AIMC Topic: Transcriptome

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Integrative transcriptomic analysis reveals oligodendrocyte lineage switching in multiple sclerosis.

Life science alliance Aug 4, 2025
Multiple sclerosis (MS) is a chronic disease of the central nervous system. The occurrence of MS is a phased process while its cause is still unclear. Here, by combining white matter single-nucleus transcriptomic datasets from MS and control samples,...
Male Middle Aged Gene Expression Profiling Transcriptome Female Adult Animals White Matter Cell Lineage Oligodendrocyte Precursor Cells Oligodendroglia Microglia Cell Differentiation Multiple Sclerosis Humans
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Prediction of the risk of transplant rejection based on RNA sequencing data of PBMCs before transplantation.

Scientific reports Aug 4, 2025
Novel methods for detecting transplant rejection are craved, since conventional methods can detect ongoing rejection that may sometimes have already caused irreversible damage in transplanted organs. Here, we applied a transcriptomics database of rec...
Transcriptome Sequence Analysis, RNA Graft Rejection Liver Transplantation Kidney Transplantation Leukocytes, Mononuclear Gene Expression Profiling Humans Machine Learning
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Combining mucosal microbiome and host multi-omics data shows prognostic potential in paediatric ulcerative colitis.

Nature communications Aug 4, 2025
Current first-line treatments of paediatric ulcerative colitis (UC) maintain a 6-month remission in only half of the patients. Relapse prediction at diagnosis could enable earlier introduction of immunosuppressants. We collected intestinal biopsies f...
Female Animals Male Transcriptome Humans Interleukin-10 Prognosis Gastrointestinal Microbiome Colitis, Ulcerative Intestinal Mucosa Mice Recurrence Bacteria Multiomics Mice, Knockout Adolescent Epigenomics Interferon-gamma Child, Preschool Child
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Integrated transcriptomic and functional modeling reveals AKT and mTOR synergy in colorectal cancer.

Scientific reports Jul 31, 2025
Colorectal cancer (CRC) treatment remains challenging due to genetic heterogeneity and resistance mechanisms. To address this, we developed a drug discovery pipeline using patient-derived primary CRC cultures with diverse genomic profiles. These cult...
TOR Serine-Threonine Kinases High-Throughput Screening Assays Drug Synergism Everolimus MTOR Inhibitors Transcriptome Cell Line, Tumor Proto-Oncogene Proteins c-akt Humans Colorectal Neoplasms
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CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

BMC biology Jul 30, 2025
BACKGROUND: The advent of single-cell RNA sequencing (scRNA-seq) has provided unprecedented insights into cancer cellular diversity, enabling a comprehensive understanding of cancer at the single-cell level. However, identifying cancer cells remains ...
Single-Cell Gene Expression Analysis Sequence Analysis, RNA Neoplasms Transcriptome Humans Single-Cell Analysis Machine Learning RNA-Seq
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CYCLONE: recycle contrastive learning for integrating single-cell gene expression data.

BMC bioinformatics Jul 30, 2025
BACKGROUND: Combining single-cell transcriptome sequencing results from several batches reduces batch effect, which improves our understanding of cellular identity and function.
Single-Cell Analysis Gene Expression Profiling Transcriptome Machine Learning Humans Algorithms
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SpaSEG: unsupervised deep learning for multi-task analysis of spatially resolved transcriptomics.

Genome biology Jul 29, 2025
Spatially resolved transcriptomics (SRT) for characterizing spatial cellular heterogeneities in tissue environments requires systematic analytical approaches to elucidate gene expression variations within their physiological context. Here, we introdu...
Carcinoma, Ductal, Breast Humans Transcriptome Female Deep Learning Breast Neoplasms Unsupervised Machine Learning Gene Expression Profiling
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Integrative transcriptomics and metabolomics reveal neuroendocrine-lipid crosstalk and adenosine signaling in broiler under heat stress.

BMC genomics Jul 29, 2025
BACKGROUND: Heat stress (HS) is a significant challenge in poultry, negatively impacting feed efficiency and survival. These adaptive responses could lead to disrupted lipid metabolism, impaired immunity, and neural damage. We hypothesized that the n...
Chickens Heat-Shock Response Signal Transduction Adenosine Hypothalamus Metabolomics Lipid Metabolism Animals Gene Expression Profiling Transcriptome Neurosecretory Systems
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Interpretable machine learning-guided single-cell mapping deciphers multi-lineage pancreatic dysregulation in type 2 diabetes.

Cardiovascular diabetology Jul 24, 2025
BACKGROUND: Pancreatic cellular heterogeneity is fundamental to systemic metabolic regulation, yet its pathological remodeling in diabetes remains poorly characterized.
Single-Cell Analysis Phenotype RNA-Seq Animals Humans Pancreas Signal Transduction Male Machine Learning Cell Lineage Pancreatic Neoplasms Transcriptome Pancreatic Stellate Cells Diabetes Mellitus, Type 2
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An autoencoder learning method for predicting breast cancer subtypes.

PloS one Jul 23, 2025
Heterogeneity of breast cancer poses several challenges for detection and treatment. With next-generation sequencing, we can now map the transcriptional profile of each patient's breast tissue, which has the potential for identifying and characterizi...
Transcriptome Breast Neoplasms Gene Expression Regulation, Neoplastic Humans Machine Learning Female Biomarkers, Tumor Gene Expression Profiling Autoencoder
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