{"entity": "researcher", "timestamp": "2026-04-13T04:33:03.296Z", "family": "Jun", "given": "Seong-Hwan", "initials": "SH", "orcid": "0000-0001-8924-0075", "affiliations": ["SciLifeLab, School of EECS, KTH Royal Institute of Technology, Stockholm, Sweden.", "Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e49aa3ca14b490eb378dbd956efaffc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e49aa3ca14b490eb378dbd956efaffc"}}, "publications": [{"entity": "publication", "iuid": "a8f955e41ebd42daa2b3966499fa8248", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a8f955e41ebd42daa2b3966499fa8248.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a8f955e41ebd42daa2b3966499fa8248"}}, "title": "Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.", "authors": [{"family": "Jun", "given": "Seong-Hwan", "initials": "SH", "orcid": "0000-0001-8924-0075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e49aa3ca14b490eb378dbd956efaffc.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "O'Flanagan", "given": "Ciara", "initials": "C"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55acae2b727144ddac3ac6bfe51fc74d.json"}}, {"family": "Aparicio", "given": "Samuel", "initials": "S", "orcid": "0000-0002-0487-9599", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0772d0f35bde4d4ca46b93eaaf7b96cf.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Roth", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3422-8823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4f921580aec4734ad538c0bc3e70b02.json"}}, {"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": "2023-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "982", "issn-l": "2041-1723"}, "abstract": "Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.", "doi": "10.1038/s41467-023-36202-y", "pmid": "36813776", "labels": {"SciLifeLab Fellow": null, "Camilla Engblom": null}, "xrefs": [{"db": "pmc", "key": "PMC9946941"}, {"db": "pii", "key": "10.1038/s41467-023-36202-y"}], "notes": [], "created": "2023-06-01T06:49:27.955Z", "modified": "2023-06-01T06:49:28.457Z"}]}