{"id":"https://openalex.org/W4408925696","doi":"https://doi.org/10.1109/tcbbio.2025.3555170","title":"scCMP: A Deep Learning Method for Identifying Clonal Mutational Profiles From Single-Cell Genomic Data","display_name":"scCMP: A Deep Learning Method for Identifying Clonal Mutational Profiles From Single-Cell Genomic Data","publication_year":2025,"publication_date":"2025-03-27","ids":{"openalex":"https://openalex.org/W4408925696","doi":"https://doi.org/10.1109/tcbbio.2025.3555170","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811320"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3555170","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3555170","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE 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/A5011001187","display_name":"Junlei Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junlei Zhou","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100745104","display_name":"Ruixiang Li","orcid":"https://orcid.org/0000-0003-3057-0496"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruixiang Li","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065978622","display_name":"Fangyuan Shi","orcid":"https://orcid.org/0000-0003-4185-8129"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangyuan Shi","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074640570","display_name":"Xianhao Huo","orcid":"https://orcid.org/0000-0002-2612-8390"},"institutions":[{"id":"https://openalex.org/I4210127460","display_name":"Ningxia Medical University","ror":"https://ror.org/02h8a1848","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210127460"]},{"id":"https://openalex.org/I4210139449","display_name":"Ningxia Medical University General Hospital","ror":"https://ror.org/049dkqr57","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210139449"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianhao Huo","raw_affiliation_strings":["Department of Neurosurgery, General Hospital, Ningxia Medical University, Yinchuan, China","Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China"],"affiliations":[{"raw_affiliation_string":"Department of Neurosurgery, General Hospital, Ningxia Medical University, Yinchuan, China","institution_ids":["https://openalex.org/I4210139449","https://openalex.org/I4210127460"]},{"raw_affiliation_string":"Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China","institution_ids":["https://openalex.org/I4210127460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030739481","display_name":"Fang Du","orcid":"https://orcid.org/0000-0002-7958-9609"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fang Du","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000095054","display_name":"Zhenhua Yu","orcid":"https://orcid.org/0000-0001-6526-6991"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenhua Yu","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5011001187"],"corresponding_institution_ids":["https://openalex.org/I21642278"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05177131,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"4","first_page":"1378","last_page":"1387"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9581999778747559,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9581999778747559,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9467999935150146,"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/computational-biology","display_name":"Computational biology","score":0.5989313125610352},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4555867314338684},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4520060420036316},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4423132538795471},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4095957279205322},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.381006121635437}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5989313125610352},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4555867314338684},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4520060420036316},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4423132538795471},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4095957279205322},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.381006121635437}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3555170","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3555170","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811320","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811320","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 transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4047386877","display_name":null,"funder_award_id":"2023BEG02009","funder_id":"https://openalex.org/F4320334010","funder_display_name":"Key Research and Development Program of Ningxia"},{"id":"https://openalex.org/G4266403100","display_name":null,"funder_award_id":"32460159","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5103070055","display_name":null,"funder_award_id":"2023AAC05006","funder_id":"https://openalex.org/F4320322877","funder_display_name":"Natural Science Foundation of Ningxia Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322877","display_name":"Natural Science Foundation of Ningxia Province","ror":null},{"id":"https://openalex.org/F4320334010","display_name":"Key Research and Development Program of Ningxia","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1987246402","https://openalex.org/W2113054345","https://openalex.org/W2157305458","https://openalex.org/W2169658215","https://openalex.org/W2346273585","https://openalex.org/W2510746232","https://openalex.org/W2754025713","https://openalex.org/W2803194497","https://openalex.org/W2900850487","https://openalex.org/W2924124844","https://openalex.org/W2950983802","https://openalex.org/W2951343553","https://openalex.org/W2963163009","https://openalex.org/W2980586637","https://openalex.org/W2988773550","https://openalex.org/W3017999335","https://openalex.org/W3018522957","https://openalex.org/W3049084893","https://openalex.org/W3082136743","https://openalex.org/W3083230937","https://openalex.org/W3087547719","https://openalex.org/W3102434595","https://openalex.org/W3112466552","https://openalex.org/W3138516171","https://openalex.org/W3139417289","https://openalex.org/W3164692211","https://openalex.org/W3164736847","https://openalex.org/W3171986076","https://openalex.org/W3196734882","https://openalex.org/W4220764708","https://openalex.org/W4229368127","https://openalex.org/W4294127637","https://openalex.org/W4309158976","https://openalex.org/W4310947643","https://openalex.org/W4311232381","https://openalex.org/W4327683140","https://openalex.org/W4361190647","https://openalex.org/W4383186693","https://openalex.org/W4386075611","https://openalex.org/W4386857837","https://openalex.org/W4392393054","https://openalex.org/W4395660260","https://openalex.org/W6745316256","https://openalex.org/W6802648153"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2731899572","https://openalex.org/W3215138031","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4321369474","https://openalex.org/W4285208911","https://openalex.org/W3082895349","https://openalex.org/W4213079790","https://openalex.org/W2248239756"],"abstract_inverted_index":{"Accurately":[0],"inferring":[1],"clonal":[2,12,37,89,127],"mutational":[3,38,90,166],"profiles":[4,167],"is":[5],"essential":[6],"for":[7,125],"understanding":[8],"intra-tumor":[9],"heterogeneity":[10],"and":[11,25,65,97,106,113,143,172],"selection":[13],"during":[14],"tumor":[15],"evolution.":[16],"Single-cell":[17],"multi-modal":[18,48],"genomic":[19,183],"data,":[20],"such":[21],"as":[22],"copy":[23,63,104],"numbers":[24],"point":[26,66,107],"mutations,":[27],"can":[28],"be":[29],"integrated":[30],"to":[31,61,86,101],"deliver":[32],"multiple":[33],"views":[34],"of":[35,41,46,69,134],"the":[36,42,117,132,162,174],"patterns.":[39],"Despite":[40],"fact":[43],"that":[44],"integration":[45],"single-cell":[47,103,139,182],"data":[49,68],"has":[50],"been":[51],"extensively":[52],"explored":[53],"in":[54,180],"existing":[55],"studies,":[56],"computational":[57],"methods":[58],"specifically":[59],"developed":[60],"integrate":[62,102],"number":[64,105],"mutation":[67,108],"single":[70],"cells":[71,163],"are":[72],"still":[73],"highly":[74],"needed.":[75],"We":[76,129],"introduce":[77],"a":[78,169],"deep":[79],"joint":[80],"representation":[81],"learning":[82],"framework":[83],"called":[84],"scCMP,":[85],"accurately":[87,160],"identify":[88],"profiles.":[91],"scCMP":[92,135,159],"employs":[93],"hybrid":[94],"Transformer-CNN":[95],"architectures":[96],"graph":[98],"convolutional":[99],"networks":[100],"data.":[109,184],"By":[110],"fusing":[111],"individual":[112],"commonality":[114],"information":[115],"among":[116],"two":[118],"modalities,":[119],"it":[120],"generates":[121],"meaningful":[122],"cell":[123],"embeddings":[124],"identifying":[126],"clusters.":[128],"comprehensively":[130],"evaluate":[131],"effectiveness":[133],"on":[136,149],"five":[137],"real":[138],"DNA":[140],"sequencing":[141],"datasets,":[142],"further":[144],"showcase":[145],"its":[146,178],"good":[147],"scalability":[148],"datasets":[150],"generated":[151],"from":[152],"other":[153],"omics":[154],"technologies.":[155],"The":[156],"results":[157],"show":[158],"aggregates":[161],"with":[164],"similar":[165],"into":[168],"same":[170],"cluster,":[171],"surpasses":[173],"state-of-the-art":[175],"methods,":[176],"indicating":[177],"advantage":[179],"integrating":[181]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
