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Sequence Analysis, RNA

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Metabolic reprogramming and macrophage expansion define ACPA-negative rheumatoid arthritis: insights from single-cell RNA sequencing.

Frontiers in immunology 39830504
BACKGROUND: Anti-citrullinated peptide antibodies (ACPA)-negative (ACPA-) rheumatoid arthritis (RA) presents significant diagnostic and therapeutic challenges due to the absence of specific biomarkers, underscoring the need to elucidate its distincti...
Adult Aged Anti-Citrullinated Protein Antibodies Arthritis, Rheumatoid Biomarkers Cellular Reprogramming Female Gene Regulatory Networks Humans Leukocytes, Mononuclear Macrophages Male Metabolic Reprogramming Middle Aged Sequence Analysis, RNA Single-Cell Analysis Synovial Membrane
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Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics.

Briefings in bioinformatics 39814561
Recent advances in single-cell RNA-Sequencing (scRNA-Seq) technologies have revolutionized our ability to gather molecular insights into different phenotypes at the level of individual cells. The analysis of the resulting data poses significant chall...
Algorithms Alzheimer Disease COVID-19 Deep Learning Gene Expression Profiling Humans Lupus Erythematosus, Systemic Neural Networks, Computer Phenotype SARS-CoV-2 Sequence Analysis, RNA Single-Cell Analysis Transcriptome
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Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks.

Briefings in bioinformatics 39800872
Single-cell multi-omics techniques, which enable the simultaneous measurement of multiple modalities such as RNA gene expression and Assay for Transposase-Accessible Chromatin (ATAC) within individual cells, have become a powerful tool for decipherin...
Chromatin Immunoprecipitation Sequencing Computational Biology Gene Regulatory Networks Graph Neural Networks Humans Neural Networks, Computer RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Single-Cell Gene Expression Analysis
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Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.

PLoS computational biology 39775239
The 3D structure of RNA critically influences its functionality, and understanding this structure is vital for deciphering RNA biology. Experimental methods for determining RNA structures are labour-intensive, expensive, and time-consuming. Computati...
Benchmarking Computational Biology Deep Learning Nucleic Acid Conformation RNA Sequence Alignment Sequence Analysis, RNA
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Unveiling the Immune Landscape of Delirium through Single-Cell RNA Sequencing and Machine Learning: Towards Precision Diagnosis and Therapy.

Psychogeriatrics : the official journal of the Japanese Psychogeriatric Society 39814058
BACKGROUND: Postoperative delirium (POD) poses significant clinical challenges regarding its diagnosis and treatment. Identifying biomarkers that can predict and diagnose POD is crucial for improving patient outcomes.
Aged Biomarkers Case-Control Studies Delirium Female Humans Leukocytes, Mononuclear Machine Learning Male Middle Aged Phosphatidylinositol 3-Kinases Postoperative Complications Precision Medicine Proto-Oncogene Proteins c-akt Sequence Analysis, RNA Signal Transduction Single-Cell Analysis
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SenPred: a single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden.

Genome medicine 39810225
BACKGROUND: Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required. However, emerging scRNA-seq datasets h...
Cellular Senescence Fibroblasts Humans Machine Learning RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Skin Transcriptome
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The role of mitophagy-related genes in prognosis and immunotherapy of cutaneous melanoma: a comprehensive analysis based on single-cell RNA sequencing and machine learning.

Immunologic research 39799269
Mitophagy, the selective degradation of mitochondria by autophagy, plays a crucial role in cancer progression and therapy response. This study aims to elucidate the role of mitophagy-related genes (MRGs) in cutaneous melanoma (CM) through single-cell...
Biomarkers, Tumor Gene Expression Profiling Gene Expression Regulation, Neoplastic Gene Regulatory Networks Humans Immunotherapy Machine Learning Melanoma Melanoma, Cutaneous Malignant Mitophagy Prognosis Sequence Analysis, RNA Single-Cell Analysis Skin Neoplasms Transcriptome Tumor Microenvironment
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Integrated RNA sequencing analysis and machine learning identifies a metabolism-related prognostic signature in clear cell renal cell carcinoma.

Scientific reports 39799252
The connection between metabolic reprogramming and tumor progression has been demonstrated in an increasing number of researches. However, further research is required to identify how metabolic reprogramming affects interpatient heterogeneity and pro...
Biomarkers, Tumor Carcinoma, Renal Cell Cell Line, Tumor Female gamma-Glutamyltransferase Gene Expression Regulation, Neoplastic Humans Kidney Neoplasms Machine Learning Male Middle Aged Prognosis Sequence Analysis, RNA Single-Cell Analysis
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Combining machine learning and single-cell sequencing to identify key immune genes in sepsis.

Scientific reports 39789158
This research aimed to identify novel indicators for sepsis by analyzing RNA sequencing data from peripheral blood samples obtained from sepsis patients (n = 23) and healthy controls (n = 10). 5148 differentially expressed genes were identified using...
Aged Algorithms Case-Control Studies Female Gene Expression Profiling Humans Machine Learning Male Middle Aged Sepsis Sequence Analysis, RNA Single-Cell Analysis
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CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data.

Cell genomics 39788105
Exploratory analysis of single-cell RNA sequencing (scRNA-seq) typically relies on hard clustering over two-dimensional projections like uniform manifold approximation and projection (UMAP). However, such methods can severely distort the data and hav...
Animals Brain Gene Expression Profiling Humans Mice RNA-Seq Sequence Analysis, RNA Single-Cell Analysis Single-Cell Gene Expression Analysis Unsupervised Machine Learning
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