{"id":"https://openalex.org/W4387526413","doi":"https://doi.org/10.1371/journal.pcbi.1011544","title":"Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors","display_name":"Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors","publication_year":2023,"publication_date":"2023-10-11","ids":{"openalex":"https://openalex.org/W4387526413","doi":"https://doi.org/10.1371/journal.pcbi.1011544","pmid":"https://pubmed.ncbi.nlm.nih.gov/37819942"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011544","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011544","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011544","any_repository_has_fulltext":true},"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 Urbana-Champaign, Urbana-Champaign, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign, Urbana-Champaign, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073096739","display_name":"Chuanyi Zhang","orcid":"https://orcid.org/0000-0002-6359-0904"},"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":"Chuanyi Zhang","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Illinois Urbana-Champaign, Urbana-Champaign, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Illinois Urbana-Champaign, Urbana-Champaign, Illinois, United States of America","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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Idoia Ochoa","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Illinois Urbana-Champaign, Urbana-Champaign, Illinois, United States of America","Department of Electrical and Electronics Engineering, University of Navarre, Donostia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Illinois Urbana-Champaign, Urbana-Champaign, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Electrical and Electronics Engineering, University of Navarre, Donostia, Spain","institution_ids":[]}]},{"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":true,"raw_author_name":"Mohammed El-Kebir","raw_affiliation_strings":["Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana-Champaign, Illinois, United States of America","Department of Electrical and Electronics Engineering, University of Navarre, Donostia, Spain"],"raw_orcid":"https://orcid.org/0000-0002-1468-2407","affiliations":[{"raw_affiliation_string":"Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana-Champaign, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Electrical and Electronics Engineering, University of Navarre, Donostia, Spain","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5019093448","https://openalex.org/A5045294377","https://openalex.org/A5073096739","https://openalex.org/A5089040838"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.9736,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.94050517,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"19","issue":"10","first_page":"e1011544","last_page":"e1011544"},"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/T10449","display_name":"Renal cell carcinoma treatment","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory 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/dna-sequencing","display_name":"DNA sequencing","score":0.6290538907051086},{"id":"https://openalex.org/keywords/single-cell-sequencing","display_name":"Single cell sequencing","score":0.6159312725067139},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5428022146224976},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5264421701431274},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.4633738398551941},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4339442253112793},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4295712113380432},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4276340901851654},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.41744425892829895},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38915178179740906},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37545979022979736},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.32507264614105225},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24316948652267456},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.22525548934936523},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.22163930535316467},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.19900894165039062},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16177892684936523},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13403257727622986},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1203845739364624}],"concepts":[{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6290538907051086},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.6159312725067139},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5428022146224976},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5264421701431274},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.4633738398551941},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4339442253112793},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4295712113380432},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4276340901851654},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.41744425892829895},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38915178179740906},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37545979022979736},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.32507264614105225},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24316948652267456},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.22525548934936523},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.22163930535316467},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.19900894165039062},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16177892684936523},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13403257727622986},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1203845739364624},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"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":"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":"D014197","descriptor_name":"Trees","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014197","descriptor_name":"Trees","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014197","descriptor_name":"Trees","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014197","descriptor_name":"Trees","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011544","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011544","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37819942","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37819942","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10593221","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10593221","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10593221/pdf/pcbi.1011544.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:b2bcedd832354c0c98dea5a390a71839","is_oa":true,"landing_page_url":"https://doaj.org/article/b2bcedd832354c0c98dea5a390a71839","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 10, p e1011544 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011544","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011544","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2489399592","display_name":null,"funder_award_id":"CCF-2046488","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G481696606","display_name":null,"funder_award_id":"PID2021-126718OA-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G4820762032","display_name":"CAREER: Algorithms for Comprehensive and Cost-effective Cancer Phylogeny Inference from Multi-omics Single-cell Sequencing Data","funder_award_id":"2046488","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310598","display_name":"Amazon Web Services","ror":"https://ror.org/04mv4n011"},{"id":"https://openalex.org/F4320321705","display_name":"Eusko Jaurlaritza","ror":"https://ror.org/00pz2fp31"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null},{"id":"https://openalex.org/F8115879620","display_name":"Cancer Center at Illinois","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1967304777","https://openalex.org/W2114843025","https://openalex.org/W2121947440","https://openalex.org/W2122392334","https://openalex.org/W2147476214","https://openalex.org/W2149441684","https://openalex.org/W2150752820","https://openalex.org/W2346273585","https://openalex.org/W2358053195","https://openalex.org/W2571353615","https://openalex.org/W2579382924","https://openalex.org/W2800852522","https://openalex.org/W2886125669","https://openalex.org/W2890035501","https://openalex.org/W2894573839","https://openalex.org/W2970198863","https://openalex.org/W2980515223","https://openalex.org/W2980586637","https://openalex.org/W2985155561","https://openalex.org/W2990360822","https://openalex.org/W3000756465","https://openalex.org/W3005450619","https://openalex.org/W3017999335","https://openalex.org/W3025790441","https://openalex.org/W3042855708","https://openalex.org/W3082136743","https://openalex.org/W3093815480","https://openalex.org/W3094802395","https://openalex.org/W3129513070","https://openalex.org/W3137654632","https://openalex.org/W3187058898","https://openalex.org/W3214767163","https://openalex.org/W3217485783","https://openalex.org/W4205558434","https://openalex.org/W4220655002","https://openalex.org/W4220762854","https://openalex.org/W4221027182","https://openalex.org/W4226106538","https://openalex.org/W4226383395","https://openalex.org/W4226487144","https://openalex.org/W4280510216","https://openalex.org/W4281699160","https://openalex.org/W4283322370","https://openalex.org/W4288442931","https://openalex.org/W4294295915","https://openalex.org/W4297859984","https://openalex.org/W4300689221","https://openalex.org/W4309013615","https://openalex.org/W4310415757","https://openalex.org/W4383340915","https://openalex.org/W4385948422","https://openalex.org/W4396213728","https://openalex.org/W6748398605"],"related_works":["https://openalex.org/W2760231366","https://openalex.org/W3029015202","https://openalex.org/W3031411603","https://openalex.org/W2359210733","https://openalex.org/W2619166255","https://openalex.org/W2472738690","https://openalex.org/W2136661588","https://openalex.org/W2095901358","https://openalex.org/W4223616223","https://openalex.org/W2981194801"],"abstract_inverted_index":{"Emerging":[0],"ultra-low":[1,60,100],"coverage":[2,41,61,101],"single-cell":[3],"DNA":[4],"sequencing":[5,23,36],"(scDNA-seq)":[6],"technologies":[7,24],"have":[8],"enabled":[9],"high":[10],"resolution":[11],"evolutionary":[12,121],"studies":[13],"of":[14,35,40,47,57,69,80,86,104,126,133],"copy":[15],"number":[16],"aberrations":[17],"(CNAs)":[18],"within":[19],"tumors.":[20],"While":[21],"these":[22],"are":[25],"well":[26,139],"suited":[27],"for":[28,44],"identifying":[29,119],"CNAs":[30],"due":[31],"to":[32,53,75,94,157,166],"the":[33,38,45,55,78,83,116,124,127,131,150,155],"uniformity":[34],"coverage,":[37],"sparsity":[39],"poses":[42],"challenges":[43],"study":[46],"single-nucleotide":[48],"variants":[49],"(SNVs).":[50],"In":[51],"order":[52],"maximize":[54],"utility":[56],"increasingly":[58],"available":[59],"scDNA-seq":[62,102],"data":[63,103,117,137,156],"and":[64,163],"obtain":[65],"a":[66,92,96,105,109],"comprehensive":[67],"understanding":[68],"tumor":[70,87],"evolution,":[71],"it":[72],"is":[73],"important":[74],"also":[76],"analyze":[77],"evolution":[79],"SNVs":[81],"from":[82,99],"same":[84],"set":[85],"cells.":[88],"We":[89,129],"present":[90],"Phertilizer,":[91],"method":[93,113],"infer":[95],"clonal":[97,161],"tree":[98],"tumor.":[106,128],"Based":[107],"on":[108,135,141],"probabilistic":[110],"model,":[111],"our":[112],"recursively":[114],"partitions":[115],"by":[118],"key":[120],"events":[122],"in":[123,154],"history":[125],"demonstrate":[130],"performance":[132],"Phertilizer":[134,147],"simulated":[136],"as":[138,140],"two":[142],"real":[143],"datasets,":[144],"finding":[145],"that":[146],"effectively":[148],"utilizes":[149],"copy-number":[151],"signal":[152],"inherent":[153],"more":[158],"accurately":[159],"uncover":[160],"structure":[162],"genotypes":[164],"compared":[165],"previous":[167],"methods.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}