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

Parra, R. G., Papadopoulos, N., Ahumada-Arranz, L., El Kholtei, J., Mottelson, N., Horokhovsky, Y., et al. (2019). Reconstructing complex lineage trees from scRNA-seq data using MERLoT. Nucleic Acids Research, 47(17), 8961-8974. doi:10.1093/nar/gkz706.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-20A2-F Version Permalink: http://hdl.handle.net/21.11116/0000-0005-20A6-B
Genre: Journal Article

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 Creators:
Parra, R. G., Author
Papadopoulos, N.1, Author              
Ahumada-Arranz, L., Author
El Kholtei, J., Author
Mottelson, N., Author
Horokhovsky, Y.2, Author              
Treutlein, B., Author
Söding, J.1, Author              
Affiliations:
1Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1933286              
2Research Group of Quantitative and System Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_2466694              

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 Abstract: 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 (https://github.com/soedinglab/ 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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Language(s): eng - English
 Dates: 2019-08-202019-09-26
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1093/nar/gkz706
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 47 (17) Sequence Number: - Start / End Page: 8961 - 8974 Identifier: -