{"id":"https://openalex.org/W4403462031","doi":"https://doi.org/10.1093/bib/bbae516","title":"Reconstructing tumor clonal heterogeneity and evolutionary relationships based on tumor DNA sequencing data","display_name":"Reconstructing tumor clonal heterogeneity and evolutionary relationships based on tumor DNA sequencing data","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4403462031","doi":"https://doi.org/10.1093/bib/bbae516","pmid":"https://pubmed.ncbi.nlm.nih.gov/39413797"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae516","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae516/59812693/bbae516.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae516/59812693/bbae516.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101829825","display_name":"Zhen Wang","orcid":"https://orcid.org/0000-0001-9934-7845"},"institutions":[{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]},{"id":"https://openalex.org/I4210145090","display_name":"Affiliated Zhongshan Hospital of Dalian University","ror":"https://ror.org/041ts2d40","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210145090"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhen Wang","raw_affiliation_strings":["College of Information Engineering, Dalian University , Dalian, Liaoning,","The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Dalian University , Dalian, Liaoning,","institution_ids":["https://openalex.org/I4210092944"]},{"raw_affiliation_string":"The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,","institution_ids":["https://openalex.org/I4210145090"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037049001","display_name":"Yanhua Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanhua Fang","raw_affiliation_strings":["School of Bioengineering, Dalian University of Technology , Dalian 116024,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Bioengineering, Dalian University of Technology , Dalian 116024,","institution_ids":["https://openalex.org/I4210092944","https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100653706","display_name":"Ruoyu Wang","orcid":"https://orcid.org/0000-0002-0422-6408"},"institutions":[{"id":"https://openalex.org/I4210145090","display_name":"Affiliated Zhongshan Hospital of Dalian University","ror":"https://ror.org/041ts2d40","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210145090"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruoyu Wang","raw_affiliation_strings":["The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,","institution_ids":["https://openalex.org/I4210145090"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102805534","display_name":"Liwen Kong","orcid":"https://orcid.org/0009-0008-0548-9550"},"institutions":[{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liwen Kong","raw_affiliation_strings":["College of Information Engineering, Dalian University , Dalian, Liaoning,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Dalian University , Dalian, Liaoning,","institution_ids":["https://openalex.org/I4210092944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101903949","display_name":"Shanshan Liang","orcid":"https://orcid.org/0000-0002-1644-4496"},"institutions":[{"id":"https://openalex.org/I4210145090","display_name":"Affiliated Zhongshan Hospital of Dalian University","ror":"https://ror.org/041ts2d40","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210145090"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shanshan Liang","raw_affiliation_strings":["The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,"],"raw_orcid":"https://orcid.org/0000-0002-1644-4496","affiliations":[{"raw_affiliation_string":"The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,","institution_ids":["https://openalex.org/I4210145090"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007499353","display_name":"Shuai Tao","orcid":"https://orcid.org/0000-0003-2223-0205"},"institutions":[{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]},{"id":"https://openalex.org/I4210145090","display_name":"Affiliated Zhongshan Hospital of Dalian University","ror":"https://ror.org/041ts2d40","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210145090"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuai Tao","raw_affiliation_strings":["College of Information Engineering, Dalian University , Dalian, Liaoning,","The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Dalian University , Dalian, Liaoning,","institution_ids":["https://openalex.org/I4210092944"]},{"raw_affiliation_string":"The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,","institution_ids":["https://openalex.org/I4210145090"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101829825"],"corresponding_institution_ids":["https://openalex.org/I4210092944","https://openalex.org/I4210145090"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.8337,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.94501328,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9958999752998352,"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"}},{"id":"https://openalex.org/T11369","display_name":"Genetic factors in colorectal cancer","score":0.9919999837875366,"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/tumor-heterogeneity","display_name":"Tumor heterogeneity","score":0.7864444255828857},{"id":"https://openalex.org/keywords/somatic-evolution-in-cancer","display_name":"Somatic evolution in cancer","score":0.6908090710639954},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5478023886680603},{"id":"https://openalex.org/keywords/single-cell-sequencing","display_name":"Single cell sequencing","score":0.5475940108299255},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5158182978630066},{"id":"https://openalex.org/keywords/genetic-heterogeneity","display_name":"Genetic heterogeneity","score":0.49478334188461304},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.46178773045539856},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.45175468921661377},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4501863420009613},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.39927899837493896},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3529863953590393},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.32890865206718445},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32579803466796875},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.30378586053848267},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2711476683616638},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.23038586974143982},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.1782827377319336},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1413322389125824},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12893101572990417}],"concepts":[{"id":"https://openalex.org/C3018028425","wikidata":"https://www.wikidata.org/wiki/Q15917291","display_name":"Tumor heterogeneity","level":3,"score":0.7864444255828857},{"id":"https://openalex.org/C113968399","wikidata":"https://www.wikidata.org/wiki/Q7559241","display_name":"Somatic evolution in cancer","level":3,"score":0.6908090710639954},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5478023886680603},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.5475940108299255},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5158182978630066},{"id":"https://openalex.org/C64618202","wikidata":"https://www.wikidata.org/wiki/Q3733697","display_name":"Genetic heterogeneity","level":4,"score":0.49478334188461304},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.46178773045539856},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.45175468921661377},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4501863420009613},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.39927899837493896},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3529863953590393},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.32890865206718445},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32579803466796875},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.30378586053848267},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2711476683616638},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.23038586974143982},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.1782827377319336},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1413322389125824},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12893101572990417}],"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":"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018740","descriptor_name":"Genetic Heterogeneity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018740","descriptor_name":"Genetic Heterogeneity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018740","descriptor_name":"Genetic Heterogeneity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018740","descriptor_name":"Genetic Heterogeneity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae516","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae516/59812693/bbae516.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39413797","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39413797","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11483135","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11483135","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11483135/pdf/bbae516.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae516","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae516/59812693/bbae516.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5497337755","display_name":null,"funder_award_id":"2021RD02","funder_id":"https://openalex.org/F4320326152","funder_display_name":"Dalian Science and Technology Bureau"},{"id":"https://openalex.org/G8531643622","display_name":null,"funder_award_id":"82172822","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320326152","display_name":"Dalian Science and Technology Bureau","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403462031.pdf","grobid_xml":"https://content.openalex.org/works/W4403462031.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1979115864","https://openalex.org/W2002295829","https://openalex.org/W2015182193","https://openalex.org/W2096027508","https://openalex.org/W2107751484","https://openalex.org/W2111874706","https://openalex.org/W2114095872","https://openalex.org/W2147476214","https://openalex.org/W2153056550","https://openalex.org/W2482614962","https://openalex.org/W2594380361","https://openalex.org/W2734435792","https://openalex.org/W2735315721","https://openalex.org/W2756005140","https://openalex.org/W2972062354","https://openalex.org/W3005312895","https://openalex.org/W3024627825","https://openalex.org/W3049719740","https://openalex.org/W3111170609","https://openalex.org/W3119672763","https://openalex.org/W3121739983","https://openalex.org/W3132555860","https://openalex.org/W3191658244","https://openalex.org/W3213410277","https://openalex.org/W4210639945","https://openalex.org/W4282030512","https://openalex.org/W4289274885","https://openalex.org/W4293435090","https://openalex.org/W4295487521","https://openalex.org/W4322617375","https://openalex.org/W4323320213","https://openalex.org/W4362524621","https://openalex.org/W4385214497","https://openalex.org/W4386916256","https://openalex.org/W4389080354"],"related_works":["https://openalex.org/W4385655613","https://openalex.org/W2172478731","https://openalex.org/W2736713143","https://openalex.org/W3120290214","https://openalex.org/W2982310169","https://openalex.org/W2123562597","https://openalex.org/W2058896898","https://openalex.org/W4200499036","https://openalex.org/W2914039047","https://openalex.org/W2898752464"],"abstract_inverted_index":{"The":[0],"heterogeneity":[1,113,147],"of":[2,10,38,56,99,110],"tumor":[3,12,21,25,57,111,139,156,180],"clones":[4],"drives":[5],"the":[6,36,49,53,91,95,144],"selection":[7],"and":[8,19,46,71,94,97,105,114,124,129,159,166,185],"evolution":[9,22,157,181],"distinct":[11],"cell":[13,80],"populations,":[14],"resulting":[15],"in":[16,48,132,179],"an":[17],"intricate":[18],"dynamic":[20],"process.":[23],"While":[24],"bulk":[26],"DNA":[27],"sequencing":[28,135],"helps":[29],"elucidate":[30],"intratumor":[31],"heterogeneity,":[32],"challenges":[33],"such":[34],"as":[35],"misidentification":[37],"mutation":[39,85],"multiplicity":[40,86],"due":[41],"to":[42,155,174],"copy":[43],"number":[44],"variations":[45],"uncertainties":[47],"reconstruction":[50,92],"process":[51,93],"hinder":[52],"accurate":[54],"inference":[55],"evolution.":[58],"In":[59],"this":[60],"study,":[61],"we":[62],"introduce":[63],"a":[64,152,176],"novel":[65],"approach,":[66],"REconstructing":[67],"Tumor":[68],"Clonal":[69],"Heterogeneity":[70],"Evolutionary":[72],"Relationships":[73],"(RETCHER),":[74],"which":[75],"characterizes":[76],"more":[77],"realistic":[78],"cancer":[79],"fractions":[81],"by":[82],"accurately":[83,106],"identifying":[84],"while":[87],"considering":[88],"uncertainty":[89],"during":[90],"credibility":[96],"reasonableness":[98],"subclone":[100,127],"clustering.":[101],"This":[102,170],"method":[103],"comprehensively":[104],"infers":[107,125],"multiple":[108],"forms":[109],"clonal":[112,146],"phylogenetic":[115],"relationships.":[116],"RETCHER":[117,150,187],"outperforms":[118],"existing":[119],"methods":[120],"on":[121],"simulated":[122],"data":[123,136],"clearer":[126],"structures":[128],"evolutionary":[130],"relationships":[131],"real":[133],"multisample":[134],"from":[137],"five":[138],"types.":[140],"By":[141],"precisely":[142],"analysing":[143],"complex":[145],"within":[148],"tumors,":[149],"provides":[151],"new":[153],"approach":[154,171],"research":[158],"offers":[160],"scientific":[161],"evidence":[162],"for":[163,190],"developing":[164],"precise":[165],"personalized":[167],"treatment":[168],"strategies.":[169],"is":[172,188],"expected":[173],"play":[175],"significant":[177],"role":[178],"research,":[182],"clinical":[183],"diagnosis,":[184],"treatment.":[186],"available":[189],"free":[191],"at":[192],"https://github.com/zlsys3/RETCHER.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-05T09:01:59.212387","created_date":"2025-10-10T00:00:00"}
