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Nucleic Acids Res. 2019 Aug 20. pii: gkz706. doi: 10.1093/nar/gkz706. [Epub ahead of print]

Reconstructing complex lineage trees from scRNA-seq data using MERLoT.

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Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany.
Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.


Advances in single-cell transcriptomics techniques are revolutionizing studies of cellular differentiation and heterogeneity. It has become possible to track the trajectory of thousands of genes across the cellular lineage trees that represent the temporal emergence of cell types during dynamic processes. However, reconstruction of cellular lineage trees with more than a few cell fates has proved challenging. We present MERLoT (, a flexible and user-friendly tool to reconstruct complex lineage trees from single-cell transcriptomics data. It can impute temporal gene expression profiles along the reconstructed tree. We show MERLoT's capabilities on various real cases and hundreds of simulated datasets.


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