{"id":"https://openalex.org/W1965001144","doi":"https://doi.org/10.1371/journal.pcbi.1003740","title":"Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics","display_name":"Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics","publication_year":2014,"publication_date":"2014-07-31","ids":{"openalex":"https://openalex.org/W1965001144","doi":"https://doi.org/10.1371/journal.pcbi.1003740","mag":"1965001144","pmid":"https://pubmed.ncbi.nlm.nih.gov/25078894"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003740","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003740","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003740&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.1003740&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110461875","display_name":"Salim A. Chowdhury","orcid":null},"institutions":[{"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/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":"Salim Akhter Chowdhury","raw_affiliation_strings":["Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America; Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America; Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":[]},{"raw_affiliation_string":"Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139","https://openalex.org/I170201317"]},{"raw_affiliation_string":"Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027859218","display_name":"Stanley E. Shackney","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111451","display_name":"Oncotherapeutics (United States)","ror":"https://ror.org/01s33dn56","country_code":"US","type":"company","lineage":["https://openalex.org/I4210111451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stanley E. Shackney","raw_affiliation_strings":["Intelligent Oncotherapeutics, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Intelligent Oncotherapeutics, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I4210111451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068597889","display_name":"Kerstin Heselmeyer\u2010Haddad","orcid":"https://orcid.org/0000-0001-7349-7407"},"institutions":[{"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kerstin Heselmeyer-Haddad","raw_affiliation_strings":["Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210149717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031392514","display_name":"Thomas Ried","orcid":"https://orcid.org/0000-0002-0767-6009"},"institutions":[{"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thomas Ried","raw_affiliation_strings":["Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210149717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000317216","display_name":"Alejandro A. Sch\u00e4ffer","orcid":"https://orcid.org/0000-0002-2147-8033"},"institutions":[{"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alejandro A. Sch\u00e4ffer","raw_affiliation_strings":["Computational Biology Branch, NCBI, NIH, Bethesda, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Branch, NCBI, NIH, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051953313","display_name":"Russell Schwartz","orcid":"https://orcid.org/0000-0002-4970-2252"},"institutions":[{"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":["Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":[]},{"raw_affiliation_string":"Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000317216","https://openalex.org/A5027859218","https://openalex.org/A5031392514","https://openalex.org/A5051953313","https://openalex.org/A5068597889","https://openalex.org/A5110461875"],"corresponding_institution_ids":["https://openalex.org/I170201317","https://openalex.org/I4210109390","https://openalex.org/I4210111451","https://openalex.org/I4210149717","https://openalex.org/I74973139"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.2272,"has_fulltext":true,"cited_by_count":63,"citation_normalized_percentile":{"value":0.86892883,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"10","issue":"7","first_page":"e1003740","last_page":"e1003740"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9991000294685364,"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/T11369","display_name":"Genetic factors in colorectal cancer","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.5873565673828125},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5754156112670898},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5191485285758972},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5005462169647217},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4945974051952362},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.48236459493637085},{"id":"https://openalex.org/keywords/fluorescence-in-situ-hybridization","display_name":"Fluorescence in situ hybridization","score":0.4622355103492737},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.435019314289093},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41430792212486267},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3992065191268921},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32964223623275757},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29987508058547974}],"concepts":[{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.5873565673828125},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5754156112670898},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5191485285758972},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5005462169647217},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4945974051952362},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.48236459493637085},{"id":"https://openalex.org/C2777542201","wikidata":"https://www.wikidata.org/wiki/Q1336182","display_name":"Fluorescence in situ hybridization","level":4,"score":0.4622355103492737},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.435019314289093},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41430792212486267},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3992065191268921},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32964223623275757},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29987508058547974}],"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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"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":"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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","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":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1003740","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003740","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003740&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:25078894","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25078894","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:repository.cmu.edu:biology-1418","is_oa":true,"landing_page_url":"http://repository.cmu.edu/cgi/viewcontent.cgi?article=1418&context=biology","pdf_url":null,"source":{"id":"https://openalex.org/S4306400668","display_name":"Research Showcase @ Carnegie Mellon University (Carnegie Mellon University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I74973139","host_organization_name":"Carnegie Mellon University","host_organization_lineage":["https://openalex.org/I74973139"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Department of Biological Sciences","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003740","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003740","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:9c0a317dca5747d0b9732543c2a6e84e","is_oa":true,"landing_page_url":"https://doaj.org/article/9c0a317dca5747d0b9732543c2a6e84e","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 10, Iss 7, p e1003740 (2014)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/6097193","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Algorithms_to_model_single_gene_single_chromosome_and_whole_genome_copy_number_changes_jointly_in_tumor_phylogenetics_/6097193","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":"pmh:oai:pubmedcentral.nih.gov:4117424","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4117424","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,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"doi:10.1184/r1/6097193.v1","is_oa":true,"landing_page_url":"https://doi.org/10.1184/r1/6097193.v1","pdf_url":null,"source":{"id":"https://openalex.org/S7407050927","display_name":"KiltHub Repository","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003740","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003740","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003740&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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5600000023841858}],"awards":[{"id":"https://openalex.org/G23638424","display_name":null,"funder_award_id":"R01 AI076318","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G282064752","display_name":null,"funder_award_id":"R01 CA140214","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5018101021","display_name":null,"funder_award_id":"1R01AI076318","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G599804571","display_name":null,"funder_award_id":"1R01AI076318","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G6007312454","display_name":null,"funder_award_id":"1R01CA140214","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6108461572","display_name":null,"funder_award_id":"1R01AI076318","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6273398171","display_name":null,"funder_award_id":"1R01CA140214","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G642247123","display_name":null,"funder_award_id":"1R01AI076318","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6449555329","display_name":null,"funder_award_id":"1R01CA140214","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1965001144.pdf","grobid_xml":"https://content.openalex.org/works/W1965001144.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W84886273","https://openalex.org/W1564772657","https://openalex.org/W1967304777","https://openalex.org/W1973919890","https://openalex.org/W1989891384","https://openalex.org/W1990986005","https://openalex.org/W1993326251","https://openalex.org/W1994638693","https://openalex.org/W1997803921","https://openalex.org/W2000111986","https://openalex.org/W2000338341","https://openalex.org/W2001258296","https://openalex.org/W2008271309","https://openalex.org/W2009569945","https://openalex.org/W2010414816","https://openalex.org/W2011091959","https://openalex.org/W2018027299","https://openalex.org/W2032388424","https://openalex.org/W2032518018","https://openalex.org/W2034629821","https://openalex.org/W2039577063","https://openalex.org/W2041380745","https://openalex.org/W2042536531","https://openalex.org/W2053256077","https://openalex.org/W2060425093","https://openalex.org/W2061285646","https://openalex.org/W2061760261","https://openalex.org/W2065288894","https://openalex.org/W2067256262","https://openalex.org/W2070968409","https://openalex.org/W2080365963","https://openalex.org/W2080677621","https://openalex.org/W2081184407","https://openalex.org/W2086757725","https://openalex.org/W2091870725","https://openalex.org/W2096420865","https://openalex.org/W2096659508","https://openalex.org/W2097706568","https://openalex.org/W2098814509","https://openalex.org/W2105341274","https://openalex.org/W2105644651","https://openalex.org/W2108531996","https://openalex.org/W2109077054","https://openalex.org/W2110779257","https://openalex.org/W2114571550","https://openalex.org/W2114991871","https://openalex.org/W2116168419","https://openalex.org/W2117649404","https://openalex.org/W2117687396","https://openalex.org/W2119185338","https://openalex.org/W2123576600","https://openalex.org/W2126903025","https://openalex.org/W2127214385","https://openalex.org/W2139212919","https://openalex.org/W2144208087","https://openalex.org/W2146489738","https://openalex.org/W2147117379","https://openalex.org/W2148819091","https://openalex.org/W2148847151","https://openalex.org/W2148930557","https://openalex.org/W2150575159","https://openalex.org/W2152207030","https://openalex.org/W2153603480","https://openalex.org/W2160076878","https://openalex.org/W2167278498","https://openalex.org/W2168156874","https://openalex.org/W2222512263","https://openalex.org/W2610167300","https://openalex.org/W3094430305","https://openalex.org/W4247715064"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2949296710","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082","https://openalex.org/W1974895455"],"abstract_inverted_index":{"We":[0,108,140],"present":[1],"methods":[2,32,74,145,176],"to":[3,50,58,113,170,181],"construct":[4],"phylogenetic":[5],"models":[6],"of":[7,22,56,85,94,133],"tumor":[8,66,126],"progression":[9],"at":[10,19],"the":[11,20,28,81,106,144,164,197],"cellular":[12],"level":[13],"that":[14,163],"include":[15],"copy":[16,82,91],"number":[17,83,92],"changes":[18,93],"scale":[21],"single":[23,95,134],"genes,":[24],"entire":[25],"chromosomes,":[26],"and":[27,142,149,156,167,180],"whole":[29],"genome.":[30,107],"The":[31],"are":[33],"designed":[34],"for":[35,75,124,177],"data":[36,129,148,152],"collected":[37],"by":[38,90,136],"fluorescence":[39],"in":[40,65,105,120],"situ":[41],"hybridization":[42],"(FISH),":[43],"an":[44,77],"experimental":[45],"technique":[46],"especially":[47],"well":[48],"suited":[49],"characterizing":[51],"intratumor":[52],"heterogeneity":[53],"using":[54],"counts":[55],"probes":[57,98,104],"genetic":[59],"regions":[60],"frequently":[61],"gained":[62],"or":[63,102],"lost":[64],"development.":[67],"Here,":[68],"we":[69],"develop":[70,114],"new":[71,165],"provably":[72],"optimal":[73],"computing":[76],"edit":[78],"distance":[79],"between":[80],"states":[84],"two":[86],"cells":[87,135],"given":[88],"evolution":[89],"probes,":[96],"all":[97,103],"on":[99,128,146,184],"a":[100,115],"chromosome,":[101],"then":[109],"apply":[110],"this":[111,137],"theory":[112],"practical":[116],"heuristic":[117],"algorithm,":[118],"implemented":[119],"publicly":[121],"available":[122],"software,":[123],"inferring":[125],"phylogenies":[127],"from":[130,153,193,196],"potentially":[131],"hundreds":[132],"evolutionary":[138],"model.":[139],"demonstrate":[141],"validate":[143],"simulated":[147],"published":[150],"FISH":[151],"cervical":[154],"cancers":[155],"breast":[157],"cancers.":[158],"Our":[159],"computational":[160],"experiments":[161],"show":[162],"model":[166],"algorithm":[168],"lead":[169],"more":[171],"parsimonious":[172],"trees":[173],"than":[174],"prior":[175],"single-tumor":[178],"phylogenetics":[179],"improved":[182],"performance":[183],"various":[185],"classification":[186],"tasks,":[187],"such":[188],"as":[189],"distinguishing":[190],"primary":[191],"tumors":[192],"metastases":[194],"obtained":[195],"same":[198],"patient":[199],"population.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":8}],"updated_date":"2026-07-01T08:55:40.977307","created_date":"2025-10-10T00:00:00"}
