID:19648141 [18]
  • Apollo: a community resource for genome annotation editing. PMID:19439563 [19]
  • PopGenIE: The Populus Genome Integrative Explorer. PMID:19383103 [20]
  • Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. PMID:18845581 [21]
  • GMODWeb: a web framework for the Generic Model Organism Database. PMID:18570664 [22]
  • FishMap: a community resource for zebrafish genomics. PMID:18554176 [23] (GBrowse-related)
  • Using the Generic Genome Browser (GBrowse). PMID:18428797 [24]
  • MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. PMID:18025269 [25]
  • SmedGD: the Schmidtea mediterranea genome database. PMID:17881371 [26]
  • The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PMID:17712414 [27]
  • Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. PMID:17668053 [28]
  • A Chado case study: an ontology-based modular schema for representing genome-associated biological information. PMID:17646315 [29]
  • Celsius: a community resource for Affymetrix microarray data PMID:17570842 [30] PDF
  • Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. PMID:17389913 [31] (See YSB.)
  • The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. PMID:17287974 [32]
  • AphidBase: a database for aphid genomic resources. PMID:17237053 [33]
  • DroSpeGe: rapid access database for new Drosophila species genomes. PMID:17202166 [34] PDF
  • T1DBase: integration and presentation of complex data for type 1 diabetes research. PMID:17169983 [35]
  • Gbrowse Moby: a Web-based browser for BioMoby Services. PMID:17147784 [36]
  • ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. PMID:17142227 [37] PDF
  • Expanded protein information at SGD: new pages and proteome browser. PMID:17142221 [38]
  • SwissRegulon: a database of genome-wide annotations of regulatory sites. PMID:17130146 [39]
  • KISS: the kinetoplastid RNA editing sequence search tool. PMID:17123956 [40]
  • BeetleBase: the model organism database for Tribolium castaneum. PMID:17090595 [41] PDF
  • Xanthusbase: adapting wikipedia principles to a model organism database. PMID:17090585 [42]
  • SynView: a GBrowse-compatible approach to visualizing comparative genome data. PMID:16844709 [43]
  • OryGenesDB: a database for rice reverse genetics. PMID:16381969 [44]
  • dictyBase, the model organism database for Dictyostelium discoideum. PMID:16381903 [45]
  • Galaxy: a platform for interactive large-scale genome analysis. PMID:16169926 [46]
  • SynBrowse: a synteny browser for comparative sequence analysis. PMID:15994196 [47] PDF
  • FPC Web tools for rice, maize, and distribution. PMID:15888684 [48]
  • 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. PMID:15805491 [49]
  • wFleaBase: the Daphnia genome database. PMID:15752432 [50] PDF
  • The Legume Information System (LIS): an integrated information resource for comparative legume biology. PMID:15608283 [51]
  • Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. PMID:15608211 [52]
  • Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. PMID:15601538 [53]
  • Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. PMID:15488149 [54]
  • ATIDB: Arabidopsis thaliana insertion database. PMID:12582244 [55] PDF
  • Apollo: a sequence annotation editor. PMID:12537571 [56] PDF
  • The generic genome browser (GBrowse): a building block for a model organism system database. PMID:12368253 [57] 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:20836076
  9. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20738864
  10. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20627860
  11. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20482635
  12. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20069535
  13. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20034392
  14. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19957275
  15. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19820115
  16. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19732458
  17. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19683474
  18. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19648141
  19. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19439563
  20. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19383103
  21. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18845581
  22. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18570664
  23. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18554176
  24. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18428797
  25. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18025269
  26. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17881371
  27. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17712414
  28. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17668053
  29. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17646315
  30. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17570842
  31. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17389913
  32. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17287974
  33. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17237053
  34. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17202166
  35. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17169983
  36. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17147784
  37. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17142227
  38. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17142221
  39. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17130146
  40. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17123956
  41. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17090595
  42. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17090585
  43. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:16844709
  44. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:16381969
  45. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:16381903
  46. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:16169926
  47. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15994196
  48. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15888684
  49. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15805491
  50. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15752432
  51. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15608283
  52. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15608211
  53. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15601538
  54. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:15488149
  55. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12582244
  56. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12537571
  57. ↑ 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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