AIMC Topic: Organ Specificity

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Deep learning deciphers the related role of master regulators and G-quadruplexes in tissue specification.

Scientific reports Jul 2, 2025
G-quadruplexes (GQs) are non-canonical DNA structures encoded by G-flipons with potential roles in gene regulation and chromatin structure. Here, we explore the role of G-flipons in tissue specification. We present a deep learning-based framework for...
Humans Deep Learning G-Quadruplexes Promoter Regions, Genetic Organ Specificity Gene Expression Regulation Genome, Human DNA
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CMImpute: cross-species and tissue imputation of species-level DNA methylation samples across mammalian species.

Genome biology May 20, 2025
The large-scale application of the mammalian methylation array has substantially expanded the availability of DNA methylation data in mammalian species. However, this data captures only a small portion of species-tissue combinations. To address this,...
Organ Specificity Mammals Species Specificity Animals Software Humans DNA Methylation
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Investigation of cell development and tissue structure network based on natural Language processing of scRNA-seq data.

Journal of translational medicine Mar 4, 2025
BACKGROUND: Single-cell multi-omics technologies, particularly single-cell RNA sequencing (scRNA-seq), have revolutionized our understanding of cellular heterogeneity and development by providing insights into gene expression at the single-cell level...
Animals Single-Cell Analysis RNA-Seq Humans Organ Specificity Sequence Analysis, RNA Natural Language Processing Gene Regulatory Networks Cell Differentiation Single-Cell Gene Expression Analysis
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Tisslet tissues-based learning estimation for transcriptomics.

BMC bioinformatics Feb 25, 2025
In the context of multi-omics data analytics for various diseases, transcriptome-wide association studies leveraging genetically predicted gene expression hold promise for identifying novel regions linked to complex traits. However, existing methods ...
Algorithms Gene Expression Profiling Transcriptome Humans Machine Learning Organ Specificity Computational Biology
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Tissue-aware interpretation of genetic variants advances the etiology of rare diseases.

Molecular systems biology Sep 16, 2024
Pathogenic variants underlying Mendelian diseases often disrupt the normal physiology of a few tissues and organs. However, variant effect prediction tools that aim to identify pathogenic variants are typically oblivious to tissue contexts. Here we r...
Genetic Predisposition to Disease Computational Biology Organ Specificity Rare Diseases Genetic Variation Humans Machine Learning
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Current genomic deep learning models display decreased performance in cell type-specific accessible regions.

Genome biology Aug 1, 2024
BACKGROUND: A number of deep learning models have been developed to predict epigenetic features such as chromatin accessibility from DNA sequence. Model evaluations commonly report performance genome-wide; however, cis regulatory elements (CREs), whi...
Chromatin Organ Specificity Regulatory Sequences, Nucleic Acid Humans Deep Learning Epigenesis, Genetic Models, Genetic Genomics
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Self-supervised learning for characterising histomorphological diversity and spatial RNA expression prediction across 23 human tissue types.

Nature communications Jul 13, 2024
As vast histological archives are digitised, there is a pressing need to be able to associate specific tissue substructures and incident pathology to disease outcomes without arduous annotation. Here, we learn self-supervised representations using a ...
Supervised Machine Learning RNA Organ Specificity Humans Gene Expression Profiling Image Processing, Computer-Assisted
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Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks.

Journal of translational medicine Jul 3, 2024
BACKGROUND: Cell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation at...
Humans Neural Networks, Computer Organ Specificity DNA Methylation Cell-Free Nucleic Acids Algorithms Genome, Human Neoplasms
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Tissue specific tumor-gene link prediction through sampling based GNN using a heterogeneous network.

Medical & biological engineering & computing Apr 18, 2024
A tissue sample is a valuable resource for understanding a patient's symptoms and health status in relation to tumor growth. Recent research seeks to establish a connection between tissue-specific tumor samples and genetic markers (genes). This break...
Gene Expression Regulation, Neoplastic Humans Organ Specificity Neural Networks, Computer Neoplasms Algorithms ROC Curve Gene Regulatory Networks Biomarkers, Tumor
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Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.

Nature Dec 12, 2023
Enhancers control gene expression and have crucial roles in development and homeostasis. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning t...
Transposases Enhancer Elements, Genetic Animals Datasets as Topic Organ Specificity Chromatin Neural Networks, Computer Embryo, Nonmammalian Deep Learning Synthetic Biology Reproducibility of Results Drosophila melanogaster Single-Cell Analysis
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