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FlyBase 2.0: the next generation

Jim Thurmond, Joshua L Goodman, Victor B Strelets, Helen Attrill, L Sian Gramates, Steven J Marygold, Beverley B Matthews, Gillian Millburn, Giulia Antonazzo, Vitor Trovisco, Thomas C Kaufman, Brian R Calvi (+34 others)
2018 Nucleic Acids Research  
At the beginning of 2018, 'FlyBase 2.0' was released with a significantly improved user interface and new tools.  ...  With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase  ...  ACKNOWLEDGEMENTS We would like to thanks the other PIs, curators, and developers of FlyBase for their comments on the manuscript. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gky1003 pmid:30364959 fatcat:edyizmh3fjcuhkbwrq7fdsyooe

FlyBase: anatomical data, images and queries

G. Grumbling
2006 Nucleic Acids Research  
FlyBase (http://flybase.org/) is a database of genetic and genomic data on the model organism Drosophila melanogaster and the entire insect family Drosophilidae.  ...  The FlyBase Consortium curates, annotates, integrates and maintains a wide variety of data within this domain.  ...  ACKNOWLEDGEMENTS FlyBase is supported by the National Human Genome Research Institute (USA), grant P41-HG00739.  ... 
doi:10.1093/nar/gkj068 pmid:16381917 pmcid:PMC1347431 fatcat:b7f7zxzr65f5jhq375slrtfpma

FlyBase: integration and improvements to query tools

R. J. Wilson, J. L. Goodman, V. B. Strelets
2007 Nucleic Acids Research  
FlyBase (http://flybase.org) is the primary resource for molecular and genetic information on the Drosophilidae.  ...  Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder.  ...  ACKNOWLEDGEMENTS FlyBase is supported by the U.S.  ... 
doi:10.1093/nar/gkm930 pmid:18160408 pmcid:PMC2238994 fatcat:ioblhziscnactksgzsbe4lidri

An RNAi-mediated screen identifies novel targets for next-generation antiepileptic drugs based on increased expression of the homeostatic regulator pumilio

Wei-Hsiang Lin, Miaomiao He, Yuen Ngan Fan, Richard A. Baines
2018 Journal of neurogenetics  
Thus, novel targets are required to catalyse the design of next-generation AEDs.  ...  We further show that chemical inhibitors of protein products of some of the genes targeted are similarly anticonvulsant.  ...  Acknowledgements We are grateful to members of the Baines group for help and advice during the course of this work. We specifically thank Dr.  ... 
doi:10.1080/01677063.2018.1465570 pmid:29718742 pmcid:PMC5989157 fatcat:hb7a4qqf5fadlm7i2dapydzkdi

DoOR 2.0 - Comprehensive Mapping ofDrosophila melanogasterOdorant Responses [article]

Daniel Muench, C. Giovanni Galizia
2015 bioRxiv   pre-print
The DoOR project combines all availableDrosophilaodorant response data into a single consensus response matrix.  ...  In this study, we add to the odor-response profiles for four odorant receptors (Or10a, Or42b, Or47b, Or56a).  ...  We thank Veith Grabe for contributing an antennal lobe map optimized for mapping the  ... 
doi:10.1101/027920 fatcat:t4gpiqwrzzferj7jdjstedthym

Using GBrowse 2.0 to visualize and share next-generation sequence data

L. D. Stein
2013 Briefings in Bioinformatics  
As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files.  ...  FUNDING This work was funded by grant #P41 G02223 from the National Human Genome Research Institute at the US National Institutes of Health, and by the Ministry of Economic Development and Innovation,  ...  Acknowledgements The author wishes to thank Dr Scott Cain for assistance with configuring and testing the VMs and four anonymous reviewers who contributed many helpful suggestions during manuscript preparation  ... 
doi:10.1093/bib/bbt001 pmid:23376193 pmcid:PMC3603216 fatcat:47agmtkgwvfaxej5rpaaudet5a

DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses

Daniel Münch, C. Giovanni Galizia
2016 Scientific Reports  
At the time of uploading this preprint, a preview of the DoOR 2.0 webpage is available at: http://neuro.uni.kn/DoOR/2.0 peer-reviewed)  ...  In this study, we add to the odor-response profiles for four odorant receptors (Or10a, Or42b, Or47b, Or56a).  ...  We thank Veith Grabe for contributing an antennal lobe map optimized for mapping the  ... 
doi:10.1038/srep21841 pmid:26912260 pmcid:PMC4766438 fatcat:ix27jmmlpnbfli6ip6qwy5gf2m

The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context

Fabio Marchiano, Margaux Haering, Bianca Hermine Habermann
2022 Nucleic Acids Research  
To fill this gap, we upgraded the mitoXplorer platform to version 2.0 (mitoXplorer 2.0).  ...  We demonstrate the usefulness of these functions in three specific use cases. mitoXplorer 2.0 is freely available without login at http://mitoxplorer2.ibdm.univ-mrs.fr.  ...  ACKNOWLEDGEMENTS We thank Alice Carrier, Benoit Giannesini, Frank Schnorrer, Nuno Luis, Jerome Avellaneda, and the members of the IBDM Computational Biology team for helpful discussion on mitoXplorer 2.0  ... 
doi:10.1093/nar/gkac306 pmid:35524562 pmcid:PMC9252804 fatcat:4dzf7lfdmbegtaweij7ajiu74e

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species

2019 Nucleic Acids Research  
We believe the new annotation of enhancers in EnhancerAtlas 2.0 will facilitate users to perform useful functional analysis of enhancers in various genomes.  ...  The updated version is a huge expansion of the first version, which only contains the enhancers in human cells. In addition, we predicted enhancer-target gene relationships in human, mouse and fly.  ...  ACKNOWLEDGEMENTS We thank the members from Qian' lab for discussion.  ... 
doi:10.1093/nar/gkz980 pmid:31740966 pmcid:PMC7145677 fatcat:cmn5ieqwvbet7a3rkdkuzhij7m

The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research

Nathalie Percie du Sert, Viki Hurst, Amrita Ahluwalia, Sabina Alam, Marc T. Avey, Monya Baker, William J. Browne, Alejandra Clark, Innes C. Cuthill, Ulrich Dirnagl, Michael Emerson, Paul Garner (+17 others)
2020 PLoS Biology  
Here, we introduce ARRIVE 2.0. The guidelines have been updated and information reorganised to facilitate their use in practice.  ...  We used a Delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the "ARRIVE Essential 10," which constitutes the minimum requirement, and the "Recommended Set," which describes  ...  With minimisation, the treatment allocated to the next animal/sample depends on the characteristics of those animals/samples already assigned.  ... 
doi:10.1371/journal.pbio.3000410 pmid:32663219 fatcat:qzlrm33ugzfeppyjmac2drgmre

Reporting animal research: Explanation and elaboration for the ARRIVE guidelines 2.0

Nathalie Percie du Sert, Amrita Ahluwalia, Sabina Alam, Marc T. Avey, Monya Baker, William J. Browne, Alejandra Clark, Innes C. Cuthill, Ulrich Dirnagl, Michael Emerson, Paul Garner, Stephen T. Holgate (+17 others)
2020 PLoS Biology  
It provides further information about each of the 21 items in ARRIVE 2.0, including the rationale and supporting evidence for their inclusion in the guidelines, elaboration of details to report, and examples  ...  Transparent and accurate reporting is vital to this process; it allows readers to assess the reliability of the findings and repeat or build upon the work of other researchers.  ...  With minimisation, the treatment allocated to the next animal/sample depends on the characteristics of those animals/samples already assigned.  ... 
doi:10.1371/journal.pbio.3000411 pmid:32663221 fatcat:wgeagtfdxvgzrhb5m5r23fbdre

A bioinformatics pipeline for the assessment of the evolutionary relationship of some Drosophila species based on class II transposons mapping [article]

Nicoleta Denisa Constantin, Alexandru Marian Bologa, Attila Cristian Ratiu, Alexandru Al. Ecovoiu
2022 bioRxiv   pre-print
Genome sequencing allowed the identification of the high content of transposons in various model organisms.  ...  Here, we present a bioinformatics pipeline developed to estimate the evolutionary relationship between Drosophila melanogaster and other Drosophilidae based on the comparative analysis of the presence  ...  ARTIST version 2.0 (www.genomeartist.ro) for the mapping step.  ... 
doi:10.1101/2022.09.13.507812 fatcat:nzqiimj2bjhired34m6xkrj6fi

Re-annotation of eight Drosophila genomes

Haiwang Yang, Maria Jaime, Maxi Polihronakis, Kelvin Kanegawa, Therese Markow, Kenneth Kaneshiro, Brian Oliver
2018 Life Science Alliance  
We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on D. melanogaster that best matched the extensively curated annotation  ...  The sequenced genomes of the Drosophila phylogeny are a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system.  ...  This research was supported in part by the Intramural Research Program of the NIH, the NIDDK.  ... 
doi:10.26508/lsa.201800156 fatcat:s2nz2uepszbdtixypgpy66mfge

B.2.16 is a non-lethal modifier of the Dark82 mosaic eye phenotype in Drosophila melanogaster [article]

Alysia D Vrailas-Mortimer, Nitish Aggarwal, Neha N Ahmed, Ian M Alberts, Masa Alhawasli, Ibrahim A Aljerdi, Brooke M Allen, Ahmad M Alnajar, Michael A Anderson, Ryan Armstong, Chace C Avery, Eric J Avila (+68 others)
2021 microPublication Biology  
FlyBase 2.0: the next generation. Nucleic Acids Res 47: D759-D765. PMID: 30364959. Funding: A.  ...  FlyBase Consortium.. 2017.  ... 
doi:10.17912/micropub.biology.000359 pmid:33474526 pmcid:PMC7812380 fatcat:warelgawdjdorf56xb7w3mol24

Evaluation of Different Reference Based Annotation Strategies Using RNA-Seq – A Case Study in Drososphila pseudoobscura

Nicola Palmieri, Viola Nolte, Anton Suvorov, Carolin Kosiol, Christian Schlötterer, Dongxiao Zhu
2012 PLoS ONE  
Using data from both sexes of two adult strains of D. pseudoobscura we detected alternative splicing for about 30% of the FlyBase multiple-exon genes.  ...  evaluated the potential of RNA-Seq to improve the annotation of Drosophila pseudoobscura.  ...  Author Contributions Conceived and designed the experiments: CS CK. Performed the experiments: VN. Analyzed the data: NP AS. Wrote the paper: NP AS CS.  ... 
doi:10.1371/journal.pone.0046415 pmid:23056304 pmcid:PMC3463616 fatcat:bueiwcaipvhyblyidau5x4jcsm
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