A Database of Drosophila Genes & Genomes

FB2008_06, released July 3, 2008
 

FlyBase Publications

  • 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.
  • A. Bhutkar, W.M. Gelbart, T.F. Smith, (2007).
    Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study.
    Genome Biol. 8: R236.
  • A. Bhutkar, S.M. Russo, T.F. Smith, W.M. Gelbart, (2007).
    Genome-scale analysis of positionally relocated genes.
    Genome Res 17: 1880-1887.
  • 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.
  • Drosophila 12 Genomes Consortium., (2007).
    Evolution of genes and genomes on the Drosophila phylogeny.
    Nature 450: 203-218.
  • N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).
    Integrating natural language processing with FlyBase curation.
    Pac Symp Biocomput. 2007;:245-56.
  • M.F. Lin, et al., (2007).
    Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
    Genome Res 17: 1823-1836.
  • 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.
  • A. Stark et al., (2007).
    Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
    Nature 450: 219-232.
  • A. Bhutkar, S. Russo, T.F. Smith, W.M. Gelbart, (2006).
    Techniques for multi-genome synteny analysis to overcome assembly limitations.
    Genome Inf. Ser., 17: 152-161.
  • 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.
  • 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]
    (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.
  • 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.
  • 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]
    (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]
    (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]
  • 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]
  • 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]
  • 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]
    (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.
  • Rachel Drysdale, (2001).
    Phenotypic data in FlyBase.
    Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01]
    (Reproduced with permission from Briefings in Bioinformatics)
  • 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]
    (Reproduced with permission from NAR Online )
  • The FlyBase Consortium (1998).
    FlyBase - A Drosophila database.
    Nucleic Acids Res., 26:85-88
  • The FlyBase Consortium (1997).
    FlyBase - A Drosophila database.
    Nucleic Acids Res., 25:63-66
  • The FlyBase Consortium (1996).
    FlyBase - The Drosophila database.
    Nucleic Acids Res., 24:53-56
  • The FlyBase Consortium (1995).
    Proposed genetic nomenclature for Drosophila melanogaster.
    Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.
  • The FlyBase Consortium (1994).
    FlyBase - The Drosophila database.
    Nucleic Acids Res., 22:3456-3458
  • M. Ashburner and R. Drysdale (1994).
    FlyBase - The Drosophila genetic database.
    Development 120:2077-2079
  • M. Ashburner (1993).
    FlyBase.
    GNome News 13:19-20.