DeepEvo

DeepEvo

<p dir="ltr">The identification of adaptively driven genes underlying human evolutionary traits remains a key challenge in evolutionary genomics. Here we present DeepEvo, an interpretable Siamese neural network that predicts cross-species expression differences from orthologous seque...

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Bibliografiska uppgifter
Huvudupphovsman:	Juntian Qi (22578974) (author)
Publicerad:	2025
Ämnen:	Bioinformatic methods development Genomics and transcriptomics Sequence analysis Human evolution Adaptively driven genes Cis-regulatory elements Siamese neural networks
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liverRegression code.
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<b>Supplementary files</b> - G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa
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Data Sheet 1_Genome-wide identification and expression profiling of bHLH transcription factors associated with ferulic acid biosynthesis in Angelica sinensis.zip
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Table 1_Genome-wide identification and expression profiling of bHLH transcription factors associated with ferulic acid biosynthesis in Angelica sinensis.xlsx
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Supplementary Figures from Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis
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Quantitative performance comparison of our method and five multilayer network ranking baselines on the GAC dataset across multiple evaluation metrics.
av: Fatemeh Keikha (20917848)
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Classification performance across the three simulation settings.
av: Fatemeh Keikha (20917848)
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Comparison of Gene Discovery and Performance Evaluation with Baseline Methods.
av: Fatemeh Keikha (20917848)
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Case study on Esophageal Squamous Cell Carcinoma (ESCC).
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Ablation studies and performance evaluation under varying training conditions.
av: Fatemeh Keikha (20917848)
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classification results on simulated datasets and biomarkers and classification results for GAC dataset.
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Simulation networks and gene expression analysis across disease states.
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Overview of the TransMarker framework for identifying DNBs from single cell time course data.
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Robustness analysis of the entropic regularization parameter in the Gromov–Wasserstein alignment step of TransMarker.
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Robustness of TransMarker concerning the selection and completeness of the prior knowledge network.
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UpSet diagram illustrating the overlap of DNBs selected by our method and top-ranked genes by the 13 baseline centrality-based ranking algorithms.
av: Fatemeh Keikha (20917848)
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Functional enrichment analysis of the 28 DNB genes identified for ESCC.
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Functional enrichment analysis of the DNBs identified for GAC.
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Publicerad: (2025)

Mean expression levels of biomarker genes across various disease states.
av: Fatemeh Keikha (20917848)
Publicerad: (2025)

Gene regulatory networks for different states of GAC post-rewiring.
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Publicerad: (2025)

UMAP visualizations of extracted CD8<sup> + </sup> T and CD4<sup> + </sup> T cell barcodes, employed for downstream subsequent single-cell trajectory and classification analyses.
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GHRAT: Global Heat Risk Assessment Toolbox
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Full list of metrics, indicators, and health-related outcomes used in PAICE rapid literature
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Data Sheet 1_Adaptive laboratory evolution enhances cell yield and lipid production of Chlorella sorokiniana under mildly cold conditions.pdf
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Structural variants of <i>Fragaria vesca</i>
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Gene expression data of <i>Fragaria vesca</i>
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Supplementary file 1_SLC11A1 protein as a key regulator of iron metabolism, ferroptosis mediator, and putative therapeutic target in nonalcoholic fatty liver disease: an integrated bioinformatics analysis.zip
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Data Sheet 2_MRI-based radiomic clustering identifies a glioblastoma subtype enriched for neural stemness and proliferative programs.pdf
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Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
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Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
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Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
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Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
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Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
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Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
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Publicerad: (2025)

Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
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Publicerad: (2025)

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