Difference between revisions of "FlyBase:About"

Latest revision as of 14:17, 15 October 2024

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
   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)
   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

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) 36–48 DOI:10.1080/15476286.2024.2408523

Marygold SJ (2024)

The alpha-ketoacid dehydrogenase complexes of Drosophila melanogaster.

MicroPubl Biol. 001209 DOI:10.17912/micropub.biology.001209 FBrf0259508

Alliance of Genome Resources Consortium (2024)

Updates to the Alliance of Genome Resources Central Infrastructure.

Genetics 227(1) iyae049 DOI:10.1093/genetics/iyae049 FBrf0259417

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) 2848-2864 DOI:10.1093/nar/gkae139 FBrf0259352

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) iyad211 DOI:10.1093/genetics/iyad211 FBrf0259457

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) dev202255 DOI:10.1242/dev.202255 FBrf0258673

2023

Attrill H (2023)

Comparing the history of signalling pathway research using the research publication record of representative genes.

MicroPubl Biol. 000998 DOI:10.17912/micropub.biology.000998 FBrf0258056

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/gkad331 FBrf0256969

Marygold SJ and the FlyBase Consortium (2023)

Exploring FlyBase Data Using QuickSearch (Updated protocol)

Current Protocols 3:e731. DOI:10.1002/cpz1.731 FBrf0256232

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.2023.1076533 FBrf0255719

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_1 FBrf0254317

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. 000560 DOI:10.17912/micropub.biology.000560 FBrf0253514

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 FBrf0253076

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 FBrf0253213

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) iyab235 DOI:10.1093/genetics/iyab235 FBrf0252867

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. 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.2021.04.021 FBrf0249044

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.2021.648481 FBrf0248570

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

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 <ftp://ftp.flybase.org/>.

FlyBase software is made available under either the MIT License (Expat) or the BSD 3-Clause.

All annotations and data produced by FlyBase that are accessible from flybase.org are distributed under a Creative 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 of FAIRsharing. FlyBase is also is registered at the re3data.org repository and is an ELIXIR-UK service.

We are now members of the Global Biodata Coalition and our application is under review with Core Trust Seal.

The primary means of disseminating FlyBase data is through our web site (http://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 our 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:

Lindsley and Zimm (1992)

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
   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 #: 2035515 BBSRC 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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FlyBase Consortium

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