{"id":"https://openalex.org/W2105341274","doi":"https://doi.org/10.1093/bioinformatics/btt205","title":"Phylogenetic analysis of multiprobe fluorescence <i>in situ</i> hybridization data from tumor cell populations","display_name":"Phylogenetic analysis of multiprobe fluorescence <i>in situ</i> hybridization data from tumor cell populations","publication_year":2013,"publication_date":"2013-06-19","ids":{"openalex":"https://openalex.org/W2105341274","doi":"https://doi.org/10.1093/bioinformatics/btt205","mag":"2105341274","pmid":"https://pubmed.ncbi.nlm.nih.gov/23812984"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt205","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i189/18534342/btt205.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,"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"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i189/18534342/btt205.pdf","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/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":["Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA. sachowdh@andrew.cmu.edu","Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA. sachowdh@andrew.cmu.edu","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational Biology, Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA","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"]},{"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":"Stanley E. Shackney","raw_affiliation_strings":["Intelligent Oncotherapeutics, Pittsburgh, PA 15243, USA,","Carnegie Mellon University, Pittsburgh, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Intelligent Oncotherapeutics, Pittsburgh, PA 15243, USA,","institution_ids":["https://openalex.org/I4210111451"]},{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh, United States","institution_ids":["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"},"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"]},{"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":["Genetics Branch, Center for Cancer Research, NCI, NIH,","Carnegie Mellon University, Pittsburgh, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genetics Branch, Center for Cancer Research, NCI, NIH,","institution_ids":["https://openalex.org/I4210149717"]},{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh, United States","institution_ids":["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"},"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"]},{"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":["Genetics Branch, Center for Cancer Research, NCI, NIH,","Carnegie Mellon University, Pittsburgh, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genetics Branch, Center for Cancer Research, NCI, NIH,","institution_ids":["https://openalex.org/I4210149717"]},{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh, United States","institution_ids":["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"},"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":false,"raw_author_name":"Alejandro A. Sch\u00e4ffer","raw_affiliation_strings":["Carnegie Mellon University, Pittsburgh, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh, United States","institution_ids":["https://openalex.org/I74973139"]}]},{"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":false,"raw_author_name":"Russell Schwartz","raw_affiliation_strings":["Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA","Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA,","Carnegie Mellon University, Pittsburgh, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA,","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh, United States","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.3984,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.95935908,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"13","first_page":"i189","last_page":"i198"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.7300000190734863,"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"}},"topics":[{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.7300000190734863,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.16009999811649323,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.017500000074505806,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7641435861587524},{"id":"https://openalex.org/keywords/in-situ","display_name":"In situ","score":0.6920199394226074},{"id":"https://openalex.org/keywords/fluorescence-in-situ-hybridization","display_name":"Fluorescence in situ hybridization","score":0.6434124708175659},{"id":"https://openalex.org/keywords/phylogenetic-relationship","display_name":"Phylogenetic relationship","score":0.6071171164512634},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5234983563423157},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4983973503112793},{"id":"https://openalex.org/keywords/fluorescence","display_name":"Fluorescence","score":0.47123250365257263},{"id":"https://openalex.org/keywords/in-situ-hybridization","display_name":"In situ hybridization","score":0.46607065200805664},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4345461130142212},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.38768988847732544},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31144240498542786},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14655610918998718},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12322092056274414},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0743761658668518},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.05727505683898926}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7641435861587524},{"id":"https://openalex.org/C2777822432","wikidata":"https://www.wikidata.org/wiki/Q216681","display_name":"In situ","level":2,"score":0.6920199394226074},{"id":"https://openalex.org/C2777542201","wikidata":"https://www.wikidata.org/wiki/Q1336182","display_name":"Fluorescence in situ hybridization","level":4,"score":0.6434124708175659},{"id":"https://openalex.org/C2992072516","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetic relationship","level":4,"score":0.6071171164512634},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5234983563423157},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4983973503112793},{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.47123250365257263},{"id":"https://openalex.org/C81439078","wikidata":"https://www.wikidata.org/wiki/Q2304142","display_name":"In situ hybridization","level":4,"score":0.46607065200805664},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4345461130142212},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.38768988847732544},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31144240498542786},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14655610918998718},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12322092056274414},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0743761658668518},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.05727505683898926},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D002583","descriptor_name":"Uterine Cervical Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D012984","descriptor_name":"Software","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":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btt205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt205","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i189/18534342/btt205.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,"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":"pmid:23812984","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23812984","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:repository.cmu.edu:biology-1426","is_oa":false,"landing_page_url":"http://repository.cmu.edu/biology/418","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Department of Biological Sciences","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2688164","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3694640","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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"},{"id":"pmh:oai:pubmedcentral.nih.gov:3694640","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3694640","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt205","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i189/18534342/btt205.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,"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":[],"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/G6374948078","display_name":null,"funder_award_id":"Z99 CA999999","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/W2105341274.pdf","grobid_xml":"https://content.openalex.org/works/W2105341274.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W84886273","https://openalex.org/W1564772657","https://openalex.org/W1967304777","https://openalex.org/W1990085600","https://openalex.org/W1990986005","https://openalex.org/W1994638693","https://openalex.org/W1996668544","https://openalex.org/W2000111986","https://openalex.org/W2000338341","https://openalex.org/W2008534472","https://openalex.org/W2009569945","https://openalex.org/W2010414816","https://openalex.org/W2020112047","https://openalex.org/W2032388424","https://openalex.org/W2032518018","https://openalex.org/W2042536531","https://openalex.org/W2064086982","https://openalex.org/W2065288894","https://openalex.org/W2080677621","https://openalex.org/W2081184407","https://openalex.org/W2091870725","https://openalex.org/W2096420865","https://openalex.org/W2098608887","https://openalex.org/W2105644651","https://openalex.org/W2108531996","https://openalex.org/W2110779257","https://openalex.org/W2114991871","https://openalex.org/W2116168419","https://openalex.org/W2117649404","https://openalex.org/W2117687396","https://openalex.org/W2123576600","https://openalex.org/W2124442734","https://openalex.org/W2126903025","https://openalex.org/W2139212919","https://openalex.org/W2143071116","https://openalex.org/W2146489738","https://openalex.org/W2148930557","https://openalex.org/W2150575159","https://openalex.org/W2152054694","https://openalex.org/W2155239253","https://openalex.org/W2160076878","https://openalex.org/W2167278498","https://openalex.org/W2169666080","https://openalex.org/W2500374022","https://openalex.org/W4247715064","https://openalex.org/W6634024494","https://openalex.org/W6652718379","https://openalex.org/W6677398440"],"related_works":["https://openalex.org/W1431904956","https://openalex.org/W1974583777","https://openalex.org/W3085510013","https://openalex.org/W2037370208","https://openalex.org/W2269144480","https://openalex.org/W1968072793","https://openalex.org/W2389590026","https://openalex.org/W3097541692","https://openalex.org/W2913396030","https://openalex.org/W4391517987"],"abstract_inverted_index":{"MOTIVATION:":[0],"Development":[1],"and":[2,110,136,201,215,220],"progression":[3,65,130,163],"of":[4,13,22,24,31,41,54,60,66,82,87,107,113,128,142,151,154],"solid":[5],"tumors":[6,35,68],"can":[7,177],"be":[8,46,178],"attributed":[9],"to":[10,78,100,124,139,191],"a":[11,55,140],"process":[12,44],"mutations,":[14],"which":[15,75],"typically":[16],"includes":[17],"changes":[18],"in":[19,71,85,187],"the":[20,155,167,174,216],"number":[21,134,195],"copies":[23],"genes":[25,84],"or":[26,52],"genomic":[27],"regions.":[28],"Although":[29],"comparisons":[30],"cells":[32,53,109],"within":[33],"single":[34,88,108],"show":[36],"extensive":[37],"heterogeneity,":[38],"recurring":[39],"features":[40,181],"their":[42],"evolutionary":[43,103],"may":[45],"discerned":[47],"by":[48],"comparing":[49],"multiple":[50],"regions":[51],"tumor.":[56],"A":[57],"useful":[58],"source":[59],"data":[61,95,135,144,217,232],"for":[62,92,182,207],"studying":[63],"likely":[64,102,126,161],"individual":[67],"is":[69],"fluorescence":[70],"situ":[72],"hybridization":[73],"(FISH),":[74],"allows":[76],"one":[77],"count":[79],"copy":[80,133,194],"numbers":[81],"several":[83],"hundreds":[86],"cells.":[89],"Novel":[90],"algorithms":[91],"interpreting":[93],"such":[94],"phylogenetically":[96],"are":[97,225,233],"needed,":[98],"however,":[99],"reconstruct":[101],"trajectories":[104],"from":[105,145,173],"states":[106],"facilitate":[111],"analysis":[112],"tumor":[114,129,162,199],"evolution.":[115],"RESULTS:":[116],"In":[117],"this":[118],"article,":[119],"we":[120],"develop":[121],"phylogenetic":[122],"methods":[123],"infer":[125],"models":[127],"using":[131],"FISH":[132,143,211],"apply":[137],"them":[138],"study":[141],"two":[146],"cancer":[147,222],"types.":[148],"Statistical":[149],"analyses":[150],"topological":[152],"characteristics":[153],"tree-based":[156],"model":[157],"provide":[158],"insights":[159],"into":[160],"pathways":[164],"consistent":[165],"with":[166],"prior":[168],"literature.":[169],"Furthermore,":[170],"tree":[171,212],"statistics":[172],"resulting":[175],"phylogenies":[176],"used":[179],"as":[180],"prediction":[183],"methods.":[184],"This":[185],"results":[186],"improved":[188],"accuracy,":[189],"relative":[190],"unstructured":[192],"gene":[193],"data,":[196],"at":[197,227,235],"predicting":[198],"state":[200],"future":[202],"metastasis.":[203],"AVAILABILITY:":[204],"Source":[205],"code":[206],"software":[208],"that":[209],"does":[210],"building":[213],"(FISHtrees)":[214],"on":[218],"cervical":[219],"breast":[221],"examined":[223],"here":[224],"available":[226,234],"ftp://ftp.ncbi.nlm.nih.gov/pub/FISHtrees.":[228],"SUPPLEMENTARY":[229],"INFORMATION:":[230],"Supplementary":[231],"Bioinformatics":[236],"online.":[237]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}