{"id":"https://openalex.org/W4379620532","doi":"https://doi.org/10.1109/tcbb.2023.3283534","title":"Construction of Gene Expression Patterns to Identify Critical Genes Under SARS-CoV-2 Infection Conditions","display_name":"Construction of Gene Expression Patterns to Identify Critical Genes Under SARS-CoV-2 Infection Conditions","publication_year":2023,"publication_date":"2023-06-07","ids":{"openalex":"https://openalex.org/W4379620532","doi":"https://doi.org/10.1109/tcbb.2023.3283534","pmid":"https://pubmed.ncbi.nlm.nih.gov/37285245"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3283534","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3283534","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/A5101825361","display_name":"Yu Xiao","orcid":"https://orcid.org/0000-0002-1985-6840"},"institutions":[{"id":"https://openalex.org/I141962983","display_name":"Shanghai University of Engineering Science","ror":"https://ror.org/0557b9y08","country_code":"CN","type":"education","lineage":["https://openalex.org/I141962983"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Yu","raw_affiliation_strings":["School of Computer Engineering and Technology, Shanghai University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0002-1985-6840","affiliations":[{"raw_affiliation_string":"School of Computer Engineering and Technology, Shanghai University, Shanghai, China","institution_ids":["https://openalex.org/I141962983"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100367608","display_name":"Weimin Li","orcid":"https://orcid.org/0000-0001-9803-2745"},"institutions":[{"id":"https://openalex.org/I141962983","display_name":"Shanghai University of Engineering Science","ror":"https://ror.org/0557b9y08","country_code":"CN","type":"education","lineage":["https://openalex.org/I141962983"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weimin Li","raw_affiliation_strings":["School of Computer Engineering and Technology, Shanghai University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0001-9803-2745","affiliations":[{"raw_affiliation_string":"School of Computer Engineering and Technology, Shanghai University, Shanghai, China","institution_ids":["https://openalex.org/I141962983"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055189079","display_name":"Jianjia Wang","orcid":"https://orcid.org/0000-0003-1983-1632"},"institutions":[{"id":"https://openalex.org/I141962983","display_name":"Shanghai University of Engineering Science","ror":"https://ror.org/0557b9y08","country_code":"CN","type":"education","lineage":["https://openalex.org/I141962983"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianjia Wang","raw_affiliation_strings":["School of Computer Engineering and Technology, Shanghai University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0003-1983-1632","affiliations":[{"raw_affiliation_string":"School of Computer Engineering and Technology, Shanghai University, Shanghai, China","institution_ids":["https://openalex.org/I141962983"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083539852","display_name":"Xing Wu","orcid":"https://orcid.org/0000-0001-5331-022X"},"institutions":[{"id":"https://openalex.org/I141962983","display_name":"Shanghai University of Engineering Science","ror":"https://ror.org/0557b9y08","country_code":"CN","type":"education","lineage":["https://openalex.org/I141962983"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xing Wu","raw_affiliation_strings":["School of Computer Engineering and Technology, Shanghai University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0001-5331-022X","affiliations":[{"raw_affiliation_string":"School of Computer Engineering and Technology, Shanghai University, Shanghai, China","institution_ids":["https://openalex.org/I141962983"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013752041","display_name":"Bin Sheng","orcid":"https://orcid.org/0000-0003-4601-446X"},"institutions":[{"id":"https://openalex.org/I141962983","display_name":"Shanghai University of Engineering Science","ror":"https://ror.org/0557b9y08","country_code":"CN","type":"education","lineage":["https://openalex.org/I141962983"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Sheng","raw_affiliation_strings":["School of Computer Engineering and Technology, Shanghai University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0003-4601-446X","affiliations":[{"raw_affiliation_string":"School of Computer Engineering and Technology, Shanghai University, Shanghai, China","institution_ids":["https://openalex.org/I141962983"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I141962983"],"apc_list":null,"apc_paid":null,"fwci":0.2691,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.61120015,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"21","issue":"4","first_page":"607","last_page":"618"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9914000034332275,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.989799976348877,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.7407729029655457},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.688971996307373},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.6857552528381348},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5343747735023499},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.46880605816841125},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.44806233048439026},{"id":"https://openalex.org/keywords/coronavirus","display_name":"Coronavirus","score":0.44422098994255066},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.4244832992553711},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4234233498573303},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.3704746961593628},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.26992037892341614},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.09102311730384827},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.08173960447311401}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.7407729029655457},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.688971996307373},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.6857552528381348},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5343747735023499},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.46880605816841125},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.44806233048439026},{"id":"https://openalex.org/C2777648638","wikidata":"https://www.wikidata.org/wiki/Q57751738","display_name":"Coronavirus","level":5,"score":0.44422098994255066},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.4244832992553711},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4234233498573303},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3704746961593628},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.26992037892341614},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.09102311730384827},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.08173960447311401},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":2,"locations":[{"id":"doi:10.1109/tcbb.2023.3283534","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3283534","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:37285245","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37285245","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.8500000238418579,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G6285256369","display_name":null,"funder_award_id":"2019YFE0190500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1542426682","https://openalex.org/W1971937094","https://openalex.org/W1978493656","https://openalex.org/W1996221647","https://openalex.org/W2049295438","https://openalex.org/W2055538060","https://openalex.org/W2056716515","https://openalex.org/W2075761732","https://openalex.org/W2085841467","https://openalex.org/W2097795961","https://openalex.org/W2101181377","https://openalex.org/W2103017472","https://openalex.org/W2103912979","https://openalex.org/W2118446779","https://openalex.org/W2125209314","https://openalex.org/W2136850043","https://openalex.org/W2146980885","https://openalex.org/W2150318080","https://openalex.org/W2159675211","https://openalex.org/W2176118516","https://openalex.org/W2215765065","https://openalex.org/W2225391592","https://openalex.org/W2414035669","https://openalex.org/W2555803041","https://openalex.org/W2569951966","https://openalex.org/W2767674461","https://openalex.org/W2768463336","https://openalex.org/W2769640901","https://openalex.org/W2806512480","https://openalex.org/W2979437960","https://openalex.org/W3001118548","https://openalex.org/W3006645647","https://openalex.org/W3013843138","https://openalex.org/W3021582812","https://openalex.org/W3022522270","https://openalex.org/W3024836211","https://openalex.org/W3036509671","https://openalex.org/W3041960835","https://openalex.org/W3087310313","https://openalex.org/W3091765099","https://openalex.org/W3092296275","https://openalex.org/W3106565768","https://openalex.org/W3106935950","https://openalex.org/W3107527779","https://openalex.org/W3110939623","https://openalex.org/W3111713404","https://openalex.org/W3119327744","https://openalex.org/W3124115765","https://openalex.org/W3126184947","https://openalex.org/W3152563552","https://openalex.org/W3152638763","https://openalex.org/W3154144457","https://openalex.org/W3158741652","https://openalex.org/W3158759620","https://openalex.org/W3161422088","https://openalex.org/W3163781793","https://openalex.org/W3176910263","https://openalex.org/W3194731995","https://openalex.org/W3204162860","https://openalex.org/W3213294911","https://openalex.org/W3217748719","https://openalex.org/W4210964945","https://openalex.org/W4226356622","https://openalex.org/W4230727741","https://openalex.org/W4281489087","https://openalex.org/W4289537189","https://openalex.org/W4292267310","https://openalex.org/W4295182961","https://openalex.org/W4312887577","https://openalex.org/W4320472890","https://openalex.org/W4328055021","https://openalex.org/W4361224469","https://openalex.org/W6783948510"],"related_works":["https://openalex.org/W2052655934","https://openalex.org/W104645380","https://openalex.org/W2027213253","https://openalex.org/W2023641020","https://openalex.org/W2017047508","https://openalex.org/W2165201120","https://openalex.org/W2188530857","https://openalex.org/W2041199873","https://openalex.org/W3151254369","https://openalex.org/W2613929436"],"abstract_inverted_index":{"Severe":[0],"Acute":[1],"Respiratory":[2],"Syndrome":[3],"Coronavirus":[4],"2":[5],"(SARS-CoV-2)":[6],"is":[7],"a":[8,80],"positive-stranded":[9],"single-stranded":[10],"RNA":[11],"virus":[12,147],"with":[13],"an":[14],"envelope":[15],"frequently":[16],"altered":[17],"by":[18,123,149],"unstable":[19],"genetic":[20],"material,":[21],"making":[22,66],"it":[23,67],"extremely":[24],"difficult":[25,68],"for":[26,48,83],"vaccines,":[27],"drugs,":[28],"and":[29,129,141],"diagnostics":[30],"to":[31,69,96,110,145],"work.":[32],"Understanding":[33],"SARS-CoV-2":[34,88,146],"infection":[35,89],"mechanisms":[36],"requires":[37],"studying":[38],"gene":[39,50,64,71,85,124],"expression":[40,51,72,86,93,99],"changes.":[41],"Deep":[42],"learning":[43],"methods":[44],"are":[45],"often":[46],"considered":[47],"large-scale":[49],"profiling":[52],"data.":[53],"Data":[54],"feature-oriented":[55],"analysis,":[56],"however,":[57],"neglects":[58],"the":[59,106],"biological":[60],"process":[61],"nature":[62],"of":[63],"expression,":[65],"describe":[70],"behaviors":[73],"accurately.":[74],"In":[75],"this":[76,102],"article,":[77],"we":[78,104],"propose":[79],"novel":[81],"scheme":[82],"modeling":[84],"during":[87],"as":[90],"networks":[91],"(gene":[92],"modes,":[94],"GEM),":[95],"characterize":[97],"their":[98],"behaviors.":[100],"On":[101],"basis,":[103],"investigated":[105],"relationships":[107],"among":[108],"GEMs":[109],"determine":[111],"SARS-CoV-2's":[112],"core":[113],"radiation":[114],"mode.":[115],"Our":[116],"final":[117],"experiments":[118],"identified":[119],"key":[120],"COVID-19":[121],"genes":[122,143],"function":[125],"enrichment,":[126],"protein":[127],"interaction,":[128],"module":[130],"mining.":[131],"Experimental":[132],"results":[133],"show":[134],"that":[135],"ATG10,":[136],"ATG14,":[137],"MAP1LC3B,":[138],"OPTN,":[139],"WDR45,":[140],"WIPI1":[142],"contribute":[144],"spread":[148],"affecting":[150],"autophagy.":[151]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}