Difference between revisions of "FlyBase:About"
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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: | 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: | ||
− | :Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby M, dos Santos G Goodman JL, Goutte-Gattat D, Jenkins V, Kaufman T, Larkin A, Matthews B, Millburn G, Strelets VB, and the FlyBase Consortium (2022) '''FlyBase: a guided tour of highlighted features.''' [https://academic.oup.com/genetics/article/220/4/iyac035/6546290 | + | :Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby M, dos Santos G Goodman JL, Goutte-Gattat D, Jenkins V, Kaufman T, Larkin A, Matthews B, Millburn G, Strelets VB, and the FlyBase Consortium (2022) '''FlyBase: a guided tour of highlighted features.''' [https://academic.oup.com/genetics/article/220/4/iyac035/6546290 Genetics, Volume 220, Issue 4, April 2022, iyac035] |
N.B. You should also state the FlyBase release (e.g. FB2022_03) 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. | N.B. You should also state the FlyBase release (e.g. FB2022_03) 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. |
Revision as of 01:44, 14 June 2022
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) Kris Broll Lynn Crosby Gil dos Santos Kathleen Falls L. Sian Gramates Victoria Jenkins Ian Longden Beverley Matthews Jolene Seme 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) Giulia Antonazzo Helen Attrill Damien Goutte-Gattat Aoife Larkin Steven Marygold Alex McLachlan Gillian Millburn Arzu Ozturk-Colak Clare Pilgrim Vitor Trovisco
- FlyBase-Indiana
- Department of Biology, Indiana University
- 1001 East 3rd Street
- Bloomington, Indiana 47405-7005
- USA
Thomas Kaufman (Co-PI) Brian Calvi (Co-PI) Josh Goodman Victor Strelets Jim Thurmond Pravija Krishna
- FlyBase-NewMexico
- Department of Biology, Castetter Hall - Room 200
- University of New Mexico,
- Albuquerque, New Mexico 87131
- USA
Richard Cripps (Co-PI) TyAnna Lovato
FlyBase Publications
- 2022
- Marygold SJ, Chan PP, Lowe TM (2022)
- Systematic identification of tRNA genes in Drosophila melanogaster.
- MicroPubl Biol. 000560 DOI:10.17912/micropub.biology.000560
- 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) iyac035 DOI:10.1093/genetics/iyac035
- Alliance of Genome Resources Consortium (2022)
- Harmonizing model organism data in the Alliance of Genome Resources.
- Genetics 220(4) iyac022 DOI:10.1093/genetics/iyac022
- 2021
- Liu Y, Li JSS, Rodiger J, Comjean A, Attrill H, Antonazzo G, Brown NH, Hu Y, Perrimon N (2021)
- FlyPhoneDB: An integrated web-based resource for cell-cell communication prediction in Drosophila.
- Genetics 220(3) iyab235 DOI:10.1093/genetics/iyab235
- 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. 000410 DOI:10.17912/micropub.biology.000410 FBrf0249415
- 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 648481 DOI:10.3389/fphys.2021.648481FBrf0248570
- The Gene Ontology Consortium (2021)
- The Gene Ontology resource: enriching a GOld mine.
- Nucleic Acids Res. 49(D1) D325–D334 DOI:10.1093/nar/gkaa1113 FBrf0247877
- 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–D907 DOI:10.1093/nar/gkaa1026 FBrf0247700
- RNAcentral Consortium (2021)
- RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
- Nucleic Acids Res. 49(D1) D212–D220 DOI: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. 000320 DOI:10.17912/micropub.biology.000320 FBrf0247389
- 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) 200149 DOI: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 baaa037 DOI: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 baz152 DOI:10.1093/database/baz152 FBrf0244633
- 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) 49-61 DOI:10.1080/19336934.2019.1710076 FBrf0245686
- The Alliance of Genome Resources Consortium (2020)
- Alliance of Genome Resources Portal: unified model organism research platform.
- Nucleic Acids Res 48(D1) D650–D658 DOI:10.1093/nar/gkz813 FBrf0245774
- 2019
- The Alliance of Genome Resources (2019)
- Building a Modern Data Ecosystem for Model Organism Databases.
- Genetics 213(4):1189-1196 DOI:10.1534/genetics.119.302523 FBrf0244239
- 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 DOI: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 bay144 DOI:10.1093/database/bay144 FBrf0241253
- 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–D765 DOI:10.1093/nar/gky1003 FBrf0241170
- The RNAcentral Consortium (2019)
- RNAcentral: a hub of information for non-coding RNA sequences.
- Nucleic Acids Res. 47(D1) D221–D229 DOI: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–D338 DOI: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) 47:277-289 DOI:10.1038/s41684-018-0150-4 FBrf0241113
- 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 DOI:10.1007%2F978-1-4939-7737-6_16 FBrf0238904
- 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 DOI:10.1534/g3.117.043885 FBrf0236248
- The Gene Ontology Consortium. (2017)
- Expansion of the Gene Ontology knowledgebase and resources
- Nucleic Acids Res. 45(D1):D331-D338 DOI: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-D671 DOI:10.1093/nar/gkw1016 FBrf0234415
- Marygold SJ, Attrill H, Lasko P. (2017)
- The Translation Factors of Drosophila melanogaster.
- Fly 11(1):65-74 DOI:10.1080/19336934.2016.1220464 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 DOI:10.1002/cpbi.19 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 DOI:10.1007/978-1-4939-6371-3_1 FBrf0233766)
- Kahsai L, Millburn GH, Cook KR. (2016)
- Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster.
- G3 (Bethesda). 6(8):2665-2670 DOI:10.1534/g3.116.030940 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 DOI:10.1242/dmm.023317 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 DOI:10.1093/nar/gkv1046 FBrf0230602
- 2015
- Lu J, Marygold SJ, Gharib WH and Suter B. (2015)
- The aminoacyl-tRNA synthetases of Drosophila melanogaster.
- Fly 9(2):53-61 DOI:10.1080/19336934.2015.1101196 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 DOI:10.1534/g3.115.018929 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 DOI:10.1534/g3.115.018937 FBrf0229217
- Gene Ontology Consortium. (2015)
- Gene Ontology Consortium: going forward.
- Nucleic Acids Res. 43(Database issue):D1049-56 DOI: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-D697 DOI:10.1093/nar/gku1099 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 DOI: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. bau086 DOI: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. bau074 DOI: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. bau033 DOI: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):D780-8 DOI:10.1093/nar/gkt1092 FBrf0223749
- 2013
- Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)
- The Drosophila anatomy ontology.
- J. Biomed. Semantics 4(1):32 DOI:10.1186/2041-1480-4-32 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 DOI:10.1186/2041-1480-4-30 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 DOI:10.7717/peerj.148 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 DOI:10.1093/nar/gks1024 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 DOI:10.1371/journal.pone.0060847 FBrf0221415
- 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:bas039 DOI:10.1093/database/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 DOI:10.1093/database/bas024 FBrf0218522
- McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)
- FlyBase 101 – the basics of navigating FlyBase.
- Nucleic Acids Res. 40 (Database issue):D706-14 DOI:10.1093/nar/gkr1030 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 DOI:10.1186/1471-2105-13-1 FBrf0218533
- Gene Ontology Consortium (2012)
- The Gene Ontology: enhancements for 2011.
- Nucleic Acids Res. 40(Database issue):D559-64 DOI: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 12:175 DOI:10.1186/1471-2105-12-175 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 DOI:10.1101/gr.107854.110 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 DOI: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):D331-5 DOI: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):D443-7 DOI:10.1093/nar/gkp910 FBrf0209611
- 2009
- St. Pierre S and McQuilton P (2009)
- Inside FlyBase (Biocuration as a career).
- Fly 3(1):112-114 DOI:10.4161/fly.3.1.7769 FBrf0213427
- Reference Genome Group of the Gene Ontology Consortium (2009)
- The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
- PLoS Comput Biol. 5(7):e1000431 DOI:10.1371/journal.pcbi.1000431
- 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 DOI:10.1093/nar/gkn788 FBrf0206621
- Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)
- The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
- BMC Bioinformatics. 10:59 DOI:10.1186/1471-2105-10-59 FBrf0207486
- 2008
- Drysdale R, and The FlyBase Consortium, (2008)
- FlyBase : a database for the Drosophila research community.
- Methods Mol. Biol. 420: 45-59 DOI:10.1007/978-1-59745-583-1_3 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 DOI: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 9:193 DOI:10.1186/1471-2105-9-193 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 DOI:10.1093/nar/gkm930 FBrf0203012
- 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-r216 FBrf0205398
- 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 DOI:10.1093/nar/gkl827 FBrf0194786
- Drosophila 12 Genomes Consortium. (2007)
- Evolution of genes and genomes on the Drosophila phylogeny.
- Nature 450(7167):203-218 DOI:10.1038/nature06341 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 DOI:10.1101/gr.6679507 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 DOI:10.1093/bioinformatics/btm189 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 DOI:10.1038/nature06340 FBrf0200674
- 2006
- Grumbling G, Strelets V and The FlyBase Consortium (2006)
- FlyBase: anatomical data, images and queries.
- Nucleic Acids Res. 34:D484-D488 DOI:10.1093/nar/gkj068 FBrf0191339
- 2005
- Drysdale RA, Crosby MA and the FlyBase Consortium (2005)
- FlyBase : Genes and gene models.
- Nucleic Acids Res., 33: D390-D395 DOI:10.1093/nar/gki046 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 DOI:10.1101/gr.3059305 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. DOI:10.1002/0471250953.bi0906s12 FBrf0206380
- 2003
- The FlyBase Consortium, (2003)
- The FlyBase Database of the Drosophila Genome Projects and community literature.
- Nucleic Acids Res. 31:172-175 DOI:10.1093/nar/gkg094 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 DOI:10.1093/bfgp/2.2.128 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 DOI:10.1186/gb-2002-3-12-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 DOI:10.1186/gb-2002-3-12-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 DOI:10.1186/gb-2002-3-12-research0083 FBrf0155827
- The FlyBase Consortium (2002)
- The FlyBase Database of the Drosophila Genome Projects and community literature.
- Nucleic Acids Res. 30:106-108 DOI:10.1093/nar/30.1.106 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 DOI:10.1093/bib/2.1.68 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 DOI:10.1093/nar/27.1.85 FBrf0107356
- 1998
- The FlyBase Consortium (1998)
- FlyBase - A Drosophila database.
- Nucleic Acids Res. 26:85-88 DOI:10.1093/nar/26.1.85 FBrf0100346
- 1997
- The FlyBase Consortium (1997)
- FlyBase - A Drosophila database.
- Nucleic Acids Res. 25:63-66 DOI:10.1093/nar/25.1.63 FBrf0093096
- 1996
- The FlyBase Consortium (1996)
- FlyBase - The Drosophila database.
- Nucleic Acids Res. 24:53-56 DOI:10.1093/nar/24.1.53 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 DOI:10.1093/nar/22.17.3456 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:
- Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby M, dos Santos G Goodman JL, Goutte-Gattat D, Jenkins V, Kaufman T, Larkin A, Matthews B, Millburn G, Strelets VB, and the FlyBase Consortium (2022) FlyBase: a guided tour of highlighted features. Genetics, Volume 220, Issue 4, April 2022, iyac035
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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.
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). 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) 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 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 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 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 Sinzi Pop 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 Carol Sutherland 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
FlyBase Support
1. "FlyBase: A Drosophila Genomic and Genetic Database" NHGRI Award #: (U41HG000739)
2. "Making connections with GO: an integrative approach to highlighting medically relevant Drosophila dataBritish Medical Research Council" Medical Research Council Award #: MR/N030117
3. "BBSRC-NSF/BIO: Integrative analysis and Visualisation of Fly Cell Atlas datasets to enable cross-species comparisons" NSF Award # DBI-2035515 BBSRC, London Award #: BB/T014008
4. “Virtual Fly Brain” Wellcome Trust, London 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 databases" NGHRI Award #: S454486
7. FlyBase Users all over the world