{"entity": "researcher", "timestamp": "2026-08-23T09:27:17.913Z", "family": "Koptagel", "given": "Hazal", "initials": "H", "orcid": "0000-0002-6234-4656", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/71be5a3974f04deb9b297b854fdbe9d8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/71be5a3974f04deb9b297b854fdbe9d8"}}, "publications": [{"entity": "publication", "iuid": "7a63db880140488fb011829c9166cfb5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a63db880140488fb011829c9166cfb5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a63db880140488fb011829c9166cfb5"}}, "title": "Scuphr: A probabilistic framework for cell lineage tree reconstruction.", "authors": [{"family": "Koptagel", "given": "Hazal", "initials": "H", "orcid": "0000-0002-6234-4656", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71be5a3974f04deb9b297b854fdbe9d8.json"}}, {"family": "Jun", "given": "Seong-Hwan", "initials": "SH"}, {"family": "H\u00e5rd", "given": "Joanna", "initials": "J"}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "20", "issue": "5", "pages": "e1012094", "issn-l": "1553-734X"}, "abstract": "Cell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method's robustness is investigated using various synthetic datasets and a biological dataset of 18 cells.", "doi": "10.1371/journal.pcbi.1012094", "pmid": "38723024", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11125557"}, {"db": "pii", "key": "PCOMPBIOL-D-22-01820"}], "notes": [], "created": "2026-08-20T12:43:18.048Z", "modified": "2026-08-20T12:43:18.134Z"}, {"entity": "publication", "iuid": "b0043f55bb154a948f43788b67940f4e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b0043f55bb154a948f43788b67940f4e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b0043f55bb154a948f43788b67940f4e"}}, "title": "Scuphr: A probabilistic framework for cell lineage tree reconstruction", "authors": [{"family": "Koptagel", "given": "Hazal", "initials": "H", "orcid": "0000-0002-6234-4656", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71be5a3974f04deb9b297b854fdbe9d8.json"}}, {"family": "Jun", "given": "Seong Hwan", "initials": "SH", "orcid": "0000-0001-8924-0075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e49aa3ca14b490eb378dbd956efaffc.json"}}, {"family": "H\u00e5rd", "given": "Joanna", "initials": "J"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}], "type": "posted-content", "published": "2018-06-29", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/357442", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:10:36.917Z", "modified": "2026-08-20T11:10:36.964Z"}]}