1-20 of 10889
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Schematic overview of data collection and processing steps for the AFED. Open Access
Published: 18 April 2025
Figure 2.
Schematic overview of data collection and processing steps for the AFED.
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Previously predicted large gene cluster is accurately delineated in two bio... Open Access
Published: 18 April 2025
Figure 3.
Previously predicted large gene cluster is accurately delineated in two biosynthetic gene clusters. Using co-expression analysis cluster 21 [ 26 ] is shown to be comprised of two distinct gene clusters: imizoquin (blue) and aspirochlorine (yellow).
Journal Article
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling Open Access
Database, Volume 2025, 2025, baaf033, https://doi.org/10.1093/database/baaf033
Published: 18 April 2025
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The AFED interface provides five tools utilizing NCBI RNA-seq data. (a) Bar... Open Access
Published: 18 April 2025
Figure 1.
The AFED interface provides five tools utilizing NCBI RNA-seq data. (a) Bar plot tool showing TPM or VST expression values across all samples for a single gene. (b) Heatmap tool of specific genes and samples from selected bioprojects. (c) Co-expression network visualization of selected genes and the
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GrameneOrzya site infrastructure and its components. The Ensembl data cores... Open Access
Published: 05 April 2025
Figure 2.
GrameneOrzya site infrastructure and its components. The Ensembl data cores for genomes, genetic variation, and comparative analyses (protein and DNA) were installed on a dedicated 250 GB Linux CentOS image with 16 GB memory and 2 CPUs. The core layer, represented in yellow, and the outer layer, dep
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Community curations in GrameneOryza interface. (a) Homology-based gene stru... Open Access
Published: 05 April 2025
Figure 6.
Community curations in GrameneOryza interface. (a) Homology-based gene structure inspection interface allows users to flag problematic models for further inspection and improvement. (b) Paper tab displays the functions curated by RAP-DB and GeneRIF, but also prompts users to enter their curation of
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Identification of PTVs using the GrameneOryza interface. (a) Germplasm: dis... Open Access
Published: 05 April 2025
Figure 5.
Identification of PTVs using the GrameneOryza interface. (a) Germplasm: displays a list of germplasms containing predicted loss-of-function alleles for the GS3 gene. Clicking the hyperlinked text “Variant image” will bring you to the Ensembl genome browser’s gene page Variant Image panel. Clicking
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The detail page in mirTarCLASH. (a) The query settings for the miRNA–mRNA p... Open Access
Published: 05 April 2025
Figure 3.
The detail page in mirTarCLASH. (a) The query settings for the miRNA–mRNA pair under investigation. (b) The confidence filters for the listed pairs. The detailed search results of a specific miRNA–target transcript pair in the tabular (c) and graphical (d) view.
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The detail page in mirTarCLASH. (a) The query settings for the miRNA–mRNA p... Open Access
Published: 05 April 2025
Figure 3.
The detail page in mirTarCLASH. (a) The query settings for the miRNA–mRNA pair under investigation. (b) The confidence filters for the listed pairs. The detailed search results of a specific miRNA–target transcript pair in the tabular (c) and graphical (d) view.
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The search mode in mirTarCLASH. (a) The query settings. (b) The query resul... Open Access
Published: 05 April 2025
Figure 2.
The search mode in mirTarCLASH. (a) The query settings. (b) The query result table. Click the “Show detail” link, and the detailed chimera analysis information for the pair will be provided.
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The browse mode in mirTarCLASH. (a) The browse settings. (b) The listed miR... Open Access
Published: 05 April 2025
Figure 4.
The browse mode in mirTarCLASH. (a) The browse settings. (b) The listed miRNA results when users intend to browse by miRNA. (c) The listed mRNA results when users intend to browse by mRNA. Click the “Show detail” link or the “Show miRNA details” link, and the detailed chimeric read information of th
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A systems level view of the core functionality of the GrameneOryza site. (a... Open Access
Published: 05 April 2025
Figure 1.
A systems level view of the core functionality of the GrameneOryza site. (a) Input data: omics data to load to the core database, this includes processed data as well as metadata, (b) Databases: build core database as well as database for search, (c) Analysis workflow: in-house workflows to generate
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GrameneOryza user interface: (a) Search: textual query search for genes. (b... Open Access
Published: 05 April 2025
Figure 3.
GrameneOryza user interface: (a) Search: textual query search for genes. (b) Quick links to Genome Browser, News, Release Notes, Guides, and Feedback form. (c) Tool and services panel with access to curated and published rice genes and other Gramene pansites as well as tools like BLAST, CLIMtools fo
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The detail page in mirTarCLASH. (a) The query settings for the miRNA–mRNA p... Open Access
Published: 05 April 2025
Figure 3.
The detail page in mirTarCLASH. (a) The query settings for the miRNA–mRNA pair under investigation. (b) The confidence filters for the listed pairs. The detailed search results of a specific miRNA–target transcript pair in the tabular (c) and graphical (d) view.
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The browse mode in mirTarCLASH. (a) The browse settings. (b) The listed miR... Open Access
Published: 05 April 2025
Figure 4.
The browse mode in mirTarCLASH. (a) The browse settings. (b) The listed miRNA results when users intend to browse by miRNA. (c) The listed mRNA results when users intend to browse by mRNA. Click the “Show detail” link or the “Show miRNA details” link, and the detailed chimeric read information of th
Journal Article
mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments Open Access
Database, Volume 2025, 2025, baaf023, https://doi.org/10.1093/database/baaf023
Published: 05 April 2025
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GrameneOrzya site infrastructure and its components. The Ensembl data cores... Open Access
Published: 05 April 2025
Figure 2.
GrameneOrzya site infrastructure and its components. The Ensembl data cores for genomes, genetic variation, and comparative analyses (protein and DNA) were installed on a dedicated 250 GB Linux CentOS image with 16 GB memory and 2 CPUs. The core layer, represented in yellow, and the outer layer, dep
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Use Case for finding copy number variations (CNVs) using GrameneOryza inter... Open Access
Published: 05 April 2025
Figure 4.
Use Case for finding copy number variations (CNVs) using GrameneOryza interface: (a) Gene Search: Keyword search produces many hits in different categories. One of the hits in the category “gene” is the rice version of SLB OsSLB1 . (b) Homology View: the neighborhood view shows CNV across the lands
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The browse mode in mirTarCLASH. (a) The browse settings. (b) The listed miR... Open Access
Published: 05 April 2025
Figure 4.
The browse mode in mirTarCLASH. (a) The browse settings. (b) The listed miRNA results when users intend to browse by miRNA. (c) The listed mRNA results when users intend to browse by mRNA. Click the “Show detail” link or the “Show miRNA details” link, and the detailed chimeric read information of th
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Use Case for finding copy number variations (CNVs) using GrameneOryza inter... Open Access
Published: 05 April 2025
Figure 4.
Use Case for finding copy number variations (CNVs) using GrameneOryza interface: (a) Gene Search: Keyword search produces many hits in different categories. One of the hits in the category “gene” is the rice version of SLB OsSLB1 . (b) Homology View: the neighborhood view shows CNV across the lands
