AIMC Topic: Gene Expression Regulation

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ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.

Nature communications Jan 2, 2025
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the...
Humans Machine Learning Animals Single-Cell Analysis Gene Expression Regulation Nucleic Acid Conformation Regulatory Sequences, Nucleic Acid Chromatin Chromatin Immunoprecipitation Sequencing Mice Computational Biology Transcription Factors DNA
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Integrative analysis of PANoptosis-related genes in diabetic retinopathy: machine learning identification and experimental validation.

Frontiers in immunology Dec 4, 2024
BACKGROUND: Diabetic retinopathy (DR) is a major complication of diabetes, leading to severe vision impairment. Understanding the molecular mechanisms, particularly PANoptosis, underlying DR is crucial for identifying potential biomarkers and therape...
Regulated Cell Death Human Umbilical Vein Endothelial Cells Random Forest CD4-Positive T-Lymphocytes Molecular Targeted Therapy Humans Gene Expression Regulation Memory T Cells ROC Curve Diabetic Retinopathy Fatty Acid Synthase, Type I RNA-Seq Machine Learning Phospholipid Transfer Proteins Gene Regulatory Networks Biomarkers Nomograms
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Extending visual range of bacteria with upconversion nanoparticles and constructing NIR-responsive bio-microrobots.

Journal of colloid and interface science Dec 1, 2024
The motility of bacteria is crucial for navigating competitive environments and is closely linked to physiological activities essential for their survival, such as biofilm development. Precise regulation of bacterial motility enhances our understandi...
Infrared Rays Spheroids, Cellular Optogenetics Methyl-Accepting Chemotaxis Proteins Drug Delivery Systems Neoplasms Cell Line, Tumor Humans Nanoparticles Escherichia coli Robotics Bacterial Proteins Gene Expression Regulation
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Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Nov 28, 2024
Recent advances in spatial transcriptomics have enabled simultaneous preservation of high-throughput gene expression profiles and the spatial context, enabling high-resolution exploration of distinct regional characterization in tissue. To effectivel...
Humans Mice Gene Expression Regulation Machine Learning Animals Gene Expression Profiling Transcriptome
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Potential diagnostic biomarkers in heart failure: Suppressed immune-associated genes identified by bioinformatic analysis and machine learning.

European journal of pharmacology Nov 23, 2024
Heart failure (HF) threatens tens of millions of people's health worldwide, which is the terminal stage in the development of majority cardiovascular diseases. Recently, an increasing number of studies have demonstrated that bioinformatics and machin...
Myocardial Infarction Heart Failure Gene Expression Regulation Biomarkers Humans Animals Computational Biology Databases, Genetic Machine Learning Male Disease Models, Animal Support Vector Machine Mice Mice, Inbred C57BL
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The diagnostic value investigation of programmed cell death genes in heart failure.

BMC cardiovascular disorders Nov 22, 2024
BACKGROUND: We aimed to identify the potential diagnostic markers and associated molecular mechanisms based on programmed cell death (PCD)-related genes in patients with heart failure (HF).
Heart Failure Plasminogen Activator Inhibitor 1 Gene Expression Regulation Apoptosis Regulatory Proteins Case-Control Studies Protein Interaction Maps Gene Regulatory Networks Nomograms Databases, Genetic Apoptosis Predictive Value of Tests Genetic Markers Machine Learning Reproducibility of Results Gene Expression Profiling Transcriptome Humans
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SDC4 protein action and related key genes in nonhealing diabetic foot ulcers based on bioinformatics analysis and machine learning.

International journal of biological macromolecules Nov 17, 2024
Diabetic foot ulcers (DFU) is a complication associated with diabetes characterised by high morbidity, disability, and mortality, involving chronic inflammation and infiltration of multiple immune cells. We aimed to identify the critical genes in non...
Humans Machine Learning Gene Expression Profiling Transcriptome Syndecan-4 Single-Cell Analysis Computational Biology Diabetic Foot Gene Expression Regulation
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Identification of TXN and F5 as novel diagnostic gene biomarkers of the severe asthma based on bioinformatics and machine learning analysis.

Autoimmunity Nov 12, 2024
Asthma poses a major threat to human health. The aim of this study was to identify genetic markers of severe asthma and analyze the relationship between key genes and immune infiltration. Differentially expressed genes (DEGs) were first screened by d...
Humans Machine Learning Biomarkers Asthma MicroRNAs Gene Expression Regulation Thioredoxins Severity of Illness Index Gene Expression Profiling Transcriptome Computational Biology
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Identification and validation of interferon-stimulated gene 15 as a biomarker for dermatomyositis by integrated bioinformatics analysis and machine learning.

Frontiers in immunology Nov 4, 2024
BACKGROUND: Dermatomyositis (DM) is an autoimmune disease that primarily affects the skin and muscles. It can lead to increased mortality, particularly when patients develop associated malignancies or experience fatal complications such as pulmonary ...
Ubiquitins Biomarkers Molecular Docking Simulation Gene Expression Profiling Case-Control Studies Humans Skin ROC Curve Machine Learning Gene Regulatory Networks Dermatomyositis Cytokines Computational Biology Gene Expression Regulation Biopsy Molecular Targeted Therapy
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Identification of metabolism related biomarkers in obesity based on adipose bioinformatics and machine learning.

Journal of translational medicine Oct 31, 2024
BACKGROUND: Obesity has emerged as a growing global public health concern over recent decades. Obesity prevalence exhibits substantial global variation, ranging from less than 5% in regions like China, Japan, and Africa to rates exceeding 75% in urba...
Mice Computational Biology Databases, Genetic Mice, Inbred C57BL Obesity Adipose Tissue Gene Expression Regulation Animals Male Gene Expression Profiling Humans Gene Regulatory Networks Machine Learning Biomarkers
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