Match!

FlyBase at 25: looking to the future

Published on Jan 4, 2017in Nucleic Acids Research11.147
路 DOI :10.1093/nar/gkw1016
L. Sian Gramates9
Estimated H-index: 9
(Harvard University),
Steven J. Marygold14
Estimated H-index: 14
(University of Cambridge)
+ 15 AuthorsPinglei Zhou7
Estimated H-index: 7
(Harvard University)
Abstract
  • References (39)
  • Citations (355)
馃摉 Papers frequently viewed together
3 Authors (Michael I. Love, ..., Simon Anders)
10.6k Citations
14.1k Citations
13.4k Citations
78% of Scinapse members use related papers. After signing in, all features are FREE.
References39
Newest
#1Gillian H. Millburn (University of Cambridge)H-Index: 14
#2Madeline A. Crosby (Harvard University)H-Index: 19
Last. Susan Tweedie (University of Cambridge)H-Index: 24
view all 4 authors...
The use of Drosophila melanogaster as a model for studying human disease is well established, reflected by the steady increase in both the number and proportion of fly papers describing human disease models in recent years. In this article, we highlight recent efforts to improve the availability and accessibility of the disease model information in FlyBase (http://flybase.org), the model organism database for Drosophila . FlyBase has recently introduced Human Disease Model Reports, each of which...
29 CitationsSource
#1Robert D. Finn (EMBL-EBI: European Bioinformatics Institute)H-Index: 47
#2Penelope Coggill (EMBL-EBI: European Bioinformatics Institute)H-Index: 3
Last. Alex Bateman (EMBL-EBI: European Bioinformatics Institute)H-Index: 71
view all 13 authors...
In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stabilit...
2,619 CitationsSource
#1Helen Attrill (University of Cambridge)H-Index: 4
#2Kathleen Falls (Harvard University)H-Index: 10
Last. Steven J. Marygold (University of Cambridge)H-Index: 14
view all 7 authors...
Many publications describe sets of genes or gene products that share a common biology. For example, genome-wide studies and phylogenetic analyses identify genes related in sequence; high-throughput genetic and molecular screens reveal functionally related gene products; and advanced proteomic methods can determine the subunit composition of multi-protein complexes. It is useful for such gene collections to be presented as discrete lists within the appropriate Model Organism Database (MOD) so tha...
227 CitationsSource
#1Steven J. Marygold (University of Cambridge)H-Index: 14
#2Madeline A. Crosby (Harvard University)H-Index: 19
Last. Joshua L. Goodman (IU: Indiana University)H-Index: 3
view all 3 authors...
For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic and high-throughput technologies add to the quantity and diversity of available data and resources. FlyBase has taken several approaches to respond to these changes in the research land...
24 CitationsSource
#1Janan T. EppigH-Index: 49
#2Joel E. RichardsonH-Index: 36
Last. Carol J. BultH-Index: 54
view all 6 authors...
Summary The Mouse Genome Database (MGD, www.informatics.jax.org) is the international scientific database for genetic, genomic, and biological data on the laboratory mouse to support the research requirements of the biomedical community. To accomplish this goal, MGD provides broad data coverage, serves as the authoritative standard for mouse nomenclature for genes, mutants, and strains, and curates and integrates many types of data from literature and electronic sources. Among the key data sets ...
11 CitationsSource
#1Beverley B. Matthews (Harvard University)H-Index: 9
#2Gilberto dos Santos (Harvard University)H-Index: 5
Last. William M. Gelbart (Harvard University)H-Index: 86
view all 12 authors...
We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription star...
19 CitationsSource
#1Madeline A. Crosby (Harvard University)H-Index: 19
#2L. Sian Gramates (Harvard University)H-Index: 9
Last. William M. Gelbart (Harvard University)H-Index: 86
view all 11 authors...
In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron process...
9 CitationsSource
#1Sonal Nagarkar-Jaiswal (BCM: Baylor College of Medicine)H-Index: 10
#2Steven Z. DeLuca (CIS: Carnegie Institution for Science)H-Index: 3
Last. Hugo J. BellenH-Index: 90
view all 9 authors...
Previously, we described a large collection of Minos-Mediated Integration Cassettes (MiMICs) that contain two phiC31 recombinase target sites and allow the generation of a new exon that encodes a protein tag when the MiMIC is inserted in a codon intron (Nagarkar-Jaiswal et al., 2015). These modified genes permit numerous applications including assessment of protein expression pattern, identification of protein interaction partners by immunoprecipitation followed by mass spec, and reversible remo...
71 CitationsSource
#1Sonal Nagarkar-Jaiswal (BCM: Baylor College of Medicine)H-Index: 10
#2Pei Tseng Lee (BCM: Baylor College of Medicine)H-Index: 2
Last. Hugo J. BellenH-Index: 90
view all 17 authors...
In the last few decades, technical advances in altering the genes of organisms have led to many discoveries about how genes work. For example, it is now possible to add a specific DNA sequence to a gene so that the protein it makes will carry a 鈥榯ag鈥 that enables us to track it in cells. One such tag is called green fluorescent protein (GFP) and it is often used to study other proteins in living cells because it produces green fluorescence that can be detected under a microscope. It is labor int...
156 CitationsSource
#1Roger A. Hoskins (LBNL: Lawrence Berkeley National Laboratory)H-Index: 34
#2Joseph W. Carlson (LBNL: Lawrence Berkeley National Laboratory)H-Index: 32
Last. Susan E. Celniker (LBNL: Lawrence Berkeley National Laboratory)H-Index: 55
view all 28 authors...
Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21...
156 CitationsSource
Cited By355
Newest
File name: Supplementary Table S1. Title: Differentially gene expression results. Caption: Sequencing statistics for all the strains analyzed in this work, and expression values for all differentially expressed genes in each strain. Genes previously reported as oxidative stress responsive genes are also listed.-- File name: Supplementary Table S2. Title: Gene ontology enrichment analysis. Caption: Significant gene ontology clusters according to DAVID functional annotation tool for pairs of strai...
2 CitationsSource
#1Murillo F. Rodrigues (UO: University of Oregon)H-Index: 1
#2Maria D. Vibranovski (USP: University of S茫o Paulo)H-Index: 18
Last. Rodrigo Cogni (USP: University of S茫o Paulo)H-Index: 15
view all 3 authors...
Spatial and seasonal variation in the environment are ubiquitous. Covariation between a trait and space is often interpreted as the result of selection, but demography can complicate inference. Finding seasonal changes driven by selection is challenging, given effect sizes are small and the environment is subject to stochastic changes within seasons. Drosophila melanogaster is known to harbor polymorphisms that change with latitude and seasons. Identifying the role of selection in driving latitu...
Source
#1Gabriele Selvaggio (GAU: University of G枚ttingen)
#2Alexey I. Chizhik (GAU: University of G枚ttingen)H-Index: 16
Last. Zhiyi Lv (GAU: University of G枚ttingen)H-Index: 4
view all 18 authors...
Imaging of complex (biological) samples in the near-infrared (NIR) is beneficial due to reduced light scattering, absorption, phototoxicity, and autofluorescence. However, there are few NIR fluorescent materials known and suitable for biomedical applications. Here we exfoliate the layered pigment CaCuSi4O10 (Egyptian Blue, EB) via ball milling and facile tip sonication into NIR fluorescent nanosheets (EB-NS). The size of EB-NS can be tailored to diameters <20鈥塶m and heights down to 1鈥塶m. EB-NS f...
Source
#1Dayana Yahalomi (TAU: Tel Aviv University)H-Index: 1
#2Stephen D. Atkinson (OSU: Oregon State University)H-Index: 19
Last. Doroth茅e Huchon (TAU: Tel Aviv University)H-Index: 27
view all 8 authors...
Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria-related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no...
Source
#1Marta Bozek (LMU: Ludwig Maximilian University of Munich)
#2Nicolas Gompel (LMU: Ludwig Maximilian University of Munich)H-Index: 14
Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Instead, recent studies focusing on the quantitative nature of accessibility signal reveal subtle differe...
Source
#1Avisha Chowdhury (NUS: National University of Singapore)
#2Cassandra M. Modahl (NUS: National University of Singapore)H-Index: 6
Last. Julien PomponH-Index: 14
view all 8 authors...
Arbovirus infection of Aedes aegypti salivary glands (SGs) determines transmission. However, there is a dearth of knowledge on SG immunity. Here, we characterized SG immune response to dengue, Zika and chikungunya viruses using high-throughput transcriptomics. The three viruses regulate components of Toll, IMD and JNK pathways. However, silencing of Toll and IMD components showed variable effects on SG infection by each virus. In contrast, regulation of JNK pathway produced consistent responses....
Source
#1Cheng-I J. Ma (U of T: University of Toronto)
#2Yitong Yang (U of T: University of Toronto)
Last. Julie A. Brill (U of T: University of Toronto)H-Index: 27
view all 8 authors...
Regulated secretion is a fundamental cellular process in which biologically active molecules stored in long-lasting secretory granules (SGs) are secreted in response to external stimuli. Many studies have described mechanisms responsible for biogenesis and secretion of SGs, but how SGs mature remains poorly understood. In a genetic screen, we discovered a large number of endolysosomal trafficking genes required for proper SG maturation, indicating that maturation of SGs might occur in a manner s...
Source
#1Courtney M. Schroeder (Fred Hutchinson Cancer Research Center)H-Index: 1
#2John R Valenzuela (Fred Hutchinson Cancer Research Center)
Last. Harmit S. Malik (Fred Hutchinson Cancer Research Center)H-Index: 54
view all 5 authors...
Many cytoskeletal proteins perform fundamental biological processes and are evolutionarily ancient. For example, the superfamily of actin-related proteins (Arps) specialized early in eukaryotic evolution for diverse cellular roles in the cytoplasm and the nucleus. Despite its strict conservation across eukaryotes, we find that the Arp superfamily has undergone dramatic lineage-specific diversification in Drosophila. Our phylogenomic analyses reveal four independent Arp gene duplications that occ...
Source
#1Alison Pischedda (Columbia University)H-Index: 9
#2Michael P. Shahandeh (UCSB: University of California, Santa Barbara)H-Index: 2
Last. Thomas L. Turner (UCSB: University of California, Santa Barbara)H-Index: 17
view all 3 authors...
The behaviors of closely related species can be remarkably different, and these differences have important ecological and evolutionary consequences. Although the recent boom in genotype-phenotype studies has led to a greater understanding of the genetic architecture and evolution of a variety of traits, studies identifying the genetic basis of behaviors are, comparatively, still lacking. This is likely because they are complex and environmentally sensitive phenotypes, making them difficult to me...
Source
Source