{"id":"https://openalex.org/W4391724177","doi":"https://doi.org/10.1093/bib/bbae022","title":"On the core segmentation algorithms of copy number variation detection tools","display_name":"On the core segmentation algorithms of copy number variation detection tools","publication_year":2024,"publication_date":"2024-01-22","ids":{"openalex":"https://openalex.org/W4391724177","doi":"https://doi.org/10.1093/bib/bbae022","pmid":"https://pubmed.ncbi.nlm.nih.gov/38340093"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae022","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae022/56648189/bbae022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae022/56648189/bbae022.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yibo Zhang","orcid":"https://orcid.org/0009-0004-7363-6509"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yibo Zhang","raw_affiliation_strings":["Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an , China"],"raw_orcid":"https://orcid.org/0009-0004-7363-6509","affiliations":[{"raw_affiliation_string":"Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an , China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100665055","display_name":"Wenyu Liu","orcid":"https://orcid.org/0000-0003-1103-6888"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenyu Liu","raw_affiliation_strings":["Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an , China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023726254","display_name":"Junbo Duan","orcid":"https://orcid.org/0000-0001-7170-3772"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junbo Duan","raw_affiliation_strings":["Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi\u2019an Jiaotong University , Xi\u2019an , China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5023726254"],"corresponding_institution_ids":["https://openalex.org/I87445476"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":6.0753,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.96365155,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"25","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9998000264167786,"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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9839000105857849,"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":0.982200026512146,"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/segmentation","display_name":"Segmentation","score":0.695274829864502},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.6917588710784912},{"id":"https://openalex.org/keywords/core","display_name":"Core (optical fiber)","score":0.6152885556221008},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6068859696388245},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.49353063106536865},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.47449469566345215},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3561483323574066},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3260471820831299},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07941249012947083},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07204851508140564},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.05387851595878601}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.695274829864502},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.6917588710784912},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.6152885556221008},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6068859696388245},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.49353063106536865},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.47449469566345215},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3561483323574066},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3260471820831299},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07941249012947083},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07204851508140564},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.05387851595878601},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae022","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae022/56648189/bbae022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38340093","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38340093","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},{"id":"pmh:oai:pubmedcentral.nih.gov:10858679","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10858679","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10858679/pdf/bbae022.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae022","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae022/56648189/bbae022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4166441612","display_name":"\u57fa\u4e8e\u7a00\u758f\u8868\u8fbe\u6a21\u578b\u7684\u591a\u7ec4\u5b66\u6570\u636e\u878d\u5408\u7814\u7a76\u53ca\u5176\u5728\u62f7\u8d1d\u6570\u53d8\u5f02\u76f8\u5173\u75be\u75c5\u7684\u5e94\u7528","funder_award_id":"61771381","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391724177.pdf"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W1966936568","https://openalex.org/W1976555450","https://openalex.org/W1979271879","https://openalex.org/W1991133427","https://openalex.org/W2001616137","https://openalex.org/W2007321142","https://openalex.org/W2012016911","https://openalex.org/W2012151892","https://openalex.org/W2014010495","https://openalex.org/W2032247293","https://openalex.org/W2035593347","https://openalex.org/W2052549259","https://openalex.org/W2068206509","https://openalex.org/W2083870688","https://openalex.org/W2090144921","https://openalex.org/W2092203068","https://openalex.org/W2106650442","https://openalex.org/W2107126369","https://openalex.org/W2108698786","https://openalex.org/W2110553133","https://openalex.org/W2112706474","https://openalex.org/W2113649367","https://openalex.org/W2116034738","https://openalex.org/W2116126626","https://openalex.org/W2120950849","https://openalex.org/W2121144826","https://openalex.org/W2121743948","https://openalex.org/W2126298009","https://openalex.org/W2133174470","https://openalex.org/W2134672574","https://openalex.org/W2137779717","https://openalex.org/W2138603354","https://openalex.org/W2139747296","https://openalex.org/W2140869203","https://openalex.org/W2149681218","https://openalex.org/W2150506261","https://openalex.org/W2160612450","https://openalex.org/W2162927194","https://openalex.org/W2166657289","https://openalex.org/W2167722550","https://openalex.org/W2170551349","https://openalex.org/W2171777347","https://openalex.org/W2317016310","https://openalex.org/W2337209831","https://openalex.org/W2513883126","https://openalex.org/W2602431927","https://openalex.org/W2617530335","https://openalex.org/W2757817643","https://openalex.org/W2761867792","https://openalex.org/W2775698023","https://openalex.org/W2796391389","https://openalex.org/W2920746096","https://openalex.org/W2921879097","https://openalex.org/W2949028980","https://openalex.org/W2952509678","https://openalex.org/W2984210223","https://openalex.org/W2991679800","https://openalex.org/W2997875816","https://openalex.org/W3004837829","https://openalex.org/W3090102164","https://openalex.org/W3135142572","https://openalex.org/W3184462571","https://openalex.org/W3196621914","https://openalex.org/W3213662367","https://openalex.org/W4207053933","https://openalex.org/W4213201562","https://openalex.org/W4225472640","https://openalex.org/W4296640609","https://openalex.org/W4386033437","https://openalex.org/W6760415315","https://openalex.org/W6769981132","https://openalex.org/W6772368147"],"related_works":["https://openalex.org/W2386430105","https://openalex.org/W2356521405","https://openalex.org/W2038534795","https://openalex.org/W2384358604","https://openalex.org/W1567829292","https://openalex.org/W2513883126","https://openalex.org/W3001063351","https://openalex.org/W3196905815","https://openalex.org/W2351370765","https://openalex.org/W3118014344"],"abstract_inverted_index":{"Shotgun":[0],"sequencing":[1,69,104,173,208],"is":[2,169,177,222],"a":[3,35,115,120,160],"high-throughput":[4],"method":[5],"used":[6],"to":[7,29,186,235],"detect":[8],"copy":[9],"number":[10],"variants":[11],"(CNVs).":[12],"Although":[13],"there":[14],"are":[15],"numerous":[16],"CNV":[17,41,100,240],"detection":[18,42,59],"tools":[19,43,56,238],"based":[20],"on":[21],"shotgun":[22],"sequencing,":[23,196],"their":[24,219],"quality":[25],"varies":[26],"significantly,":[27],"leading":[28],"performance":[30,92],"discrepancies.":[31],"Therefore,":[32],"we":[33,89,118],"conducted":[34],"comprehensive":[36],"analysis":[37],"of":[38,54,93,111],"next-generation":[39],"sequencing-based":[40],"over":[44],"the":[45,52,62,74,91,139,145,216],"past":[46],"decade.":[47],"Our":[48],"findings":[49],"revealed":[50],"that":[51],"majority":[53],"mainstream":[55,124],"employ":[57],"similar":[58],"rationale:":[60],"calculates":[61],"so-called":[63],"read":[64],"depth":[65],"signal":[66,75],"from":[67],"aligned":[68],"reads":[70],"and":[71,108,231],"then":[72],"segments":[73,184],"by":[76],"utilizing":[77],"either":[78],"circular":[79],"binary":[80],"segmentation":[81,97],"(CBS)":[82],"or":[83],"hidden":[84],"Markov":[85],"model":[86,122],"(HMM).":[87],"Hence,":[88],"compared":[90,185,201,214],"those":[94],"two":[95],"core":[96],"algorithms":[98],"in":[99,180],"detection,":[101],"considering":[102],"varying":[103],"depths,":[105,174],"segment":[106],"lengths":[107],"complex":[109,192],"types":[110],"CNVs.":[112],"To":[113],"ensure":[114],"fair":[116],"comparison,":[117],"designed":[119],"parametrical":[121],"using":[123],"statistical":[125],"distributions,":[126],"which":[127],"allows":[128],"for":[129,233,239],"pre-excluding":[130],"bias":[131],"correction":[132],"such":[133],"as":[134],"guanine-cytosine":[135],"(GC)":[136],"content":[137],"during":[138],"preprocessing":[140],"step.":[141],"The":[142],"results":[143],"indicate":[144],"following":[146],"key":[147],"points:":[148],"(1)":[149],"Under":[150],"ideal":[151],"conditions,":[152,167],"CBS":[153,176],"demonstrates":[154,198],"high":[155,161],"precision,":[156],"while":[157,175,218],"HMM":[158,168,197,210],"exhibits":[159],"recall":[162],"rate.":[163],"(2)":[164],"For":[165],"practical":[166],"advantageous":[170],"at":[171],"lower":[172],"more":[178,199],"competitive":[179],"detecting":[181],"small":[182],"variant":[183],"HMM.":[187],"(3)":[188],"In":[189],"case":[190],"involving":[191],"CNVs":[193],"resembling":[194],"real":[195],"robustness":[200],"with":[202,215],"CBS.":[203],"(4)":[204],"When":[205],"facing":[206],"large-scale":[207],"data,":[209],"costs":[211],"less":[212],"time":[213],"CBS,":[217],"memory":[220],"usage":[221],"approximately":[223],"equal.":[224],"This":[225],"can":[226],"provide":[227],"an":[228],"important":[229],"guidance":[230],"reference":[232],"researchers":[234],"develop":[236],"new":[237],"detection.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}
