AIMC Topic: Sequence Analysis, RNA

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scMUSCL: multi-source transfer learning for clustering scRNA-seq data.

Bioinformatics (Oxford, England)
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) analysis relies heavily on effective clustering to facilitate numerous downstream applications. Although several machine learning methods have been developed to enhance single-cell clustering, most a...

scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery.

Briefings in bioinformatics
Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) produces vast amounts of individual cell profiling data. Its analysis presents a significant challenge in accurately annotating cell types and their associated biomarkers. Different pipelines ...

Machine learning-augmented m6A-Seq analysis without a reference genome.

Briefings in bioinformatics
Methylated RNA m6A immunoprecipitation sequencing (m6A-Seq) is a powerful technique for investigating transcriptome-wide m6A modification. However, most of the existing m6A-Seq protocols rely on reference genomes, limiting their use in species lackin...

Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering.

Briefings in bioinformatics
Clustering is pivotal in deciphering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data. However, it suffers from several challenges in handling the high dimensionality and complexity of scRNA-seq data. Especially when employing gr...

Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data.

Briefings in bioinformatics
Single-cell sequencing has advanced our understanding of cellular heterogeneity and disease pathology, offering insights into cellular behavior and immune mechanisms. However, extracting meaningful phenotype-related features is challenging due to noi...

Study on the mechanism of action of the active ingredient of Calculus Bovis in the treatment of sepsis by integrating single-cell sequencing and machine learning.

Medicine
BACKGROUND: Sepsis, a complex inflammatory condition with high mortality rates, lacks effective treatments. This study explores the therapeutic mechanisms of Calculus Bovis in sepsis using network pharmacology and RNA sequencing.

adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks.

Bioinformatics (Oxford, England)
MOTIVATION: Several machine learning (ML) algorithms dedicated to the detection of healthy and diseased cell types from single-cell RNA sequencing (scRNA-seq) data have been proposed for biomedical purposes. This raises concerns about their vulnerabi...

CoupleVAE: coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data.

Briefings in bioinformatics
With the rapid advances in single-cell sequencing technology, it is now feasible to conduct in-depth genetic analysis in individual cells. Study on the dynamics of single cells in response to perturbations is of great significance for understanding t...

Optimizing sample size for supervised machine learning with bulk transcriptomic sequencing: a learning curve approach.

Briefings in bioinformatics
Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate classification accuracy without undue resource allocat...

COME: contrastive mapping learning for spatial reconstruction of single-cell RNA sequencing data.

Bioinformatics (Oxford, England)
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) enables high-throughput transcriptomic profiling at single-cell resolution. The inherent spatial location is crucial for understanding how single cells orchestrate multicellular functions and drive d...