用 moslin 绘制跨时间点的系谱追踪细胞图

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-10-21 DOI:10.1186/s13059-024-03422-4

Marius Lange, Zoe Piran, Michal Klein, Bastiaan Spanjaard, Dominik Klein, Jan Philipp Junker, Fabian J. Theis, Mor Nitzan

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引用次数: 0

摘要

同时分析单细胞基因表达和细胞系历史对研究细胞决策具有巨大的潜力。最近的计算方法将这两种模式结合到细胞轨迹中；然而，它们无法在破坏性时间序列实验中利用所有可用的系谱信息。在这里，我们介绍了基于 Gromov-Wasserstein 模型的 moslin，该模型可根据细胞系和基因表达信息将各时间点的细胞概况结合起来。我们通过模拟验证了我们的方法，并在秀丽隐杆线虫胚胎发育过程中演示了 moslin 如何预测命运概率和推定决策驱动基因。最后，我们利用 moslin 在斑马鱼心脏再生过程中划分瞬时激活的成纤维细胞状态之间的系谱关系。

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Mapping lineage-traced cells across time points with moslin

Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making. Recent computational approaches combine both modalities into cellular trajectories; however, they cannot make use of all available lineage information in destructive time-series experiments. Here, we present moslin, a Gromov-Wasserstein-based model to couple cellular profiles across time points based on lineage and gene expression information. We validate our approach in simulations and demonstrate on Caenorhabditis elegans embryonic development how moslin predicts fate probabilities and putative decision driver genes. Finally, we use moslin to delineate lineage relationships among transiently activated fibroblast states during zebrafish heart regeneration.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.