Difference between revisions of "FlyBase:About"

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The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.
 
The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.
  
Please use the contact FlyBase form to write to us.
+
Please use the [http://{{flybaseorg}}/cgi-bin/mailto-fbhelp.html contact FlyBase] form to write to us.
  
 
:'''FlyBase-Harvard'''
 
:'''FlyBase-Harvard'''
Line 10: Line 10:
 
:USA
 
:USA
  
     William Gelbart (PI)
+
     Norbert Perrimon (PI)
 +
    Susan Russo Gelbart (PD)
 +
    Julie Agapite
 
     Kris Broll
 
     Kris Broll
 
     Lynn Crosby
 
     Lynn Crosby
     Gil dos Santos
+
     Gilberto dos Santos
     David Emmert
+
     Kathleen Falls
 
     L. Sian Gramates
 
     L. Sian Gramates
     Kathleen Falls
+
     Victoria Jenkins
 +
    Ian Longden
 
     Beverley Matthews
 
     Beverley Matthews
     Susan Russo
+
     Carol Sutherland
     Andy Schroeder
+
     Christopher Tabone
    Susan St. Pierre
 
 
     Pinglei Zhou
 
     Pinglei Zhou
 
     Mark Zytkovicz
 
     Mark Zytkovicz
  
 
:'''FlyBase-Cambridge'''
 
:'''FlyBase-Cambridge'''
:Department of Genetics, University of Cambridge
+
:Department of Physiology, Development and Neuroscience, University of Cambridge
:Downing Street, Cambridge CB2 3EH
+
:Downing Street, Cambridge CB2 3DY
 
:UK
 
:UK
  
 
     Nick Brown (PI)
 
     Nick Brown (PI)
     Boris Adryan
+
     Giulia Antonazzo
 
     Helen Attrill
 
     Helen Attrill
     Marta Costa
+
     Phani Garapati
 +
    Aoife Larkin
 
     Steven Marygold
 
     Steven Marygold
    Peter McQuilton
 
 
     Gillian Millburn
 
     Gillian Millburn
     Laura Ponting
+
     Clare Pilgrim
     Ray Stefancsik
+
     Sinzi Pop
     Susan Tweedie
+
     Vitor Trovisco
 +
    Pepe Urbano
  
 
:'''FlyBase-Indiana'''
 
:'''FlyBase-Indiana'''
Line 47: Line 50:
  
 
     Thomas Kaufman (PI)
 
     Thomas Kaufman (PI)
     Kathy Matthews (PI)
+
     Brian Calvi (PI)
 
     Josh Goodman
 
     Josh Goodman
    Gary Grumbling
 
 
     Victor Strelets
 
     Victor Strelets
 
     Jim Thurmond
 
     Jim Thurmond
 +
   
  
 
:'''FlyBase-NewMexico'''
 
:'''FlyBase-NewMexico'''
Line 61: Line 64:
 
     Maggie Werner-Washburne (PI)
 
     Maggie Werner-Washburne (PI)
 
     Richard Cripps (PI)
 
     Richard Cripps (PI)
     Harriett Platero
+
     Phillip Baker
  
 
==FlyBase Publications==
 
==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).  
+
:'''2019'''
:FlyBase: improvements to the bibliography.  
+
 
:Nucleic Acids Res. 41(D1):D751-D757. [FBrf0220350]
+
:Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium. (2019)
 +
:    '''Annotation of gene product function from high-throughput studies using the Gene Ontology.'''
 +
:    [https://doi.org/10.1093/database/baz007 Database 2019 baz007]
 +
 
 +
 
 +
:Garapati  PV, Zhang J, Rey AJ and Marygold SJ (2019)
 +
:    '''Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase'''
 +
:    [https://doi.org/10.1093/database/bay144 Database 2019 bay144]
 +
 
 +
 
 +
:Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn M, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR and the FlyBase Consortium. (2019)
 +
:    '''FlyBase 2.0: the next generation.'''
 +
:    [https://doi.org/10.1093/nar/gky1003 Nucleic Acids Res. 47(D1) D759–D765]
 +
 
 +
 
 +
:The RNAcentral Consortium (2019)
 +
:    '''RNAcentral: a hub of information for non-coding RNA sequences.'''
 +
:    [https://doi.org/10.1093/nar/gky1034 Nucleic Acids Res. 47(D1) D221–D229]
 +
 
 +
 
 +
:The Gene Ontology Consortium (2019)
 +
:    '''The Gene Ontology Resource: 20 years and still GOing strong.'''
 +
:    [https://doi.org/10.1093/nar/gky1055 Nucleic Acids Res. 47(D1) D330–D338]
 +
 
 +
 
 +
:'''2018'''
 +
 
 +
:Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE and Smith C. (2018)
 +
:    '''Model organism data evolving in support of translational medicine.'''
 +
:    [https://doi.org/10.1038/s41684-018-0150-4 Lab Anim (NY) 47:277-289]
 +
 
 +
 
 +
:Rey AJ, Attrill H, Marygold SJ and The FlyBase Consortium. (2018)
 +
:    '''Using FlyBase to Find Functionally Related Drosophila Genes.'''
 +
:    [https://link.springer.com/protocol/10.1007%2F978-1-4939-7737-6_16 Eukaryotic Genomic Databases: Methods and Protocols (M. Kollmar, ed.) pp. 493-512. Springer, New York] [http://{{flybaseorg}}/reports/FBrf0238904.html (FBrf0238904)] [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996772 (PMC5996772)]
 +
 
 +
 
 +
:'''2017'''
 +
 
 +
:Hu Y, Comjean A, Mohr SE; FlyBase Consortium, Perrimon N. (2017)
 +
:    '''Gene2Function: An Integrated Online Resource for Gene Function Discovery.'''
 +
:    [https://doi.org/10.1534/g3.117.043885 G3 (Bethesda) 7(8):2855-2858] [http://{{flybaseorg}}/reports/FBrf0236248.html (FBrf0236248)]
 +
 
 +
 
 +
:The Gene Ontology Consortium. (2017)
 +
:    '''Expansion of the Gene Ontology knowledgebase and resources'''
 +
:    [https://doi.org/10.1093/nar/gkw1108 Nucleic Acids Res. 45(D1):D331-D338]
 +
 
 +
 
 +
:Gramates LS, Marygold SJ, dos Santos G, Urbano J-M, Antonazzo G, Matthews BB, Rey AJ, Tabone CJ, Crosby MA, Emmert DB, Falls K, Goodman JL, Hu Y, Ponting L, Schroeder AJ, Strelets VB, Thurmond J, Zhou P and the FlyBase Consortium. (2017)
 +
:    '''FlyBase at 25: looking to the future.'''
 +
:    [https://doi.org/10.1093/nar/gkw1016 Nucleic Acids Res. 45(D1):D663-D671] [http://{{flybaseorg}}/reports/FBrf0234415.html (FBrf0234415)]
 +
 
 +
 
 +
:Marygold SJ, Attrill H, Lasko P. (2017)
 +
:    '''The Translation Factors of Drosophila melanogaster.'''
 +
:    [https://doi.org/10.1080/19336934.2016.1220464 Fly 11(1):65-74] [http://{{flybaseorg}}/reports/FBrf0233552.html (FBrf0233552)]
 +
 
 +
 
 +
:'''2016'''
 +
 
 +
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)
 +
:    '''Exploring FlyBase Data Using QuickSearch.'''
 +
:    [https://doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]
 +
 
 +
 
 +
:Marygold SJ, Crosby MA, Goodman JL and The FlyBase Consortium. (2016)
 +
:    '''Using FlyBase, a Database of Drosophila Genes and Genomes.'''
 +
:    [https://doi.org/10.1007/978-1-4939-6371-3_1 Drosophila: Methods and Protocols, Second edition, vol. 1478 (C. Dahmann, ed.) pp. 1-31. Springer, New York] [http://{{flybaseorg}}/reports/FBrf0233766.html (FBrf0233766)] [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5107610/ (PMC5107610)]
 +
 
 +
 
 +
:Kahsai L, Millburn GH, Cook KR. (2016)
 +
:    '''Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster.'''
 +
:    [https://doi.org/10.1534/g3.116.030940 G3 (Bethesda). 6(8):2665-2670] [http://{{flybaseorg}}/reports/FBrf0233125.html (FBrf0233125)]
 +
 
 +
 
 +
:Millburn GH, Crosby MA, Gramates LS, Tweedie S; FlyBase Consortium. (2016)
 +
:    '''FlyBase portals to human disease research using Drosophila models.'''
 +
:    [https://doi.org/10.1242/dmm.023317 Dis. Model Mech. 9(3):245-252] [http://{{flybaseorg}}/reports/FBrf0231138.html (FBrf0231138)]
 +
 
 +
 
 +
:Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ; the FlyBase Consortium. (2016)
 +
:    '''FlyBase: establishing a Gene Group resource for Drosophila melanogaster.'''
 +
:    [https://doi.org/10.1093/nar/gkv1046 Nucleic Acids Res. 44(D1):D786-D792] [http://{{flybaseorg}}/reports/FBrf0230602.html (FBrf0230602)]
 +
 
 +
 
 +
:'''2015'''
 +
 
 +
:Lu J, Marygold SJ, Gharib WH and Suter B. (2015)
 +
:    '''The aminoacyl-tRNA synthetases of Drosophila melanogaster.'''
 +
:    [http://dx.doi.org/10.1080/19336934.2015.1101196 Fly 9(2):53-61] [http://{{flybaseorg}}/reports/FBrf0230668.html (FBrf0230668)]
 +
 
 +
 
 +
:Matthews BB, dos Santos G, Crosby MA, Emmert DB, St Pierre SE, Gramates LS, Zhou P, Schroeder AJ, Falls K, Strelets V, Russo SM, Gelbart WM, and the FlyBase Consortium. (2015)
 +
:    '''Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.'''
 +
:    [http://dx.doi.org/10.1534/g3.115.018929 G3 (Bethesda) 5:1721-1736] [http://{{flybaseorg}}/reports/FBrf0229216.html (FBrf0229216)]
 +
 
 +
 
 +
:Crosby MA, Gramates LS, dos Santos G, Matthews BB, St Pierre SE, Zhou P, Schroeder AJ, Falls K, Emmert DB, Russo SM, Gelbart WM., and the FlyBase Consortium. (2015)
 +
:    '''Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.'''
 +
:    [http://dx.doi.org/10.1534/g3.115.018937 G3 (Bethesda) 5:1737-1749] [http://{{flybaseorg}}/reports/FBrf0229217.html (FBrf0229217)]
 +
 
 +
 
 +
: Gene Ontology Consortium. (2015)
 +
:    '''Gene Ontology Consortium: going forward.'''
 +
:    [http://dx.doi.org/10.1093/nar/gku1179 Nucleic Acids Res. 43(Database issue):D1049-56]
 +
 
 +
 
 +
:Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)
 +
:    '''FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.'''
 +
:    [http://dx.doi.org/10.1093/nar/gku1099 Nucleic Acids Res. 43(Database issue): D690-D697] [http://{{flybaseorg}}/reports/FBrf0227324.html (FBrf0227324)]
 +
 
 +
 
 +
:'''2014'''
 +
 
 +
:Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. (2014)
 +
:    '''Representing kidney development using the gene ontology.'''
 +
:    [http://dx.doi.org/10.1371/journal.pone.0099864 PLoS One. 9(6):e99864]
 +
 
 +
 
 +
:Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. (2014)
 +
:    '''Overview of the gene ontology task at BioCreative IV.'''
 +
:    [http://dx.doi.org/10.1093/database/bau086 Database 2014. bau086]
 +
 
 +
 
 +
:Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z (2014)
 +
:    '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''
 +
:    [http://dx.doi.org/10.1093/database/bau074 Database 2014. bau074]
 +
 
 +
 
 +
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)
 +
:    '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''
 +
:    [http://dx.doi.org/10.1093/database/bau033 Database 2014. bau033]
 +
 
 +
 
 +
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)
 +
:    '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''
 +
:    [http://dx.doi.org/10.1093/nar/gkt1092 Nucleic Acids Res. 42(Database issue):D780-8] [http://{{flybaseorg}}/reports/FBrf0223749.html (FBrf0223749)]
 +
 
 +
 
 +
:'''2013'''
 +
 
 +
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)
 +
:    '''The Drosophila anatomy ontology.'''
 +
:    [http://dx.doi.org/10.1186/2041-1480-4-32 J. Biomed. Semantics 4(1):32] [http://{{flybaseorg}}/reports/FBrf0223849.html (FBrf0223849)]
 +
 
 +
 
 +
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV. (2013)
 +
:    '''The Drosophila phenotype ontology.'''
 +
:    [http://dx.doi.org/10.1186/2041-1480-4-30 J. Biomed. Semantics 4(1):30] [http://{{flybaseorg}}/reports/FBrf0223876.html (FBrf0223876)]
 +
 
 +
 
 +
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)
 +
:    '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''
 +
:   [http://dx.doi.org/10.7717/peerj.148 PeerJ. 1:e148] [http://{{flybaseorg}}/reports/FBrf0222712.html (FBrf0222712)]
 +
 
 +
 
 +
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)
 +
:    '''FlyBase: improvements to the bibliography.'''
 +
:   [http://dx.doi.org/10.1093/nar/gks1024 Nucleic Acids Res. 41(Database issue):D751-D757] [http://{{flybaseorg}}/reports/FBrf0220350.html (FBrf0220350)]
 +
 
 +
 
 +
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)
 +
:    '''Systematic analysis of experimental phenotype data reveals gene functions.'''
 +
:    [http://dx.doi.org/10.1371/journal.pone.0060847 PLoS One. 8(4):e60847] [http://{{flybaseorg}}/reports/FBrf0221415.html (FBrf0221415)]
 +
 
 +
 
 +
:Gene Ontology Consortium (2013)
 +
:    '''Gene Ontology annotations and resources.'''
 +
:    [http://dx.doi.org/10.1093/nar/gks1050 Nucleic Acids Res. 41(Database issue):D530-5.]
 +
 
  
 +
:'''2012'''
  
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013).  
+
:McQuilton P and the FlyBase Consortium (2012)
:Systematic analysis of experimental phenotype data reveals gene functions.  
+
:    '''Opportunities for text mining in the FlyBase genetic literature curation workflow.'''
:PLoS One. 8(4):e60847. PMID: 23626672
+
:   [http://dx.doi.org/10.1093/database/bas039 Database 2012:bas039] [http://{{flybaseorg}}/reports/FBrf0219955.html (FBrf0219955)]
  
  
:McQuilton P and the FlyBase Consortium (2012).
+
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)
:Opportunities for text mining in the FlyBase genetic literature curation workflow.  
+
:   '''Directly e-mailing authors of newly published papers encourages community curation.'''
:Database 2012:bas039. [FBrf0219955]
+
:   [http://dx.doi.org/10.1093/database/bas024 Database 2012:bas024] [http://{{flybaseorg}}/reports/FBrf0218522.html (FBrf0218522)]
  
  
:Gene Ontology Consortium (2012).
+
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)
:Gene Ontology annotations and resources.  
+
:   '''FlyBase 101 – the basics of navigating FlyBase.'''
:Nucleic Acids Res. 41(Database issue):D530-5. doi: 10.1093/nar/gks1050. PubMed PMID: 23161678; PubMed Central PMCID: PMC3531070.
+
:   [http://dx.doi.org/10.1093/nar/gkr1030 Nucleic Acids Res. 40 (Database issue):D706-14] [http://{{flybaseorg}}/reports/FBrf0217108.html (FBrf0217108)]
  
  
:S.M. Bunt, G.B. Grumbling, H.I. Field, S.J. Marygold, N.H. Brown, G.H. Millburn and the FlyBase Consortium (2012).
+
: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)
:Directly e-mailing authors of newly published papers encourages community curation.  
+
:   '''Automatic categorization of diverse experimental information in the bioscience literature.'''
:Database 2012; doi: 10.1093/database/bas024. [FBrf0218522]
+
:   [http://dx.doi.org/10.1186/1471-2105-13-16 BMC Bioinformatics. 13(1):16] [http://{{flybaseorg}}/reports/FBrf0218533.html (FBrf0218533)]
  
  
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012).
+
:Gene Ontology Consortium (2012)
:FlyBase 101 – the basics of navigating FlyBase.  
+
:   '''The Gene Ontology: enhancements for 2011.'''
:Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108]
+
:   [http://dx.doi.org/10.1093/nar/gkr1028 Nucleic Acids Res. 40(Database issue):D559-64]
   
+
 
 +
 
 +
:'''2011'''
 +
 
 +
:Rangarajan A, Schedl T, Yook K, Chan J, Haenel S, Otis L, Faelten S, DePellegrin‑Connelly T, Isaacson R, Skrzypek MS, Marygold SJ, Stefancsik R, Cherry JM, Sternberg PW and Müller H-M (2011)
 +
:    '''Toward an interactive article: integrating journals and biological databases.'''
 +
:    [http://dx.doi.org/10.1186/1471-2105-12-175 BMC Bioinformatics 12:175] [http://{{flybaseorg}}/reports/FBrf0214821.html (FBrf0214821)]
 +
 
 +
 
 +
:Daines, B., Wang, H., Wang, L., Li, Y., Han, Y., Emmert, D., Gelbart, W., Wang, X., Li, W., Gibbs, R., Chen, R. (2011).
 +
:    '''The Drosophila melanogaster transcriptome by paired-end RNA sequencing.'''
 +
:    [http://dx.doi.org/10.1101/gr.107854.110 Genome Res. 21(2): 315--324] [http://{{flybaseorg}}/reports/FBrf0213064.html (FBrf0213064)]
 +
 
 +
 
 +
: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.'''
 +
:    [http://dx.doi.org/10.1016/j.ydbio.2011.03.011 Dev Biol. 354(1):9-17]
 +
 
  
: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).
+
:'''2010'''
:    Automatic categorization of diverse experimental information in the bioscience literature.
 
:    BMC Bioinformatics. 13(1):16. [FBrf0218533]
 
   
 
  
:Gene Ontology Consortium (2012).
+
:Gene Ontology Consortium (2010)
:    The Gene Ontology: enhancements for 2011.
+
:    '''The Gene Ontology in 2010: extensions and refinements.'''
:    Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568; PubMed Central PMCID: PMC3245151.
+
:    [http://dx.doi.org/10.1093/nar/gkp1018 Nucleic Acids Res. 38(Database issue):D331-5]
   
 
  
: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]
 
  
 +
: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.'''
 +
:    [http://dx.doi.org/10.1093/nar/gkp910 Nucleic Acids Res. 38(Database issue):D443-7] [http://{{flybaseorg}}/reports/FBrf0209611.html (FBrf0209611)]
  
:    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.
 
  
 +
:'''2009'''
 
      
 
      
:Gene Ontology Consortium (2009).
+
:St. Pierre S and McQuilton P (2009)
:    The Gene Ontology in 2010: extensions and refinements.
+
:    '''Inside FlyBase (Biocuration as a career).'''
:    Nucleic Acids Res. 38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. PubMed PMID: 19920128; PubMed Central PMCID: PMC2808930.
+
:    [http://dx.doi.org/10.4161/fly.3.1.7769 Fly 3(1):112-114] [http://{{flybaseorg}}/reports/FBrf0213427.html (FBrf0213427)]
  
 
      
 
      
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).
+
:Reference Genome Group of the Gene Ontology Consortium (2009)
:    FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.
+
:    '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''
:    Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132; PubMed Central PMCID: PMC2808907. [FBrf0209611]
+
:    [http://dx.doi.org/10.1371/journal.pcbi.1000431 PLoS Comput Biol. 5(7):e1000431]
  
 
      
 
      
:S. St. Pierre, P. McQuilton (2009).
+
:Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi‑Sutherland D, Schroeder A, Seal R, Zhang H; FlyBase Consortium (2009)
:    Inside FlyBase (Biocuration as a career).
+
:    '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''
:    Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427]
+
:    [http://dx.doi.org/10.1093/nar/gkn788 Nucleic Acids Res. 37(Database issue):D555-D559] [http://{{flybaseorg}}/reports/FBrf0206621.html (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.'''
 +
:    [http://dx.doi.org/10.1186/1471-2105-10-59 BMC Bioinformatics. 10:59] [http://{{flybaseorg}}/reports/FBrf0207486.html (FBrf0207486)]
 
      
 
      
: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.
 
  
 +
:'''2008'''
 +
 +
:Drysdale R, and The FlyBase Consortium, (2008)
 +
:    '''FlyBase : a database for the Drosophila research community.'''
 +
:    [http://dx.doi.org/10.1007/978-1-59745-583-1_3 Methods Mol. Biol. 420: 45-59] [http://{{flybaseorg}}/reports/FBrf0205804.html (FBrf0205804)]
 
      
 
      
: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.
+
:Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, Rhee SY (2008)
:    Nucleic Acids Res. 37: D555-D559; doi:10.1093/nar/gkn788. [FBrf0206621]
+
:    '''Big data: The future of biocuration.'''
 +
:    [http://dx.doi.org/10.1038/455047a Nature 455(7209):47-50]
  
 
      
 
      
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).
+
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)
:    The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
+
:    '''Natural language processing in aid of FlyBase curators.'''
:    BMC Bioinformatics. 10:59. doi: 10.1186/1471-2105-10-59. PubMed PMID: 19210778; PubMed Central PMCID: PMC2648944. [FBrf0207486]
+
:    [http://dx.doi.org/10.1186/1471-2105-9-193 BMC Bioinformatics 9:193] [http://{{flybaseorg}}/reports/FBrf0206381.html (FBrf0206381)]
  
 
      
 
      
:R. Drysdale, and The FlyBase Consortium, (2008).
+
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)
:    FlyBase : a database for the Drosophila research community.
+
:    '''FlyBase: integration and improvements to query tools.'''
:    Methods Molec. Biol. 420: 45-59. [FBrf0205804]
+
:    [http://dx.doi.org/10.1093/nar/gkm930 Nucleic Acids Res. 36:D588-D593] [http://{{flybaseorg}}/reports/FBrf0203012.html (FBrf0203012)]
 +
   
  
 +
:'''2007'''
 +
 +
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)
 +
:    '''FlyBase: genomes by the dozen.'''
 +
:    [http://dx.doi.org/10.1093/nar/gkl827 Nucleic Acids Res. 35:D486-D491] [http://{{flybaseorg}}/reports/FBrf0194786.html (FBrf0194786)]
 
      
 
      
: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]
 
  
 +
:Drosophila 12 Genomes Consortium. (2007)
 +
:    '''Evolution of genes and genomes on the Drosophila phylogeny.'''
 +
:    [http://dx.doi.org/10.1038/nature06341 Nature 450(7167):203-218] [http://{{flybaseorg}}/reports/FBrf0200326.html (FBrf0200326)]
 +
 +
   
 +
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)
 +
:    '''Integrating natural language processing with FlyBase curation.'''
 +
:    Pac Symp Biocomput. 2007:245-56 [http://{{flybaseorg}}/reports/FBrf0206379.html (FBrf0206379)]
 
      
 
      
: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]
 
  
 +
:Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL Jr, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M.. (2007)
 +
:    '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''
 +
:    [http://dx.doi.org/10.1101/gr.6679507 Genome Res. 17(12):1823-1836] [http://{{flybaseorg}}/reports/FBrf0202906.html (FBrf0202906)]
 
      
 
      
: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]
 
  
 +
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)
 +
:    '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''
 +
:    [http://dx.doi.org/10.1093/bioinformatics/btm189 Bioinformatics 23(13):i337-346] [http://{{flybaseorg}}/reports/FBrf0201050.html (FBrf0201050)]
 
      
 
      
: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]
 
  
 +
:Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M (2007)
 +
:    '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''
 +
:    [http://dx.doi.org/10.1038/nature06340 Nature 450(7167):219-232] [http://{{flybaseorg}}/reports/FBrf0200674.html (FBrf0200674)]
 
      
 
      
:Drosophila 12 Genomes Consortium., (2007).
+
 
:    Evolution of genes and genomes on the Drosophila phylogeny.
+
:'''2006'''
:    Nature 450: 203-218. [FBrf0200326]
+
 
 +
:Grumbling G, Strelets V and The FlyBase Consortium (2006)
 +
:    '''FlyBase: anatomical data, images and queries.'''
 +
:    [http://dx.doi.org/10.1093/nar/gkj068 Nucleic Acids Res. 34:D484-D488] [http://{{flybaseorg}}/reports/FBrf0191339.html (FBrf0191339)]
 +
 
 +
 
 +
:'''2005'''
 +
 
 +
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)
 +
:    '''FlyBase : Genes and gene models.'''
 +
:    [http://dx.doi.org/10.1093/nar/gki046 Nucleic Acids Res., 33: D390-D395] [http://{{flybaseorg}}/reports/FBrf0184221.html (FBrf0184221)]
  
 
      
 
      
:N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).
+
:Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. (2005)
:    Integrating natural language processing with FlyBase curation.
+
:    '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''
:    Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]
+
:    [http://dx.doi.org/10.1101/gr.3059305 Genome Res. 15(1):1-18] [http://{{flybaseorg}}/reports/FBrf0184012.html (FBrf0184012)]
 +
   
  
 +
:Zhou P, Emmert D, Zhang P (2005)
 +
:    '''Using chado to store genome annotation data.'''
 +
:    Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [http://{{flybaseorg}}/reports/FBrf0206380.html (FBrf0206380)]
 
      
 
      
: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]
 
  
   
+
:'''2003'''
: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]
 
  
   
+
:The FlyBase Consortium, (2003)
:A. Stark et al., (2007).
+
:    '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''
:    Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
+
:    [http://dx.doi.org/10.1093/nar/gkg094 Nucleic Acids Res. 31:172-175] [http://{{flybaseorg}}/reports/FBrf0159266.html (FBrf0159266)]
:    Nature 450: 219-232. [FBrf0200674]
 
  
 
      
 
      
:G. Grumbling, V. Strelets and The FlyBase Consortium, (2006).
+
:Drysdale R (2003)
:    FlyBase: anatomical data, images and queries.
+
:    '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''
:    Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]
+
:    Briefings in Functional Genomics and Proteomics 2(2):128--134 [http://{{flybaseorg}}/reports/FBrf0167361.html (FBrf0167361)]
  
   
 
: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 )
 
  
   
+
:'''2002'''
:S. Richards et al., (2005).
+
 
:    Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
+
:Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM and Lewis SE. (2002)
:    Genome Res., 15: 1-18. [FBrf0184012]
+
:    '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''
 +
:    [http://dx.doi.org/10.1186/gb-2002-3-12-research0081 Genome Biol. 3:research0081] [http://{{flybaseorg}}/reports/FBrf0155825.html (FBrf0155825)]
 +
  
 +
:Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ and Clamp ME. (2002)
 +
:    '''Apollo: a sequence annotation editor.'''
 +
:    [http://dx.doi.org/10.1186/gb-2002-3-12-research0082 Genome Biol. 3(12):research0082] [http://{{flybaseorg}}/reports/FBrf0155826.html (FBrf0155826)]
 
      
 
      
: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]
 
  
 +
:Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfield EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey ADNJ, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM and Lewis SE. (2002)
 +
:    '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''
 +
:    [http://dx.doi.org/10.1186/gb-2002-3-12-research0083 Genome Biol. 3:research0083] [http://{{flybaseorg}}/reports/FBrf0155827.html (FBrf0155827)]
 
      
 
      
: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 )
 
  
   
+
:The FlyBase Consortium (2002)
:Rachel Drysdale, (2003).
+
:    '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''
:    The Drosophila melanogaster genome sequencing and annotation projects: A status report.
+
:    [http://dx.doi.org/10.1093/nar/30.1.106 Nucleic Acids Res. 30:106-108] [http://{{flybaseorg}}/reports/FBrf0141697.html (FBrf0141697)]
:    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)'''
+
:'''2001'''
  
 
+
:Matthews K and Cook K (2001)
::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).
+
:   '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''
::   An integrated computational pipeline and database to support whole-genome sequence annotation.
+
:    In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [http://{{flybaseorg}}/reports/FBrf0185967.html (FBrf0185967)]
::    Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]
+
   
  
 +
:Drysdale R (2001)
 +
:    '''Phenotypic data in FlyBase.'''
 +
:    Brief. Bioinform. 2(1):68-80 [http://{{flybaseorg}}/reports/FBrf0137187.html (FBrf0137187)]
 
    
 
    
::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]
 
  
 +
:'''1999'''
 +
 +
:FlyBase (1999)
 +
:    '''FlyBase: Genomic and post-genomic viewpoints.'''
 +
:    In S. Letovsky (Ed.)
 +
:    Bioinformatics: Databases and Systems 141-150 [http://{{flybaseorg}}/reports/FBrf0111589.html (FBrf0111589)]
 
      
 
      
::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.
+
:The FlyBase Consortium, (1999)
::   Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]
+
:    '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''
 +
:   [http://dx.doi.org/10.1093/nar/27.1.85 Nucleic Acids Res. 27:85-88] [http://{{flybaseorg}}/reports/FBrf0107356.html (FBrf0107356)]
  
 
      
 
      
:The FlyBase Consortium, (2002).
+
:'''1998'''
:    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 )
 
  
 +
:The FlyBase Consortium (1998)
 +
:    '''FlyBase - A Drosophila database.'''
 +
:    [http://dx.doi.org/10.1093/nar/26.1.85 Nucleic Acids Res. 26:85-88] [http://{{flybaseorg}}/reports/FBrf0100346.html (FBrf0100346)]
 
      
 
      
: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]
 
  
 +
:'''1997'''
 +
 +
:The FlyBase Consortium (1997)
 +
:    '''FlyBase - A Drosophila database.'''
 +
:    [http://dx.doi.org/10.1093/nar/25.1.63 Nucleic Acids Res. 25:63-66] [http://{{flybaseorg}}/reports/FBrf0093096.html (FBrf0093096)]
 
      
 
      
: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]
 
  
 +
:'''1996'''
 +
 +
:The FlyBase Consortium (1996)
 +
:    '''FlyBase - The Drosophila database.'''
 +
:    [http://dx.doi.org/10.1093/nar/24.1.53 Nucleic Acids Res. 24:53-56] [http://{{flybaseorg}}/reports/FBrf0085043.html (FBrf0085043)]
 
      
 
      
: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 )
 
  
   
+
:'''1995'''
:The FlyBase Consortium (1998).
+
 
:    FlyBase - A Drosophila database.
+
:The FlyBase Consortium (1995)
:    Nucleic Acids Res., 26:85-88 [FBrf0100346]
+
:    '''Proposed genetic nomenclature for Drosophila melanogaster.'''
 +
:    Trends in Genetics: Genetic Nomenclature Guide 26-29. [http://{{flybaseorg}}/reports/FBrf0078422.html (FBrf0078422)]
 +
 
 +
 
 +
:'''1994'''
  
   
+
:The FlyBase Consortium (1994)
:The FlyBase Consortium (1997).
+
:    '''FlyBase - The Drosophila database.'''
:    FlyBase - A Drosophila database.
+
:    [http://dx.doi.org/10.1093/nar/22.17.3456 Nucleic Acids Res. 22(17):3456-3458] [http://{{flybaseorg}}/reports/FBrf0077015.html (FBrf0077015)]
:    Nucleic Acids Res., 25:63-66 [FBrf0093096]
 
  
   
 
:The FlyBase Consortium (1996).
 
:    FlyBase - The Drosophila database.
 
:    Nucleic Acids Res., 24:53-56 [FBrf0085043]
 
  
   
+
:Ashburner M and Drysdale R (1994)
:The FlyBase Consortium (1995).
+
:    '''FlyBase - The Drosophila genetic database.'''
:    Proposed genetic nomenclature for Drosophila melanogaster.
+
:    Development 120:2077-2079 [http://{{flybaseorg}}/reports/FBrf0072526.html (FBrf0072526)]
:    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]
 
  
   
+
:'''1993'''
:M. Ashburner and R. Drysdale (1994).
 
:    FlyBase - The Drosophila genetic database.
 
:    Development 120:2077-2079 [FBrf0072526]
 
  
   
+
:Ashburner M (1993)
:M. Ashburner (1993).
+
:    '''FlyBase.'''
:    FlyBase.
+
:    GNome News 13:19-20 [http://{{flybaseorg}}/reports/FBrf0058642.html (FBrf0058642)]
:    GNome News 13:19-20. [FBrf0058642]
 
  
 
==Citing FlyBase==
 
==Citing FlyBase==
We suggest FlyBase be referenced in publications in the following manner:
+
 
: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]:
+
If you have used FlyBase during your research project, we urge you to cite us in your published work. We recommend that you use our latest ''Nucleic Acids Research:Database issue'' publication:
 +
:Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn M, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR and the FlyBase Consortium. (2019) '''FlyBase 2.0: the next generation.'''  [http://dx.doi.org/10.1093/nar/gky1003 Nucleic Acids Res. 47(D1) D759–D765]
 +
 
 +
 
 +
N.B. You should also state the FlyBase release (e.g. FB2018_06) used for any data obtained/analysed using FlyBase, as data content is updated with each web release. The current release number is found in the header and footer of every FlyBase page.
 +
 
 +
Information on citing genes or fly lines (alleles, deficiencies, transgenes, insertions) can be found in our [[FlyBase:Author Guidelines|Author Guidelines article]].
 +
 
 +
Please see the related '''video tutorials''' [https://www.youtube.com/watch?v=16SGlcASOL4 How to cite FlyBase] and [https://www.youtube.com/watch?v=HsoWqclXMng Author Guidelines].
 +
 
 
==FlyBase Copyright==
 
==FlyBase Copyright==
 
===The Copyright of FlyBase===
 
===The Copyright of FlyBase===
Copyright ©1993-2006 by The Genetics Society of America.
 
All Rights Reserved.
 
  
FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <ftp://flybase.net/flybase/>.
+
FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <ftp://ftp.flybase.org/>.
  
 
This publication may be copied for non-commercial, scientific uses by individuals or organizations (including for-profit organizations). FlyBase is freely distributed to the scientific community on the understanding that it will not be used for commercial gain by any organization. Any commercial use of this publication, or any parts thereof, is expressly prohibited without permission in writing from the FlyBase consortium.
 
This publication may be copied for non-commercial, scientific uses by individuals or organizations (including for-profit organizations). FlyBase is freely distributed to the scientific community on the understanding that it will not be used for commercial gain by any organization. Any commercial use of this publication, or any parts thereof, is expressly prohibited without permission in writing from the FlyBase consortium.
  
 
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.
 
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.
Warranty
+
 
 +
===Warranty===
  
 
FlyBase and the Genetics Society of America make no warranty of any kind with respect to the subject matter included herein. FlyBase and the Genetics Society of America specifically disclaim all warranties, expressed, implied or otherwise, including without limitation, all warranties of merchantability, fitness for a particular purpose, or non-infringement.
 
FlyBase and the Genetics Society of America make no warranty of any kind with respect to the subject matter included herein. FlyBase and the Genetics Society of America specifically disclaim all warranties, expressed, implied or otherwise, including without limitation, all warranties of merchantability, fitness for a particular purpose, or non-infringement.
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By viewing or using this information the user agrees that in no event shall FlyBase or the Genetics Society of America be liable for any special, incidental, indirect, or consequential damages of any kind, or any damages whatsoever, whether or not advised of the possibility of damage, arising out of or in connection with the use or performance of this information.
 
By viewing or using this information the user agrees that in no event shall FlyBase or the Genetics Society of America be liable for any special, incidental, indirect, or consequential damages of any kind, or any damages whatsoever, whether or not advised of the possibility of damage, arising out of or in connection with the use or performance of this information.
Disclaimer
 
  
Information in FlyBase is curated from the scientific literature, including unrefereed sources such as abstracts, reviews, and personal communications. With the partial exception of map data, statements of fact are not vetted by FlyBase. Users should remember that published information is not always correct information and are encouraged to use FlyBase as a guide to the literature rather than as a substitute for it.  
+
===Disclaimer===
 +
 
 +
Information in FlyBase is curated from the scientific literature, including unrefereed sources such as abstracts, reviews, and personal communications. With the partial exception of map data, statements of fact are not vetted by FlyBase. Users should remember that published information is not always correct information and are encouraged to use FlyBase as a guide to the literature rather than as a substitute for it.
  
 
===BIOSIS Copyright===
 
===BIOSIS Copyright===
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1250 Sixth Avenue, San Diego, California 92101-4311
 
1250 Sixth Avenue, San Diego, California 92101-4311
  
FlyBase is based on the information contained in Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992), however we no longer redistribute the complete text of the book.  
+
FlyBase is based on the information contained in Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992), however we no longer redistribute the complete text of the book.
 +
 
 
==FlyBase Data Sources==
 
==FlyBase Data Sources==
  
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:'''Natural transposon insertion data'''
 
:'''Natural transposon insertion data'''
 
:
 
:
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]
+
:[http://{{flybaseorg}}/reports/FBrf0155828.html Kaminker J. et al. 2002]
 
:
 
:
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]
+
:[http://{{flybaseorg}}/reports/FBrf0184336.html Quesneville H. et al. 2005]
  
 
'''Stock Lists Submitted to FlyBase'''
 
'''Stock Lists Submitted to FlyBase'''
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FlyBase thanks these former members of the FlyBase consortium for their contribution:
 
FlyBase thanks these former members of the FlyBase consortium for their contribution:
  
 +
    Boris Adryan
 
     Manish Anand
 
     Manish Anand
 
     Michael Ashburner
 
     Michael Ashburner
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     Russell Collins
 
     Russell Collins
 
     Kim Cook
 
     Kim Cook
 +
    Marta Costa
 +
    Bryon Czoch
 
     Anthony DeAngelo
 
     Anthony DeAngelo
 
     Aubrey de Grey
 
     Aubrey de Grey
 
     Rachel Drysdale
 
     Rachel Drysdale
 +
    David Emmert
 +
    Silvie Fexova
 
     Helen Field
 
     Helen Field
 
     Rebecca Foulger
 
     Rebecca Foulger
 
     Erwin Frise
 
     Erwin Frise
 +
    William Gelbart
 
     Mark Gibson
 
     Mark Gibson
 
     Don Gilbert
 
     Don Gilbert
 +
    Gary Grumbling
 
     Janet Gulotta
 
     Janet Gulotta
 
     Cyrus Harmon
 
     Cyrus Harmon
 
     Nomi Harris
 
     Nomi Harris
 
     Gregg Helt
 
     Gregg Helt
 +
    Alex Holmes
 
     Pavel Hradecky
 
     Pavel Hradecky
 
     Yanmei Huang
 
     Yanmei Huang
 +
    Tamsin Jones
 
     Josh Kaminker
 
     Josh Kaminker
 
     Kerry Knight
 
     Kerry Knight
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     Guo-chun Liao
 
     Guo-chun Liao
 
     Anne Loraine
 
     Anne Loraine
 +
    Kathy Matthews
 
     Glenn McAlpine
 
     Glenn McAlpine
 +
    Peter McQuilton
 
     John Merriam
 
     John Merriam
 
     Sima Misra
 
     Sima Misra
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     David Osumi-Sutherland
 
     David Osumi-Sutherland
 
     Dawn Palmer
 
     Dawn Palmer
 +
    Harriet Platero
 +
    Laura Ponting
 
     Simon Prochnik
 
     Simon Prochnik
 
     Simon Reeve
 
     Simon Reeve
 +
    Alix Rey
 
     John Richter
 
     John Richter
 
     Wayne Rindone
 
     Wayne Rindone
 
     Margo Roark
 
     Margo Roark
 
     Gerry Rubin
 
     Gerry Rubin
 +
    Susan St. Pierre
 +
    Andrew Schroeder
 
     Ruth Seal
 
     Ruth Seal
 
     Carolyn Shemen
 
     Carolyn Shemen
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     Chris Smith
 
     Chris Smith
 
     Frank Smutniak
 
     Frank Smutniak
 +
    Nicole Staudt
 +
    Ray Stefancsik
 
     Jon Tupy
 
     Jon Tupy
 +
    Susan Tweedie
 
     Edwin Wang
 
     Edwin Wang
 
     Eddy Wellbourne
 
     Eddy Wellbourne
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==FlyBase Support==
 
==FlyBase Support==
 
FlyBase is supported by a grant from the National Human Genome Research Institute at the
 
FlyBase is supported by a grant from the National Human Genome Research Institute at the
U.S. National Institutes of Health #P41 HG000739.
+
U.S. National Institutes of Health [https://projectreporter.nih.gov/project_info_description.cfm?aid=9043157&icde=30422530 #U41 HG000739].
 
 
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.
 
  
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.
+
Support is also provided by the British Medical Research Council ([http://gtr.rcuk.ac.uk/projects?ref=MR%2FN030117%2F1 #MR/N030117/1]) and [[FlyBase:List_of_Contributors|FlyBase Users]] all over the world.
  
 
[[Category:FlyBase]]
 
[[Category:FlyBase]]
 +
[[Category:DONE]]

Latest revision as of 12:07, 6 June 2019

FlyBase Consortium

The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.

Please use the contact FlyBase form to write to us.

FlyBase-Harvard
Biological Laboratories, Harvard University
16 Divinity Avenue
Cambridge, Massachusetts 02138
USA
   Norbert Perrimon (PI)
   Susan Russo Gelbart (PD)
   Julie Agapite
   Kris Broll
   Lynn Crosby
   Gilberto dos Santos
   Kathleen Falls
   L. Sian Gramates
   Victoria Jenkins
   Ian Longden
   Beverley Matthews
   Carol Sutherland
   Christopher Tabone
   Pinglei Zhou
   Mark Zytkovicz
FlyBase-Cambridge
Department of Physiology, Development and Neuroscience, University of Cambridge
Downing Street, Cambridge CB2 3DY
UK
   Nick Brown (PI)
   Giulia Antonazzo
   Helen Attrill
   Phani Garapati
   Aoife Larkin
   Steven Marygold
   Gillian Millburn
   Clare Pilgrim
   Sinzi Pop
   Vitor Trovisco
   Pepe Urbano
FlyBase-Indiana
Department of Biology, Indiana University
1001 East 3rd Street
Bloomington, Indiana 47405-7005
USA
   Thomas Kaufman (PI)
   Brian Calvi (PI)
   Josh Goodman
   Victor Strelets
   Jim Thurmond
   
FlyBase-NewMexico
Department of Biology, Castetter Hall - Room 200
University of New Mexico,
Albuquerque, New Mexico 87131
USA
   Maggie Werner-Washburne (PI)
   Richard Cripps (PI)
   Phillip Baker

FlyBase Publications

2019
Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium. (2019)
Annotation of gene product function from high-throughput studies using the Gene Ontology.
Database 2019 baz007


Garapati PV, Zhang J, Rey AJ and Marygold SJ (2019)
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase
Database 2019 bay144


Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn M, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR and the FlyBase Consortium. (2019)
FlyBase 2.0: the next generation.
Nucleic Acids Res. 47(D1) D759–D765


The RNAcentral Consortium (2019)
RNAcentral: a hub of information for non-coding RNA sequences.
Nucleic Acids Res. 47(D1) D221–D229


The Gene Ontology Consortium (2019)
The Gene Ontology Resource: 20 years and still GOing strong.
Nucleic Acids Res. 47(D1) D330–D338


2018
Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE and Smith C. (2018)
Model organism data evolving in support of translational medicine.
Lab Anim (NY) 47:277-289


Rey AJ, Attrill H, Marygold SJ and The FlyBase Consortium. (2018)
Using FlyBase to Find Functionally Related Drosophila Genes.
Eukaryotic Genomic Databases: Methods and Protocols (M. Kollmar, ed.) pp. 493-512. Springer, New York (FBrf0238904) (PMC5996772)


2017
Hu Y, Comjean A, Mohr SE; FlyBase Consortium, Perrimon N. (2017)
Gene2Function: An Integrated Online Resource for Gene Function Discovery.
G3 (Bethesda) 7(8):2855-2858 (FBrf0236248)


The Gene Ontology Consortium. (2017)
Expansion of the Gene Ontology knowledgebase and resources
Nucleic Acids Res. 45(D1):D331-D338


Gramates LS, Marygold SJ, dos Santos G, Urbano J-M, Antonazzo G, Matthews BB, Rey AJ, Tabone CJ, Crosby MA, Emmert DB, Falls K, Goodman JL, Hu Y, Ponting L, Schroeder AJ, Strelets VB, Thurmond J, Zhou P and the FlyBase Consortium. (2017)
FlyBase at 25: looking to the future.
Nucleic Acids Res. 45(D1):D663-D671 (FBrf0234415)


Marygold SJ, Attrill H, Lasko P. (2017)
The Translation Factors of Drosophila melanogaster.
Fly 11(1):65-74 (FBrf0233552)


2016
Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)
Exploring FlyBase Data Using QuickSearch.
Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23 (FBrf0234167)


Marygold SJ, Crosby MA, Goodman JL and The FlyBase Consortium. (2016)
Using FlyBase, a Database of Drosophila Genes and Genomes.
Drosophila: Methods and Protocols, Second edition, vol. 1478 (C. Dahmann, ed.) pp. 1-31. Springer, New York (FBrf0233766) (PMC5107610)


Kahsai L, Millburn GH, Cook KR. (2016)
Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster.
G3 (Bethesda). 6(8):2665-2670 (FBrf0233125)


Millburn GH, Crosby MA, Gramates LS, Tweedie S; FlyBase Consortium. (2016)
FlyBase portals to human disease research using Drosophila models.
Dis. Model Mech. 9(3):245-252 (FBrf0231138)


Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ; the FlyBase Consortium. (2016)
FlyBase: establishing a Gene Group resource for Drosophila melanogaster.
Nucleic Acids Res. 44(D1):D786-D792 (FBrf0230602)


2015
Lu J, Marygold SJ, Gharib WH and Suter B. (2015)
The aminoacyl-tRNA synthetases of Drosophila melanogaster.
Fly 9(2):53-61 (FBrf0230668)


Matthews BB, dos Santos G, Crosby MA, Emmert DB, St Pierre SE, Gramates LS, Zhou P, Schroeder AJ, Falls K, Strelets V, Russo SM, Gelbart WM, and the FlyBase Consortium. (2015)
Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.
G3 (Bethesda) 5:1721-1736 (FBrf0229216)


Crosby MA, Gramates LS, dos Santos G, Matthews BB, St Pierre SE, Zhou P, Schroeder AJ, Falls K, Emmert DB, Russo SM, Gelbart WM., and the FlyBase Consortium. (2015)
Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.
G3 (Bethesda) 5:1737-1749 (FBrf0229217)


Gene Ontology Consortium. (2015)
Gene Ontology Consortium: going forward.
Nucleic Acids Res. 43(Database issue):D1049-56


Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.
Nucleic Acids Res. 43(Database issue): D690-D697 (FBrf0227324)


2014
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. (2014)
Representing kidney development using the gene ontology.
PLoS One. 9(6):e99864


Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. (2014)
Overview of the gene ontology task at BioCreative IV.
Database 2014. bau086


Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z (2014)
BC4GO: a full-text corpus for the BioCreative IV GO Task.
Database 2014. bau074


Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Database 2014. bau033


St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)
FlyBase 102 - advanced approaches to interrogating FlyBase.
Nucleic Acids Res. 42(Database issue):D780-8 (FBrf0223749)


2013
Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)
The Drosophila anatomy ontology.
J. Biomed. Semantics 4(1):32 (FBrf0223849)


Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV. (2013)
The Drosophila phenotype ontology.
J. Biomed. Semantics 4(1):30 (FBrf0223876)


Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)
On the reproducibility of science: unique identification of research resources in the biomedical literature.
PeerJ. 1:e148 (FBrf0222712)


Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)
FlyBase: improvements to the bibliography.
Nucleic Acids Res. 41(Database issue):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 (FBrf0221415)


Gene Ontology Consortium (2013)
Gene Ontology annotations and resources.
Nucleic Acids Res. 41(Database issue):D530-5.


2012
McQuilton P and the FlyBase Consortium (2012)
Opportunities for text mining in the FlyBase genetic literature curation workflow.
Database 2012:bas039 (FBrf0219955)


Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)
Directly e-mailing authors of newly published papers encourages community curation.
Database 2012: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


2011
Rangarajan A, Schedl T, Yook K, Chan J, Haenel S, Otis L, Faelten S, DePellegrin‑Connelly T, Isaacson R, Skrzypek MS, Marygold SJ, Stefancsik R, Cherry JM, Sternberg PW and Müller H-M (2011)
Toward an interactive article: integrating journals and biological databases.
BMC Bioinformatics 12:175 (FBrf0214821)


Daines, B., Wang, H., Wang, L., Li, Y., Han, Y., Emmert, D., Gelbart, W., Wang, X., Li, W., Gibbs, R., Chen, R. (2011).
The Drosophila melanogaster transcriptome by paired-end RNA sequencing.
Genome Res. 21(2): 315--324 (FBrf0213064)


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


2010
Gene Ontology Consortium (2010)
The Gene Ontology in 2010: extensions and refinements.
Nucleic Acids Res. 38(Database issue):D331-5


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 (FBrf0209611)


2009
St. Pierre S and McQuilton P (2009)
Inside FlyBase (Biocuration as a career).
Fly 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


Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi‑Sutherland D, Schroeder A, Seal R, Zhang H; FlyBase Consortium (2009)
FlyBase: enhancing Drosophila Gene Ontology annotations.
Nucleic Acids Res. 37(Database issue):D555-D559 (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 (FBrf0207486)


2008
Drysdale R, and The FlyBase Consortium, (2008)
FlyBase : a database for the Drosophila research community.
Methods Mol. Biol. 420: 45-59 (FBrf0205804)


Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, Rhee SY (2008)
Big data: The future of biocuration.
Nature 455(7209):47-50


Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)
Natural language processing in aid of FlyBase curators.
BMC Bioinformatics 9:193 (FBrf0206381)


Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)
FlyBase: integration and improvements to query tools.
Nucleic Acids Res. 36:D588-D593 (FBrf0203012)


2007
Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)
FlyBase: genomes by the dozen.
Nucleic Acids Res. 35:D486-D491 (FBrf0194786)


Drosophila 12 Genomes Consortium. (2007)
Evolution of genes and genomes on the Drosophila phylogeny.
Nature 450(7167):203-218 (FBrf0200326)


Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)
Integrating natural language processing with FlyBase curation.
Pac Symp Biocomput. 2007:245-56 (FBrf0206379)


Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL Jr, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M.. (2007)
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
Genome Res. 17(12):1823-1836 (FBrf0202906)


Mungall CJ, Emmert DB and the FlyBase Consortium (2007)
A Chado case study: an ontology-based modular schema for representing genome-associated biological information.
Bioinformatics 23(13):i337-346 (FBrf0201050)


Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M (2007)
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Nature 450(7167):219-232 (FBrf0200674)


2006
Grumbling G, Strelets V and The FlyBase Consortium (2006)
FlyBase: anatomical data, images and queries.
Nucleic Acids Res. 34:D484-D488 (FBrf0191339)


2005
Drysdale RA, Crosby MA and the FlyBase Consortium (2005)
FlyBase : Genes and gene models.
Nucleic Acids Res., 33: D390-D395 (FBrf0184221)


Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. (2005)
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
Genome Res. 15(1):1-18 (FBrf0184012)


Zhou P, Emmert D, Zhang P (2005)
Using chado to store genome annotation data.
Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. (FBrf0206380)


2003
The FlyBase Consortium, (2003)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 31:172-175 (FBrf0159266)


Drysdale R (2003)
The Drosophila melanogaster genome sequencing and annotation projects: A status report.
Briefings in Functional Genomics and Proteomics 2(2):128--134 (FBrf0167361)


2002
Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM and Lewis SE. (2002)
An integrated computational pipeline and database to support whole-genome sequence annotation.
Genome Biol. 3:research0081 (FBrf0155825)


Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ and Clamp ME. (2002)
Apollo: a sequence annotation editor.
Genome Biol. 3(12):research0082 (FBrf0155826)


Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfield EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey ADNJ, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM and Lewis SE. (2002)
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
Genome Biol. 3:research0083 (FBrf0155827)


The FlyBase Consortium (2002)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 30:106-108 (FBrf0141697)


2001
Matthews K and Cook K (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)


Drysdale R (2001)
Phenotypic data in FlyBase.
Brief. Bioinform. 2(1):68-80 (FBrf0137187)


1999
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 (FBrf0107356)


1998
The FlyBase Consortium (1998)
FlyBase - A Drosophila database.
Nucleic Acids Res. 26:85-88 (FBrf0100346)


1997
The FlyBase Consortium (1997)
FlyBase - A Drosophila database.
Nucleic Acids Res. 25:63-66 (FBrf0093096)


1996
The FlyBase Consortium (1996)
FlyBase - The Drosophila database.
Nucleic Acids Res. 24:53-56 (FBrf0085043)


1995
The FlyBase Consortium (1995)
Proposed genetic nomenclature for Drosophila melanogaster.
Trends in Genetics: Genetic Nomenclature Guide 26-29. (FBrf0078422)


1994
The FlyBase Consortium (1994)
FlyBase - The Drosophila database.
Nucleic Acids Res. 22(17):3456-3458 (FBrf0077015)


Ashburner M and Drysdale R (1994)
FlyBase - The Drosophila genetic database.
Development 120:2077-2079 (FBrf0072526)


1993
Ashburner M (1993)
FlyBase.
GNome News 13:19-20 (FBrf0058642)

Citing FlyBase

If you have used FlyBase during your research project, we urge you to cite us in your published work. We recommend that you use our latest Nucleic Acids Research:Database issue publication:

Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn M, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR and the FlyBase Consortium. (2019) FlyBase 2.0: the next generation. Nucleic Acids Res. 47(D1) D759–D765


N.B. You should also state the FlyBase release (e.g. FB2018_06) used for any data obtained/analysed using FlyBase, as data content is updated with each web release. The current release number is found in the header and footer of every FlyBase page.

Information on citing genes or fly lines (alleles, deficiencies, transgenes, insertions) can be found in our Author Guidelines article.

Please see the related video tutorials How to cite FlyBase and Author Guidelines.

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The Copyright of FlyBase

FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <ftp://ftp.flybase.org/>.

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Disclaimer

Information in FlyBase is curated from the scientific literature, including unrefereed sources such as abstracts, reviews, and personal communications. With the partial exception of map data, statements of fact are not vetted by FlyBase. Users should remember that published information is not always correct information and are encouraged to use FlyBase as a guide to the literature rather than as a substitute for it.

BIOSIS Copyright

The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:

"This database is copyrighted by Biological Abstracts Inc. (BIOSIS®). All rights reserved. No part of the information may be reproduced in hard copy, machine-readable form or other form without advance written permission from BIOSIS. Information has been obtained from public sources believed to be reliable. BIOSIS makes a diligent effort to provide complete and accurate representation of the bioscientific and other literature in its publications and services. However, BIOSIS does not guarantee the accuracy, adequacy, or completeness of any information and BIOSIS makes no warranties or representations of any kind, express or implied, including but not limited to warranties of merchantability or fitness for particular purpose. BIOSIS disclaims all liability for errors or omissions that may exist and shall not be liable for any incidental, consequential or other damages (whether resulting from negligence or otherwise) including, without limitation, exemplary damages or lost profits arising out of or in connection with the use of this database. Errors or omissions may be reported to Biological Abstracts Inc., 2100 Arch Street, Philadelphia, PA 19103-1399."

Herskowitz's Bibliography Copyright

The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:

"Bibliography on the genetics of Drosophila: Part 5, by Irwin H. Herskowitz is reproduced with the permission of Macmillan Publishing Company. Copyright ©1969 by Macmillan Publishing Company. "

"Bibliography on the genetics of Drosophila: Part 6, by Irwin H. Herskowitz is reproduced with the permission of Macmillan Publishing Company. Copyright ©1974 by Macmillan Publishing Company."

Lindsley and Zimm (1992)

Lindsley and Zimm (1992) - The New Redbook The Genome of Drosophila melanogaster Dan L. Lindsley & Georgianna G. Zimm Copyright 1992 By Academic Press, Inc. All Rights Reserved.

ISBN 0-12-450990-8 Academic Press, Inc. 1250 Sixth Avenue, San Diego, California 92101-4311

FlyBase is based on the information contained in Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992), however we no longer redistribute the complete text of the book.

FlyBase Data Sources

The Red Book

Lindsley and Zimm (1992) The Genome of Drosophila melanogaster

Bibliographies

The major sources that have been incorporated into the FlyBase Bibliography:

Bibliography from The Genetics of Drosophila. T. H. Morgan, C. B. Bridges and A. H. Sturtevant, 1925. Bibliographica Genetica II: 1-262. 'S-Gravenhage, Martinus Nijhoff.
Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.
Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.
Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.
Commonwealth Agricultural Bureaux. Slough: Farnham Royal.
Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.
Indiana University Publications.
Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.
McGraw-Hill Book Company, Inc.
Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.
Macmillan Publishing Company, Inc.
Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.
Macmillan Publishing Company, Inc.
Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.
Drosophila Information Service 51: 159-193.
Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.
Drosophila Information Service 52:186-226.
Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.
Drosophila Information Service 53: 219-244.
Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.
Drosophila Information Service 55: 218-262.
Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.
Drosophila Information Service 56: 199-210.
Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.
Drosophila Information Service 58: 227-270.
Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.
Drosophila Information Service 59: 163-207.
Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).
Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.
Drosophila Information Service 40: 105-126.
Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.
Drosophila Information Service: 58: 215-226.
Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.
Drosophila Information Service 66: 198-208.
Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.
Drosophila Information Service 70: 110-117.
Bibliography on Drosophila ananassae. B. N. Singh, 1991.
Drosophila Information Service 70: 205-211.
The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.
Dowden, Hutchinson and Ross Publications, Inc.
Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).
M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.
In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.
Blackie Publications. Glasgow, Scotland.
End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.
A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).
January 1993 with regular subsequent updates.
References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.
Japan Scientific Societies Press and Karger, Tokyo and Basel.
References from the Environmental Mutagen Information Center (EMIC) database.
MEDLINE (National Library of Medicine, Washington).
Searched on the Text Word DROSOPHIL. Searched from 1966 to date.
BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.
References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.
References from John Merriam's Genevent database of molecular data.
Drosophila records from the Zoological Record, volume 115 (1978) to 2008.
Jeff Hall's bibliography on neurogenetics of Drosophila.

External Databases

Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ) UniProtKB InterPro

Journal Articles and Books

Publications relevant to Drosophila from various journals and books.

Drosophila Conference Abstracts

The following abstracts were curated until 2008.

GSA Annual Drosophila Research Conference Abstracts

European Drosophila Research Conference Abstracts

Personal Communications to FlyBase

Information and observations provided by the Fly Community

Direct Submission of High-Throughput Data

Proteomics data
Center for Model Organism Proteomes --
(SystemsX and Research Priority Project of the University of Zurich, Switzerland)
Microarrays (Oligos, cDNAs)
Affymetrix, Santa Clara, CA (Affy v1, Affy v2)
Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)
Tiling BACs
Berkeley Drosophila Genome Project

Insertion Collection Data

Transgene insertion data
Gene Disruption Project (2005 - present)(Bellen et. al., 2004)
Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)
DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)
P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)
P{GawB} Project, GETDB, Japan (2002 - 2004)
NCI lethals (2002 - 2004)(Oh et. al., 2003)
P{GT1} Project, Ed Ryder, Cambridge, UK (2004)
Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)
Natural transposon insertion data
Kaminker J. et al. 2002
Quesneville H. et al. 2005

Stock Lists Submitted to FlyBase

Bloomington Drosophila Stock Center

Drosophila Genetic Resource Center

UC San Diego Drosophila Species Stock Center

Exelixis Drosophila Stock Collection at Harvard Medical School

Nusslein-Volhard laboratory

Garcia-Bellido laboratory

Carpenter laboratory

People

The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.

An e-mail address list compiled and maintained by Dr. John Haynie (1992)

Records of the Bloomington Drosophila Stock Center (1992)

The distribution list of Drosophila Information Newsletter (1992)

A subset of the Genetics Society of America's mailing and membership list (1992)

The mailing list for the European Drosophila Research Conference (1992)

FlyBase Alumni

FlyBase thanks these former members of the FlyBase consortium for their contribution:

   Boris Adryan
   Manish Anand
   Michael Ashburner
   Leyla Bayraktaroglu
   Ben Berman
   Brian Bettencourt
   Lee Bitsoi
   Pete Brokstein
   Stephanie Bunt
   Heather Butler
   Kathy Campbell
   Russell Collins
   Kim Cook
   Marta Costa
   Bryon Czoch
   Anthony DeAngelo
   Aubrey de Grey
   Rachel Drysdale
   David Emmert
   Silvie Fexova
   Helen Field
   Rebecca Foulger
   Erwin Frise
   William Gelbart
   Mark Gibson
   Don Gilbert
   Gary Grumbling
   Janet Gulotta
   Cyrus Harmon
   Nomi Harris
   Gregg Helt
   Alex Holmes
   Pavel Hradecky
   Yanmei Huang
   Tamsin Jones
   Josh Kaminker
   Kerry Knight
   Sophia Kossida
   Rob Kulathinal
   Julia Lamenza
   Joe Lemaire
   Stan Letovsky
   Suzanna Lewis
   Paul Leyland
   Guo-chun Liao
   Anne Loraine
   Kathy Matthews
   Glenn McAlpine
   Peter McQuilton
   John Merriam
   Sima Misra
   Emanuel Mongin
   Chris Mungall
   Tatiana Murnikova
   Catherine Nelson
   David Osumi-Sutherland
   Dawn Palmer
   Harriet Platero
   Laura Ponting
   Simon Prochnik
   Simon Reeve
   Alix Rey
   John Richter
   Wayne Rindone
   Margo Roark
   Gerry Rubin
   Susan St. Pierre
   Andrew Schroeder
   Ruth Seal
   Carolyn Shemen
   Hardik Sheth
   Nihar Sheth
   Shengqiang Shu
   David Simas
   Chris Smith
   Frank Smutniak
   Nicole Staudt
   Ray Stefancsik
   Jon Tupy
   Susan Tweedie
   Edwin Wang
   Eddy Wellbourne
   Eleanor Whitfield
   Colin Wiel
   Mark Williams
   Robert Wilson
   J.D. Wong
   Chihiro Yamada
   Mark Yandell
   Haiyan Zhang
   Peili Zhang

FlyBase Support

FlyBase is supported by a grant from the National Human Genome Research Institute at the U.S. National Institutes of Health #U41 HG000739.

Support is also provided by the British Medical Research Council (#MR/N030117/1) and FlyBase Users all over the world.