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Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees

Lookup NU author(s): 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.

Publication metadata

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


DOI: 10.1016/j.cels.2021.05.008

PubMed id: 34146472


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Funder referenceFunder name
Paul G. Allen Frontiers Group Prime Awarding Agency and HFSP (RGP0002/2016) to I.S.-M. and M.J.T.