{"id":"https://openalex.org/W4284888900","doi":"https://doi.org/10.1093/bib/bbac264","title":"Resolving single-cell copy number profiling for large datasets","display_name":"Resolving single-cell copy number profiling for large datasets","publication_year":2022,"publication_date":"2022-07-08","ids":{"openalex":"https://openalex.org/W4284888900","doi":"https://doi.org/10.1093/bib/bbac264","pmid":"https://pubmed.ncbi.nlm.nih.gov/35801503"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac264","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac264","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029082731","display_name":"Ruohan Wang","orcid":"https://orcid.org/0000-0003-2327-2888"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Wang Ruohan","raw_affiliation_strings":["Department of Computer Science at City University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science at City University of Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhang Yuwei","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Zhang Yuwei","raw_affiliation_strings":["Department of Computer Science at City University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science at City University of Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Wang Mengbo","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Wang Mengbo","raw_affiliation_strings":["Department of Computer Science at City University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science at City University of Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Feng Xikang","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Xikang","raw_affiliation_strings":["School of Software, Northwestern Polytechnical University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Northwestern Polytechnical University","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Wang Jianping","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Wang Jianping","raw_affiliation_strings":["Department of Computer Science at City University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science at City University of Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031252587","display_name":"Li Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Li Shuai Cheng","raw_affiliation_strings":["Department of Computer Science at City University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science at City University of Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5031252587"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.7655,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.86256506,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"4","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":0.9995999932289124,"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":0.9995999932289124,"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":0.9976000189781189,"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":0.9968000054359436,"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/computer-science","display_name":"Computer science","score":0.6917172074317932},{"id":"https://openalex.org/keywords/breakpoint","display_name":"Breakpoint","score":0.6291580200195312},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5159940719604492},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.48492175340652466},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.48358482122421265},{"id":"https://openalex.org/keywords/entropy","display_name":"Entropy (arrow of time)","score":0.4410651922225952},{"id":"https://openalex.org/keywords/mixture-model","display_name":"Mixture model","score":0.41428709030151367},{"id":"https://openalex.org/keywords/structural-variation","display_name":"Structural variation","score":0.4100933074951172},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4058893024921417},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40360382199287415},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3517102003097534},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2880933880805969},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22650766372680664},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.1728469431400299},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16764315962791443},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13660699129104614}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6917172074317932},{"id":"https://openalex.org/C206936463","wikidata":"https://www.wikidata.org/wiki/Q634179","display_name":"Breakpoint","level":4,"score":0.6291580200195312},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5159940719604492},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.48492175340652466},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.48358482122421265},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.4410651922225952},{"id":"https://openalex.org/C61224824","wikidata":"https://www.wikidata.org/wiki/Q2260434","display_name":"Mixture model","level":2,"score":0.41428709030151367},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.4100933074951172},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4058893024921417},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40360382199287415},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3517102003097534},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2880933880805969},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22650766372680664},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.1728469431400299},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16764315962791443},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13660699129104614},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"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":"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"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":"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":2,"locations":[{"id":"doi:10.1093/bib/bbac264","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac264","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35801503","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35801503","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}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7300000190734863,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1579730317","https://openalex.org/W1966313764","https://openalex.org/W1974113747","https://openalex.org/W2011728187","https://openalex.org/W2012151892","https://openalex.org/W2030017878","https://openalex.org/W2032518018","https://openalex.org/W2048527505","https://openalex.org/W2068674866","https://openalex.org/W2088470456","https://openalex.org/W2094295010","https://openalex.org/W2102941013","https://openalex.org/W2106619117","https://openalex.org/W2107751484","https://openalex.org/W2108234281","https://openalex.org/W2113574907","https://openalex.org/W2126903025","https://openalex.org/W2133174470","https://openalex.org/W2140548491","https://openalex.org/W2142769937","https://openalex.org/W2149118757","https://openalex.org/W2155707112","https://openalex.org/W2332292689","https://openalex.org/W2338678442","https://openalex.org/W2571353615","https://openalex.org/W2583245795","https://openalex.org/W2762374429","https://openalex.org/W2786672974","https://openalex.org/W2885386724","https://openalex.org/W2924124844","https://openalex.org/W2952708922","https://openalex.org/W2969486796","https://openalex.org/W2978221280","https://openalex.org/W2997123690","https://openalex.org/W3012982892","https://openalex.org/W3023438254","https://openalex.org/W3027826979","https://openalex.org/W3041828825","https://openalex.org/W3049025136","https://openalex.org/W3121637338","https://openalex.org/W3123988232","https://openalex.org/W3137654632","https://openalex.org/W3207172363","https://openalex.org/W3207337285","https://openalex.org/W4234217873","https://openalex.org/W4243367687","https://openalex.org/W4247053599","https://openalex.org/W6748816842","https://openalex.org/W6753185613","https://openalex.org/W6772440719","https://openalex.org/W6775277851"],"related_works":["https://openalex.org/W4361892629","https://openalex.org/W3134412476","https://openalex.org/W2160911017","https://openalex.org/W2005276393","https://openalex.org/W2091911799","https://openalex.org/W3005131427","https://openalex.org/W2029233263","https://openalex.org/W2142819802","https://openalex.org/W2072462056","https://openalex.org/W2465436886"],"abstract_inverted_index":{"The":[0],"advances":[1],"of":[2,14,24,29,127],"single-cell":[3],"DNA":[4],"sequencing":[5,180,191],"(scDNA-seq)":[6],"enable":[7],"us":[8],"to":[9,60,71,129,166,178],"characterize":[10],"the":[11,18,27,62,80,87,92,98,102,105,109,138,169,201],"genetic":[12],"heterogeneity":[13],"cancer":[15,185,196],"cells.":[16,116],"However,":[17],"high":[19],"noise":[20,128],"and":[21,43,125,187,204],"low":[22],"coverage":[23],"scDNA-seq":[25],"impede":[26],"estimation":[28],"copy":[30,63,110],"number":[31],"variations":[32],"(CNVs).":[33],"In":[34],"addition,":[35],"existing":[36],"tools":[37,164],"suffer":[38],"from":[39,101,182,193],"intensive":[40],"execution":[41],"time":[42,170],"often":[44],"fail":[45,165],"on":[46],"large":[47,154],"datasets.":[48],"Here,":[49],"we":[50],"propose":[51],"SeCNV,":[52],"an":[53],"efficient":[54],"method":[55],"that":[56],"leverages":[57],"structural":[58,99],"entropy,":[59],"profile":[61],"numbers.":[64],"SeCNV":[65,90,107,132,151,177,198,208],"adopts":[66],"a":[67,73,134],"local":[68],"Gaussian":[69],"kernel":[70],"construct":[72],"matrix,":[74],"depth":[75],"congruent":[76],"map":[77],"(DCM),":[78],"capturing":[79],"similarities":[81],"between":[82],"any":[83],"two":[84,183],"bins":[85],"along":[86],"genome.":[88],"Then,":[89],"partitions":[91],"genome":[93],"into":[94],"segments":[95],"by":[96],"minimizing":[97],"entropy":[100],"DCM.":[103],"With":[104],"partition,":[106],"estimates":[108],"numbers":[111],"within":[112,159,168],"each":[113],"segment":[114],"for":[115,144],"We":[117,175],"simulate":[118],"nine":[119],"datasets":[120,155,181,192],"with":[121],"various":[122],"breakpoint":[123,145],"distributions":[124],"amplitudes":[126],"benchmark":[130],"SeCNV.":[131],"achieves":[133],"robust":[135],"performance,":[136],"i.e.":[137,172],"F1-scores":[139],"are":[140],"higher":[141],"than":[142],"0.95":[143],"detections,":[146],"significantly":[147],"outperforming":[148],"state-of-the-art":[149],"methods.":[150],"successfully":[152,199],"processes":[153],"(>50":[156],"000":[157],"cells)":[158],"4":[160],"min,":[161],"while":[162],"other":[163],"finish":[167],"limit,":[171],"120":[173],"h.":[174],"apply":[176],"single-nucleus":[179],"breast":[184,195],"patients":[186],"acoustic":[188],"cell":[189],"tagmentation":[190],"eight":[194],"patients.":[197],"reproduces":[200],"distinct":[202],"subclones":[203],"infers":[205],"tumor":[206],"heterogeneity.":[207],"is":[209],"available":[210],"at":[211],"https://github.com/deepomicslab/SeCNV.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
