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.

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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. ↑ McCallum J et al. AlliumMap-A comparative genomics resource for cultivated Allium vegetables. BMC Genomics 2012 13:168.
    DOI:10.1186/1471-2164-13-168 PMCID:PMC3423043 PMID:22559261
  2. ↑ Di Génova A et al. SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. Database (Oxford) 2011 2011:bar050.
    DOI:10.1093/database/bar050 PMCID:PMC3225076 PMID:22120661
  3. ↑ Ficklin SP et al. Tripal: a construction toolkit for online genome databases. Database (Oxford) 2011 2011:bar044.
    DOI:10.1093/database/bar044 PMCID:PMC3263599 PMID:21959868
  4. ↑ Visendi P et al. TparvaDB: a database to support Theileria parva vaccine development. Database (Oxford) 2011 2011:bar015.
    DOI:10.1093/database/bar015 PMCID:PMC3092609 PMID:21546359
  5. ↑ Papanicolaou A and Heckel DG. The GMOD Drupal bioinformatic server framework. Bioinformatics 2010 26:3119-24.
    DOI:10.1093/bioinformatics/btq599 PMCID:PMC2995126 PMID:20971988
  6. ↑ Arnaiz O and Sperling L. ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res. 2011 39:D632-6.
    DOI:10.1093/nar/gkq918 PMCID:PMC3013783 PMID:20952411
  7. ↑ Bombarely A et al. The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res. 2011 39:D1149-55.
    DOI:10.1093/nar/gkq866 PMCID:PMC3013765 PMID:20935049
  8. ↑ McKay SJ, Vergara IA, and Stajich JE. Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics 2010 Chapter 9:Unit 9.12.
    DOI:10.1002/0471250953.bi0912s31 PMCID:PMC3162311 PMID:20836076
  9. ↑ Goecks J, Nekrutenko A, Taylor J, and Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010 11:R86.
    DOI:10.1186/gb-2010-11-8-r86 PMCID:PMC2945788 PMID:20738864
  10. ↑ Sen TZ et al. Choosing a genome browser for a Model Organism Database: surveying the maize community. Database (Oxford) 2010 2010:baq007.
    DOI:10.1093/database/baq007 PMCID:PMC2911842 PMID:20627860
  11. ↑ Legeai F et al. AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. Insect Mol. Biol. 2010 19 Suppl 2:5-12.
    DOI:10.1111/j.1365-2583.2009.00930.x PMID:20482635
  12. ↑ Blankenberg D et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 2010 Chapter 19:Unit 19.10.1-21.
    DOI:10.1002/0471142727.mb1910s89 PMID:20069535
  13. ↑ Papanicolaou A, Stierli R, Ffrench-Constant RH, and Heckel DG. Next generation transcriptomes for next generation genomes using est2assembly. BMC Bioinformatics 2009 10:447.
    DOI:10.1186/1471-2105-10-447 PMCID:PMC3087352 PMID:20034392
  14. ↑ Donlin MJ. Using the Generic Genome Browser (GBrowse). Curr Protoc Bioinformatics 2009 Chapter 9:Unit 9.9.
    DOI:10.1002/0471250953.bi0909s28 PMID:19957275
  15. ↑ Kim HS et al. BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. Nucleic Acids Res. 2010 38:D437-42.
    DOI:10.1093/nar/gkp807 PMCID:PMC2808946 PMID:19820115
  16. ↑ Cheng F, Chen W, Richards E, Deng L, and Zeng C. SNP@Evolution: a hierarchical database of positive selection on the human genome. BMC Evol. Biol. 2009 9:221.
    DOI:10.1186/1471-2148-9-221 PMCID:PMC2755008 PMID:19732458
  17. ↑ Bhardwaj A, Bhartiya D, Kumar N, Open Source Drug Discovery Consortium, and Scaria V. TBrowse: an integrative genomics map of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2009 89:386-7.
    DOI:10.1016/j.tube.2009.07.005 PMID:19683474
  18. ↑ Youens-Clark K, Faga B, Yap IV, Stein L, and Ware D. CMap 1.01: a comparative mapping application for the Internet. Bioinformatics 2009 25:3040-2.
    DOI:10.1093/bioinformatics/btp458 PMCID:PMC2773250 PMID:19648141
  19. ↑ Lee E, Harris N, Gibson M, Chetty R, and Lewis S. Apollo: a community resource for genome annotation editing. Bioinformatics 2009 25:1836-7.
    DOI:10.1093/bioinformatics/btp314 PMCID:PMC2705230 PMID:19439563
  20. ↑ Sjödin A, Street NR, Sandberg G, Gustafsson P, and Jansson S. The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome. New Phytol. 2009 182:1013-25.
    DOI:10.1111/j.1469-8137.2009.02807.x PMID:19383103
  21. ↑ Carver T et al. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008 24:2672-6.
    DOI:10.1093/bioinformatics/btn529 PMCID:PMC2606163 PMID:18845581
  22. ↑ O'Connor BD et al. GMODWeb: a web framework for the Generic Model Organism Database. Genome Biol. 2008 9:R102.
    DOI:10.1186/gb-2008-9-6-r102 PMCID:PMC2481422 PMID:18570664
  23. ↑ Meli R et al. FishMap: a community resource for zebrafish genomics. Zebrafish 2008 5:125-30.
    DOI:10.1089/zeb.2008.0531 PMID:18554176
  24. ↑ Donlin MJ. Using the Generic Genome Browser (GBrowse). Curr Protoc Bioinformatics 2007 Chapter 9:Unit 9.9.
    DOI:10.1002/0471250953.bi0909s17 PMID:18428797
  25. ↑ Cantarel BL et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008 18:188-96.
    DOI:10.1101/gr.6743907 PMCID:PMC2134774 PMID:18025269
  26. ↑ Robb SM, Ross E, and Sánchez Alvarado A. SmedGD: the Schmidtea mediterranea genome database. Nucleic Acids Res. 2008 36:D599-606.
    DOI:10.1093/nar/gkm684 PMCID:PMC2238899 PMID:17881371
  27. ↑ Heinicke S et al. The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PLoS ONE 2007 2:e766.
    DOI:10.1371/journal.pone.0000766 PMCID:PMC1942082 PMID:17712414
  28. ↑ Suga K, Welch DM, Tanaka Y, Sakakura Y, and Hagiwara A. Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. PLoS ONE 2007 2:e671.
    DOI:10.1371/journal.pone.0000671 PMCID:PMC1925144 PMID:17668053
  29. ↑ Mungall CJ, Emmert DB, and FlyBase Consortium. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics 2007 23:i337-46.
    DOI:10.1093/bioinformatics/btm189 PMID:17646315
  30. ↑ Day A, Carlson MR, Dong J, O'Connor BD, and Nelson SF. Celsius: a community resource for Affymetrix microarray data. Genome Biol. 2007 8:R112.
    DOI:10.1186/gb-2007-8-6-r112 PMCID:PMC2394754 PMID:17570842
  31. ↑ Schacherer J et al. Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS ONE 2007 2:e322.
    DOI:10.1371/journal.pone.0000322 PMCID:PMC1829191 PMID:17389913
  32. ↑ Shultz JL, Kazi S, Bashir R, Afzal JA, and Lightfoot DA. The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor. Appl. Genet. 2007 114:1081-90.
    DOI:10.1007/s00122-007-0501-9 PMID:17287974
  33. ↑ Gauthier JP, Legeai F, Zasadzinski A, Rispe C, and Tagu D. AphidBase: a database for aphid genomic resources. Bioinformatics 2007 23:783-4.
    DOI:10.1093/bioinformatics/btl682 PMID:17237053
  34. ↑ Gilbert DG. DroSpeGe: rapid access database for new Drosophila species genomes. Nucleic Acids Res. 2007 35:D480-5.
    DOI:10.1093/nar/gkl997 PMCID:PMC1899099 PMID:17202166
  35. ↑ Hulbert EM et al. T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res. 2007 35:D742-6.
    DOI:10.1093/nar/gkl933 PMCID:PMC1781218 PMID:17169983
  36. ↑ Wilkinson M. Gbrowse Moby: a Web-based browser for BioMoby Services. Source Code Biol Med 2006 1:4.
    DOI:10.1186/1751-0473-1-4 PMCID:PMC1636335 PMID:17147784
  37. ↑ Arnaiz O, Cain S, Cohen J, and Sperling L. ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res. 2007 35:D439-44.
    DOI:10.1093/nar/gkl777 PMCID:PMC1669747 PMID:17142227
  38. ↑ Nash R et al. Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res. 2007 35:D468-71.
    DOI:10.1093/nar/gkl931 PMCID:PMC1669759 PMID:17142221
  39. ↑ Pachkov M, Erb I, Molina N, and van Nimwegen E. SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res. 2007 35:D127-31.
    DOI:10.1093/nar/gkl857 PMCID:PMC1716717 PMID:17130146
  40. ↑ Ochsenreiter T, Cipriano M, and Hajduk SL. KISS: the kinetoplastid RNA editing sequence search tool. RNA 2007 13:1-4.
    DOI:10.1261/rna.232907 PMCID:PMC1705751 PMID:17123956
  41. ↑ Wang L, Wang S, Li Y, Paradesi MS, and Brown SJ. BeetleBase: the model organism database for Tribolium castaneum. Nucleic Acids Res. 2007 35:D476-9.
    DOI:10.1093/nar/gkl776 PMCID:PMC1669707 PMID:17090595
  42. ↑ Arshinoff BI et al. Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res. 2007 35:D422-6.
    DOI:10.1093/nar/gkl881 PMCID:PMC1669732 PMID:17090585
  43. ↑ Wang H, Su Y, Mackey AJ, Kraemer ET, and Kissinger JC. SynView: a GBrowse-compatible approach to visualizing comparative genome data. Bioinformatics 2006 22:2308-9.
    DOI:10.1093/bioinformatics/btl389 PMID:16844709
  44. ↑ Droc G et al. OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res. 2006 34:D736-40.
    DOI:10.1093/nar/gkj012 PMCID:PMC1347375 PMID:16381969
  45. ↑ Chisholm RL et al. dictyBase, the model organism database for Dictyostelium discoideum. Nucleic Acids Res. 2006 34:D423-7.
    DOI:10.1093/nar/gkj090 PMCID:PMC1347453 PMID:16381903
  46. ↑ Giardine B et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005 15:1451-5.
    DOI:10.1101/gr.4086505 PMCID:PMC1240089 PMID:16169926
  47. ↑ Pan X, Stein L, and Brendel V. SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics 2005 21:3461-8.
    DOI:10.1093/bioinformatics/bti555 PMID:15994196
  48. ↑ Pampanwar V et al. FPC Web tools for rice, maize, and distribution. Plant Physiol. 2005 138:116-26.
    DOI:10.1104/pp.104.056291 PMCID:PMC1104167 PMID:15888684
  49. ↑ Katari MS, Balija V, Wilson RK, Martienssen RA, and McCombie WR. 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. 2005 15:496-504.
    DOI:10.1101/gr.3239105 PMCID:PMC1074364 PMID:15805491
  50. ↑ Colbourne JK, Singan VR, and Gilbert DG. wFleaBase: the Daphnia genome database. BMC Bioinformatics 2005 6:45.
    DOI:10.1186/1471-2105-6-45 PMCID:PMC555599 PMID:15752432
  51. ↑ Gonzales MD et al. The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucleic Acids Res. 2005 33:D660-5.
    DOI:10.1093/nar/gki128 PMCID:PMC540082 PMID:15608283
  52. ↑ Winsor GL et al. Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res. 2005 33:D338-43.
    DOI:10.1093/nar/gki047 PMCID:PMC540001 PMID:15608211
  53. ↑ Burren OS et al. Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. Hum. Genomics 2004 1:98-109.
    PMCID:PMC3525068 PMID:15601538
  54. ↑ Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, and Sherlock G. Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 2004 5:151.
    DOI:10.1186/1471-2105-5-151 PMCID:PMC528725 PMID:15488149
  55. ↑ Pan X et al. ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Res. 2003 31:1245-51.
    PMCID:PMC150240 PMID:12582244
  56. ↑ Lewis SE et al. Apollo: a sequence annotation editor. Genome Biol. 2002 3:RESEARCH0082.
    PMCID:PMC151184 PMID:12537571
  57. ↑ Stein LD et al. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 12:1599-610.
    DOI:10.1101/gr.403602 PMCID:PMC187535 PMID:12368253


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