AIMC Topic: Transcriptome
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Integrated analysis of shared gene expression signatures and immune microenvironment heterogeneity in type 2 diabetes mellitus and colorectal cancer.
Scientific reports
Jul 1, 2025
Emerging evidence suggests a bidirectional relationship between colorectal cancer (CRC) and type 2 diabetes mellitus (T2DM), yet the shared molecular mechanisms and prognostic biomarkers remain poorly characterized. This study aimed to identify novel...
Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data.
Nature communications
Jul 1, 2025
During cell-cell communication (CCC), pathways activated by different ligand-receptor pairs may have crosstalk with each other. While multiple methods have been developed to infer CCC networks and their downstream response using single-cell RNA-seq d...
Screening biomarkers related to cholesterol metabolism in osteoarthritis based on transcriptomics.
Scientific reports
Jul 1, 2025
Cholesterol metabolism-related genes (CMRGs) have been associated with osteoarthritis (OA), but their specific regulatory mechanisms remain unclear. This study aimed to investigate the role of CMRGs in OA and provide new insights into its treatment. ...
Identification of pyroptosis related genes and subtypes in atherosclerosis using multiomic and single cell analysis.
Scientific reports
Jul 1, 2025
Atherosclerosis (AS), the leading cause of cardiovascular diseases, is a chronic inflammatory disorder involving lipid metabolism, immune dysregulation, and cell death. Pyroptosis, a form of inflammatory programmed cell death, is implicated in AS pro...
CellMemory: hierarchical interpretation of out-of-distribution cells using bottlenecked transformer.
Genome biology
Jun 23, 2025
Machine learning methods, especially Transformer architectures, have been widely employed in single-cell omics studies. However, interpretability and accurate representation of out-of-distribution (OOD) cells remains challenging. Inspired by the glob...
WISP2/CCN5 revealed as a potential diagnostic biomarker for endometriosis based on machine learning and single-cell transcriptomic analysis.
Functional & integrative genomics
Jun 19, 2025
OBJECTIVE: Endometriosis is a prevalent gynecological disease characterized by the ectopic growth of functional endometrial tissue outside the uterine cavity, affecting millions of women worldwide. Currently, the definitive diagnosis relies on invasi...
Generative prediction of causal gene sets responsible for complex traits.
Proceedings of the National Academy of Sciences of the United States of America
Jun 12, 2025
The relationship between genotype and phenotype remains an outstanding question for organism-level traits because these traits are generally . The challenge arises from complex traits being determined by a combination of multiple genes (or loci), whi...
Exploring the molecular mechanisms of lactylation-related biological functions and immune regulation in sepsis-associated acute kidney injury.
Clinical and experimental medicine
Jun 12, 2025
Lactylation, a novel post-translational modification, has been implicated in various pathophysiological processes; however, its role in sepsis-associated acute kidney injury (SA-AKI) remains unclear. This study aimed to investigate the expression pat...
Neurodegeneration Promotes Tumorigenesis in Colorectal Cancer: Insights From Single-Cell and Spatial Multiomics.
JCO precision oncology
Jun 6, 2025
PURPOSE: Colorectal cancer (CRC) ranks third in global incidence and second in mortality, with rates increasing among younger populations. The enteric nervous system (ENS) is crucial for gastrointestinal function, and its dysfunction is associated wi...
Machine learning and multi-omics analysis reveal key regulators of proneural-mesenchymal transition in glioblastoma.
Scientific reports
Jun 5, 2025
Glioblastoma (GBM) is classified into subtypes according to the molecular expression profile; the proneural subtype has a relatively good prognosis, and the mesenchymal type is the most aggressive form with the worst prognosis. GBM undergoes proneura...
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