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Journal Article
Correction to: The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study
Database, Volume 2025, 2025, baae131, https://doi.org/10.1093/database/baae131
Published: 13 January 2025
Journal Article
DisGeNet: a disease-centric interaction database among diseases and various associated genes
Database, Volume 2025, 2025, baae122, https://doi.org/10.1093/database/baae122
Published: 11 January 2025
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Genome catalogues were created for each system. HoloFood-derived metagenome...
Published: 11 January 2025
Figure 2.
Genome catalogues were created for each system. HoloFood-derived metagenome-assembled genomes were combined with other publicly available chicken and fish data to produce genome catalogues for the MGnify Genomes resource [ 11 ]. In this example, the HoloFood genome clusters with three other genomes
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The data collection process of DisGeNet: (a) the collection of node informa...
Published: 11 January 2025
Figure 2.
The data collection process of DisGeNet: (a) the collection of node information and (b) the collection of link information.
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A general use process of DisGeNet: (a) the interface of the search module w...
Published: 11 January 2025
Figure 5.
A general use process of DisGeNet: (a) the interface of the search module with “AIDS” input as the retrieved disease in the “Search” page (disease name used as an example), (b) fuzzy search result page of “AIDS”, (c) filtering links by node types, (d) the search results shown in a list manner, and (
Journal Article
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production
Database, Volume 2025, 2025, baae112, https://doi.org/10.1093/database/baae112
Published: 11 January 2025
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Overview of the multiomic samples available in the HoloFood Data Portal for...
Published: 11 January 2025
Figure 3.
Overview of the multiomic samples available in the HoloFood Data Portal for each system. Different multiomics sample sets were extracted from animals in multiple trials and time points. Each row shows how many individual animals are available covering that multi-omic combination. Combinations are sh
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Screenshot showing a sample detail page for a metagenomic sample (left). Th...
Published: 11 January 2025
Figure 5.
Screenshot showing a sample detail page for a metagenomic sample (left). The analysis of metagenomic samples is performed by and stored in MGnify [ 9 ]. The data portal shows a summary of this MGnify data and links to MGnify where users can browse the analysis dataset (right).
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The statistics of DisGeNet: (a) six types of links network, (b) four types ...
Published: 11 January 2025
Figure 1.
The statistics of DisGeNet: (a) six types of links network, (b) four types of nodes, (c) statistics of links, and (d) the top 50 diseases associated with genes.
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Interface of DisGeNet: (a) search for all associations and interactions, an...
Published: 11 January 2025
Figure 4.
Interface of DisGeNet: (a) search for all associations and interactions, and (b) browse all associations and interactions.
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Other functions in DisGeNet: (a) get data via “Download” or “API,” (b) disc...
Published: 11 January 2025
Figure 6.
Other functions in DisGeNet: (a) get data via “Download” or “API,” (b) discussion and feedback in DisGeNet, (c) data statistics in DisGeNet, and (d) learn more about DisGeNet through the “Help” interface.
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The schema used for HoloFood animals and samples registered in BioSamples [...
Published: 11 January 2025
Figure 1.
The schema used for HoloFood animals and samples registered in BioSamples [ 8 ]. Individual animals are accessed as BioSamples, with metadata sections as shown on the left. Most of these metadata sections are shared between the two systems. Extraction-level (derived) samples are registered separatel
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The primary dataset available in the data portal is a list of samples (regi...
Published: 11 January 2025
Figure 4.
The primary dataset available in the data portal is a list of samples (registered in BioSamples). The sample list (in the background of this composite screenshot) can be partitioned along different axes: in this case by system, omic type, and treatment. It can also be partitioned by host, as shown b
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Statistical comparison of data in DisGeNet: (a) node data and (b) link data...
Published: 11 January 2025
Figure 3.
Statistical comparison of data in DisGeNet: (a) node data and (b) link data.
Journal Article
GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries
Database, Volume 2024, 2024, baae130, https://doi.org/10.1093/database/baae130
Published: 27 December 2024
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GeniePool 2.0 user interface. Genomic coordinates for either a single varia...
Published: 27 December 2024
Figure 1.
GeniePool 2.0 user interface. Genomic coordinates for either a single variant or co-occurrence of two variants are searched within NGS samples from SRA. Resulting variants can be filtered by sample attributes. Selected variants will provide information about each variant and its study.
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Clinical tests complete-blood-count (CBC) and morphology analysis are used ...
Published: 25 December 2024
Figure 1.
Clinical tests complete-blood-count (CBC) and morphology analysis are used for anemia diagnosis.
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Visual results of image segmentation using the GAN network at different epo...
Published: 25 December 2024
Figure 9.
Visual results of image segmentation using the GAN network at different epochs.
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Training and validation accuracy and loss for both datasets regarding the c...
Published: 25 December 2024
Figure 11.
Training and validation accuracy and loss for both datasets regarding the classification of VGG16 and MobileNet.
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(a) Training progress of Atten_UNet on AneRBC-I and AneRBC-II. (b) IoU and ...
Published: 25 December 2024
Figure A1.
(a) Training progress of Atten_UNet on AneRBC-I and AneRBC-II. (b) IoU and Dice-Coefficient of UNet on AneRBC-I and AneRBC-II. (c) IoU and Dice-Coefficient of LinkNet on AneRBC-I and AneRBC-II.
