{"id":"https://openalex.org/W4292369550","doi":"https://doi.org/10.1186/s12859-022-04890-w","title":"SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances","display_name":"SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances","publication_year":2022,"publication_date":"2022-08-19","ids":{"openalex":"https://openalex.org/W4292369550","doi":"https://doi.org/10.1186/s12859-022-04890-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/35986254","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/9392257"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04890-w","doi":"https://doi.org/10.1186/s12859-022-04890-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04890-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04890-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04890-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053504865","display_name":"Sandra Hui","orcid":"https://orcid.org/0000-0002-3534-6998","observed_orcids":["https://orcid.org/0000-0002-3534-6998"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sandra Hui","raw_affiliation_strings":["Center for Computational Biology, University of California, Berkeley, Berkeley, 94720, USA"],"raw_orcid":"https://orcid.org/0000-0002-3534-6998","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, University of California, Berkeley, Berkeley, 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088476239","display_name":"Rasmus Nielsen","orcid":"https://orcid.org/0000-0003-0513-6591","observed_orcids":["https://orcid.org/0000-0003-0513-6591"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rasmus Nielsen","raw_affiliation_strings":["Center for Computational Biology, University of California, Berkeley, Berkeley, 94720, USA","Department of Integrative Biology, University of California, Berkeley, Berkeley, 94720, USA","Department of Statistics, University of California, Berkeley, Berkeley, 94720, USA"],"raw_orcid":"https://orcid.org/0000-0003-0513-6591","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, University of California, Berkeley, Berkeley, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Integrative Biology, University of California, Berkeley, Berkeley, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Statistics, University of California, Berkeley, Berkeley, 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053504865","https://openalex.org/A5088476239"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":2690,"currency":"USD","value_usd":2690},"apc_paid":{"value":2690,"currency":"USD","value_usd":2690},"fwci":0.105,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.30734112,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"23","issue":"1","first_page":"348","last_page":"348"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9452999830245972,"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":0.9452999830245972,"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":0.0333000011742115,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.011500000022351742,"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/tumor-phylogeny","display_name":"tumor phylogeny","score":0.7570000290870667},{"id":"https://openalex.org/keywords/tumor-evolution","display_name":"tumor evolution","score":0.777999997138977},{"id":"https://openalex.org/keywords/somatic-copy-number-alterations","display_name":"somatic copy number alterations","score":0.8859999775886536},{"id":"https://openalex.org/keywords/single-cell-whole-genome-sequencing","display_name":"single-cell whole-genome sequencing","score":0.8339999914169312},{"id":"https://openalex.org/keywords/joint-inference","display_name":"joint inference","score":0.4650000035762787}],"concepts":[{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.7311335802078247},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6893875002861023},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6392793655395508},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.6186845898628235},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5723159313201904},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5595751404762268},{"id":"https://openalex.org/C166608930","wikidata":"https://www.wikidata.org/wiki/Q5169175","display_name":"Copy number analysis","level":5,"score":0.48879215121269226},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.44219186902046204},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.43670955300331116},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4115898013114929},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38811376690864563},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.35975903272628784},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32291561365127563},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20877599716186523},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.14936798810958862},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.13594484329223633},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1157495379447937},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"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":"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":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","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":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-022-04890-w","doi":"https://doi.org/10.1186/s12859-022-04890-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04890-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04890-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/2022.05.12.491742","doi":"https://doi.org/10.1101/2022.05.12.491742","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.05.12.491742","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/05/13/2022.05.12.491742.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:9392257","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9392257","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmid:35986254","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35986254","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,"listed_in":[],"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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9xd7z6mv","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9xd7z6mv","pdf_url":"https://escholarship.org/content/qt9xd7z6mv/qt9xd7z6mv.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"BMC Bioinformatics, vol 23, iss 1","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:9622caffbc3844b48c7cc296da3935b7","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/9622caffbc3844b48c7cc296da3935b7","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,"listed_in":[],"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":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-23 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04890-w","doi":"https://doi.org/10.1186/s12859-022-04890-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04890-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04890-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1093856126","display_name":"Enabling Precision Genomics Using Adaptive Variation","funder_award_id":"R01GM138634","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4292369550.pdf","grobid_xml":"https://content.openalex.org/works/W4292369550.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1483627327","https://openalex.org/W1814244002","https://openalex.org/W1978302017","https://openalex.org/W1991133427","https://openalex.org/W2007321142","https://openalex.org/W2011728187","https://openalex.org/W2032518018","https://openalex.org/W2036897871","https://openalex.org/W2060425093","https://openalex.org/W2077574412","https://openalex.org/W2086699924","https://openalex.org/W2088735033","https://openalex.org/W2090079179","https://openalex.org/W2097706568","https://openalex.org/W2102424972","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2117801354","https://openalex.org/W2121180999","https://openalex.org/W2125838338","https://openalex.org/W2128599926","https://openalex.org/W2131271579","https://openalex.org/W2140628770","https://openalex.org/W2142384583","https://openalex.org/W2153056550","https://openalex.org/W2170551349","https://openalex.org/W2406445961","https://openalex.org/W2414771725","https://openalex.org/W2513727910","https://openalex.org/W2579382924","https://openalex.org/W2583245795","https://openalex.org/W2588969809","https://openalex.org/W2767035748","https://openalex.org/W2781608882","https://openalex.org/W2883251903","https://openalex.org/W2898580681","https://openalex.org/W2997797797","https://openalex.org/W3004295003","https://openalex.org/W3004647847","https://openalex.org/W3005127469","https://openalex.org/W3007172120","https://openalex.org/W3007196669","https://openalex.org/W3009737049","https://openalex.org/W3027826979","https://openalex.org/W3049025136","https://openalex.org/W3082136743","https://openalex.org/W3087547719","https://openalex.org/W4207053933","https://openalex.org/W4254687493","https://openalex.org/W4282591735","https://openalex.org/W4407514551"],"related_works":["https://openalex.org/W4207053933","https://openalex.org/W7204511406","https://openalex.org/W7203804048","https://openalex.org/W4405385451","https://openalex.org/W6976836034","https://openalex.org/W4414162556","https://openalex.org/W4407514551","https://openalex.org/W4409739458","https://openalex.org/W7020714010","https://openalex.org/W7125614877"],"abstract_inverted_index":{"BACKGROUND:":[0],"Single":[1],"cell":[2,22,49,79,108,135],"whole":[3,136],"genome":[4,137],"tumor":[5,48,131,138,147],"sequencing":[6,80,109,139],"can":[7],"yield":[8],"novel":[9],"insights":[10],"into":[11],"the":[12,31,113,116],"evolutionary":[13,33],"history":[14],"of":[15,35,115,146],"somatic":[16],"copy":[17,23,52,70,92,122],"number":[18,24,53,71,93,123],"alterations.":[19],"Existing":[20],"single":[21,78,107,134],"calling":[25,69,94],"methods":[26,45],"do":[27],"not":[28],"explicitly":[29],"model":[30],"shared":[32],"process":[34],"multiple":[36,141],"cells,":[37,142],"and":[38,73,95,125],"generally":[39],"analyze":[40],"cells":[41],"independently.":[42],"Additionally,":[43],"existing":[44],"for":[46,67,77,129],"estimating":[47,74],"phylogenies":[50,132],"using":[51],"profiles":[54,124],"are":[55],"sensitive":[56],"to":[57,104,111],"profile":[58],"estimation":[59,97],"errors.":[60],"RESULTS:":[61],"We":[62,101],"present":[63],"SCONCE2,":[64],"a":[65,126],"method":[66],"jointly":[68,120],"alterations":[72],"pairwise":[75],"distances":[76],"data.":[81],"Using":[82],"simulations,":[83],"we":[84],"show":[85],"that":[86],"SCONCE2":[87,103,119],"has":[88],"higher":[89],"accuracy":[90],"in":[91,133],"phylogeny":[96],"than":[98],"competing":[99],"methods.":[100],"apply":[102],"previously":[105],"published":[106],"data":[110],"illustrate":[112],"utility":[114],"method.":[117],"CONCLUSIONS:":[118],"estimates":[121],"distance":[127],"metric":[128],"inferring":[130],"across":[140],"enabling":[143],"deeper":[144],"understandings":[145],"evolution.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2022-08-20T00:00:00"}