Publications

From GMOD

Jump to: navigation, search

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] (See YSB.)
  • 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
  • Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. [27]

Bibliography

  1. ↑ Lewis SE et al. (2002) Apollo: a sequence annotation editor. Genome Biol 3: RESEARCH0082 PubMed
  2. ↑ Stein LD et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12: 1599-610 PubMed
  3. ↑ Pan X et al. (2003) ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Res 31: 1245-51 PubMed
  4. ↑ Gilbert DG (2007) DroSpeGe: rapid access database for new Drosophila species genomes. Nucleic Acids Res 35: D480-5 PubMed
  5. ↑ Arnaiz O et al. (2007) ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res 35: D439-44 PubMed
  6. ↑ Colbourne JK et al. (2005) wFleaBase: the Daphnia genome database. BMC Bioinformatics 6: 45 PubMed
  7. ↑ Wang L et al. (2007) BeetleBase: the model organism database for Tribolium castaneum. Nucleic Acids Res 35: D476-9 PubMed
  8. ↑ Gauthier JP et al. (2007) AphidBase: a database for aphid genomic resources. Bioinformatics 23: 783-4 PubMed
  9. ↑ Ochsenreiter T et al. (2007) KISS: the kinetoplastid RNA editing sequence search tool. RNA 13: 1-4 PubMed
  10. ↑ Arshinoff BI et al. (2007) Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res 35: D422-6 PubMed
  11. ↑ Droc G et al. (2006) OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res 34: D736-40 PubMed
  12. ↑ Pan X et al. (2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics 21: 3461-8 PubMed
  13. ↑ Pampanwar V et al. (2005) FPC Web tools for rice, maize, and distribution. Plant Physiol 138: 116-26 PubMed
  14. ↑ Katari MS et al. (2005) 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. Genome Res 15: 496-504 PubMed
  15. ↑ Gonzales MD et al. (2005) The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucleic Acids Res 33: D660-5 PubMed
  16. ↑ Schacherer J et al. (2007) Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS ONE 2: e322 PubMed
  17. ↑ Shultz JL et al. (2007) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114: 1081-90 PubMed
  18. ↑ Hulbert EM et al. (2007) T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res 35: D742-6 PubMed
  19. ↑ Wilkinson M (2006) Gbrowse Moby: a Web-based browser for BioMoby Services. Source Code Biol Med 1: 4 PubMed
  20. ↑ Nash R et al. (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35: D468-71 PubMed
  21. ↑ Pachkov M et al. (2007) SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res 35: D127-31 PubMed
  22. ↑ Wang H et al. (2006) SynView: a GBrowse-compatible approach to visualizing comparative genome data. Bioinformatics 22: 2308-9 PubMed
  23. ↑ Winsor GL et al. (2005) Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res 33: D338-43 PubMed
  24. ↑ Burren OS et al. (2004) Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. Hum Genomics 1: 98-109 PubMed
  25. ↑ Mungall CJ & Emmert DB (2007) A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics 23: i337-46 PubMed
  26. ↑ Day A et al. (2007) Celsius: a community resource for Affymetrix microarray data. Genome Biol 8: R112 PubMed
  27. ↑ Awad IA et al. (2004) Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 5: 151 PubMed


Adding Citations

Enter them into the Articles section. Example:

<ref name=PMID:15752432/>

Retrieved from "http://gmod.org/wiki/Publications"
Personal tools
developers