{"id":"https://openalex.org/W4414162556","doi":"https://doi.org/10.1177/15578666251374694","title":"Pharming: Joint Clonal Tree Reconstruction of Single-Nucleotide Variant and Copy Number Aberration Evolution from Single-Cell DNA Sequencing of Tumors","display_name":"Pharming: Joint Clonal Tree Reconstruction of Single-Nucleotide Variant and Copy Number Aberration Evolution from Single-Cell DNA Sequencing of Tumors","publication_year":2025,"publication_date":"2025-09-13","ids":{"openalex":"https://openalex.org/W4414162556","doi":"https://doi.org/10.1177/15578666251374694","pmid":"https://pubmed.ncbi.nlm.nih.gov/40944534"},"language":"en","primary_location":{"id":"doi:10.1177/15578666251374694","is_oa":false,"landing_page_url":"https://doi.org/10.1177/15578666251374694","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019093448","display_name":"Leah L. Weber","orcid":"https://orcid.org/0000-0002-6378-5648"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Leah L. Weber","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064661665","display_name":"A. A. M. Hart","orcid":"https://orcid.org/0000-0002-1942-524X"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anna Hart","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045294377","display_name":"Idoia Ochoa","orcid":"https://orcid.org/0000-0003-1864-7868"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I4210125320","display_name":"Gobierno de Navarra","ror":"https://ror.org/025qq4838","country_code":"ES","type":"government","lineage":["https://openalex.org/I4210088234","https://openalex.org/I4210125320"]}],"countries":["ES","US"],"is_corresponding":false,"raw_author_name":"Idoia Ochoa","raw_affiliation_strings":["Department of Electrical &amp; Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA","Department of Electrical and Electronics Engineering, Tecnun, University of Navarra, Donostia, Spain","Department of Electrical & Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical &amp; Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Electrical and Electronics Engineering, Tecnun, University of Navarra, Donostia, Spain","institution_ids":["https://openalex.org/I4210125320"]},{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089040838","display_name":"Mohammed El-Kebir","orcid":"https://orcid.org/0000-0002-1468-2407"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammed El-Kebir","raw_affiliation_strings":["Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA","Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA"],"raw_orcid":"https://orcid.org/0000-0002-1468-2407","affiliations":[{"raw_affiliation_string":"Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5019093448"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":null,"apc_paid":null,"fwci":0.7417,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.75881133,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"33","issue":"1","first_page":"2","last_page":"18"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","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/T11642","display_name":"Genomics and Rare Diseases","score":0.986299991607666,"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/dna-sequencing","display_name":"DNA sequencing","score":0.6202999949455261},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5910999774932861},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5728999972343445},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.4715999960899353},{"id":"https://openalex.org/keywords/single-cell-sequencing","display_name":"Single cell sequencing","score":0.46470001339912415},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4074000120162964},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.37610000371932983},{"id":"https://openalex.org/keywords/coalescent-theory","display_name":"Coalescent theory","score":0.34709998965263367}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6851000189781189},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6202999949455261},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5910999774932861},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5728999972343445},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5641000270843506},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.4715999960899353},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.46470001339912415},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4196000099182129},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4074000120162964},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.37610000371932983},{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.34709998965263367},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3463999927043915},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.3441999852657318},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.31619998812675476},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.30970001220703125},{"id":"https://openalex.org/C99983632","wikidata":"https://www.wikidata.org/wiki/Q1087765","display_name":"Chromothripsis","level":5,"score":0.28679999709129333},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2773999869823456},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.26570001244544983},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.26260000467300415},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.2590999901294708},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.25119999051094055},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2508000135421753}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1177/15578666251374694","is_oa":false,"landing_page_url":"https://doi.org/10.1177/15578666251374694","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:40944534","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40944534","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G474467374","display_name":null,"funder_award_id":"2046488","funder_id":"https://openalex.org/F4320337387","funder_display_name":"Division of Computing and Communication Foundations"}],"funders":[{"id":"https://openalex.org/F4320337387","display_name":"Division of Computing and Communication Foundations","ror":"https://ror.org/01mng8331"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1853989166","https://openalex.org/W1967304777","https://openalex.org/W2002295829","https://openalex.org/W2122392334","https://openalex.org/W2346273585","https://openalex.org/W2886125669","https://openalex.org/W2890035501","https://openalex.org/W2980515223","https://openalex.org/W2980586637","https://openalex.org/W2985155561","https://openalex.org/W3017999335","https://openalex.org/W3082136743","https://openalex.org/W3137654632","https://openalex.org/W3194323428","https://openalex.org/W4214521270","https://openalex.org/W4220655002","https://openalex.org/W4220858033","https://openalex.org/W4225546915","https://openalex.org/W4226047574","https://openalex.org/W4226106538","https://openalex.org/W4283322370","https://openalex.org/W4307658070","https://openalex.org/W4385835596","https://openalex.org/W4387526413","https://openalex.org/W4388520420","https://openalex.org/W4388911943","https://openalex.org/W4389199685","https://openalex.org/W4391380737","https://openalex.org/W4409210243"],"related_works":["https://openalex.org/W2223496461","https://openalex.org/W2359210733","https://openalex.org/W2372203775","https://openalex.org/W1596598103","https://openalex.org/W2619166255","https://openalex.org/W4313342334","https://openalex.org/W2805859037","https://openalex.org/W4320709878","https://openalex.org/W2364288480","https://openalex.org/W2063433671"],"abstract_inverted_index":{"Cancer":[0],"arises":[1],"through":[2],"an":[3],"evolutionary":[4,29,104,126],"process":[5],"in":[6,40,55,69,152,156],"which":[7,41],"somatic":[8],"mutations,":[9],"including":[10,200],"single-nucleotide":[11],"variants":[12],"(SNVs)":[13],"and":[14,45,108,130,146,197,219],"copy":[15,66,142],"number":[16,67,143],"aberrations":[17],"(CNAs),":[18],"drive":[19],"the":[20,38,46,62,73,88,98,103,124,138,147,201,214],"development":[21],"of":[22,52,65,77,92,128,141,195,205],"a":[23,83,115,186,206],"malignant,":[24],"heterogeneous":[25],"tumor.":[26],"Reconstructing":[27],"this":[28,111],"history":[30,127],"from":[31],"sequencing":[32,59,75,80,229],"data":[33],"is":[34,135],"critical":[35],"for":[36,85,165,216,224],"understanding":[37],"order":[39,157],"mutations":[42],"are":[43],"acquired":[44],"dynamic":[47],"interplay":[48],"between":[49,106],"different":[50],"types":[51],"alterations.":[53],"Advances":[54],"modern":[56],"whole-genome":[57,208],"single-cell":[58,227],"now":[60],"enable":[61,159],"accurate":[63],"inference":[64,119,144,179,223],"profiles":[68],"individual":[70],"cells.":[71],"However,":[72],"low":[74],"coverage":[76],"these":[78],"low-pass":[79],"technologies":[81,230],"poses":[82],"challenge":[84],"reliably":[86],"inferring":[87],"presence":[89],"or":[90],"absence":[91],"SNVs":[93,107,129,150],"within":[94],"tumor":[95,117,162,177,221],"cells,":[96],"limiting":[97],"ability":[99],"to":[100,136,158,185],"simultaneously":[101],"study":[102],"relationships":[105],"CNAs.":[109,131],"In":[110],"work,":[112],"we":[113,182],"introduce":[114],"novel":[116],"phylogeny":[118,163,178,222],"method,":[120],"Pharming,":[121],"that":[122,149,173],"infers":[123],"joint":[125,193],"Our":[132],"key":[133],"insight":[134],"leverage":[137],"high":[139],"accuracy":[140],"methods":[145],"fact":[148],"co-occur":[151],"regions":[153],"with":[154,232],"CNAs":[155],"more":[160,217],"precise":[161],"reconstruction":[164,194],"both":[166],"alteration":[167],"types.":[168],"We":[169],"demonstrate":[170],"via":[171],"simulations":[172],"Pharming":[174,184,212],"outperforms":[175],"state-of-the-art":[176],"methods.":[180],"Additionally,":[181],"apply":[183],"triple-negative":[187],"breast":[188],"cancer":[189],"case,":[190],"achieving":[191],"high-resolution,":[192],"CNA":[196],"SNV":[198],"evolution,":[199],"de":[202],"novo":[203],"detection":[204],"clonal":[207],"duplication":[209],"event.":[210],"Thus,":[211],"offers":[213],"potential":[215],"comprehensive":[218],"detailed":[220],"high-throughput,":[225],"low-coverage":[226],"DNA":[228],"compared":[231],"existing":[233],"approaches.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
