{"id":"https://openalex.org/W4390970653","doi":"https://doi.org/10.1109/bibm58861.2023.10386053","title":"Using Biological Processes as Prior Knowledge Identifies New Microglial Immune Signatures at Single Cell Level in Alzheimer\u2019s Disease","display_name":"Using Biological Processes as Prior Knowledge Identifies New Microglial Immune Signatures at Single Cell Level in Alzheimer\u2019s Disease","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390970653","doi":"https://doi.org/10.1109/bibm58861.2023.10386053"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10386053","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10386053","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5100377483","display_name":"Chenyu Zhang","orcid":"https://orcid.org/0000-0002-6739-4724"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chenyu Zhang","raw_affiliation_strings":["University of Connecticut,Computer Science and Engineering Department,Storrs,CT,USA,06269"],"affiliations":[{"raw_affiliation_string":"University of Connecticut,Computer Science and Engineering Department,Storrs,CT,USA,06269","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100726968","display_name":"Honglin Wang","orcid":"https://orcid.org/0009-0004-6408-0772"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Honglin Wang","raw_affiliation_strings":["University of Connecticut,Computer Science and Engineering Department,Storrs,CT,USA,06269"],"affiliations":[{"raw_affiliation_string":"University of Connecticut,Computer Science and Engineering Department,Storrs,CT,USA,06269","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076114384","display_name":"Seung-Hyun Hong","orcid":"https://orcid.org/0000-0003-2848-6666"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seung-Hyun Hong","raw_affiliation_strings":["University of Connecticut,Computer Science and Engineering Department,Storrs,CT,USA,06269"],"affiliations":[{"raw_affiliation_string":"University of Connecticut,Computer Science and Engineering Department,Storrs,CT,USA,06269","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038360689","display_name":"Riqiang Yan","orcid":"https://orcid.org/0000-0001-7195-7617"},"institutions":[{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"funder","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Riqiang Yan","raw_affiliation_strings":["University of Connecticut Health Center,Department of Neuroscience,Farmington,CT,USA,06030"],"affiliations":[{"raw_affiliation_string":"University of Connecticut Health Center,Department of Neuroscience,Farmington,CT,USA,06030","institution_ids":["https://openalex.org/I75929689"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112474888","display_name":"Dong\u2010Guk Shin","orcid":"https://orcid.org/0009-0004-4649-7363"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong-Guk Shin","raw_affiliation_strings":["University of Connecticut,Computer Science and Engineering Department,Storrs,CT,USA,06269"],"affiliations":[{"raw_affiliation_string":"University of Connecticut,Computer Science and Engineering Department,Storrs,CT,USA,06269","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100377483"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":null,"apc_paid":null,"fwci":0.3788,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.62726376,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"3756","last_page":"3763"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11266","display_name":"Neuroinflammation and Neurodegeneration Mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2808","display_name":"Neurology"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11266","display_name":"Neuroinflammation and Neurodegeneration Mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2808","display_name":"Neurology"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12955","display_name":"Atherosclerosis and Cardiovascular Diseases","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11313","display_name":"Immune cells in cancer","score":0.9894999861717224,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.6340692043304443},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.5592336058616638},{"id":"https://openalex.org/keywords/microglia","display_name":"Microglia","score":0.4894810914993286},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.47602492570877075},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47252801060676575},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.3946585953235626},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37900078296661377},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33241918683052063},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3164557218551636},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.2024114429950714},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1143253743648529},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.11072242259979248}],"concepts":[{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.6340692043304443},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.5592336058616638},{"id":"https://openalex.org/C2779830541","wikidata":"https://www.wikidata.org/wiki/Q1622829","display_name":"Microglia","level":3,"score":0.4894810914993286},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.47602492570877075},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47252801060676575},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.3946585953235626},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37900078296661377},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33241918683052063},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3164557218551636},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.2024114429950714},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1143253743648529},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.11072242259979248},{"id":"https://openalex.org/C2776914184","wikidata":"https://www.wikidata.org/wiki/Q101991","display_name":"Inflammation","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10386053","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10386053","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1987971958","https://openalex.org/W2082290707","https://openalex.org/W2124667416","https://openalex.org/W2128049108","https://openalex.org/W2598326928","https://openalex.org/W2612288104","https://openalex.org/W2622807556","https://openalex.org/W2624988670","https://openalex.org/W2773035279","https://openalex.org/W2774947569","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2804685648","https://openalex.org/W2845591014","https://openalex.org/W2897249806","https://openalex.org/W2991414673","https://openalex.org/W2998795963","https://openalex.org/W3003257820","https://openalex.org/W3106188259","https://openalex.org/W3152525961","https://openalex.org/W3179788429","https://openalex.org/W3180524530","https://openalex.org/W4245436919","https://openalex.org/W4249273120","https://openalex.org/W4283029637","https://openalex.org/W4288421326","https://openalex.org/W4313526657","https://openalex.org/W4318984787","https://openalex.org/W4321748231","https://openalex.org/W4323542992","https://openalex.org/W4367336636"],"related_works":["https://openalex.org/W2885325217","https://openalex.org/W2546440307","https://openalex.org/W4287448745","https://openalex.org/W3130437983","https://openalex.org/W3048533658","https://openalex.org/W3176323037","https://openalex.org/W2076096323","https://openalex.org/W4308968236","https://openalex.org/W2972440269","https://openalex.org/W4210834908"],"abstract_inverted_index":{"The":[0,127],"brain\u2019s":[1],"resident":[2],"immune":[3,102,169],"cells,":[4,148],"microglia,":[5],"play":[6],"important":[7],"roles":[8],"in":[9,87,180],"the":[10,38,81,88,183,191],"pathological":[11],"process":[12],"of":[13,41,56,116,125,129,147,193,202],"Alzheimer's":[14],"disease":[15,67],"(AD).":[16],"Upon":[17],"encountering":[18],"amyloid-\u03b2":[19],"(A\u03b2)":[20],"plaque":[21],"accumulation,":[22],"microglia":[23,58,69],"change":[24],"its":[25],"state":[26,40,61],"to":[27,31,66,144,157,167,182],"produce":[28],"proinflammatory":[29],"cytokines":[30],"uptake":[32],"and":[33,104,171,207],"clear":[34],"A\u03b2":[35],"but":[36],"during":[37],"chronic":[39],"neuroinflammation":[42],"they":[43],"become":[44],"responsible":[45,162],"for":[46,101],"neurodegeneration.":[47],"In":[48,108],"this":[49,109,130],"paper":[50],"we":[51],"propose":[52],"a":[53,200],"new":[54],"method":[55,78,112,134,198],"analyzing":[57],"undergoing":[59],"multi-stage":[60],"changes":[62],"from":[63,80],"homeostasis":[64],"(HOM)":[65],"associated":[68],"(DAM).":[70],"Our":[71],"single":[72],"cell":[73,196],"gene":[74,211],"expression":[75,212],"data":[76],"analysis":[77],"differs":[79],"conventional":[82],"marker":[83],"based":[84],"subtyping":[85],"methods":[86],"sense":[89],"that":[90],"it":[91],"uses":[92],"prior":[93],"knowledge,":[94],"namely,":[95],"Gene":[96],"Ontology\u2019s":[97],"Biological":[98,154],"Processes":[99],"known":[100],"functions":[103],"other":[105],"related":[106],"ones.":[107],"regard,":[110],"our":[111,194],"can":[113,139,151,177],"be":[114,158,178],"thought":[115],"supervised":[117],"clustering":[118,197],"rather":[119],"than":[120],"UMAP/tSNE":[121],"style":[122],"unbiased":[123],"subgrouping":[124],"cells.":[126],"strengths":[128],"\"prior":[131,187],"knowledge\"":[132],"using":[133,199],"are":[135],"multi-faceted:":[136],"(i)":[137],"one":[138,150],"assign":[140],"meaningful":[141],"functional":[142],"nomenclatures":[143],"identified":[145,179],"subtypes":[146],"(ii)":[149],"refine":[152],"GO":[153],"Process":[155],"genes":[156],"context-specific":[159,174],"(e.g.,":[160],"phagocytosis":[161],"by":[163],"\"microglia\"":[164],"as":[165,186],"opposed":[166],"\"general":[168],"cells\"),":[170],"(iii)":[172],"additional":[173],"biological":[175],"processes":[176],"addition":[181],"ones":[184],"used":[185],"knowledge\".":[188],"We":[189],"illustrate":[190],"advantages":[192],"semi-supervised":[195],"set":[201],"publicly":[203],"available":[204],"human":[205],"AD":[206,209],"mouse":[208],"model":[210],"datasets.":[213]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
