Publications

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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.

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

GMOD on Mendeley

If you use Mendeley, please join the GMOD group and contribute GMOD and GMOD-related papers to the pool there. The following feed shows papers recently added to the GMOD Mendeley group.

Articles

Sorted by PubMed ID, highest (most recent) first. This listing is compatible with the Mendeley web importer and has embedded COiNs bibliographic data.

  • Canto: An online tool for community literature curation DOI:10.1093/bioinformatics/btu103 [1]
  • AlliumMap-a comparative genomics resource for cultivated Allium vegetables. PMID:22559261 [2]
  • SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. PMID:22120661 [3]
  • Tripal: a construction toolkit for online genome databases. PMID:21959868 [4]
  • TparvaDB: a database to support Theileria parva vaccine development. PMID:21546359 [5]
  • The GMOD Drupal bioinformatic server framework. PMID:20971988 [6]
  • ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. PMID:20952411 [7]
  • The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. PMID:20935049 [8]
  • Using the Generic Synteny Browser (GBrowse_syn) PMID:20836076 [9]
  • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. PMID:20738864 [10]
  • Choosing a genome browser for a Model Organism Database: surveying the Maize community. PMID:20627860 [11] PDF
  • AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. PMID:20482635 [12]
  • Galaxy: a web-based genome analysis tool for experimentalists". PMID:20069535 [13]
  • Next generation transcriptomes for next generation genomes using est2assembly. PMID:20034392 [14]
  • Using the Generic Genome Browser (GBrowse). PMID:19957275 [15]
  • BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. PMID:19820115 [16]
  • SNP@Evolution: a hierarchical database of positive selection on the human genome. PMID:19732458 [17] (GBrowse-related)
  • TBrowse: an integrative genomics map of Mycobacterium tuberculosis. PMID:19683474 [18] (GBrowse-related)
  • CMap 1.01: a comparative mapping application for the Internet. PMID:19648141 [19]
  • Apollo: a community resource for genome annotation editing. PMID:19439563 [20]
  • PopGenIE: The Populus Genome Integrative Explorer. PMID:19383103 [21]
  • Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. PMID:18845581 [22]
  • GMODWeb: a web framework for the Generic Model Organism Database. PMID:18570664 [23]
  • FishMap: a community resource for zebrafish genomics. PMID:18554176 [24] (GBrowse-related)
  • Using the Generic Genome Browser (GBrowse). PMID:18428797 [25]
  • MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. PMID:18025269 [26]
  • SmedGD: the Schmidtea mediterranea genome database. PMID:17881371 [27]
  • The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PMID:17712414 [28]
  • Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. PMID:17668053 [29]
  • A Chado case study: an ontology-based modular schema for representing genome-associated biological information. PMID:17646315 [30]
  • Celsius: a community resource for Affymetrix microarray data PMID:17570842 [31] PDF
  • Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. PMID:17389913 [32] (See YSB.)
  • The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. PMID:17287974 [33]
  • AphidBase: a database for aphid genomic resources. PMID:17237053 [34]
  • DroSpeGe: rapid access database for new Drosophila species genomes. PMID:17202166 [35] PDF
  • T1DBase: integration and presentation of complex data for type 1 diabetes research. PMID:17169983 [36]
  • Gbrowse Moby: a Web-based browser for BioMoby Services. PMID:17147784 [37]
  • ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. PMID:17142227 [38] PDF
  • Expanded protein information at SGD: new pages and proteome browser. PMID:17142221 [39]
  • SwissRegulon: a database of genome-wide annotations of regulatory sites. PMID:17130146 [40]
  • KISS: the kinetoplastid RNA editing sequence search tool. PMID:17123956 [41]
  • BeetleBase: the model organism database for Tribolium castaneum. PMID:17090595 [42] PDF
  • Xanthusbase: adapting wikipedia principles to a model organism database. PMID:17090585 [43]
  • SynView: a GBrowse-compatible approach to visualizing comparative genome data. PMID:16844709 [44]
  • OryGenesDB: a database for rice reverse genetics. PMID:16381969 [45]
  • dictyBase, the model organism database for Dictyostelium discoideum. PMID:16381903 [46]
  • Galaxy: a platform for interactive large-scale genome analysis. PMID:16169926 [47]
  • SynBrowse: a synteny browser for comparative sequence analysis. PMID:15994196 [48] PDF
  • FPC Web tools for rice, maize, and distribution. PMID:15888684 [49]
  • 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 [50]
  • wFleaBase: the Daphnia genome database. PMID:15752432 [51] PDF
  • The Legume Information System (LIS): an integrated information resource for comparative legume biology. PMID:15608283 [52]
  • Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. PMID:15608211 [53]
  • Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. PMID:15601538 [54]
  • Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. PMID:15488149 [55]
  • ATIDB: Arabidopsis thaliana insertion database. PMID:12582244 [56] PDF
  • Apollo: a sequence annotation editor. PMID:12537571 [57] PDF
  • The generic genome browser (GBrowse): a building block for a model organism system database. PMID:12368253 [58] PDF



Adding Citations

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