AIMC Topic: Sequence Analysis, RNA
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Single-cell RNA sequencing and machine learning provide candidate drugs against drug-tolerant persister cells in colorectal cancer.
Biochimica et biophysica acta. Molecular basis of disease
Jan 25, 2025
Drug resistance often stems from drug-tolerant persister (DTP) cells in cancer. These cells arise from various lineages and exhibit complex dynamics. However, effectively targeting DTP cells remains challenging. We used single-cell RNA sequencing (sc...
KanCell: dissecting cellular heterogeneity in biological tissues through integrated single-cell and spatial transcriptomics.
Journal of genetics and genomics = Yi chuan xue bao
Jan 23, 2025
KanCell is a deep learning model based on Kolmogorov-Arnold networks (KAN) designed to enhance cellular heterogeneity analysis by integrating single-cell RNA sequencing and spatial transcriptomics (ST) data. ST technologies provide insights into gene...
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
Jan 14, 2025
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...
Immunometabolic alterations in type 2 diabetes mellitus revealed by single-cell RNA sequencing: insights into subtypes and therapeutic targets.
Frontiers in immunology
Jan 14, 2025
BACKGROUND: Type 2 Diabetes Mellitus (T2DM) represents a major global health challenge, marked by chronic hyperglycemia, insulin resistance, and immune system dysfunction. Immune cells, including T cells and monocytes, play a pivotal role in driving ...
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
Jan 11, 2025
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...
Immunotherapy
Sequence Analysis, RNA
Gene Expression Regulation, Neoplastic
Melanoma, Cutaneous Malignant
Transcriptome
Single-Cell Analysis
Gene Regulatory Networks
Mitophagy
Machine Learning
Prognosis
Melanoma
Skin Neoplasms
Tumor Microenvironment
Biomarkers, Tumor
Gene Expression Profiling
Humans
Integrated RNA sequencing analysis and machine learning identifies a metabolism-related prognostic signature in clear cell renal cell carcinoma.
Scientific reports
Jan 11, 2025
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...
Combining machine learning and single-cell sequencing to identify key immune genes in sepsis.
Scientific reports
Jan 10, 2025
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...
Metabolic reprogramming and macrophage expansion define ACPA-negative rheumatoid arthritis: insights from single-cell RNA sequencing.
Frontiers in immunology
Jan 3, 2025
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...
Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.
PLoS computational biology
Dec 30, 2024
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...
Application of deep learning models on single-cell RNA sequencing analysis uncovers novel markers of double negative T cells.
Scientific reports
Dec 28, 2024
Double negative T (DNT) cells are a unique subset of CD3 + TCRαβ + T lymphocytes that lack CD4, CD8, or NK1.1 expression and constitute 3-5% of the total T cell population in C57BL/6 mice. They have increasingly gained recognition for their novel rol...
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