{"id":"https://openalex.org/W4411969836","doi":"https://doi.org/10.3389/fbinf.2025.1615834","title":"GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data","display_name":"GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data","publication_year":2025,"publication_date":"2025-07-02","ids":{"openalex":"https://openalex.org/W4411969836","doi":"https://doi.org/10.3389/fbinf.2025.1615834","pmid":"https://pubmed.ncbi.nlm.nih.gov/40672519"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1615834","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1615834","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1615834/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1615834/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037221822","display_name":"R. Tobin","orcid":null},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan M. Tobin","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, United States","Institute of Genomic and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute of Genomic and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018210315","display_name":"Shikha Singh","orcid":"https://orcid.org/0009-0008-5712-2793"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shikha Singh","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, United States","Institute of Genomic and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute of Genomic and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100680948","display_name":"Sudhir Kumar","orcid":"https://orcid.org/0000-0002-9918-8212"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, United States","Institute of Genomic and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute of Genomic and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062480014","display_name":"Sayaka Miura","orcid":"https://orcid.org/0000-0001-9881-2848"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]},{"id":"https://openalex.org/I368840534","display_name":"University of Mississippi","ror":"https://ror.org/02teq1165","country_code":"US","type":"education","lineage":["https://openalex.org/I368840534","https://openalex.org/I4210141039"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sayaka Miura","raw_affiliation_strings":["Department of Biology, University of Mississippi, University, MS, United States","Institute of Genomic and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Mississippi, University, MS, United States","institution_ids":["https://openalex.org/I368840534"]},{"raw_affiliation_string":"Institute of Genomic and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5062480014"],"corresponding_institution_ids":["https://openalex.org/I368840534","https://openalex.org/I84392919"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.8353,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.74984596,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"5","issue":null,"first_page":"1615834","last_page":"1615834"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9984999895095825,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9835000038146973,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/clone","display_name":"clone (Java method)","score":0.7401116490364075},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.6156038641929626},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5822948217391968},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5663469433784485},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49434852600097656},{"id":"https://openalex.org/keywords/prostate-cancer","display_name":"Prostate cancer","score":0.4917753040790558},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.4414571225643158},{"id":"https://openalex.org/keywords/tumor-heterogeneity","display_name":"Tumor heterogeneity","score":0.42444857954978943},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.382408082485199},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.36040616035461426},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2613716125488281},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24366438388824463}],"concepts":[{"id":"https://openalex.org/C81089528","wikidata":"https://www.wikidata.org/wiki/Q5134986","display_name":"clone (Java method)","level":3,"score":0.7401116490364075},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6156038641929626},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5822948217391968},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5663469433784485},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49434852600097656},{"id":"https://openalex.org/C2780192828","wikidata":"https://www.wikidata.org/wiki/Q181257","display_name":"Prostate cancer","level":3,"score":0.4917753040790558},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4414571225643158},{"id":"https://openalex.org/C3018028425","wikidata":"https://www.wikidata.org/wiki/Q15917291","display_name":"Tumor heterogeneity","level":3,"score":0.42444857954978943},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.382408082485199},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.36040616035461426},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2613716125488281},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24366438388824463}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1615834","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1615834","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1615834/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40672519","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40672519","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:924129934f4244efa925343cc5681f42","is_oa":true,"landing_page_url":"https://doaj.org/article/924129934f4244efa925343cc5681f42","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12263698","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12263698","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1615834","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1615834","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1615834/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411969836.pdf","grobid_xml":"https://content.openalex.org/works/W4411969836.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1973702005","https://openalex.org/W1987012261","https://openalex.org/W2015182193","https://openalex.org/W2032518018","https://openalex.org/W2097706568","https://openalex.org/W2114095872","https://openalex.org/W2121552166","https://openalex.org/W2122392334","https://openalex.org/W2133360663","https://openalex.org/W2150677022","https://openalex.org/W2204695746","https://openalex.org/W2346273585","https://openalex.org/W2515462796","https://openalex.org/W2588969809","https://openalex.org/W2609243345","https://openalex.org/W2795707203","https://openalex.org/W2797282777","https://openalex.org/W2802415313","https://openalex.org/W2806004564","https://openalex.org/W2947410234","https://openalex.org/W2977250149","https://openalex.org/W2991495852","https://openalex.org/W3002685488","https://openalex.org/W3008591269","https://openalex.org/W3015646919","https://openalex.org/W3117558845","https://openalex.org/W3121105779","https://openalex.org/W3126201322","https://openalex.org/W4214576283","https://openalex.org/W4226106538","https://openalex.org/W4283274128","https://openalex.org/W4365137707","https://openalex.org/W4365137743","https://openalex.org/W4376956725","https://openalex.org/W4385490759","https://openalex.org/W4385955982","https://openalex.org/W4387569866"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2377327490","https://openalex.org/W2560253012","https://openalex.org/W1524590520","https://openalex.org/W2412288087","https://openalex.org/W2371792548","https://openalex.org/W1697705604","https://openalex.org/W2419862115","https://openalex.org/W2017092658","https://openalex.org/W2770713575"],"abstract_inverted_index":{"DNA":[0],"sequencing":[1],"technologies":[2],"are":[3],"widely":[4],"used":[5],"to":[6,22,60,71,74,105],"study":[7,89],"tumor":[8,35,62,91,106],"evolution":[9,63,92,107],"within":[10,33],"a":[11,54,87],"cancer":[12,28,96],"patient.":[13],"However,":[14],"analyses":[15],"require":[16],"various":[17],"computational":[18,100],"methods,":[19],"including":[20],"those":[21],"infer":[23],"clone":[24,31,37],"sequences":[25],"(genotypes":[26],"of":[27,42,57,90],"cell":[29,47],"populations),":[30],"frequencies":[32],"each":[34],"sample,":[36],"phylogeny,":[38],"mutational":[39,43],"tree,":[40],"dynamics":[41],"signatures,":[44],"and":[45,68,77],"metastatic":[46,94],"migration":[48],"events.":[49],"Therefore,":[50],"we":[51],"developed":[52,67],"GenoPath,":[53],"streamlined":[55],"pipeline":[56],"existing":[58],"tools":[59,70],"perform":[61],"analysis.":[64,108],"We":[65,81],"also":[66],"added":[69],"visualize":[72],"results":[73],"assist":[75],"interpretation":[76],"derive":[78],"biological":[79],"insights.":[80],"have":[82],"illustrated":[83],"GenoPath's":[84],"utility":[85],"through":[86],"case":[88],"using":[93],"prostate":[95],"data.":[97],"By":[98],"reducing":[99],"barriers,":[101],"GenoPath":[102],"broadens":[103],"access":[104],"The":[109],"software":[110],"is":[111],"available":[112],"at":[113],"https://github.com/SayakaMiura/GP.":[114]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}