Literature DB >> 33219682

FlyBase: updates to the Drosophila melanogaster knowledge base.

Aoife Larkin1, Steven J Marygold1, Giulia Antonazzo1, Helen Attrill1, Gilberto Dos Santos2, Phani V Garapati1, Joshua L Goodman3, L Sian Gramates2, Gillian Millburn1, Victor B Strelets3, Christopher J Tabone2, Jim Thurmond3.   

Abstract

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID： 33219682      PMCID： PMC7779046          DOI： 10.1093/nar/gkaa1026

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  36 in total

1.  Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes.

Authors:  Andreas Heger; Chris P Ponting
Journal:  Genome Res       Date:  2007-11-07       Impact factor: 9.043

2.  Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase.

Authors:  Phani V Garapati; Jingyao Zhang; Alix J Rey; Steven J Marygold
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

3.  Automatic categorization of diverse experimental information in the bioscience literature.

Authors:  Ruihua Fang; Gary Schindelman; Kimberly Van Auken; Jolene Fernandes; Wen Chen; Xiaodong Wang; Paul Davis; Mary Ann Tuli; Steven J Marygold; Gillian Millburn; Beverley Matthews; Haiyan Zhang; Nick Brown; William M Gelbart; Paul W Sternberg
Journal:  BMC Bioinformatics       Date:  2012-01-26       Impact factor: 3.169

4.  Directly e-mailing authors of newly published papers encourages community curation.

Authors:  Stephanie M Bunt; Gary B Grumbling; Helen I Field; Steven J Marygold; Nicholas H Brown; Gillian H Millburn
Journal:  Database (Oxford)       Date:  2012-05-02       Impact factor: 3.451

5.  KEGG: new perspectives on genomes, pathways, diseases and drugs.

Authors:  Minoru Kanehisa; Miho Furumichi; Mao Tanabe; Yoko Sato; Kanae Morishima
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

6.  The developmental proteome of Drosophila melanogaster.

Authors:  Nuria Casas-Vila; Alina Bluhm; Sergi Sayols; Nadja Dinges; Mario Dejung; Tina Altenhein; Dennis Kappei; Benjamin Altenhein; Jean-Yves Roignant; Falk Butter
Journal:  Genome Res       Date:  2017-04-05       Impact factor: 9.043

7.  Tissue-specific (ts)CRISPR as an efficient strategy for in vivo screening in Drosophila.

Authors:  Hagar Meltzer; Efrat Marom; Idan Alyagor; Oded Mayseless; Victoria Berkun; Netta Segal-Gilboa; Tamar Unger; David Luginbuhl; Oren Schuldiner
Journal:  Nat Commun       Date:  2019-05-08       Impact factor: 14.919

8.  Human Disease Ontology 2018 update: classification, content and workflow expansion.

Authors:  Lynn M Schriml; Elvira Mitraka; James Munro; Becky Tauber; Mike Schor; Lance Nickle; Victor Felix; Linda Jeng; Cynthia Bearer; Richard Lichenstein; Katharine Bisordi; Nicole Campion; Brooke Hyman; David Kurland; Connor Patrick Oates; Siobhan Kibbey; Poorna Sreekumar; Chris Le; Michelle Giglio; Carol Greene
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

9.  JBrowse: a dynamic web platform for genome visualization and analysis.

Authors:  Robert Buels; Eric Yao; Colin M Diesh; Richard D Hayes; Monica Munoz-Torres; Gregg Helt; David M Goodstein; Christine G Elsik; Suzanna E Lewis; Lincoln Stein; Ian H Holmes
Journal:  Genome Biol       Date:  2016-04-12       Impact factor: 13.583

10.  FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data.

Authors:  David P Leader; Sue A Krause; Aniruddha Pandit; Shireen A Davies; Julian A T Dow
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971
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  133 in total

1.  Labeling and Tracking Mitochondria with Photoactivation in Drosophila Embryos.

Authors:  Sayali Chowdhary; Richa Rikhy
Journal:  Bio Protoc       Date:  2022-03-05

Review 2.  A simple guide to de novo transcriptome assembly and annotation.

Authors:  Venket Raghavan; Louis Kraft; Fantin Mesny; Linda Rigerte
Journal:  Brief Bioinform       Date:  2022-03-10       Impact factor: 11.622

Review 3.  Building RNA-protein germ granules: insights from the multifaceted functions of DEAD-box helicase Vasa/Ddx4 in germline development.

Authors:  Caoling Xu; Yuzhu Cao; Jianqiang Bao
Journal:  Cell Mol Life Sci       Date:  2021-12-18       Impact factor: 9.261

4.  A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster.

Authors:  Kundan Kumar; Amol Mhetre; Girish S Ratnaparkhi; Siddhesh S Kamat
Journal:  Biochemistry       Date:  2021-04-07       Impact factor: 3.162

5.  Drosophila NSD deletion induces developmental anomalies similar to those seen in Sotos syndrome 1 patients.

Authors:  Saeyan Choi; Bokyeong Song; Hyewon Shin; Chihyun Won; Taejoon Kim; Hideki Yoshida; Daewon Lee; Jongkyeong Chung; Kyoung Sang Cho; Im-Soon Lee
Journal:  Genes Genomics       Date:  2021-04-17       Impact factor: 1.839

6.  Recurrent NFIA K125E substitution represents a loss-of-function allele: Sensitive in vitro and in vivo assays for nontruncating alleles.

Authors:  Tomoko Uehara; Rikako Sanuki; Yurie Ogura; Atsushi Yokoyama; Takeshi Yoshida; Hiroshi Futagawa; Hiroshi Yoshihashi; Mamiko Yamada; Hisato Suzuki; Toshiki Takenouchi; Kohei Matsubara; Hiromi Hirata; Kenjiro Kosaki; Toshiyuki Takano-Shimizu
Journal:  Am J Med Genet A       Date:  2021-05-11       Impact factor: 2.802

7.  Combined Transcriptomic and Proteomic Analysis of Perk Toxicity Pathways.

Authors:  Rebeka Popovic; Ivana Celardo; Yizhou Yu; Ana C Costa; Samantha H Y Loh; L Miguel Martins
Journal:  Int J Mol Sci       Date:  2021-04-27       Impact factor: 5.923

8.  Complex Genetic Interactions between Piwi and HP1a in the Repression of Transposable Elements and Tissue-Specific Genes in the Ovarian Germline.

Authors:  Artem A Ilyin; Anastasia D Stolyarenko; Nikolay Zenkin; Mikhail S Klenov
Journal:  Int J Mol Sci       Date:  2021-12-14       Impact factor: 5.923

9.  Genetic mapping and phenotypic analysis of shotH.3.2 in Drosophila melanogaster.

Authors:  Elyse M Talley; Charlie T Watts; Sonia Aboyer; Madeline G Adamson; Harriet Ab Akoto; Haley Altemus; Philip J Avella; Rebecca Bailey; Elizabeth R Bell; Katheryn L Bell; Kelsey Breneman; Jessica S Burkhart; Logan J Chanley; Savannah S Cook; Mackenzie T DesLaurier; Timothy R Dorsey; Cassandra J Doyle; Merris E Egloff; Ayoola S Fasawe; Katy K Garcia; Nathaniel P Graves; Tyler K Gray; Evan M Gustafson; Makayla J Hall; Jaden D Hayes; Lindsay J Holic; Brice A Jarvis; Piotr S Klos; Sidney Kritzmire; Lera Kuzovko; Edwyna Lainez; Shamerra McCoy; James C Mierendorf; Nicole A Neri; Caley R Neville; Kelley Osborn; Kaitlyn Parker; Megan E Parks; Kylee Peck; Robyn Pitt; Matthew E Platta; Brianna Powell; Katalina Rodriguez; Clara Ruiz; Mariah N Schaefer; Amanda B Shields; Jasmine B Smiley; Briona Stauffer; Devan Straub; John L Sweeney; Kaitlyn M Termine; Brett Thomas; Sophia D Toth; Taylor R Veile; Kayla S Walker; Paige N Webster; Brian J Woodard; Quentin L Yoder; McKenzie K Young; McKenzie L Zeedyk; Logan N Ziegler; Kayla L Bieser; David P Puthoff; Joyce Stamm; Alysia D Vrailas-Mortimer; Jacob D Kagey; Julie A Merkle
Journal:  MicroPubl Biol       Date:  2021-07-13

Review 10.  Multi-Scale Organization of the Drosophila melanogaster Genome.

Authors:  Samantha C Peterson; Kaylah B Samuelson; Stacey L Hanlon
Journal:  Genes (Basel)       Date:  2021-05-27       Impact factor: 4.096
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