AIMC Topic: RNA-Seq

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CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

BMC biology
BACKGROUND: The advent of single-cell RNA sequencing (scRNA-seq) has provided unprecedented insights into cancer cellular diversity, enabling a comprehensive understanding of cancer at the single-cell level. However, identifying cancer cells remains ...

Identification of proliferating neural progenitors in the adult human hippocampus.

Science (New York, N.Y.)
Continuous adult hippocampal neurogenesis is involved in memory formation and mood regulation but is challenging to study in humans. Difficulties finding proliferating progenitor cells called into question whether and how new neurons may be generated...

Cross modality learning of cell painting and transcriptomics data improves mechanism of action clustering and bioactivity modelling.

Scientific reports
In drug discovery, different data modalities (chemical structure, cell biology, quantum mechanics, etc.) are abundant, and their integration can help with understanding aspects of chemistry, biology, and their interactions. Within cell biology, cell ...

Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer.

BMC bioinformatics
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression by allowing researchers to analyze the transcriptomes of individual cells. This technology provides unprecedented insights into cellular heterogeneity, cellular st...

Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data.

Nature communications
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...

scGANSL: Graph Attention Network with Subspace Learning for scRNA-seq Data Clustering.

Journal of chemical information and modeling
Single-cell RNA sequencing (scRNA-seq) has become a crucial technology for analyzing cellular diversity at the single-cell level. Cell clustering is crucial in scRNA-seq data analysis as it accurately identifies distinct cell types and uncovers poten...

Identification and evaluation of biomarkers for diagnosis of chronic hepatitis B using RNA-seq.

Virus research
BACKGROUND & AIM: Chronic hepatitis B (CHB) is a global public health problem affecting hundreds of millions of people and is associated with significant morbidity and mortality of liver cancer. Exosomes originate from cells and their detection in bi...

SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution.

BMC bioinformatics
BACKGROUND: Understanding cellular heterogeneity within tissues hinges on knowledge of their spatial context. However, it is still challenging to accurately map cells to their spatial coordinates.

Error Reduction in Leukemia Machine Learning Classification With Conformal Prediction.

JCO clinical cancer informatics
PURPOSE: Recent advances in machine learning have led to the development of classifiers that predict molecular subtypes of acute lymphoblastic leukemia (ALL) using RNA-sequencing (RNA-seq) data. Although these models have shown promising results, the...