International journal of molecular sciences
Feb 13, 2024
Single-cell RNA sequencing (scRNA-seq) data reveal the complexity and diversity of cellular ecosystems and molecular interactions in various biomedical research. Hence, identifying cell types from large-scale scRNA-seq data using existing annotations...
A crucial step in the analysis of single-cell data is annotating cells to cell types and states. While a myriad of approaches has been proposed, manual labeling of cells to create training datasets remains tedious and time-consuming. In the field of ...
Marine bacteria have been considered as important participants in revealing various carbon/sulfur/nitrogen cycles of marine ecosystem. Thus, how to accurately identify rare marine bacteria without a culture process is significant and valuable. In thi...
Existing RNA velocity estimation methods strongly rely on predefined dynamics and cell-agnostic constant transcriptional kinetic rates, assumptions often violated in complex and heterogeneous single-cell RNA sequencing (scRNA-seq) data. Using a graph...
Cell imaging technology is undoubtedly a powerful tool for studying single-cell heterogeneity due to its non-invasive and visual advantages. It covers microscope hardware, software, and image analysis techniques, which are hindered by low throughput ...
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Dec 25, 2023
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characteri...
Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) da...
Enhancers control gene expression and have crucial roles in development and homeostasis. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning t...
Journal of computational biology : a journal of computational molecular cell biology
Nov 28, 2023
Intratumoral heterogeneity and the presence of cancer stem cells are challenging issues in cancer therapy. An appropriate quantification of the stemness of individual cells for assessing the potential for self-renewal and differentiation from the cel...
BACKGROUND: Feature selection is an essential task in single-cell RNA-seq (scRNA-seq) data analysis and can be critical for gene dimension reduction and downstream analyses, such as gene marker identification and cell type classification. Most popula...
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