AIMC Topic: RNA-Seq

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scCorrect: Cross-modality label transfer from scRNA-seq to scATAC-seq using domain adaptation.

Analytical biochemistry
Cell type annotation in single-cell chromatin accessibility sequencing (scATAC-seq) is crucial for enabling researchers to identify subpopulations of cells associated with specific diseases, elucidate gene regulatory networks, and discover markers in...

Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

PLoS genetics
Deep learning techniques are increasingly utilized to analyze large-scale single-cell RNA sequencing (scRNA-seq) data, offering valuable insights from complex transcriptome datasets. Geneformer, a pre-trained model using a Transformer Encoder archite...

Investigation of cell development and tissue structure network based on natural Language processing of scRNA-seq data.

Journal of translational medicine
BACKGROUND: Single-cell multi-omics technologies, particularly single-cell RNA sequencing (scRNA-seq), have revolutionized our understanding of cellular heterogeneity and development by providing insights into gene expression at the single-cell level...

Deep learning powered single-cell clustering framework with enhanced accuracy and stability.

Scientific reports
Single-cell RNA sequencing (scRNA-seq) has revolutionized the field of cellular diversity research. Unsupervised clustering, a key technique in this exploration, allows for the identification of distinct cell types within a population. Graph-based de...

scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder.

BMC bioinformatics
BACKGROUND: Single-cell RNA sequencing (scRNA-seq) has transformed biological research by offering new insights into cellular heterogeneity, developmental processes, and disease mechanisms. As scRNA-seq technology advances, its role in modern biology...

Deciphering the role of metal ion transport-related genes in T2D pathogenesis and immune cell infiltration via scRNA-seq and machine learning.

Frontiers in immunology
INTRODUCTION: Type 2 diabetes (T2D) is a complex metabolic disorder with significant global health implications. Understanding the molecular mechanisms underlying T2D is crucial for developing effective therapeutic strategies. This study employs sing...

Identifying candidate RNA-seq biomarkers for severity discrimination in chemical injuries: A machine learning and molecular dynamics approach.

International immunopharmacology
INTRODUCTION: Biomarkers play a crucial role across various fields by providing insights into biological responses to interventions. High-throughput gene expression profiling technologies facilitate the discovery of data-driven biomarkers through ext...

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
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...

Integrating single-cell RNA-Seq and machine learning to dissect tryptophan metabolism in ulcerative colitis.

Journal of translational medicine
BACKGROUND: Ulcerative colitis (UC) is a persistent inflammatory bowels disease (IBD) characterized by immune response dysregulation and metabolic disruptions. Tryptophan metabolism has been believed as a significant factor in UC pathogenesis, with s...

Integration of bulk/scRNA-seq and multiple machine learning algorithms identifies PIM1 as a biomarker associated with cuproptosis and ferroptosis in abdominal aortic aneurysm.

Frontiers in immunology
BACKGROUND: Abdominal aortic aneurysm (AAA) is a serious life-threatening vascular disease, and its ferroptosis/cuproptosis markers have not yet been characterized. This study was aiming to identify markers associated with ferroptosis/cuproptosis in ...