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细胞-细胞通信推断的进步和挑战:对工具,资源和未来方向的全面审查
Giulia Cesaro1, James Shiniti Nagai2, Nicolò Gnoato3
1Department of Information Engineering, University of Padova, Via Gradenigo 6/B, 35131, Padova, Italy.
Briefings in bioinformatics
|June 19, 2025
概括
高通量测序推进了细胞间通信研究. 本报告回顾了100多种生物信息学工具和50种单细胞和空间转录组学资源,帮助研究人员选择最佳方法.
科学领域:
- 基因组学和生物信息学
- 细胞生物学 细胞生物学
背景情况:
- 单细胞和空间转录组学的进步刺激了对细胞-细胞通信推断的兴趣.
- 在过去的六年里,已经出现了100多个生物信息学工具和50个资源.
研究的目的:
- 提供关于细胞间通信分析方法和资源的当前状态的全面报告.
- 为研究人员解决工具和资源选择方面的挑战.
- 确定该领域的局限性和未来方向.
主要方法:
- 审查和聚合现有的关于细胞-细胞通信推断工具和资源的文献.
- 对工具和资源特征的分析,包括要求,评分,范围和限制.
- 将知识整合到一个集中的网络平台中,CCC-Catalog.
主要成果:
- 在生物信息学工具和用于细胞间通信分析的配体受体数据库中存在显著的多样性.
- 工具要求,评分和推断能力的变化 (细胞间与细胞内).
- 在资源注释,物种覆盖和信号聚焦方面的差异.
结论:
- 工具/资源的丰富性和多样性给研究人员带来了挑战.
- "CCC-Catalog"旨在集中信息,并促进选择合适的方法.
- 需要进一步开发以解决局限性并推进细胞-细胞通信推断.
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