FlyBase:About

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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 thecontact 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)   Kris Broll   Lynn Crosby   Gil dos Santos   L. Sian Gramates   Victoria Jenkins   Ian Longden   Beverley Matthews   Carol Sutherland   Christopher J. Tabone   Pinglei Zhou   Mark Zytkovicz
FlyBase-Cambridge
Department of Physiology, Development and Neuroscience, University of Cambridge
Downing Street, Cambridge CB2 3DY
UK
   Nick Brown (Co-PI)   Katja Röper (Co-PI)   Giulia Antonazzo   Helen Attrill   Damien Goutte-Gattat   Aoife Larkin   Steven Marygold   Alex McLachlan   Gillian Millburn   Arzu Öztürk-Çolak   Clare Pilgrim   Rossana Zaru
FlyBase-Indiana
Department of Biology, Indiana University
1001 East 3rd Street
Bloomington, Indiana 47405-7005
USA
   Brian Calvi (Co-PI)   Seth Campbell   Josh Goodman   Victor Strelets   Jim Thurmond
FlyBase-New Mexico
Department of Biology, Castetter Hall - Room 200
University of New Mexico,
Albuquerque, New Mexico 87131
USA
   Richard Cripps (Co-PI)   TyAnna Lovato

FlyBase Publications

2025
Feuermann M, Mi H, Gaudet P, Muruganujan A, Lewis SE, Ebert D, Mushayahama T, Gene Ontology Consortium and Thomas PD (2025)
A compendium of human gene functions derived from evolutionary modelling.
NatureDOI:10.1038/s41586-025-08592-0


Zaru R and Marygold SJ (2025)
In silico identification and analysis of paralogs encoding enzymes of carbohydrate metabolism in Drosophila melanogaster.
MicroPubl Biol. 001425DOI:10.17912/micropub.biology.001425FBrf0261725


2024
Antonazzo G, Gaudet P, Lovering RC, Attrill H (2024)
Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology.
RNA Biol. 21(1) 36–48DOI:10.1080/15476286.2024.2408523


Marygold SJ (2024)
The alpha-ketoacid dehydrogenase complexes of Drosophila melanogaster.
MicroPubl Biol. 001209DOI:10.17912/micropub.biology.001209FBrf0259508


Alliance of Genome Resources Consortium (2024)
Updates to the Alliance of Genome Resources Central Infrastructure.
Genetics 227(1) iyae049DOI:10.1093/genetics/iyae049FBrf0259417


Sklias A, Cruciani S, Marchand V, Spagnuolo M, Lavergne G, Bourguignon V, Brambilla A, Dreos R, Marygold SJ, Novoa EM, Motorin Y, Roignant JY (2024)
Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster.
Nucleic Acids Res 52(6) 2848-2864DOI:10.1093/nar/gkae139FBrf0259352


Öztürk-Çolak A, Marygold SJ, Antonazzo G, Attrill H, Goutte-Gattat D, Jenkins VK, Matthews BB, Millburn G, dos Santos G, Tabone CJ, the FlyBase Consortium (2024)
FlyBase: updates to the Drosophila genes and genomes database.
Genetics 227(1) iyad211DOI:10.1093/genetics/iyad211FBrf0259457


Attrill H, Antonazzo G, Goodman JL, Thurmond J, Strelets VB, Brown NH; FlyBase Consortium (2024)
A new experimental evidence-weighted signaling pathway resource in FlyBase.
Development 151(3) dev202255DOI:10.1242/dev.202255FBrf0258673


2023
Attrill H (2023)
Comparing the history of signalling pathway research using the research publication record of representative genes.
MicroPubl Biol. 000998DOI:10.17912/micropub.biology.000998FBrf0258056


Gene Ontology Consortium (2023)
The Gene Ontology knowledgebase in 2023.
Genetics 224(1) iyad031.DOI:10.1093/genetics/iyad031


Hu Y, Comjean A, Attrill H, Antonazzo G, Thurmond J, Chen W, Li F, Chao T, Mohr SE, Brown NH, Perrimon N. (2023)
PANGEA: a new gene set enrichment tool for Drosophila and common research organisms.
Nucleic Acids Res 51(W1) W419--WW426.DOI:10.1093/nar/gkad331FBrf0256969


Marygold SJ and the FlyBase Consortium (2023)
Exploring FlyBase Data Using QuickSearch (Updated protocol)
Current Protocols 3:e731.DOI:10.1002/cpz1.731FBrf0256232


Court R, Costa M, Pilgrim C, Millburn G, Holmes A, McLachlan A, Larkin A, Matentzoglu N, Kir H, Parkinson H, Brown NH, O'Kane CJ, Armstrong JD, Jefferis GSXE, Osumi-Sutherland D. (2023)
Virtual Fly Brain-An interactive atlas of the Drosophila nervous system.
Front Physiol. 14:1076533.DOI:10.3389/fphys.2023.1076533FBrf0255719


2022
Jenkins VK, Larkin A, Thurmond J; FlyBase Consortium. (2022)
Using FlyBase: A Database of Drosophila Genes and Genetics.
Methods Mol Biol. 2540:1-34.DOI:10.1007/978-1-0716-2541-5_1FBrf0254317


Trovisco V (2022)
Featured Resource: FlyBase.
The Node: Resources


Marygold SJ, Chan PP, Lowe TM (2022)
Systematic identification of tRNA genes in Drosophila melanogaster.
MicroPubl Biol. 000560DOI:10.17912/micropub.biology.000560FBrf0253514


Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, dos Santos G, Goodman JL, Goutte-Gattat D, Jenkins VK, Kaufman T, Larkin A, Matthews BB, Millburn G, Strelets VB and the FlyBase Consortium (2022)
FlyBase: A guided tour of highlighted features.
Genetics 220(4) iyac035DOI:10.1093/genetics/iyac035FBrf0253076


Alliance of Genome Resources Consortium (2022)
Harmonizing model organism data in the Alliance of Genome Resources.
Genetics 220(4) iyac022DOI:10.1093/genetics/iyac022FBrf0253213


Liu Y, Li JSS, Rodiger J, Comjean A, Attrill H, Antonazzo G, Brown NH, Hu Y, Perrimon N (2022)
FlyPhoneDB: An integrated web-based resource for cell-cell communication prediction in Drosophila.
Genetics 220(3) iyab235DOI:10.1093/genetics/iyab235FBrf0252867


2021
Meyer H, Buhr A, Callaerts P, Schiemann R, Wolfner MF, Marygold SJ (2021)
Identification and bioinformatic analysis of neprilysin and neprilysin-like metalloendopeptidases in Drosophila melanogaster.
MicroPubl Biol. 000410DOI:10.17912/micropub.biology.000410FBrf0249415


Hu Y, Tattikota SG, Liu Y, Comjean A, Gao Y, Forman C, Kim G, Rodiger J, Papatheodorou I, Dos Santos G, Mohr SE, Perrimon N (2021)
DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.
Comput Struct Biotechnol J 19:2018-2026.DOI:10.1016/j.csbj.2021.04.021FBrf0249044


Ahn SJ and Marygold SJ (2021)
The UDP-Glycosyltransferase Family in Drosophila melanogaster: Nomenclature Update, Gene Expression and Phylogenetic Analysis.
Front Physiol 12 648481DOI:10.3389/fphys.2021.648481FBrf0248570


The Gene Ontology Consortium (2021)
The Gene Ontology resource: enriching a GOld mine.
Nucleic Acids Res. 49(D1) D325–D334DOI:10.1093/nar/gkaa1113FBrf0247877


Larkin A, Marygold SJ, Antonazzo G, Attrill H, dos Santos G, Garapati PV, Goodman JL, Gramates LS, Millburn G, Strelets VB, Tabone CJ, Thurmond J and the FlyBase Consortium (2021)
FlyBase: updates to the Drosophila melanogaster knowledge base.
Nucleic Acids Res. 49(D1) D899–D907DOI:10.1093/nar/gkaa1026FBrf0247700


RNAcentral Consortium (2021)
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
Nucleic Acids Res. 49(D1) D212–D220DOI:10.1093/nar/gkaa921


2020
Marygold SJ, Alic N, Gilmour DS, Grewal SS (2020)
In silico identification of Drosophila melanogaster genes encoding RNA polymerase subunits.
MicroPubl Biol. 000320DOI:10.17912/micropub.biology.000320FBrf0247389


Wood V, Carbon S, Harris MA, Lock A, Engel SR, Hill DP, Van Auken K, Attrill H, Feuermann M, Gaudet P, Lovering RC, Poux S, Rutherford KM and Mungall CJ (2020)
Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.
Open Biol 10(9) 200149DOI:10.1098/rsob.200149


Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, the Alliance of Genome Resources (2020)
Automated generation of gene summaries at the Alliance of Genome Resources.
Database 2020 baaa037DOI:10.1093/database/baaa037


Antonazzo G, Urbano JM, Marygold SJ, Millburn GH and Brown NH (2020)
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation.
Database 2020 baz152DOI:10.1093/database/baz152FBrf0244633


Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y and Yamaguchi M (2020)
The DNA polymerases of Drosophila melanogaster.
Fly 14(1-4) 49-61DOI:10.1080/19336934.2019.1710076FBrf0245686


The Alliance of Genome Resources Consortium (2020)
Alliance of Genome Resources Portal: unified model organism research platform.
Nucleic Acids Res 48(D1) D650–D658DOI:10.1093/nar/gkz813FBrf0245774


2019
The Alliance of Genome Resources (2019)
Building a Modern Data Ecosystem for Model Organism Databases.
Genetics 213(4):1189-1196DOI:10.1534/genetics.119.302523FBrf0244239


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 baz007DOI:10.1093/database/baz007


Garapati PV, Zhang J, Rey AJ and Marygold SJ (2019)
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase
Database 2019 bay144DOI:10.1093/database/bay144FBrf0241253


Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn G, 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–D765DOI:10.1093/nar/gky1003FBrf0241170


The RNAcentral Consortium (2019)
RNAcentral: a hub of information for non-coding RNA sequences.
Nucleic Acids Res. 47(D1) D221–D229DOI:10.1093/nar/gky1034


The Gene Ontology Consortium (2019)
The Gene Ontology Resource: 20 years and still GOing strong.
Nucleic Acids Res. 47(D1) D330–D338DOI:10.1093/nar/gky1055


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) 47:277-289DOI:10.1038/s41684-018-0150-4FBrf0241113


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 YorkDOI:10.1007%2F978-1-4939-7737-6_16FBrf0238904


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):2855-2858DOI:10.1534/g3.117.043885FBrf0236248


The Gene Ontology Consortium. (2017)
Expansion of the Gene Ontology knowledgebase and resources
Nucleic Acids Res. 45(D1):D331-D338DOI:10.1093/nar/gkw1108


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-D671DOI:10.1093/nar/gkw1016FBrf0234415


Marygold SJ, Attrill H, Lasko P. (2017)
The Translation Factors of Drosophila melanogaster.
Fly 11(1):65-74DOI:10.1080/19336934.2016.1220464FBrf0233552


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 56:1.31.1-1.31.23DOI:10.1002/cpbi.19FBrf0234167


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 YorkDOI:10.1007/978-1-4939-6371-3_1FBrf0233766)


Kahsai L, Millburn GH, Cook KR. (2016)
Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster.
G3 (Bethesda). 6(8):2665-2670DOI:10.1534/g3.116.030940FBrf0233125


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):245-252DOI:10.1242/dmm.023317FBrf0231138


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-D792DOI:10.1093/nar/gkv1046FBrf0230602


2015
Lu J, Marygold SJ, Gharib WH and Suter B. (2015)
The aminoacyl-tRNA synthetases of Drosophila melanogaster.
Fly 9(2):53-61DOI:10.1080/19336934.2015.1101196FBrf0230668


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) 5:1721-1736DOI:10.1534/g3.115.018929FBrf0229216


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) 5:1737-1749DOI:10.1534/g3.115.018937FBrf0229217


Gene Ontology Consortium. (2015)
Gene Ontology Consortium: going forward.
Nucleic Acids Res. 43(Database issue):D1049-56DOI:10.1093/nar/gku1179


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-D697DOI:10.1093/nar/gku1099FBrf0227324


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):e99864DOI:10.1371/journal.pone.0099864


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. bau086DOI:10.1093/database/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. bau074DOI:10.1093/database/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. bau033DOI:10.1093/database/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):D780-8DOI:10.1093/nar/gkt1092FBrf0223749


2013
Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)
The Drosophila anatomy ontology.
J. Biomed. Semantics 4(1):32DOI:10.1186/2041-1480-4-32FBrf0223849


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):30DOI:10.1186/2041-1480-4-30FBrf0223876


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:e148DOI:10.7717/peerj.148FBrf0222712


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-D757DOI:10.1093/nar/gks1024FBrf0220350


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):e60847DOI:10.1371/journal.pone.0060847FBrf0221415


Gene Ontology Consortium (2013)
Gene Ontology annotations and resources.
Nucleic Acids Res. 41(Database issue):D530-5.DOI:10.1093/nar/gks1050


2012
McQuilton P and the FlyBase Consortium (2012)
Opportunities for text mining in the FlyBase genetic literature curation workflow.
Database 2012:bas039DOI:10.1093/database/bas039FBrf0219955


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:bas024DOI:10.1093/database/bas024FBrf0218522


McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)
FlyBase 101 – the basics of navigating FlyBase.
Nucleic Acids Res. 40 (Database issue):D706-14DOI:10.1093/nar/gkr1030FBrf0217108


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):16DOI:10.1186/1471-2105-13-1FBrf0218533


Gene Ontology Consortium (2012)
The Gene Ontology: enhancements for 2011.
Nucleic Acids Res. 40(Database issue):D559-64DOI:10.1093/nar/gkr1028


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 12:175DOI:10.1186/1471-2105-12-175FBrf0214821


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--324DOI:10.1101/gr.107854.110FBrf0213064


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):9-17DOI:10.1016/j.ydbio.2011.03.011


2010
Gene Ontology Consortium (2010)
The Gene Ontology in 2010: extensions and refinements.
Nucleic Acids Res. 38(Database issue):D331-5DOI:10.1093/nar/gkp1018


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):D443-7DOI:10.1093/nar/gkp910FBrf0209611


2009
St. Pierre S and McQuilton P (2009)
Inside FlyBase (Biocuration as a career).
Fly 3(1):112-114DOI:10.4161/fly.3.1.7769FBrf0213427


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):e1000431DOI:10.1371/journal.pcbi.1000431


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-D559DOI:10.1093/nar/gkn788FBrf0206621


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. 10:59DOI:10.1186/1471-2105-10-59FBrf0207486


2008
Drysdale R, and The FlyBase Consortium, (2008)
FlyBase : a database for the Drosophila research community.
Methods Mol. Biol. 420: 45-59DOI:10.1007/978-1-59745-583-1_3FBrf0205804


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):47-50DOI:10.1038/455047a


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 9:193DOI:10.1186/1471-2105-9-193FBrf0206381


Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)
FlyBase: integration and improvements to query tools.
Nucleic Acids Res. 36:D588-D593DOI:10.1093/nar/gkm930FBrf0203012


2007
Marygold SJ, Roote J, Reuter G, Lambertsson A, Ashburner M, Millburn GH, Harrison PM, Yu Z, Kenmochi N, Kaufman TC, Leevers SJ, Cook KR (2017)
The ribosomal protein genes and Minute loci of Drosophila melanogaster.
Genome Biol. 2007;8(10):R216.DOI:10.1186/gb-2007-8-10-r216FBrf0205398


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-D491DOI:10.1093/nar/gkl827FBrf0194786


Drosophila 12 Genomes Consortium. (2007)
Evolution of genes and genomes on the Drosophila phylogeny.
Nature 450(7167):203-218DOI:10.1038/nature06341FBrf0200326


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


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):1823-1836DOI:10.1101/gr.6679507FBrf0202906


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):i337-346DOI:10.1093/bioinformatics/btm189FBrf0201050


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):219-232DOI:10.1038/nature06340FBrf0200674


2006
Grumbling G, Strelets V and The FlyBase Consortium (2006)
FlyBase: anatomical data, images and queries.
Nucleic Acids Res. 34:D484-D488DOI:10.1093/nar/gkj068FBrf0191339


2005
Drysdale RA, Crosby MA and the FlyBase Consortium (2005)
FlyBase : Genes and gene models.
Nucleic Acids Res., 33: D390-D395DOI:10.1093/nar/gki046FBrf0184221


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):1-18DOI:10.1101/gr.3059305FBrf0184012


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.DOI:10.1002/0471250953.bi0906s12FBrf0206380


2003
The FlyBase Consortium, (2003)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 31:172-175DOI:10.1093/nar/gkg094FBrf0159266


Drysdale R (2003)
The Drosophila melanogaster genome sequencing and annotation projects: A status report.
Briefings in Functional Genomics and Proteomics 2(2):128--134DOI:10.1093/bfgp/2.2.128FBrf0167361


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:research0081DOI:10.1186/gb-2002-3-12-research0081FBrf0155825


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):research0082DOI:10.1186/gb-2002-3-12-research0082FBrf0155826


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:research0083DOI:10.1186/gb-2002-3-12-research0083FBrf0155827


The FlyBase Consortium (2002)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 30:106-108DOI:10.1093/nar/30.1.106FBrf0141697


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):68-80DOI:10.1093/bib/2.1.68FBrf0137187


1999
FlyBase (1999)
FlyBase: Genomic and post-genomic viewpoints.
In S. Letovsky (Ed.) Bioinformatics: Databases and Systems 141-150FBrf0111589


The FlyBase Consortium, (1999)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 27:85-88DOI:10.1093/nar/27.1.85FBrf0107356


1998
The FlyBase Consortium (1998)
FlyBase - A Drosophila database.
Nucleic Acids Res. 26:85-88DOI:10.1093/nar/26.1.85FBrf0100346


1997
The FlyBase Consortium (1997)
FlyBase - A Drosophila database.
Nucleic Acids Res. 25:63-66DOI:10.1093/nar/25.1.63FBrf0093096


1996
The FlyBase Consortium (1996)
FlyBase - The Drosophila database.
Nucleic Acids Res. 24:53-56DOI:10.1093/nar/24.1.53FBrf0085043


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):3456-3458DOI:10.1093/nar/22.17.3456FBrf0077015


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


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

FlyBase Mission Statement

The aim of the FlyBase project is to provide an openly accessible centralized resource for Drosophila genetic, genomic and functional data.

FlyBase Licenses and Availability

FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <https://s3ftp.flybase.org/index.html>.

FlyBase software is made available under either theMIT License (Expat) or theBSD 3-Clause.

All annotations and data produced by FlyBase that are accessible from flybase.org are distributed under aCreative Commons Attribution 4.0 International License (CC BY 4.0). Different licensing and copyright terms may apply for data provided by these resources that are not distributed by FlyBase.

FlyBase adheres to the principle of full and unfettered data access to FlyBase data for the entire scientific community, and is a member ofFAIRsharing. FlyBase is also is registered at there3data.org repository and is anELIXIR-UK service.

We are now members of theGlobal Biodata Coalition and our application is under review withCore Trust Seal.

The primary means of disseminating FlyBase data is through our web site (https://flybase.org) which provides an interface with many options for browsing, interrogating and manipulating FlyBase data according to the needs of the user. In addition, the web site links to an S3 ftp site containing all FlyBase data in a variety of formats, including various sequence formats, archival data, and the entire FlyBase Chado database.

All FlyBase data are available for download to other resources without restriction. In addition to our web site, FlyBase shares data with other major genetic / genomic resources. Most notable among these are NCBI and UniProt. FlyBase is the authority source for data on D. melanogaster and provides files (including whole genome annotation GenBank submissions to NCBI) that are used to generate reference files such as RefSeq. D. melanogaster GenBank/RefSeq submissions are updated annually, and power users are encouraged to use these stable annotation sets in their analyses.

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.

The information contained in this publication is subject to change without notice.

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.

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 RedbookThe Genome of Drosophila melanogasterDan L. Lindsley & Georgianna G. ZimmCopyright 1992 By Academic Press, Inc.All Rights Reserved.

ISBN 0-12-450990-8Academic 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). Searching all fields with the text word DROSOPHIL* or MELANOGASTER. 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)UniProtKBInterPro

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 AbstractsEuropean 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   Julie Agapite   Manish Anand   Michael Ashburner   Phill Baker   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   Kathleen Falls   Silvie Fexova   Helen Field   Rebecca Foulger   Erwin Frise   Phani Garapati   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   Thomas Kaufman   Kerry Knight   Sophia Kossida   Pravija Krishna   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   Sinzi Pop   Simon Prochnik   Simon Reeve   Alix Rey   John Richter   Wayne Rindone   Margo Roark   Gerry Rubin   Susan St. Pierre   Andrew Schroeder   Ruth Seal   Jolene Seme   Carolyn Shemen   Hardik Sheth   Nihar Sheth   Shengqiang Shu   David Simas   Chris Smith   Frank Smutniak   Nicole Staudt   Ray Stefancsik   Vitor Trovisco   Jon Tupy   Susan Tweedie   Jose Maria Urbano   Edwin Wang   Eddy Wellbourne   Maggie Werner-Washburne   Eleanor Whitfield   Colin Wiel   Mark Williams   Robert Wilson   J.D. Wong   Chihiro Yamada   Mark Yandell   Haiyan Zhang   Peili Zhang

Grants Supporting FlyBase

1. "FlyBase: A Drosophila Genomic and Genetic Database"NHGRI Award #:U24HG013300

2. "GO annotation: maximizing the potential of Drosophila research to benefit human health"UK Medical Research Council Award #:MR/W024233/1

3. "BBSRC-NSF/BIO: Integrative analysis and Visualisation of Fly Cell Atlas datasets to enable cross-species comparisons" NSF Award #:2035515BBSRC Award #:BB/T014008/1

4. “Virtual Fly Brain”Wellcome Trust Award #:PLM13398

5. "Sustaining FlyBase: The Drosophila genomic and genetic database.“ NSF Award #:2039324

6. "Alliance Central: A Platform for sustainable development of next generation genome knowledgebases"NHGRI Award #:U24HG010859

7. "Investigating metabolic responses to high sugar diets and the onset of diabetic phenotypes"NIDDK Award #:1R01DK136945-01

8.FlyBase Users all over the world

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