{"id":"https://openalex.org/W7126057355","doi":"https://doi.org/10.1109/bibm66473.2025.11356826","title":"Integrating Single Cell RNA Sequencing Data and Protein Embeddings to Infer Cell-Cell Communication in Alzheimer's Disease","display_name":"Integrating Single Cell RNA Sequencing Data and Protein Embeddings to Infer Cell-Cell Communication in Alzheimer's Disease","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126057355","doi":"https://doi.org/10.1109/bibm66473.2025.11356826"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356826","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356826","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5042786517","display_name":"Yuting Tan","orcid":"https://orcid.org/0000-0002-3605-1307"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuting Tan","raw_affiliation_strings":["Vanderbilt University,Department of Molecular Physiology and Biophysics,Nashville,Tennessee"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Department of Molecular Physiology and Biophysics,Nashville,Tennessee","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124232536","display_name":"Yang Li","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Li","raw_affiliation_strings":["Vanderbilt University,Department of Computer Science,Nashville,Tennessee"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Department of Computer Science,Nashville,Tennessee","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100403642","display_name":"Rui Chen","orcid":"https://orcid.org/0000-0002-4341-2908"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rui Chen","raw_affiliation_strings":["Vanderbilt University,Department of Molecular Physiology and Biophysics,Nashville,Tennessee"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Department of Molecular Physiology and Biophysics,Nashville,Tennessee","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Anshul Tiwari","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anshul Tiwari","raw_affiliation_strings":["Vanderbilt University,Department of Molecular Physiology and Biophysics,Nashville,Tennessee"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Department of Molecular Physiology and Biophysics,Nashville,Tennessee","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121345714","display_name":"Zhexing Wen","orcid":null},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhexing Wen","raw_affiliation_strings":["Emory University,Department of Psychiatry and Behavioral Sciences,Atlanta,Georgia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Emory University,Department of Psychiatry and Behavioral Sciences,Atlanta,Georgia","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124267825","display_name":"Xue Zhong","orcid":null},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xue Zhong","raw_affiliation_strings":["Vanderbilt University Medical Center,Department of Medicine,Nashville,Tennessee"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University Medical Center,Department of Medicine,Nashville,Tennessee","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124231830","display_name":"Zhijun Yin","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhijun Yin","raw_affiliation_strings":["Vanderbilt University,Department of Computer Science,Nashville,Tennessee"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Department of Computer Science,Nashville,Tennessee","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015400531","display_name":"Bo Li","orcid":"https://orcid.org/0000-0002-7294-6888"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bingshan Li","raw_affiliation_strings":["Vanderbilt University,Department of Molecular Physiology and Biophysics,Nashville,Tennessee"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University,Department of Molecular Physiology and Biophysics,Nashville,Tennessee","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1227","last_page":"1234"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9865999817848206,"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":0.9865999817848206,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0034000000450760126,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/interpretability","display_name":"Interpretability","score":0.7778000235557556},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6953999996185303},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.49079999327659607},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.36320000886917114},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.35910001397132874},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.35499998927116394},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3483000099658966},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.3425000011920929}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.7778000235557556},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6953999996185303},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6583999991416931},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6184999942779541},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.49079999327659607},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4120999872684479},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3898000121116638},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.36320000886917114},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.35910001397132874},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35910001397132874},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.35499998927116394},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3483000099658966},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.3425000011920929},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.32679998874664307},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.325300008058548},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.321399986743927},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.32109999656677246},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.3151000142097473},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.31029999256134033},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.30979999899864197},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2939999997615814},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.2913999855518341},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.28119999170303345},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26600000262260437},{"id":"https://openalex.org/C155911762","wikidata":"https://www.wikidata.org/wiki/Q422321","display_name":"Blueprint","level":2,"score":0.2612000107765198}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356826","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356826","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7082701921463013,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[{"id":"https://openalex.org/G7819194233","display_name":null,"funder_award_id":"R01AG069900,R01AG089717,R01AG065611","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1043653796","https://openalex.org/W2992151131","https://openalex.org/W3007935255","https://openalex.org/W3132661792","https://openalex.org/W3187966659","https://openalex.org/W4321498274","https://openalex.org/W4327550249","https://openalex.org/W4387142593","https://openalex.org/W4390618033","https://openalex.org/W4396569073","https://openalex.org/W4401406616","https://openalex.org/W4401947164","https://openalex.org/W4403401644","https://openalex.org/W4404458588","https://openalex.org/W4412521091"],"related_works":[],"abstract_inverted_index":{"Cell-cell":[0],"communication":[1],"(CCC)":[2],"plays":[3],"a":[4,38,119,133],"critical":[5],"role":[6],"in":[7,127],"the":[8,56,62,82,109],"pathogenesis":[9],"of":[10,66,112],"Alzheimer's":[11],"disease":[12],"(AD),":[13],"yet":[14],"most":[15],"computational":[16],"methods":[17],"for":[18,122,135],"CCC":[19,67,137],"inference":[20,44],"rely":[21],"exclusively":[22],"on":[23],"transcriptomic":[24],"data,":[25],"showing":[26],"low":[27],"consistency":[28],"across":[29],"datasets":[30],"or":[31],"methods.":[32],"In":[33],"this":[34],"study,":[35],"we":[36],"present":[37],"Protein":[39],"Embedding-Infused":[40],"Cell":[41],"Talk":[42],"(PEICTalk)":[43],"method":[45],"that":[46],"integrates":[47],"singlecell":[48],"RNA-sequencing":[49],"(scRNA-seq)":[50],"data":[51],"with":[52,102],"protein":[53],"embeddings":[54],"from":[55],"ESM-2":[57],"language":[58],"model":[59],"to":[60,72],"improve":[61],"accuracy":[63],"and":[64,94,129],"interpretability":[65],"inference.":[68],"We":[69],"applied":[70],"PEICTalk":[71,87],"two":[73],"large-scale":[74],"scRNA-seq":[75],"datasets,":[76],"after":[77],"harmonizing":[78],"celltype":[79],"annotations":[80],"using":[81],"SEA-AD":[83],"taxonomy":[84],"via":[85],"MapMyCells.":[86],"outperformed":[88],"standard":[89],"tools":[90],"such":[91],"as":[92,132],"CellChat":[93],"CellPhoneDB,":[95],"identifying":[96],"more":[97],"biologically":[98],"meaningful":[99],"ligandreceptor":[100],"interactions":[101],"higher":[103],"cross-dataset":[104],"reproducibility.":[105],"Ablation":[106],"analysis":[107],"confirmed":[108],"crucial":[110],"value":[111],"protein-level":[113],"information.":[114],"This":[115],"integrative":[116],"strategy":[117],"offers":[118],"robust":[120],"foundation":[121],"uncovering":[123],"novel":[124],"intercellular":[125],"mechanisms":[126],"AD":[128],"may":[130],"serve":[131],"blueprint":[134],"future":[136],"studies.":[138]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2026-01-30T00:00:00"}