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.

Articles

Sorted by PubMed ID, highest (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]
  • Using the Generic Synteny Browser (GBrowse_syn) [8]
  • Choosing a genome browser for a Model Organism Database: surveying the Maize community. [9] PDF
  • AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. [10]
  • Next generation transcriptomes for next generation genomes using est2assembly. [11]
  • Using the Generic Genome Browser (GBrowse). [12]
  • BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. [13]
  • SNP@Evolution: a hierarchical database of positive selection on the human genome. [14] (GBrowse-related)
  • TBrowse: an integrative genomics map of Mycobacterium tuberculosis. [15] (GBrowse-related)
  • CMap 1.01: a comparative mapping application for the Internet. [16]
  • Apollo: a community resource for genome annotation editing. [17]
  • PopGenIE: The Populus Genome Integrative Explorer. [18]
  • Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. [19]
  • GMODWeb: a web framework for the Generic Model Organism Database. [20]
  • FishMap: a community resource for zebrafish genomics. [21] (GBrowse-related)
  • Using the Generic Genome Browser (GBrowse). [22]
  • MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. [23]
  • SmedGD: the Schmidtea mediterranea genome database. [24]
  • The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. [25]
  • Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. [26]
  • A Chado case study: an ontology-based modular schema for representing genome-associated biological information. [27]
  • Celsius: a community resource for Affymetrix microarray data [28] PDF
  • Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. [29] (See YSB.)
  • The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. [30]
  • AphidBase: a database for aphid genomic resources. [31]
  • DroSpeGe: rapid access database for new Drosophila species genomes. [32] PDF
  • T1DBase: integration and presentation of complex data for type 1 diabetes research. [33]
  • Gbrowse Moby: a Web-based browser for BioMoby Services. [34]
  • ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. [35] PDF
  • Expanded protein information at SGD: new pages and proteome browser. [36]
  • SwissRegulon: a database of genome-wide annotations of regulatory sites. [37]
  • KISS: the kinetoplastid RNA editing sequence search tool. [38]
  • BeetleBase: the model organism database for Tribolium castaneum. [39] PDF
  • Xanthusbase: adapting wikipedia principles to a model organism database. [40]
  • SynView: a GBrowse-compatible approach to visualizing comparative genome data. [41]
  • OryGenesDB: a database for rice reverse genetics. [42]
  • dictyBase, the model organism database for Dictyostelium discoideum. [43]
  • Galaxy: a platform for interactive large-scale genome analysis. [44]
  • SynBrowse: a synteny browser for comparative sequence analysis. [45] PDF
  • FPC Web tools for rice, maize, and distribution. [46]
  • 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. [47]
  • wFleaBase: the Daphnia genome database. [48] PDF
  • The Legume Information System (LIS): an integrated information resource for comparative legume biology. [49]
  • Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. [50]
  • Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. [51]
  • Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. [52]
  • ATIDB: Arabidopsis thaliana insertion database. [53] PDF
  • Apollo: a sequence annotation editor. [54] PDF
  • The generic genome browser (GBrowse): a building block for a model organism system database. [55] PDF

Bibliography

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  55. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:12368253


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