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Journal Article
TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf173, https://doi.org/10.1093/bib/bbaf173
Published: 21 April 2025
Journal Article
STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf174, https://doi.org/10.1093/bib/bbaf174
Published: 21 April 2025
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PAUROC of statistical tests for imputation and imputation-free methods acro...
Published: 21 April 2025
Figure 2
PAUROC of statistical tests for imputation and imputation-free methods across different MNAR ratios. (A) pAUROC in the simulation scenario for the DDA_HMiss dataset (sample size = 100, fold change = 2, missingness ratio = 0.75). (B, C) pAUROC for the simulation scenario of DDA_LMiss and DIA_LMiss da
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The bias of effect size compared to complete data in each round of simulati...
Published: 21 April 2025
Figure 4
The bias of effect size compared to complete data in each round of simulation in DDA_HMiss. The difference between the effect size of missing data (labeled as “missing” on the x -axis of each panel) or imputed data (labeled with the imputation method names) and the completed data were quantified an
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Example of the utility of taxon set enrichment analysis for detecting share...
Published: 21 April 2025
Figure 1
Example of the utility of taxon set enrichment analysis for detecting shared functional changes missed by traditional differential abundance methods.
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Overview of the taxon set enrichment analysis workflow using TaxSEA.
Published: 21 April 2025
Figure 2
Overview of the taxon set enrichment analysis workflow using TaxSEA.
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(a) Bar plot of significantly depleted taxon sets (FDR < 0.1) in IBD com...
Published: 21 April 2025
Figure 4
(a) Bar plot of significantly depleted taxon sets (FDR < 0.1) in IBD compared to controls in the Lloyd-Price et al. dataset. Abbreviations: 4HA = 4-hydroxyphenylacetic acid; 3IAA = indole-3-acetic acid. (b) Volcano plot showing depletion of SCFA producers (i.e. propionate, butyrate, or acetate pr
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A schematic illustration of imaging endophenotypes-assisted gene-environmen...
Published: 21 April 2025
Figure 1
A schematic illustration of imaging endophenotypes-assisted gene-environment interaction analysis. First, the bi-directional mapping framework incorporates genetic variations, exposomes, and endophenotypes simultaneously. The feature-interaction module identifies biologically meaningful genetics, en
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Investigation of the mediating effects of endophenotypes characteristics on...
Published: 21 April 2025
Figure 6
Investigation of the mediating effects of endophenotypes characteristics on diagnostic phenotypes caused by genetic variants (a) rs429358 (b) rs6857. ( * , <0̇5), ( ** , <0̇1), ( *** , < .001).
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Biomarker discovery for important endophenotypes on ADNI. (a) Neuroimaging-...
Published: 21 April 2025
Figure 7
Biomarker discovery for important endophenotypes on ADNI. (a) Neuroimaging-derived phenotypes (VBM). (b) Neuroimaging-derived phenotypes (FreeSurfer). (c) Plasma-derived proteomic markers. (d) CSF-derived proteomic markers. Each row is a method: (1) SMCCA; (2) adaptive SMCCA; (3) RelPMDCCA; (4) prop
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Regional plot of the top lead SNPs rs429358.
Published: 21 April 2025
Figure 8
Regional plot of the top lead SNPs rs429358.
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(a) A Manhattan plot depicting the snp-based test. (b) A separate Manhattan...
Published: 21 April 2025
Figure 9
(a) A Manhattan plot depicting the snp-based test. (b) A separate Manhattan plot was created for the gene-based test, the x -axis represents the SNP positions on the genome, while the y -axis represents the negative base-10 logarithm of the -values. Higher values on the y -axis indicate strong
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(a) The PheWAS analysis yielded results for SNP rs429358 ( ). (b) The Phe...
Published: 21 April 2025
Figure 11
(a) The PheWAS analysis yielded results for SNP rs429358 ( ). (b) The PheWAS analysis yielded results for SNP rs56131196 ( ).
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Schematic overview of our proposed approach. a , STForte processes SRT dat...
Published: 21 April 2025
Figure 1
Schematic overview of our proposed approach. a , STForte processes SRT data to extract spatial KNN graph and expression feature matrix, identifying unmeasured or low-quality locations through automatic padding or user-defined procedures. b , The spatial graph contains consistency information while
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The three-layer architecture of IDP-EDL, (a) ProtT5 encoder with LoRA is us...
Published: 21 April 2025
Figure 1
The three-layer architecture of IDP-EDL, (a) ProtT5 encoder with LoRA is used to generate the sequence embedding; (b) different deep learning algorithms are employed to capture different features between different disordered regions; (c) a meta predictor calculate final prediction results.
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Performance metrics for different methods on dataset .
Published: 21 April 2025
Figure 2
Performance metrics for different methods on dataset .
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The AUC values of IDP-EDL-L, IDP-EDL-S, IDP-EDL-G, and IDP-EDL on datasets ...
Published: 21 April 2025
Figure 3
The AUC values of IDP-EDL-L, IDP-EDL-S, IDP-EDL-G, and IDP-EDL on datasets , , and .
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The AUC values of IDP-EDL-G and IDP-EDL evaluated on the datasets with diff...
Published: 21 April 2025
Figure 4
The AUC values of IDP-EDL-G and IDP-EDL evaluated on the datasets with different ratios of LDRs and SDRs.
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Illustration of the DCOL. The blue vertical lines represent the distances b...
Published: 21 April 2025
Figure 1
Illustration of the DCOL. The blue vertical lines represent the distances between adjacent values ordered by , while the gray dotted lines represent the distances between adjacent values. (A) An example where and have a predictive relationship, and the spread of is small. (B)
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Single-omics simulation results. We conducted various simulations with diff...
Published: 21 April 2025
Figure 2
Single-omics simulation results. We conducted various simulations with different combinations of sample size (n) chosen from {500, 1000, 2000}, the number of features (p) selected from {500, 1000, 2000}, and the group size (k) picked from {5, 10, 15}. ARI scores were calculated based on the first fi
