{"id":"https://openalex.org/W4405427464","doi":"https://doi.org/10.1145/3698587.3701469","title":"MIXER: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data","display_name":"MIXER: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405427464","doi":"https://doi.org/10.1145/3698587.3701469"},"language":"en","primary_location":{"id":"doi:10.1145/3698587.3701469","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701469","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5059523099","display_name":"Tao Deng","orcid":"https://orcid.org/0000-0001-7401-311X"},"institutions":[{"id":"https://openalex.org/I4210099586","display_name":"Shenzhen Research Institute of Big Data","ror":"https://ror.org/00z1gwf89","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210099586"]},{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tao Deng","raw_affiliation_strings":["The Chinese University of Hong Kong, Shenzhen, Shenzhen Research Institute of Big Data, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong, Shenzhen, Shenzhen Research Institute of Big Data, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I4210116924","https://openalex.org/I4210099586"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111907751","display_name":"Mengqian Huang","orcid":"https://orcid.org/0009-0003-6440-0601"},"institutions":[{"id":"https://openalex.org/I158934434","display_name":"Zhongnan University of Economics and Law","ror":"https://ror.org/04yqxxq63","country_code":"CN","type":"education","lineage":["https://openalex.org/I158934434"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengqian Huang","raw_affiliation_strings":["Zhongnan University of Economics and Law, Wuhan, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Zhongnan University of Economics and Law, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I158934434"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022227779","display_name":"Kaichen Xu","orcid":"https://orcid.org/0009-0001-1768-1303"},"institutions":[{"id":"https://openalex.org/I158934434","display_name":"Zhongnan University of Economics and Law","ror":"https://ror.org/04yqxxq63","country_code":"CN","type":"education","lineage":["https://openalex.org/I158934434"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kaichen Xu","raw_affiliation_strings":["Zhongnan University of Economics and Law, Wuhan, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Zhongnan University of Economics and Law, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I158934434"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022128301","display_name":"Yan Lu","orcid":"https://orcid.org/0009-0006-6492-2321"},"institutions":[{"id":"https://openalex.org/I158934434","display_name":"Zhongnan University of Economics and Law","ror":"https://ror.org/04yqxxq63","country_code":"CN","type":"education","lineage":["https://openalex.org/I158934434"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Lu","raw_affiliation_strings":["Zhongnan University of Economics and Law, Wuhan, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Zhongnan University of Economics and Law, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I158934434"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042336372","display_name":"Siyu Chen","orcid":"https://orcid.org/0000-0002-2662-2858"},"institutions":[{"id":"https://openalex.org/I158934434","display_name":"Zhongnan University of Economics and Law","ror":"https://ror.org/04yqxxq63","country_code":"CN","type":"education","lineage":["https://openalex.org/I158934434"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siyu Chen","raw_affiliation_strings":["Zhongnan University of Economics and Law, Wuhan, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Zhongnan University of Economics and Law, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I158934434"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101286883","display_name":"Yucheng Xu","orcid":"https://orcid.org/0009-0004-9552-4305"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yucheng Xu","raw_affiliation_strings":["Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071955765","display_name":"Nina Xie","orcid":"https://orcid.org/0000-0001-8405-9576"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I4210159865","display_name":"Xiangya Hospital Central South University","ror":"https://ror.org/05c1yfj14","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159865"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Nina Xie","raw_affiliation_strings":["Xiangya Hospital, Central South University, National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China"],"affiliations":[{"raw_affiliation_string":"Xiangya Hospital, Central South University, National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China","institution_ids":["https://openalex.org/I4210159865","https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083170497","display_name":"Hao Wu","orcid":"https://orcid.org/0000-0003-1269-7354"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Wu","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065527238","display_name":"Xiaobo Sun","orcid":"https://orcid.org/0000-0001-9876-5666"},"institutions":[{"id":"https://openalex.org/I158934434","display_name":"Zhongnan University of Economics and Law","ror":"https://ror.org/04yqxxq63","country_code":"CN","type":"education","lineage":["https://openalex.org/I158934434"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaobo Sun","raw_affiliation_strings":["Zhongnan University of Economics and Law, Wuhan, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Zhongnan University of Economics and Law, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I158934434"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5059523099"],"corresponding_institution_ids":["https://openalex.org/I4210099586","https://openalex.org/I4210116924"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20484928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9866999983787537,"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":0.9866999983787537,"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/T11482","display_name":"RNA modifications and cancer","score":0.9861000180244446,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9776999950408936,"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/transcriptome","display_name":"Transcriptome","score":0.6789315342903137},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5675525665283203},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5303505063056946},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5141308903694153},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3306218981742859},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3164879083633423},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30861496925354004},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18002161383628845}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6789315342903137},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5675525665283203},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5303505063056946},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5141308903694153},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3306218981742859},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3164879083633423},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30861496925354004},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18002161383628845}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3698587.3701469","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701469","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":1,"referenced_works":["https://openalex.org/W4200404717"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W4388725868","https://openalex.org/W2104762330","https://openalex.org/W4379374180","https://openalex.org/W2523545060","https://openalex.org/W2034625591"],"abstract_inverted_index":{"Uncovering":[0],"co-expressed":[1,55,76],"genes":[2,13,190],"across":[3,162],"tissue":[4,87],"domains":[5],"and":[6,29,71,86,115,125,132,142,181,186],"cell":[7,84],"types":[8],"is":[9,199],"key":[10],"to":[11,74,111],"identifying":[12,189],"that":[14,68],"operate":[15],"together":[16],"in":[17,91,144,159,179,184,188],"biological":[18,140],"or":[19],"pathological":[20],"processes":[21],"[1].":[22],"Although":[23],"both":[24,83],"single-cell":[25],"RNA":[26],"sequencing":[27],"(scRNA-seq)":[28],"spatially-resolved":[30],"transcriptomics":[31],"(SRT)":[32],"provide":[33],"valuable":[34],"information":[35],"on":[36,43],"gene":[37,56,77,123,136,149,160,169],"co-expression,":[38],"existing":[39],"approaches":[40],"often":[41],"rely":[42],"one":[44],"data":[45,73],"type,":[46],"potentially":[47],"weakening":[48],"the":[49,80,145],"detection":[50],"of":[51,82,100,122,147],"co-functionality":[52],"signals":[53],"within":[54,151],"groups.":[57],"To":[58],"address":[59],"this":[60],"challenge,":[61],"we":[62],"propose":[63],"MIXER,":[64],"a":[65],"computational":[66],"method":[67],"integrates":[69],"scRNA-seq":[70],"SRT":[72,180],"discover":[75],"groups":[78],"at":[79,202],"levels":[81],"type":[85],"domain.":[88],"As":[89],"depicted":[90],"Fig.":[92],"1A,":[93],"MIXER":[94,155,172,198],"first":[95],"generates":[96],"highly":[97],"confident":[98],"pseudo-labels":[99],"spatial":[101,126,177,193],"domains.":[102],"It":[103],"then":[104],"utilizes":[105],"an":[106],"innovative":[107],"hierarchical":[108],"clustering":[109],"algorithm":[110],"maximize":[112],"intra-cluster":[113],"redundancy":[114],"inter-cluster":[116],"complementarity,":[117],"capturing":[118],"more":[119],"nuanced":[120],"patterns":[121,195],"co-expression":[124],"coherence":[127],"(Fig.":[128,196],"1B).":[129],"Through":[130],"enrichment":[131],"co-function":[133],"analyses,":[134],"these":[135],"clusters":[137],"demonstrate":[138],"their":[139],"relevance":[141],"utilities":[143],"discovery":[146],"novel":[148],"functions":[150],"specific":[152],"contexts.":[153],"Remarkably,":[154],"can":[156],"identify":[157],"changes":[158],"interactions":[161],"different":[163],"conditions,":[164],"offering":[165],"insights":[166],"into":[167],"disease-related":[168],"crosstalk.":[170],"Additionally,":[171],"improves":[173],"annotation":[174],"accuracy":[175],"for":[176],"spots":[178],"single":[182],"cells":[183],"scRNA-seq,":[185],"pioneers":[187],"with":[191],"designated":[192],"expression":[194],"1C).":[197],"freely":[200],"available":[201],"https://github.com/MengqianHuang/MIXER.":[203]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
