Beverley B. Matthews
Harvard University
Publications 13
#1Julie AgapiteH-Index: 1
Last.Karen YookH-Index: 7
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4 CitationsSource
#1Jim Thurmond (IU: Indiana University Bloomington)H-Index: 5
#2Joshua L. Goodman (IU: Indiana University Bloomington)H-Index: 6
Last.Phillip W. BakerH-Index: 5
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71 CitationsSource
#1L. Sian Gramates (Harvard University)H-Index: 9
#2Steven J. Marygold (University of Cambridge)H-Index: 14
Last.Pinglei Zhou (Harvard University)H-Index: 7
view all 18 authors...
355 CitationsSource
#1Steven J. Marygold (University of Cambridge)H-Index: 14
#2Giulia Antonazzo (University of Cambridge)H-Index: 4
Last.Jim Thurmond (IU: Indiana University Bloomington)H-Index: 5
view all 11 authors...
FlyBase ( is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet ...
2 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
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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
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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
#1Ruihua Fang (California Institute of Technology)H-Index: 3
#2Gary Schindelman (California Institute of Technology)H-Index: 10
Last.Paul W. Sternberg (California Institute of Technology)H-Index: 91
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Background Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and ...
21 CitationsSource
#1Michael F. LinH-Index: 23
#2Joseph W. CarlsonH-Index: 32
Last.Manolis KamvysselisH-Index: 94
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The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have developed quantitative metrics for the evolutionary signatures specific to protein-coding regions and applied them genome-wide, resulting in 1193 candidate new protein-coding exons in the D. melanogaster genome. We have reviewed these predictions by manual curation and validated a subset by directed c...
121 CitationsSource
#1Sima Misra (University of California, Berkeley)H-Index: 12
#2Madeline A. Crosby (Harvard University)H-Index: 19
Last.Suzanna E. Lewis (University of California, Berkeley)H-Index: 62
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Background: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing ea...
299 CitationsSource
#1Sima MisraH-Index: 12
#2Madeline A. CrosbyH-Index: 19
Last.Suzanna E. LewisH-Index: 62
view all 30 authors...
7 CitationsSource