AIMC Topic: Transcriptome

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scDMSC: Deep Multi-View Subspace Clustering for Single-Cell Multi-Omics Data.

IEEE journal of biomedical and health informatics
Single-cell multi-omics sequencing technology comprehensively considers various molecular features to reveal the complexity of cells information. The clustering analysis of multi-omics data provides new insight into cellular heterogeneity. However, m...

Integrating bulk RNA-seq and scRNA-seq analyses with machine learning to predict platinum response and prognosis in ovarian cancer.

Scientific reports
Platinum-based therapy is an integral part of the standard treatment for ovarian cancer. However, despite extensive research spanning several decades, the identification of dependable predictive biomarkers for platinum response in clinical practice h...

An immunohistochemistry-based classification of colorectal cancer resembling the consensus molecular subtypes using convolutional neural networks.

Scientific reports
Colorectal cancer (CRC) represents a major global disease burden with nearly 1 million cancer-related deaths annually. TNM staging has served as the foundation for predicting patient prognosis, despite variation across staging groups. The consensus m...

Integrated machine learning survival framework develops a prognostic model based on macrophage-related genes and programmed cell death signatures in a multi-sample Kidney renal clear cell carcinoma.

Cell biology and toxicology
BACKGROUND: Macrophages are closely associated with the progression of Kidney renal clear cell carcinoma (KIRC) and can influence programmed cell death (PCD) of tumour cells. To identify prognostic biomarkers for KIRC, it is essential to investigate ...

scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links.

Nature communications
Recent advancements in single-cell technologies have enabled comprehensive characterization of cellular states through transcriptomic, epigenomic, and proteomic profiling at single-cell resolution. These technologies have significantly deepened our u...

Saliva-derived transcriptomic signature for gastric cancer detection using machine learning and leveraging publicly available datasets.

Scientific reports
Saliva, a non-invasive, self-collected liquid biopsy, holds promise for early gastric cancer (GC) screening. This study aims to assess the potential of saliva as a proxy for malignant gastric transformation and its diagnostic value through transcript...

Prediction of Drug-Induced Nephrotoxicity Using Chemical Information and Transcriptomics Data.

Journal of chemical information and modeling
Prediction of drug-induced nephrotoxicity is an important task in the drug discovery and development pipeline. Chemical information-based machine learning models are used in general for nephrotoxicity prediction as a part of computational modeling. C...

CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders.

Nucleic acids research
Correcting for confounding variables is often overlooked when computing RNA-RNA correlations, even though it can profoundly affect results. We introduce CorrAdjust, a method for identifying and correcting such hidden confounders. CorrAdjust selects a...

Machine learning using scRNA-seq Combined with bulk-seq to identify lactylation-related hub genes in carotid arteriosclerosis.

Scientific reports
Atherosclerosis is a chronic inflammatory disease, this study aims to investigate the immune landscape in carotid atherosclerotic plaque formation and explore diagnostic biomarkers of lactylation-associated genes, so as to gain new insights into unde...

Machine-learning meta-analysis reveals ethylene as a central component of the molecular core in abiotic stress responses in Arabidopsis.

Nature communications
Understanding how plants adapt their physiology to overcome severe and often multifactorial stress conditions in nature is vital in light of the climate crisis. This remains a challenge given the complex nature of the underlying molecular mechanisms....