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

Autor:	Gong W; Lillehei Heart Institute, University of Minnesota, 2231 6th St S.E, 4-165 CCRB, Minneapolis, MN 55114, USA., Granados AA; California Institute of Technology, Pasadena, CA 91125, USA., Hu J; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA., Jones MG; Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA; Integrative Program of Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA., Raz O; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel., Salvador-Martínez I; Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK., Zhang H; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Chow KK; California Institute of Technology, Pasadena, CA 91125, USA., Kwak IY; Department of Applied Statistics, College of Business & Economics, Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea., Retkute R; Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK., Prusokiene A; School of Natural and Environmental Sciences, Newcastle University, Newcastle NE1 7RU, UK., Prusokas A; Department of Life Sciences, Imperial College London, London SW7 2AZ, UK., Khodaverdian A; Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA., Zhang R; Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA., Rao S; Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA., Wang R; Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA., Rennert P; EC Wise Inc., 1299 4th St #505, San Rafael, CA 94901, USA., Saipradeep VG; TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India., Sivadasan N; TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India., Rao A; TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India., Joseph T; TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India., Srinivasan R; TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India., Peng J; School of Computer Science, Northwestern Polytechnical University, Xi'an, China., Han L; School of Computer Science, Northwestern Polytechnical University, Xi'an, China., Shang X; School of Computer Science, Northwestern Polytechnical University, Xi'an, China., Garry DJ; Lillehei Heart Institute, University of Minnesota, 2231 6th St S.E, 4-165 CCRB, Minneapolis, MN 55114, USA., Yu T; Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA., Chung V; Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA., Mason M; Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA., Liu Z; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA., Guan Y; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Yosef N; Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA., Shendure J; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA., Telford MJ; Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK., Shapiro E; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel., Elowitz MB; California Institute of Technology, Pasadena, CA 91125, USA., Meyer P; T.J. Watson Research Center, IBM, Healthcare & Life Sciences, 1101 Kitchawan Rd 10598, Yorktown Heights, NY 10598, USA. Electronic address: pmeyerr@us.ibm.com.
Jazyk:	angličtina
Zdroj:	Cell systems [Cell Syst] 2021 Aug 18; Vol. 12 (8), pp. 810-826.e4. Date of Electronic Publication: 2021 Jun 18.
DOI:	10.1016/j.cels.2021.05.008
Abstrakt:	The 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. Competing Interests: Declaration of interests The authors declare no competing interests. Worm image in Figure 1 was modified from Caenorhabditis elegans hermaphrodite adult-en.svg from Wikimedia Commons by K. D. Schroeder, CC-BY-SA 3.0. The schematic cell lineage of C. elegans in Figures 1 and 6 was generated using the cell lineage web visualization tool CeLaVi available at http://celavi.pro (Salvador-Martínez et al., 2020). (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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