AIMC Topic: RNA-Seq

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Identification of mitophagy-related biomarkers in severe acute pancreatitis: integration of WGCNA, machine learning algorithms and scRNA-seq.

Frontiers in immunology
BACKGROUND: Mitophagy is a highly conserved cellular process in eukaryotic cells that selectively clears dysfunctional or damaged mitochondria through autophagy mechanisms to maintain mitochondrial homeostasis. However, the role of mitophagy in the p...

scE2EGAE: enhancing single-cell RNA-Seq data analysis through an end-to-end cell-graph-learnable graph autoencoder with differentiable edge sampling.

Biology direct
BACKGROUND: Single-cell RNA sequencing (scRNA-Seq) technology reveals biological processes and molecular-level genomic information among individual cells. Numerous computational methods, including methods based on graph neural networks (GNNs), have b...

GRLGRN: graph representation-based learning to infer gene regulatory networks from single-cell RNA-seq data.

BMC bioinformatics
BACKGROUND: A gene regulatory network (GRN) is a graph-level representation that describes the regulatory relationships between transcription factors and target genes in cells. The reconstruction of GRNs can help investigate cellular dynamics, drug d...

Molecular features and diagnostic modeling of synovium- and IPFP-derived OA macrophages in the inflammatory microenvironment via scRNA-seq and machine learning.

Journal of orthopaedic surgery and research
BACKGROUND: Osteoarthritis (OA) is the leading cause of degenerative joint disease, with total joint replacement as the only definitive cure. However, no disease-modifying therapy is currently available. Inflammation and fibrosis in the infrapatellar...

Assessing concordance between RNA-Seq and NanoString technologies in Ebola-infected nonhuman primates using machine learning.

BMC genomics
This study evaluates the concordance between RNA sequencing (RNA-Seq) and NanoString technologies for gene expression analysis in non-human primates (NHPs) infected with Ebola virus (EBOV). A detailed comparison of both platforms revealed a strong co...

Unique and shared transcriptomic signatures underlying localized scleroderma pathogenesis identified using interpretable machine learning.

JCI insight
Using transcriptomic profiling at single-cell resolution, we investigated cell-intrinsic and cell-extrinsic signatures associated with pathogenesis and inflammation-driven fibrosis in both adult and pediatric patients with localized scleroderma (LS)....

scAMZI: attention-based deep autoencoder with zero-inflated layer for clustering scRNA-seq data.

BMC genomics
BACKGROUND: Clustering scRNA-seq data plays a vital role in scRNA-seq data analysis and downstream analyses. Many computational methods have been proposed and achieved remarkable results. However, there are several limitations of these methods. First...

Mitigating ambient RNA and doublets effects on single cell transcriptomics analysis in cancer research.

Cancer letters
In cancer biology, where understanding the tumor microenvironment at high resolution is vital, ambient RNA contamination becomes a considerable problem. This hinders accurate delineation of intratumoral heterogeneity, complicates the identification o...

Deep Neural Network-Mining of Rice Drought-Responsive TF-TAG Modules by a Combinatorial Analysis of ATAC-Seq and RNA-Seq.

Plant, cell & environment
Drought is a critical risk factor that impacts rice growth and yields. Previous studies have focused on the regulatory roles of individual transcription factors in response to drought stress. However, there is limited understanding of multi-factor st...