FB2015_01, released February 24th, 2015

A Database of Drosophila Genes & Genomes

FlyBase Publications

  • S.J. Marygold, P.C. Leyland, R.L. Seal, J.L. Goodman, J.R. Thurmond, V.B. Strelets, R.J. Wilson and the FlyBase Consortium (2013).
    FlyBase: improvements to the bibliography.
    Nucleic Acids Res. 41(D1):D751-D757. [FBrf0220350]
  • Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013).
    Systematic analysis of experimental phenotype data reveals gene functions.
    PLoS One. 8(4):e60847. PMID: 23626672. [FBrf0221415]
  • McQuilton P and the FlyBase Consortium (2012).
    Opportunities for text mining in the FlyBase genetic literature curation workflow.
    Database 2012:bas039. [FBrf0219955]
  • Gene Ontology Consortium (2013).
    Gene Ontology annotations and resources.
    Nucleic Acids Res. 41(Database issue):D530-5. doi: 10.1093/nar/gks1050. PubMed PMID: 23161678; PubMed Central PMCID: PMC3531070.
  • S.M. Bunt, G.B. Grumbling, H.I. Field, S.J. Marygold, N.H. Brown, G.H. Millburn and the FlyBase Consortium (2012).
    Directly e-mailing authors of newly published papers encourages community curation.
    Database 2012; doi: 10.1093/database/bas024. [FBrf0218522]
  • McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012).
    FlyBase 101 – the basics of navigating FlyBase.
    Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108]
  • Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold S, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW (2012).
    Automatic categorization of diverse experimental information in the bioscience literature.
    BMC Bioinformatics. 13(1):16. [FBrf0218533]
  • Gene Ontology Consortium (2012).
    The Gene Ontology: enhancements for 2011.
    Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568; PubMed Central PMCID: PMC3245151.
  • A. Rangarajan, T. Schedl, K. Yook, J. Chan, S. Haenel, L. Otis, S. Faelten, T. DePellegrin‑Connelly, R. Isaacson, M.S. Skrzypek, S.J. Marygold, R. Stefancsik, J.M. Cherry, P.W. Sternberg, H‑M. Müller (2011).
    Toward an interactive article: integrating journals and biological databases.
    BMC Bioinformatics 2011, 12:175. [FBrf0214821]
  • Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).
    The representation of heart development in the gene ontology.
    Dev Biol. 354(1):9-17. doi: 10.1016/j.ydbio.2011.03.011. PubMed PMID: 21419760; PubMed Central PMCID: PMC3302178.
  • Gene Ontology Consortium (2010).
    The Gene Ontology in 2010: extensions and refinements.
    Nucleic Acids Res. 38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. PubMed PMID: 19920128; PubMed Central PMCID: PMC2808930.
  • Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010).
    FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.
    Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132; PubMed Central PMCID: PMC2808907. [FBrf0209611]
  • S. St. Pierre, P. McQuilton (2009).
    Inside FlyBase (Biocuration as a career).
    Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427]
  • Reference Genome Group of the Gene Ontology Consortium (2009).
    The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
    PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431; PubMed Central PMCID: PMC2699109.
  • S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi‑Sutherland, A. Schroeder, R. Seal, H. Zhang, and The FlyBase Consortium, (2009).
    FlyBase: enhancing Drosophila Gene Ontology annotations.
    Nucleic Acids Res. 37: D555-D559; doi:10.1093/nar/gkn788. [FBrf0206621]
  • Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).
    The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
    BMC Bioinformatics. 10:59. doi: 10.1186/1471-2105-10-59. PubMed PMID: 19210778; PubMed Central PMCID: PMC2648944. [FBrf0207486]
  • R. Drysdale, and The FlyBase Consortium, (2008).
    FlyBase : a database for the Drosophila research community.
    Methods Molec. Biol. 420: 45-59. [FBrf0205804]
  • Howe, Doug; Costanzo, Maria; Fey, Petra; Gojobori, Takashi; Hannick, Linda; Hide, Winston; Hill, David P.; Kania, Renate; Schaeffer, Mary; St Pierre, Susan; Twigger, Simon; White, Owen; Yon Rhee, Seung (2008).
    Big data: The future of biocuration.
    Nature. 455(7209):47-50. doi: 10.1038/455047a. PubMed PMID: 19182544; PubMed Central PMCID: PMC2819144. [FBrf0213427]
  • N. Karamanis, R. Seal, I. Lewin, P. McQuilton, A. Vlachos, C. Gasperin, R. Drysdale, T. Briscoe, (2008).
    Natural language processing in aid of FlyBase curators.
    BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381]
  • R.J. Wilson, J.L. Goodman, V.B. Strelets, and the FlyBase Consortium, (2008).
    FlyBase: integration and improvements to query tools.
    Nucleic Acids Res. 36: D588-D593; doi:10.1093/nar/gkm930. [FBrf0203012]
  • M.A. Crosby, J.L. Goodman, V.B. Strelets, P. Zhang, W.M Gelbart, and the FlyBase Consortium, (2007).
    FlyBase: genomes by the dozen.
    Nucleic Acids Res. 35: D486-D491; doi:10.1093/nar/gkl827. [FBrf0194786]
  • Drosophila 12 Genomes Consortium., (2007).
    Evolution of genes and genomes on the Drosophila phylogeny.
    Nature 450: 203-218. [FBrf0200326]
  • N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).
    Integrating natural language processing with FlyBase curation.
    Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]
  • M.F. Lin, et al., (2007).
    Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
    Genome Res 17: 1823-1836. [FBrf0202906]
  • C.J. Mungall, D.B. Emmert, and the FlyBase Consortium, (2007).
    A Chado case study: an ontology-based modular schema for representing genome-associated biological information.
    Bioinformatics 23: i337-346. [FBrf0201050]
  • A. Stark et al., (2007).
    Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
    Nature 450: 219-232. [FBrf0200674]
  • G. Grumbling, V. Strelets and The FlyBase Consortium, (2006).
    FlyBase: anatomical data, images and queries.
    Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]
  • R.A. Drysdale, M.A. Crosby and the FlyBase Consortium, (2005).
    FlyBase : Genes and gene models.
    Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]
    (Reproduced with permission from NAR Online )
  • S. Richards et al., (2005).
    Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
    Genome Res., 15: 1-18. [FBrf0184012]
  • P. Zhou, D. Emmert, P. Zhang, (2005).
    Using chado to store genome annotation data.
    Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]
  • The FlyBase Consortium, (2003).
    The FlyBase Database of the Drosophila Genome Projects and community literature.
    Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]
    (Reproduced with permission from NAR Online )
  • Rachel Drysdale, (2003).
    The Drosophila melanogaster genome sequencing and annotation projects: A status report.
    Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]
    (Reproduced with permission from Briefings in Functional Genomics and Proteomics)
Genome Annotation, (2002)
  • CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin and SE Lewis. (2002).
    An integrated computational pipeline and database to support whole-genome sequence annotation.
    Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]
  • SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall and ME Clamp. (2002).
    Apollo: a sequence annotation editor.
    Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]
  • S Misra, MA Crosby, CJ Mungall, BB Matthews, KS Campbell, P Hradecky, Y Huang, JS Kaminker, GH Millburn, SE Prochnik, CD Smith, JL Tupy, EJ Whitfield, L Bayraktaroglu, BP Berman, BR Bettencourt, SE Celniker, ADNJ de Grey, RA Drysdale, NL Harris, J Richter, S Russo, AJ Schroeder, SQ Shu, M Stapleton, C Yamada, M Ashburner, WM Gelbart, GM Rubin and SE Lewis. (2002).
    Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
    Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]
  • The FlyBase Consortium, (2002).
    The FlyBase Database of the Drosophila Genome Projects and community literature.
    Nucleic Acids Res., 30:106-108 pdf [ 67 kb] .. html [ 20 kb, 15-Apr-02] [FBrf0141697]
    (Reproduced with permission from NAR Online )
  • K. Matthews and K. Cook (2001).
    Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.
    In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [FBrf0185967]
  • Rachel Drysdale, (2001).
    Phenotypic data in FlyBase.
    Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01] [FBrf0137187]
    (Reproduced with permission from Briefings in Bioinformatics)
  • FlyBase (1999).
    FlyBase: Genomic and post-genomic viewpoints.
    In S. Letovsky (Ed.)
    Bioinformatics: Databases and Systems 141--150. [FBrf0111589]
  • The FlyBase Consortium, (1999).
    The FlyBase Database of the Drosophila Genome Projects and community literature.
    Nucleic Acids Res., 27:85-88 pdf [ 34 kb] .. html [ 29 kb, 10-Feb-99] [FBrf0107356]
    (Reproduced with permission from NAR Online )
  • The FlyBase Consortium (1998).
    FlyBase - A Drosophila database.
    Nucleic Acids Res., 26:85-88 [FBrf0100346]
  • The FlyBase Consortium (1997).
    FlyBase - A Drosophila database.
    Nucleic Acids Res., 25:63-66 [FBrf0093096]
  • The FlyBase Consortium (1996).
    FlyBase - The Drosophila database.
    Nucleic Acids Res., 24:53-56 [FBrf0085043]
  • The FlyBase Consortium (1995).
    Proposed genetic nomenclature for Drosophila melanogaster.
    Trends in Genetics: Genetic Nomenclature Guide, pp.26--29. [FBrf0078422]
  • The FlyBase Consortium (1994).
    FlyBase - The Drosophila database.
    Nucleic Acids Res., 22:3456-3458 [FBrf0077015]
  • M. Ashburner and R. Drysdale (1994).
    FlyBase - The Drosophila genetic database.
    Development 120:2077-2079 [FBrf0072526]
  • M. Ashburner (1993).
    GNome News 13:19-20. [FBrf0058642]