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Overview of the strategy employed to develop and expand KitBase, the Kitaak...
Published: 12 June 2026
Figure 1
Overview of the strategy employed to develop and expand KitBase, the KitaakeX rice FN mutagenized population. (A) M 0 generation KitaakeX seeds were subjected to FN irradiation, and the resulting M 1 plants were self-fertilized to produce M 2 seeds. (B) Seeds from 3268 M 2 or M 3 mutant lines w
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Genome-Wide Characterization of Mutations in 3268 FN-Induced Rice Mutant Li...
Published: 12 June 2026
Figure 2
Genome-Wide Characterization of Mutations in 3268 FN-Induced Rice Mutant Lines. (A) The number of mutant lines aligned to each reference genome (Nipponbare and KitaakeX), showing the distribution of sequencing data for comparative genomic analysis. (B) Distribution of mutant lines based on the numbe
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Representative phenotypes observed in FN-mutagenized KitaakeX rice lines. T...
Published: 12 June 2026
Figure 6
Representative phenotypes observed in FN-mutagenized KitaakeX rice lines. This figure displays a range of morphological alterations induced by FN mutagenesis in the KitaakeX population. (A) Panicle height: tall to dwarf; (B) Lethal albino seedling; (C) Leaf phenotypes: partial albino, brown and mimi
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Overview of the KitBase User Interface. (A) Main Navigation Page: Displays ...
Published: 12 June 2026
Figure 7
Overview of the KitBase User Interface. (A) Main Navigation Page: Displays the primary navigation menu at the top and bottom, facilitating access to various sections of KitBase. (B) Search Functionality: Offers multiple search options, including Mutant ID, Gene ID, Keyword, and Phenotype, enabling u
Journal Article
KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants
Database, Volume 2026, 2026, baag024, https://doi.org/10.1093/database/baag024
Published: 12 June 2026
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Comprehensive Analysis of Affected Genes in 3268 FN-Induced Rice Mutant Lin...
Published: 12 June 2026
Figure 3
Comprehensive Analysis of Affected Genes in 3268 FN-Induced Rice Mutant Lines. (A) Left: Proportion of annotated genes affected by FN-induced mutations in the Nipponbare and KitaakeX reference genomes, without subdivision of transposable element (TE) and non-TE gene categories. Right: Proportion of
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Chromosomal Distribution and Mutation Density of Affected Genes. (A) Chromo...
Published: 12 June 2026
Figure 4
Chromosomal Distribution and Mutation Density of Affected Genes. (A) Chromosomal mapping of affected genes in the Nipponbare alignment. The heatmap represents the number of distinct mutations per gene, ranging from lighter shades (yellow, indicating one mutation) to darker shades (red, indicating te
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Chromosomal Distribution and Frequency of Mutation Types in the FN-Induced ...
Published: 12 June 2026
Figure 5
Chromosomal Distribution and Frequency of Mutation Types in the FN-Induced Kitaake Rice Mutant Population. (A) Circular plot showing the distribution and frequency of mutations across the 12 rice chromosomes on a megabase scale. The plot consists of six concentric tracks, labeled A–F from outermost
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Lysins identified in the EnVhog database. (A) The number of proteins, stand...
Published: 05 June 2026
Figure 4
Lysins identified in the EnVhog database. (A) The number of proteins, standard clusters (30% sequence identity), and remote homology clusters predicted by SUBLYME, split according to lysin type (endolysin and virion associated lysin—VAL). (B) Number of representative endolysins (one per standard clu
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Domain architecture occurrences in PhaLP 2.0. More specific annotations are...
Published: 05 June 2026
Figure 5
Domain architecture occurrences in PhaLP 2.0. More specific annotations are listed below the principal architecture; only the most frequent ones are listed. Enzymatically active domains (EADs) are presented in red, cell wall-binding domains (CBDs) in blue, and miscellaneous domains in yellow. Sch
Journal Article
A similarity metric, rubric, and unified hierarchy for biomedical publication types and study designs
Database, Volume 2026, 2026, baag022, https://doi.org/10.1093/database/baag022
Published: 05 June 2026
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Hierarchical clustering of publication types by model-inferred probabilitie...
Published: 05 June 2026
Figure 3
Hierarchical clustering of publication types by model-inferred probabilities. Publication type clusters derived from pairwise model score correlations and grouped with hierarchical clustering. Cut points were chosen to delineate 13 low-level categories and 5 broader categories. Diagram showing th
Journal Article
PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery
Database, Volume 2026, 2026, baag033, https://doi.org/10.1093/database/baag033
Published: 05 June 2026
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Correlation matrix derivation. Modelled predicted probabilities were used t...
Published: 05 June 2026
Figure 1
Correlation matrix derivation. Modelled predicted probabilities were used to compute Spearman correlations for each pairwise combination of publication types. Diagram showing how predictive scores for individual articles are converted to similarity correlation values pairwise across different pub
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Distribution of pairwise correlations for PTs. Spearman correlation was com...
Published: 05 June 2026
Figure 2
Distribution of pairwise correlations for PTs. Spearman correlation was computed among model-predicted probabilities for assignment of 72 publication types forming a 72 × 72 correlation matrix. The distribution of the correlation coefficients is bimodal with one mode centred around zero, the other a
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Study overview. (A) Training SUBLYME. A first model was trained on a datase...
Published: 05 June 2026
Figure 1
Study overview. (A) Training SUBLYME. A first model was trained on a dataset of lysins (from PhaLP) and non-lysin phage proteins (from INPHARED) to distinguish between these two classes. Then, a second model was trained, using just the lysins in PhaLP, to classify lysins as endolysins or virion-asso
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Evaluation of SUBLYME. Distribution of the precision and recall of models t...
Published: 05 June 2026
Figure 2
Evaluation of SUBLYME. Distribution of the precision and recall of models trained during repeated k-fold cross-validation as a function of the decision threshold used by models to make predictions. A total of 100 models (10 repeats with 10 folds per repeat) were trained and tested for the lysin pred
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Predicted lysins in the Fernández-Ruiz dataset. (A) t-SNE projection of pro...
Published: 05 June 2026
Figure 3
Predicted lysins in the Fernández-Ruiz dataset. (A) t-SNE projection of protein embeddings for all predicted lysins. In blue, lysins predicted by SUBLYME; in red, endolysins identified by Fernández-Ruiz et al . [ 29 ]; in yellow, endolysins identified by both methods. (B) Number of occurrences of t
Journal Article
GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms
Database, Volume 2026, 2026, baag029, https://doi.org/10.1093/database/baag029
Published: 03 June 2026
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Framework for developing GUTAID. For image description, please refer to ...
Published: 03 June 2026
Figure 1
Framework for developing GUTAID. For image description, please refer to the figure legend and surrounding text.
