{"id":"https://openalex.org/W2978053672","doi":"https://doi.org/10.1109/tcbb.2019.2944827","title":"CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression","display_name":"CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression","publication_year":2019,"publication_date":"2019-10-01","ids":{"openalex":"https://openalex.org/W2978053672","doi":"https://doi.org/10.1109/tcbb.2019.2944827","mag":"2978053672","pmid":"https://pubmed.ncbi.nlm.nih.gov/31581092"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2944827","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2944827","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077204135","display_name":"Quanhua Mu","orcid":"https://orcid.org/0000-0002-6891-5616"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]},{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Quanhua Mu","raw_affiliation_strings":["Division of Life Science, Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China"],"affiliations":[{"raw_affiliation_string":"Division of Life Science, Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China","institution_ids":["https://openalex.org/I200769079","https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101451440","display_name":"Jiguang Wang","orcid":"https://orcid.org/0000-0002-6923-4097"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]},{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiguang Wang","raw_affiliation_strings":["Division of Life Science, Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China"],"affiliations":[{"raw_affiliation_string":"Division of Life Science, Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China","institution_ids":["https://openalex.org/I200769079","https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077204135"],"corresponding_institution_ids":["https://openalex.org/I200769079","https://openalex.org/I889458895"],"apc_list":null,"apc_paid":null,"fwci":0.5356,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.59649277,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"18","issue":"1","first_page":"306","last_page":"311"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9987000226974487,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9979000091552734,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6058381795883179},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5912356376647949},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5744525790214539},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5626881122589111},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.53421550989151},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5198841094970703},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.48428791761398315},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.47431349754333496},{"id":"https://openalex.org/keywords/gene-dosage","display_name":"Gene dosage","score":0.43294256925582886},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3769722580909729},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.36304971575737}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6058381795883179},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5912356376647949},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5744525790214539},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5626881122589111},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.53421550989151},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5198841094970703},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.48428791761398315},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.47431349754333496},{"id":"https://openalex.org/C55548728","wikidata":"https://www.wikidata.org/wiki/Q1465102","display_name":"Gene dosage","level":4,"score":0.43294256925582886},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3769722580909729},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.36304971575737}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2019.2944827","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2944827","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31581092","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31581092","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:repository.hkust.edu.hk:1783.1-101794","is_oa":false,"landing_page_url":"http://www.scopus.com/record/display.url?eid=2-s2.0-85100600450&origin=inward","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:repository.ust.hk:1783.1-101794","is_oa":false,"landing_page_url":"http://repository.ust.hk/ir/Record/1783.1-101794","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1591498689","display_name":null,"funder_award_id":"ITS/480/18FP","funder_id":"https://openalex.org/F4320321920","funder_display_name":"Innovation and Technology Commission"},{"id":"https://openalex.org/G4614357796","display_name":null,"funder_award_id":"ITCPD/17-9","funder_id":"https://openalex.org/F4320321920","funder_display_name":"Innovation and Technology Commission"}],"funders":[{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W571060166","https://openalex.org/W1480376833","https://openalex.org/W1812256879","https://openalex.org/W1976526581","https://openalex.org/W1982088425","https://openalex.org/W2011637823","https://openalex.org/W2030017878","https://openalex.org/W2062214822","https://openalex.org/W2090144921","https://openalex.org/W2090461073","https://openalex.org/W2096173332","https://openalex.org/W2097331151","https://openalex.org/W2109816625","https://openalex.org/W2122769974","https://openalex.org/W2133339454","https://openalex.org/W2135046866","https://openalex.org/W2142452151","https://openalex.org/W2144222696","https://openalex.org/W2149681218","https://openalex.org/W2157852151","https://openalex.org/W2263206910","https://openalex.org/W2337209831","https://openalex.org/W2366536035","https://openalex.org/W2410468716","https://openalex.org/W2546514099","https://openalex.org/W2592397787","https://openalex.org/W2603523955","https://openalex.org/W2739822787","https://openalex.org/W2756324015","https://openalex.org/W2795441313","https://openalex.org/W2802053370","https://openalex.org/W2899794439","https://openalex.org/W2914305908"],"related_works":["https://openalex.org/W2043199743","https://openalex.org/W2009966535","https://openalex.org/W1883752748","https://openalex.org/W2187207551","https://openalex.org/W2069184423","https://openalex.org/W2903984190","https://openalex.org/W2549117626","https://openalex.org/W1603543036","https://openalex.org/W2059282377","https://openalex.org/W3016874529"],"abstract_inverted_index":{"Detection":[0],"of":[1,115],"DNA":[2,22,26,33,112],"copy":[3,61,113],"number":[4,62,114],"alteration":[5],"in":[6,43,102,130],"cancer":[7,13,81,101],"cells":[8],"is":[9],"critical":[10],"to":[11,58,92],"understanding":[12],"initiation":[14],"and":[15,24,31,77,98,119,124,135],"progression.":[16],"Widely":[17],"used":[18],"methods,":[19],"such":[20],"as":[21,142],"arrays":[23],"genomic":[25],"sequencing,":[27],"are":[28,40],"relatively":[29],"expensive":[30],"require":[32],"samples":[34,82],"at":[35,146],"a":[36],"microgram":[37],"level,":[38],"which":[39],"not":[41],"avaiblable":[42],"certain":[44],"situations":[45],"like":[46],"clinical":[47],"biopsies":[48],"or":[49],"single-cell":[50],"genomes.":[51],"Here,":[52],"we":[53],"developed":[54,141],"an":[55,143],"alternative":[56],"method-CNAPE":[57],"computationally":[59],"infer":[60],"alterations":[63],"from":[64,83],"gene":[65],"expression":[66],"data.":[67],"A":[68],"prior":[69],"knowledge-aided":[70],"machine":[71],"learning":[72],"model":[73],"was":[74,140],"proposed,":[75],"trained":[76],"tested":[78],"on":[79],"9,740":[80],"The":[84],"Cancer":[85],"Genome":[86],"Atlas.":[87],"We":[88],"then":[89],"applied":[90],"CNAPE":[91,109,139],"study":[93],"gliomas,":[94],"the":[95],"most":[96],"common":[97],"aggressive":[99],"brain":[100],"adult.":[103],"Particularly,":[104],"using":[105],"RNA":[106],"sequencing":[107],"data,":[108],"respectively":[110],"predicted":[111],"chromosomes,":[116],"chromosomal":[117],"arms,":[118],"12":[120],"commonly":[121],"altered":[122],"genes,":[123],"achieved":[125],"over":[126],"80":[127],"percent":[128],"accuracy":[129],"almost":[131],"all":[132],"broad":[133],"regions":[134],"some":[136],"focal":[137],"regions.":[138],"easy-to-use":[144],"tool":[145],"https://github.com/WangLabHKUST/CNAPE.":[147]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}