{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/estimation-of-cell-lineage-trees-by-maximum","title":"Estimation of cell lineage trees by maximum-likelihood phylogenetics","arxiv_id":"1904.00117","date":"2019-03-29","proceeding":null,"authors":[],"abstract":"CRISPR technology has enabled large-scale cell lineage tracing for complex\nmulticellular organisms by mutating synthetic genomic barcodes during\norganismal development. However, these sophisticated biological tools currently\nuse ad-hoc and outmoded computational methods to reconstruct the cell lineage\ntree from the mutated barcodes. Because these methods are agnostic to the\nbiological mechanism, they are unable to take full advantage of the data's\nstructure. We propose a statistical model for the mutation process and develop\na procedure to estimate the tree topology, branch lengths, and mutation\nparameters by iteratively applying penalized maximum likelihood estimation. In\ncontrast to existing techniques, our method estimates time along each branch,\nrather than number of mutation events, thus providing a detailed account of\ntissue-type differentiation. Via simulations, we demonstrate that our method is\nsubstantially more accurate than existing approaches. Our reconstructed trees\nalso better recapitulate known aspects of zebrafish development and reproduce\nsimilar results across fish replicates.","url_abs":"http://arxiv.org/abs/1904.00117v1","url_pdf":"http://arxiv.org/pdf/1904.00117v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"estimation-of-cell-lineage-trees-by-maximum","repo_url":"https://github.com/matsengrp/gestaltamania","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}