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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Bibliográfalaš dieđut
Váldodahkki:	Juntian Qi (22578974) (author)
Almmustuhtton:	2025
Fáttát:	Bioinformatic methods development Genomics and transcriptomics Sequence analysis Human evolution Adaptively driven genes Cis-regulatory elements Siamese neural networks
Fáddágilkorat:	Lasit fáddágilkoriid Eai fáddágilkorat, Lasit vuosttaš fáddágilkora!

Geahča maid

liverRegression code.
Dahkki: Amy Stephen (22684448)
Almmustuhtton: (2025)

基于机器学习和网络药理学分析类风湿关节炎中大麻二酚治疗双靶点机制
Dahkki: xiaohua fang (22678832)
Almmustuhtton: (2025)

<b>Supplementary files</b> - G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa
Dahkki: Alain Garcia De Las Bayonas (21095624)
Almmustuhtton: (2025)

Data Sheet 1_Genome-wide identification and expression profiling of bHLH transcription factors associated with ferulic acid biosynthesis in Angelica sinensis.zip
Dahkki: Khadija Tehseen Arshad (22687526)
Almmustuhtton: (2025)

Table 1_Genome-wide identification and expression profiling of bHLH transcription factors associated with ferulic acid biosynthesis in Angelica sinensis.xlsx
Dahkki: Khadija Tehseen Arshad (22687526)
Almmustuhtton: (2025)

Processed snRNA-seq data from wild-type and <i>Pink1</i>-deficient mouse gut
Dahkki: Muhammad Junaid (14524523)
Almmustuhtton: (2025)

Supplementary Data from Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis
Dahkki: Nicole M. Rossi (15619062)
Almmustuhtton: (2025)

Supplementary Figures from Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis
Dahkki: Nicole M. Rossi (15619062)
Almmustuhtton: (2025)

Quantitative performance comparison of our method and five multilayer network ranking baselines on the GAC dataset across multiple evaluation metrics.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Classification performance across the three simulation settings.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Comparison of Gene Discovery and Performance Evaluation with Baseline Methods.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Case study on Esophageal Squamous Cell Carcinoma (ESCC).
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Ablation studies and performance evaluation under varying training conditions.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

classification results on simulated datasets and biomarkers and classification results for GAC dataset.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Simulation networks and gene expression analysis across disease states.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Overview of the TransMarker framework for identifying DNBs from single cell time course data.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Robustness analysis of the entropic regularization parameter in the Gromov–Wasserstein alignment step of TransMarker.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Robustness of TransMarker concerning the selection and completeness of the prior knowledge network.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

UpSet diagram illustrating the overlap of DNBs selected by our method and top-ranked genes by the 13 baseline centrality-based ranking algorithms.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Functional enrichment analysis of the 28 DNB genes identified for ESCC.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

Functional enrichment analysis of the DNBs identified for GAC.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

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

Gene regulatory networks for different states of GAC post-rewiring.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (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.
Dahkki: Fatemeh Keikha (20917848)
Almmustuhtton: (2025)

GHRAT: Global Heat Risk Assessment Toolbox
Dahkki: Xuewen Lei (18138637)
Almmustuhtton: (2025)

Full list of metrics, indicators, and health-related outcomes used in PAICE rapid literature
Dahkki: Rachel Juel (11796266)
Almmustuhtton: (2025)

Data Sheet 1_Adaptive laboratory evolution enhances cell yield and lipid production of Chlorella sorokiniana under mildly cold conditions.pdf
Dahkki: Shu-Yi Lu (22679327)
Almmustuhtton: (2025)

Structural variants of <i>Fragaria vesca</i>
Dahkki: Minto Odagiri (22680003)
Almmustuhtton: (2025)

Gene expression data of <i>Fragaria vesca</i>
Dahkki: Minto Odagiri (22680003)
Almmustuhtton: (2025)

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
Dahkki: Yang Wang (5921)
Almmustuhtton: (2025)

Data Sheet 1_MRI-based radiomic clustering identifies a glioblastoma subtype enriched for neural stemness and proliferative programs.csv
Dahkki: Zhongyi Zhang (219440)
Almmustuhtton: (2025)

Data Sheet 2_MRI-based radiomic clustering identifies a glioblastoma subtype enriched for neural stemness and proliferative programs.pdf
Dahkki: Zhongyi Zhang (219440)
Almmustuhtton: (2025)

<b>Minimal repeats identified by machine learning as novel cross-species markers of translation initiation sites</b>
Dahkki: Ali Mohammad Ali Maddi (11301486)
Almmustuhtton: (2025)

Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
Dahkki: Xu Hua (14954032)
Almmustuhtton: (2025)

Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
Dahkki: Xu Hua (14954032)
Almmustuhtton: (2025)

Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
Dahkki: Xu Hua (14954032)
Almmustuhtton: (2025)

Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
Dahkki: Xu Hua (14954032)
Almmustuhtton: (2025)

Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
Dahkki: Xu Hua (14954032)
Almmustuhtton: (2025)

Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
Dahkki: Xu Hua (14954032)
Almmustuhtton: (2025)

Supplementary Data from Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer
Dahkki: Xu Hua (14954032)
Almmustuhtton: (2025)

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