{"id":"https://openalex.org/W2104801871","doi":"https://doi.org/10.1093/bioinformatics/btv233","title":"Inferring models of multiscale copy number evolution for single-tumor phylogenetics","display_name":"Inferring models of multiscale copy number evolution for single-tumor phylogenetics","publication_year":2015,"publication_date":"2015-06-10","ids":{"openalex":"https://openalex.org/W2104801871","doi":"https://doi.org/10.1093/bioinformatics/btv233","mag":"2104801871","pmid":"https://pubmed.ncbi.nlm.nih.gov/26072490","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4481700"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv233","doi":"https://doi.org/10.1093/bioinformatics/btv233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i258/49014042/bioinformatics_31_12_i258.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i258/49014042/bioinformatics_31_12_i258.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110461875","display_name":"Salim Akhter Chowdhury","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Salim Akhter Chowdhury","raw_affiliation_strings":["1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210140884","https://openalex.org/I4210149717","https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041973530","display_name":"Edward Michael Gertz","orcid":"https://orcid.org/0000-0001-8390-4387","observed_orcids":["https://orcid.org/0000-0001-8390-4387"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E. Michael Gertz","raw_affiliation_strings":["1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210140884","https://openalex.org/I4210149717","https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074997587","display_name":"Darawalee Wangsa","orcid":"https://orcid.org/0000-0001-8585-3077","observed_orcids":["https://orcid.org/0000-0001-8585-3077"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Darawalee Wangsa","raw_affiliation_strings":["1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210140884","https://openalex.org/I4210149717","https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068597889","display_name":"Kerstin Heselmeyer\u2010Haddad","orcid":"https://orcid.org/0000-0001-7349-7407","observed_orcids":["https://orcid.org/0000-0001-7349-7407"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kerstin Heselmeyer-Haddad","raw_affiliation_strings":["1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210140884","https://openalex.org/I4210149717","https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031392514","display_name":"Thomas Ried","orcid":"https://orcid.org/0000-0002-0767-6009","observed_orcids":["https://orcid.org/0000-0002-0767-6009"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Ried","raw_affiliation_strings":["1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210140884","https://openalex.org/I4210149717","https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000317216","display_name":"Alejandro A. Sch\u00e4ffer","orcid":"https://orcid.org/0000-0002-2147-8033","observed_orcids":["https://orcid.org/0000-0002-2147-8033"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alejandro A. Sch\u00e4ffer","raw_affiliation_strings":["1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210140884","https://openalex.org/I4210149717","https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051953313","display_name":"Russell S. Schwartz","orcid":"https://orcid.org/0000-0002-4970-2252","observed_orcids":["https://orcid.org/0000-0002-4970-2252"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Russell Schwartz","raw_affiliation_strings":["1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA, 2Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA, 3Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA, 4Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA and 5Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210140884","https://openalex.org/I4210149717","https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5051953313"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210140884","https://openalex.org/I4210149717","https://openalex.org/I74973139"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":1.2117,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.75422062,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"31","issue":"12","first_page":"i258","last_page":"i267"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9961000084877014,"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":0.9961000084877014,"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":0.0015999999595806003,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/copy-number-evolution","display_name":"copy number evolution","score":0.9679999947547913},{"id":"https://openalex.org/keywords/tumor-progression","display_name":"tumor progression","score":0.7200000286102295},{"id":"https://openalex.org/keywords/chromosomal-abnormalities","display_name":"chromosomal abnormalities","score":0.7319999933242798},{"id":"https://openalex.org/keywords/whole-genome-doubling","display_name":"whole-genome duplication","score":0.7760000228881836},{"id":"https://openalex.org/keywords/expectation-maximization-algorithm","display_name":"expectation-maximization algorithm","score":0.7730000019073486},{"id":"https://openalex.org/keywords/cervical-cancer","display_name":"cervical cancer","score":0.7080000042915344},{"id":"https://openalex.org/keywords/tongue-cancer","display_name":"tongue cancer","score":0.9919999837875366},{"id":"https://openalex.org/keywords/metastasis-prediction","display_name":"metastasis prediction","score":0.9739999771118164}],"concepts":[{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.6702987551689148},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5117987990379333},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5107443332672119},{"id":"https://openalex.org/C124942203","wikidata":"https://www.wikidata.org/wiki/Q656638","display_name":"Comparative genomic hybridization","level":4,"score":0.48422932624816895},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48019492626190186},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4768346846103668},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.44715970754623413},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.4346626102924347},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.4325869679450989},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27561670541763306},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2712341547012329}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btv233","doi":"https://doi.org/10.1093/bioinformatics/btv233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i258/49014042/bioinformatics_31_12_i258.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4481700","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4481700","pdf_url":null,"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,"listed_in":[],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:26072490","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26072490","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,"listed_in":[],"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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.792.9674","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.792.9674","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/9a/15/btv233.PMC4481700.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/12/i258","doi":null,"is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/12/i258","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv233","doi":"https://doi.org/10.1093/bioinformatics/btv233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i258/49014042/bioinformatics_31_12_i258.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.504800021648407}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3463494533","display_name":"Inferring in vivo Capsid Assembly Kinetics from in vitro by Stochastic Simulation","funder_award_id":"R01AI076318","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8202052874","display_name":"Heterogeneous Cancer Progression from Microarray Data","funder_award_id":"R01CA140214","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2104801871.pdf","grobid_xml":"https://content.openalex.org/works/W2104801871.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1533555842","https://openalex.org/W1552426876","https://openalex.org/W1965001144","https://openalex.org/W1967304777","https://openalex.org/W1988615825","https://openalex.org/W1989891384","https://openalex.org/W1993326251","https://openalex.org/W1999207703","https://openalex.org/W2014686215","https://openalex.org/W2018027299","https://openalex.org/W2032388424","https://openalex.org/W2032518018","https://openalex.org/W2039577063","https://openalex.org/W2042536531","https://openalex.org/W2049633694","https://openalex.org/W2053256077","https://openalex.org/W2061760261","https://openalex.org/W2067256262","https://openalex.org/W2069399470","https://openalex.org/W2072023036","https://openalex.org/W2091870725","https://openalex.org/W2095325198","https://openalex.org/W2096420865","https://openalex.org/W2096659508","https://openalex.org/W2105341274","https://openalex.org/W2105644651","https://openalex.org/W2109363750","https://openalex.org/W2117649404","https://openalex.org/W2129288227","https://openalex.org/W2148300747","https://openalex.org/W2148819091","https://openalex.org/W2148930557","https://openalex.org/W2153603480","https://openalex.org/W2153938747","https://openalex.org/W2159165264","https://openalex.org/W2167030304","https://openalex.org/W2171690009","https://openalex.org/W4233815609","https://openalex.org/W6632976546"],"related_works":["https://openalex.org/W1965001144","https://openalex.org/W2562231496","https://openalex.org/W2329043717","https://openalex.org/W2026522435","https://openalex.org/W2105341274","https://openalex.org/W2522536125","https://openalex.org/W2939491123","https://openalex.org/W2802351095","https://openalex.org/W7097972951","https://openalex.org/W2769797880"],"abstract_inverted_index":{"MOTIVATION:":[0],"Phylogenetic":[1],"algorithms":[2,92,179],"have":[3],"begun":[4],"to":[5,12,98,154,165,180,205],"see":[6],"widespread":[7],"use":[8],"in":[9,17,189],"cancer":[10,30,183,202,219],"research":[11],"reconstruct":[13],"processes":[14],"of":[15,29,61,70,73,91,112,137,141,177,212],"evolution":[16,31,67,102],"tumor":[18,24,51,101,113],"progression.":[19],"Developing":[20],"reliable":[21],"phylogenies":[22,60],"for":[23,48,96,109,124,135,209,217],"data":[25,184],"requires":[26],"quantitative":[27,94],"models":[28,69,111],"that":[32],"include":[33,155],"the":[34,210],"unusual":[35],"genetic":[36],"mechanisms":[37],"by":[38,64,88],"which":[39],"tumors":[40,63],"evolve,":[41],"such":[42],"as":[43],"chromosome":[44,146],"abnormalities,":[45],"and":[46,53,76,82,93,127,144,168,200,216,227],"allow":[47],"heterogeneity":[49],"between":[50],"types":[52],"individual":[54],"patients.":[55],"Previous":[56],"work":[57],"on":[58,198],"inferring":[59,110],"single":[62,142,145],"copy":[65,118],"number":[66,119],"assumed":[68],"uniform":[71],"rates":[72,123,171],"genomic":[74,80,187],"gain":[75,126],"loss":[77,128],"across":[78],"different":[79,125],"sites":[81],"scales,":[83],"a":[84,89,107,132],"substantial":[85],"oversimplification":[86],"necessitated":[87],"lack":[90],"parameters":[95],"fitting":[97],"more":[99],"realistic":[100],"models.":[103],"RESULTS:":[104],"We":[105,130,148,158],"propose":[106,131],"framework":[108],"progression":[114,191],"from":[115],"single-cell":[116],"gene":[117,143],"data,":[120],"including":[121],"variable":[122],"events.":[129,147],"new":[133],"algorithm":[134],"identification":[136],"most":[138],"parsimonious":[139],"combinations":[140],"extend":[149],"it":[150],"via":[151],"dynamic":[152],"programming":[153],"genome":[156],"duplications.":[157],"implement":[159],"an":[160],"expectation":[161],"maximization":[162],"(EM)-like":[163],"method":[164],"estimate":[166],"mutation-specific":[167],"tumor-specific":[169],"event":[170],"concurrently":[172],"with":[173,193],"tree":[174],"reconstruction.":[175],"Application":[176],"our":[178],"real":[181],"cervical":[182,199,214],"identifies":[185],"key":[186],"events":[188],"disease":[190],"consistent":[192],"prior":[194],"literature.":[195],"Classification":[196],"experiments":[197],"tongue":[201,218],"datasets":[203,229],"lead":[204],"improved":[206],"prediction":[207],"accuracy":[208],"metastasis":[211],"primary":[213],"cancers":[215],"survival.":[220],"AVAILABILITY":[221],"AND":[222],"IMPLEMENTATION:":[223],"Our":[224],"software":[225],"(FISHtrees)":[226],"two":[228],"are":[230],"available":[231],"at":[232],"ftp://ftp.ncbi.nlm.nih.gov/pub/FISHtrees.":[233]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}