{"id":"https://openalex.org/W4387873137","doi":"https://doi.org/10.1371/journal.pcbi.1011379","title":"Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity","display_name":"Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity","publication_year":2023,"publication_date":"2023-10-23","ids":{"openalex":"https://openalex.org/W4387873137","doi":"https://doi.org/10.1371/journal.pcbi.1011379","pmid":"https://pubmed.ncbi.nlm.nih.gov/37871126"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011379","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011379","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011379&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011379&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047585596","display_name":"Thomas B.K. Watkins","orcid":"https://orcid.org/0000-0001-7414-737X"},"institutions":[{"id":"https://openalex.org/I2801081054","display_name":"The Francis Crick Institute","ror":"https://ror.org/04tnbqb63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801081054"]},{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]},{"id":"https://openalex.org/I4210088881","display_name":"London Cancer","ror":"https://ror.org/005kpb876","country_code":"GB","type":"other","lineage":["https://openalex.org/I4210088881"]},{"id":"https://openalex.org/I4210147892","display_name":"CRUK Lung Cancer Centre of Excellence","ror":"https://ror.org/04nm2mq63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210147892"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Thomas B. K. Watkins","raw_affiliation_strings":["Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom","The Francis Crick Institute, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801316944","https://openalex.org/I4210088881","https://openalex.org/I4210147892","https://openalex.org/I45129253"]},{"raw_affiliation_string":"The Francis Crick Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801081054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042286774","display_name":"Emma Colliver","orcid":"https://orcid.org/0000-0002-1497-0740"},"institutions":[{"id":"https://openalex.org/I2801081054","display_name":"The Francis Crick Institute","ror":"https://ror.org/04tnbqb63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801081054"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Emma C. Colliver","raw_affiliation_strings":["The Francis Crick Institute, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Francis Crick Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801081054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062858483","display_name":"Matthew R. Huska","orcid":"https://orcid.org/0000-0002-0912-745X"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I4577782","display_name":"Technische Universit\u00e4t Berlin","ror":"https://ror.org/03v4gjf40","country_code":"DE","type":"education","lineage":["https://openalex.org/I4577782"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthew R. Huska","raw_affiliation_strings":["Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany","Department of Electrical Engineering & Computer Science, Technische Universit\u00e4t Berlin, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany","institution_ids":["https://openalex.org/I205582932"]},{"raw_affiliation_string":"Department of Electrical Engineering & Computer Science, Technische Universit\u00e4t Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I4577782"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046622096","display_name":"Tom L. Kaufmann","orcid":"https://orcid.org/0000-0003-4374-1338"},"institutions":[{"id":"https://openalex.org/I180923762","display_name":"University of Cologne","ror":"https://ror.org/00rcxh774","country_code":"DE","type":"education","lineage":["https://openalex.org/I180923762"]},{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I4210088352","display_name":"Berliner Institut f\u00fcr Sozialforschung","ror":"https://ror.org/0043ncq27","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210088352"]},{"id":"https://openalex.org/I4210153755","display_name":"University Hospital Cologne","ror":"https://ror.org/05mxhda18","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210153755"]},{"id":"https://openalex.org/I4401727010","display_name":"Berlin Institute for the Foundations of Learning and Data","ror":"https://ror.org/05dsfb086","country_code":null,"type":"facility","lineage":["https://openalex.org/I4401727010","https://openalex.org/I4577782","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I4577782","display_name":"Technische Universit\u00e4t Berlin","ror":"https://ror.org/03v4gjf40","country_code":"DE","type":"education","lineage":["https://openalex.org/I4577782"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Tom L. Kaufmann","raw_affiliation_strings":["BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany","Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany","Department of Electrical Engineering & Computer Science, Technische Universit\u00e4t Berlin, Berlin, Germany","Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany","BIFOLD\u2014Berlin Institute for the Foundations of Learning and Data, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany","institution_ids":["https://openalex.org/I4210088352"]},{"raw_affiliation_string":"Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany","institution_ids":["https://openalex.org/I205582932"]},{"raw_affiliation_string":"Department of Electrical Engineering & Computer Science, Technische Universit\u00e4t Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I4577782"]},{"raw_affiliation_string":"Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany","institution_ids":["https://openalex.org/I4210153755","https://openalex.org/I180923762"]},{"raw_affiliation_string":"BIFOLD\u2014Berlin Institute for the Foundations of Learning and Data, Berlin, Germany","institution_ids":["https://openalex.org/I4401727010"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112099576","display_name":"Emilia L. Lim","orcid":"https://orcid.org/0009-0009-2954-1795"},"institutions":[{"id":"https://openalex.org/I2801081054","display_name":"The Francis Crick Institute","ror":"https://ror.org/04tnbqb63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801081054"]},{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]},{"id":"https://openalex.org/I4210088881","display_name":"London Cancer","ror":"https://ror.org/005kpb876","country_code":"GB","type":"other","lineage":["https://openalex.org/I4210088881"]},{"id":"https://openalex.org/I4210147892","display_name":"CRUK Lung Cancer Centre of Excellence","ror":"https://ror.org/04nm2mq63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210147892"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Emilia L. Lim","raw_affiliation_strings":["Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom","The Francis Crick Institute, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801316944","https://openalex.org/I4210088881","https://openalex.org/I4210147892","https://openalex.org/I45129253"]},{"raw_affiliation_string":"The Francis Crick Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801081054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061674163","display_name":"Cody B. Duncan","orcid":"https://orcid.org/0000-0003-3127-228X"},"institutions":[{"id":"https://openalex.org/I180923762","display_name":"University of Cologne","ror":"https://ror.org/00rcxh774","country_code":"DE","type":"education","lineage":["https://openalex.org/I180923762"]},{"id":"https://openalex.org/I4210153755","display_name":"University Hospital Cologne","ror":"https://ror.org/05mxhda18","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210153755"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Cody B. Duncan","raw_affiliation_strings":["Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3127-228X","affiliations":[{"raw_affiliation_string":"Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany","institution_ids":["https://openalex.org/I4210153755","https://openalex.org/I180923762"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081872336","display_name":"Kerstin Haase","orcid":"https://orcid.org/0000-0002-0944-5618"},"institutions":[{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Kerstin Haase","raw_affiliation_strings":["Department of Pediatric Oncology and Hematology, Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","Experimental and Clinical Research Center (ECRC) of the MDC and Charit\u00e9 Berlin, Berlin, Germany","German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany","Department of Pediatric Oncology and Hematology, Charit\u00e9\u2013Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatric Oncology and Hematology, Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Experimental and Clinical Research Center (ECRC) of the MDC and Charit\u00e9 Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]},{"raw_affiliation_string":"Department of Pediatric Oncology and Hematology, Charit\u00e9\u2013Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I7877124","https://openalex.org/I75951250"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079808888","display_name":"Peter Van Loo","orcid":"https://orcid.org/0000-0003-0292-1949"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I2801081054","display_name":"The Francis Crick Institute","ror":"https://ror.org/04tnbqb63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801081054"]}],"countries":["GB","US"],"is_corresponding":true,"raw_author_name":"Peter Van Loo","raw_affiliation_strings":["Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America","Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America","The Francis Crick Institute, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"The Francis Crick Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801081054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016475369","display_name":"Charles Swanton","orcid":"https://orcid.org/0000-0002-4299-3018"},"institutions":[{"id":"https://openalex.org/I2801081054","display_name":"The Francis Crick Institute","ror":"https://ror.org/04tnbqb63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801081054"]},{"id":"https://openalex.org/I2801259928","display_name":"Royal London Hospital","ror":"https://ror.org/019my5047","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I225661044","https://openalex.org/I2801259928"]},{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]},{"id":"https://openalex.org/I4210088881","display_name":"London Cancer","ror":"https://ror.org/005kpb876","country_code":"GB","type":"other","lineage":["https://openalex.org/I4210088881"]},{"id":"https://openalex.org/I4210147892","display_name":"CRUK Lung Cancer Centre of Excellence","ror":"https://ror.org/04nm2mq63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210147892"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Charles Swanton","raw_affiliation_strings":["Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom","Department of Medical Oncology, University College London Hospitals, London, United Kingdom","The Francis Crick Institute, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801316944","https://openalex.org/I4210088881","https://openalex.org/I4210147892","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Department of Medical Oncology, University College London Hospitals, London, United Kingdom","institution_ids":["https://openalex.org/I2801259928","https://openalex.org/I45129253"]},{"raw_affiliation_string":"The Francis Crick Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801081054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056525592","display_name":"Nicholas McGranahan","orcid":"https://orcid.org/0000-0001-9537-4045"},"institutions":[{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]},{"id":"https://openalex.org/I4210088881","display_name":"London Cancer","ror":"https://ror.org/005kpb876","country_code":"GB","type":"other","lineage":["https://openalex.org/I4210088881"]},{"id":"https://openalex.org/I4210147892","display_name":"CRUK Lung Cancer Centre of Excellence","ror":"https://ror.org/04nm2mq63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210147892"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Nicholas McGranahan","raw_affiliation_strings":["Cancer Genome Evolution Research Group, University College London Cancer Institute, London, United Kingdom","Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Genome Evolution Research Group, University College London Cancer Institute, London, United Kingdom","institution_ids":["https://openalex.org/I4210088881","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom","institution_ids":["https://openalex.org/I2801316944","https://openalex.org/I4210088881","https://openalex.org/I4210147892","https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069018848","display_name":"Roland F. Schwarz","orcid":"https://orcid.org/0000-0001-9155-4268"},"institutions":[{"id":"https://openalex.org/I180923762","display_name":"University of Cologne","ror":"https://ror.org/00rcxh774","country_code":"DE","type":"education","lineage":["https://openalex.org/I180923762"]},{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I4210088352","display_name":"Berliner Institut f\u00fcr Sozialforschung","ror":"https://ror.org/0043ncq27","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210088352"]},{"id":"https://openalex.org/I4210153755","display_name":"University Hospital Cologne","ror":"https://ror.org/05mxhda18","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210153755"]},{"id":"https://openalex.org/I4401727010","display_name":"Berlin Institute for the Foundations of Learning and Data","ror":"https://ror.org/05dsfb086","country_code":null,"type":"facility","lineage":["https://openalex.org/I4401727010","https://openalex.org/I4577782","https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Roland F. Schwarz","raw_affiliation_strings":["BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany","Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany","Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany","BIFOLD\u2014Berlin Institute for the Foundations of Learning and Data, Berlin, Germany"],"raw_orcid":"https://orcid.org/0000-0001-9155-4268","affiliations":[{"raw_affiliation_string":"BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany","institution_ids":["https://openalex.org/I4210088352"]},{"raw_affiliation_string":"Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany","institution_ids":["https://openalex.org/I205582932"]},{"raw_affiliation_string":"Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany","institution_ids":["https://openalex.org/I4210153755","https://openalex.org/I180923762"]},{"raw_affiliation_string":"BIFOLD\u2014Berlin Institute for the Foundations of Learning and Data, Berlin, Germany","institution_ids":["https://openalex.org/I4401727010"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5016475369","https://openalex.org/A5042286774","https://openalex.org/A5046622096","https://openalex.org/A5047585596","https://openalex.org/A5056525592","https://openalex.org/A5061674163","https://openalex.org/A5062858483","https://openalex.org/A5069018848","https://openalex.org/A5079808888","https://openalex.org/A5081872336","https://openalex.org/A5112099576"],"corresponding_institution_ids":["https://openalex.org/I1343551460","https://openalex.org/I17937529","https://openalex.org/I180923762","https://openalex.org/I205582932","https://openalex.org/I223822909","https://openalex.org/I2801081054","https://openalex.org/I2801259928","https://openalex.org/I2801316944","https://openalex.org/I39343248","https://openalex.org/I4210088352","https://openalex.org/I4210088881","https://openalex.org/I4210147892","https://openalex.org/I4210153755","https://openalex.org/I4401727010","https://openalex.org/I45129253","https://openalex.org/I4577782","https://openalex.org/I75951250","https://openalex.org/I7877124"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.7112,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.95193383,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"19","issue":"10","first_page":"e1011379","last_page":"e1011379"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.7828065156936646},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6370707154273987},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5895393490791321},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.5863692760467529},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5537289381027222},{"id":"https://openalex.org/keywords/phaser","display_name":"Phaser","score":0.5273289084434509},{"id":"https://openalex.org/keywords/copy-number-analysis","display_name":"Copy number analysis","score":0.5165197253227234},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.48690667748451233},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.48213669657707214},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.45474502444267273},{"id":"https://openalex.org/keywords/somatic-cell","display_name":"Somatic cell","score":0.44538912177085876},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.4129776954650879},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.3880752921104431},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2408495843410492},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14122545719146729}],"concepts":[{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.7828065156936646},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6370707154273987},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5895393490791321},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.5863692760467529},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5537289381027222},{"id":"https://openalex.org/C135393689","wikidata":"https://www.wikidata.org/wiki/Q1551588","display_name":"Phaser","level":2,"score":0.5273289084434509},{"id":"https://openalex.org/C166608930","wikidata":"https://www.wikidata.org/wiki/Q5169175","display_name":"Copy number analysis","level":5,"score":0.5165197253227234},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.48690667748451233},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.48213669657707214},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.45474502444267273},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.44538912177085876},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4129776954650879},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.3880752921104431},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2408495843410492},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14122545719146729},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1011379","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011379","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011379&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37871126","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37871126","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:edoc.mdc-berlin.de:23811","is_oa":true,"landing_page_url":"https://edoc.mdc-berlin.de/id/eprint/23811/2/23811suppl.zip","pdf_url":"https://edoc.mdc-berlin.de/id/eprint/23811/1/23811oa.pdf","source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10181788","is_oa":true,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10181788/","pdf_url":"https://discovery.ucl.ac.uk/10181788/1/journal.pcbi.1011379.pdf","source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   PLoS Computational Biology , 19  (10)    , Article e1011379. (2023)      ","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10621967","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10621967","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10621967/pdf/pcbi.1011379.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:digitalcommons.library.tmc.edu:uthgsbs_docs-3179","is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/uthgsbs_docs/2233","pdf_url":null,"source":{"id":"https://openalex.org/S4377196655","display_name":"Digital Commons-TMC (Texas Medical Center)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1337852284","host_organization_name":"Texas Medical Center","host_organization_lineage":["https://openalex.org/I1337852284"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty, Staff and Student Publications","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:813504d2d9cb4d0b820b2c0d5e22969e","is_oa":true,"landing_page_url":"https://doaj.org/article/813504d2d9cb4d0b820b2c0d5e22969e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 10, p e1011379 (2023)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/24534514","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Refphase_Multi-sample_phasing_reveals_haplotype-specific_copy_number_heterogeneity_/24534514","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"doi:10.25418/crick.24534514.v1","is_oa":true,"landing_page_url":"https://doi.org/10.25418/crick.24534514.v1","pdf_url":null,"source":{"id":"https://openalex.org/S7407051354","display_name":"The Francis Crick Institute","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011379","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011379","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011379&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1840670726","display_name":null,"funder_award_id":"RR210006","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G2721993293","display_name":null,"funder_award_id":"RSRP\\R\\210001","funder_id":"https://openalex.org/F4320320006","funder_display_name":"Royal Society"},{"id":"https://openalex.org/G3038870994","display_name":null,"funder_award_id":"211179/Z/18/Z","funder_id":"https://openalex.org/F4320320006","funder_display_name":"Royal Society"},{"id":"https://openalex.org/G3194548215","display_name":null,"funder_award_id":"C11496/A30025","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G3324096309","display_name":null,"funder_award_id":"ID16584","funder_id":"https://openalex.org/F4320320320","funder_display_name":"Rosetrees Trust"},{"id":"https://openalex.org/G3808951710","display_name":null,"funder_award_id":"CC2008","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G3957183390","display_name":null,"funder_award_id":"ref. 01IS18025A and ref 01IS18037A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4239497624","display_name":null,"funder_award_id":"C11496/A30025","funder_id":"https://openalex.org/F4320330795","funder_display_name":"CRUK Lung Cancer Centre of Excellence"},{"id":"https://openalex.org/G4275441869","display_name":null,"funder_award_id":"C416/A21999","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G4431183167","display_name":null,"funder_award_id":"A17786","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G4589978392","display_name":null,"funder_award_id":"CC2008; CC2041","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G4598959532","display_name":null,"funder_award_id":"CC2008","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G4767103862","display_name":null,"funder_award_id":"C416/","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G5579996087","display_name":null,"funder_award_id":"ID16584","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G5741171854","display_name":null,"funder_award_id":"ID16584","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G5874233344","display_name":null,"funder_award_id":"835297","funder_id":"https://openalex.org/F4320334678","funder_display_name":"European Research Council"},{"id":"https://openalex.org/G5958715125","display_name":null,"funder_award_id":"211179","funder_id":"https://openalex.org/F4320320006","funder_display_name":"Royal Society"},{"id":"https://openalex.org/G6777807394","display_name":null,"funder_award_id":"CC2008; CC2041","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G6813130969","display_name":null,"funder_award_id":"CC2041","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G6966623676","display_name":null,"funder_award_id":"CC2008; CC2041","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7269663634","display_name":null,"funder_award_id":"21-029-ASP","funder_id":"https://openalex.org/F4320315143","funder_display_name":"Mark Foundation For Cancer Research"},{"id":"https://openalex.org/G7409131040","display_name":null,"funder_award_id":"SU2C-AACR-DT23-17","funder_id":"https://openalex.org/F4320332898","funder_display_name":"Stand Up To Cancer"},{"id":"https://openalex.org/G7492514856","display_name":null,"funder_award_id":"C11496/A17786","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G7593086743","display_name":null,"funder_award_id":"CC2041","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7894469207","display_name":null,"funder_award_id":"RP/EA/180007","funder_id":"https://openalex.org/F4320320006","funder_display_name":"Royal Society"},{"id":"https://openalex.org/G8285592626","display_name":null,"funder_award_id":"211179/Z/18/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8410755691","display_name":null,"funder_award_id":"CC2041","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G8764295400","display_name":null,"funder_award_id":"835297","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8913699038","display_name":null,"funder_award_id":"CC2041","funder_id":"https://openalex.org/F4320312060","funder_display_name":"Francis Crick Institute"},{"id":"https://openalex.org/G900861293","display_name":null,"funder_award_id":"AACR-DT23-17","funder_id":"https://openalex.org/F4320332898","funder_display_name":"Stand Up To Cancer"}],"funders":[{"id":"https://openalex.org/F4320306091","display_name":"American Association for Cancer Research","ror":"https://ror.org/02fnpv153"},{"id":"https://openalex.org/F4320306260","display_name":"Breast Cancer Research Foundation","ror":"https://ror.org/0348ff195"},{"id":"https://openalex.org/F4320306997","display_name":"LUNGevity Foundation","ror":"https://ror.org/02t0s0z58"},{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320309149","display_name":"Entertainment Industry Foundation","ror":"https://ror.org/01dmpb598"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320312060","display_name":"Francis Crick Institute","ror":"https://ror.org/04tnbqb63"},{"id":"https://openalex.org/F4320315143","display_name":"Mark Foundation For Cancer Research","ror":"https://ror.org/00v7th354"},{"id":"https://openalex.org/F4320317289","display_name":"Ministerium f\u00fcr Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen","ror":null},{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"},{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320320286","display_name":"University College London","ror":"https://ror.org/02jx3x895"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320320","display_name":"Rosetrees Trust","ror":"https://ror.org/04e3zg361"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320325698","display_name":"Helmholtz Association","ror":null},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320330795","display_name":"CRUK Lung Cancer Centre of Excellence","ror":"https://ror.org/04nm2mq63"},{"id":"https://openalex.org/F4320332898","display_name":"Stand Up To Cancer","ror":"https://ror.org/01dmpb598"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387873137.pdf","grobid_xml":"https://content.openalex.org/works/W4387873137.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W1967304777","https://openalex.org/W1979693095","https://openalex.org/W1995794660","https://openalex.org/W2001658484","https://openalex.org/W2006288875","https://openalex.org/W2010873488","https://openalex.org/W2016661249","https://openalex.org/W2041993682","https://openalex.org/W2050146329","https://openalex.org/W2061539393","https://openalex.org/W2077749987","https://openalex.org/W2088735033","https://openalex.org/W2096746187","https://openalex.org/W2101979288","https://openalex.org/W2109991075","https://openalex.org/W2111307685","https://openalex.org/W2137220794","https://openalex.org/W2138345444","https://openalex.org/W2150575159","https://openalex.org/W2170490448","https://openalex.org/W2171777347","https://openalex.org/W2171892226","https://openalex.org/W2175940415","https://openalex.org/W2185207072","https://openalex.org/W2233072870","https://openalex.org/W2275877493","https://openalex.org/W2346025119","https://openalex.org/W2405513305","https://openalex.org/W2414771725","https://openalex.org/W2529241974","https://openalex.org/W2560383108","https://openalex.org/W2586629973","https://openalex.org/W2608738563","https://openalex.org/W2609243345","https://openalex.org/W2741106212","https://openalex.org/W2775981503","https://openalex.org/W2783667606","https://openalex.org/W2796079887","https://openalex.org/W2797542577","https://openalex.org/W2807848287","https://openalex.org/W2884903585","https://openalex.org/W2889721546","https://openalex.org/W2946362598","https://openalex.org/W2973350525","https://openalex.org/W2981548686","https://openalex.org/W2982060649","https://openalex.org/W2990059271","https://openalex.org/W3003504182","https://openalex.org/W3009570993","https://openalex.org/W3012749684","https://openalex.org/W3027643991","https://openalex.org/W3081916416","https://openalex.org/W3082136743","https://openalex.org/W3082714866","https://openalex.org/W3103510420","https://openalex.org/W3119400275","https://openalex.org/W3137654632","https://openalex.org/W3142571537","https://openalex.org/W3151413124","https://openalex.org/W3157220164","https://openalex.org/W3165458352","https://openalex.org/W3175892313","https://openalex.org/W3204399561","https://openalex.org/W3216618334","https://openalex.org/W4206967925","https://openalex.org/W4210516674","https://openalex.org/W4211137491","https://openalex.org/W4220873173","https://openalex.org/W4299627282","https://openalex.org/W4307658070","https://openalex.org/W4309013615","https://openalex.org/W4365137743","https://openalex.org/W4366590831"],"related_works":["https://openalex.org/W2062965527","https://openalex.org/W2133327999","https://openalex.org/W2081326723","https://openalex.org/W4291136042","https://openalex.org/W2014477412","https://openalex.org/W2032955575","https://openalex.org/W2154361640","https://openalex.org/W2003084393","https://openalex.org/W2082810381","https://openalex.org/W2580223441"],"abstract_inverted_index":{"Most":[0],"computational":[1],"methods":[2],"that":[3,40],"infer":[4,46,58],"somatic":[5],"copy":[6,48],"number":[7],"alterations":[8],"(SCNAs)":[9],"from":[10,26,95],"bulk":[11],"sequencing":[12,21],"of":[13,22,84,92],"DNA":[14],"analyse":[15],"tumour":[16,24],"samples":[17,25,94],"individually.":[18],"However,":[19],"the":[20,82],"multiple":[23],"a":[27,89],"patient's":[28],"disease":[29],"is":[30],"an":[31,38],"increasingly":[32],"common":[33],"practice.":[34],"We":[35,53],"introduce":[36],"Refphase,":[37],"algorithm":[39],"leverages":[41],"this":[42],"multi-sampling":[43],"approach":[44],"to":[45,57,66,77],"haplotype-specific":[47,59],"numbers":[49],"through":[50],"multi-sample":[51],"phasing.":[52],"demonstrate":[54],"Refphase's":[55],"ability":[56],"SCNAs":[60],"and":[61,76],"characterise":[62],"their":[63],"intra-tumour":[64],"heterogeneity,":[65],"uncover":[67],"previously":[68],"undetected":[69],"allelic":[70],"imbalance":[71],"in":[72,81,88],"low":[73],"purity":[74],"samples,":[75],"identify":[78],"parallel":[79],"evolution":[80],"context":[83],"whole":[85],"genome":[86],"doubling":[87],"pan-cancer":[90],"cohort":[91],"336":[93],"99":[96],"tumours.":[97]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}