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Lookup NU author(s): Dr Alis Prusokiene
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND).
© 2021 The AuthorsThe recent advent of CRISPR and other molecular tools enabled the reconstruction of cell lineages based on induced DNA mutations and promises to solve the ones of more complex organisms. To date, no lineage reconstruction algorithms have been rigorously examined for their performance and robustness across dataset types and number of cells. To benchmark such methods, we decided to organize a DREAM challenge using in vitro experimental intMEMOIR recordings and in silico data for a C. elegans lineage tree of about 1,000 cells and a Mus musculus tree of 10,000 cells. Some of the 22 approaches submitted had excellent performance, but structural features of the trees prevented optimal reconstructions. Using smaller sub-trees as training sets proved to be a good approach for tuning algorithms to reconstruct larger trees. The simulation and reconstruction methods here generated delineate a potential way forward for solving larger cell lineage trees such as in mouse.
Author(s): Gong W, Granados AA, Hu J, Jones MG, Raz O, Salvador-Martinez I, Zhang H, Chow K-HK, Kwak I-Y, Retkute R, Prusokas A, Prusokas A, Khodaverdian A, Zhang R, Rao S, Wang R, Rennert P, Saipradeep VG, Sivadasan N, Rao A, Joseph T, Srinivasan R, Peng J, Han L, Shang X, Garry DJ, Yu T, Chung V, Mason M, Liu Z, Guan Y, Yosef N, Shendure J, Telford MJ, Shapiro E, Elowitz MB, Meyer P
Publication type: Article
Publication status: Published
Journal: Cell Systems
Year: 2021
Volume: 12
Issue: 8
Pages: 810-826.e4
Print publication date: 18/08/2021
Online publication date: 18/06/2021
Acceptance date: 11/05/2021
Date deposited: 25/08/2021
ISSN (print): 2405-4712
ISSN (electronic): 2405-4720
Publisher: Cell Press
URL: https://doi.org/10.1016/j.cels.2021.05.008
DOI: 10.1016/j.cels.2021.05.008
PubMed id: 34146472
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