{"id":"https://openalex.org/W4383314212","doi":"https://doi.org/10.1371/journal.pcbi.1011222","title":"Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes","display_name":"Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes","publication_year":2023,"publication_date":"2023-07-06","ids":{"openalex":"https://openalex.org/W4383314212","doi":"https://doi.org/10.1371/journal.pcbi.1011222","pmid":"https://pubmed.ncbi.nlm.nih.gov/37410793"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011222","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011222","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011222&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011222&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021538432","display_name":"Shaoke Lou","orcid":"https://orcid.org/0000-0002-2626-5897"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaoke Lou","raw_affiliation_strings":["Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America","Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2626-5897","affiliations":[{"raw_affiliation_string":"Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013133039","display_name":"Mingjun Yang","orcid":"https://orcid.org/0000-0001-6341-4284"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mingjun Yang","raw_affiliation_strings":["School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-6341-4284","affiliations":[{"raw_affiliation_string":"School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London, United Kingdom","institution_ids":["https://openalex.org/I166337079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100689730","display_name":"Tianxiao Li","orcid":"https://orcid.org/0000-0002-9147-7511"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianxiao Li","raw_affiliation_strings":["Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America","Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Weihao Zhao","orcid":"https://orcid.org/0000-0002-7480-8112"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weihao Zhao","raw_affiliation_strings":["Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America","Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7480-8112","affiliations":[{"raw_affiliation_string":"Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082059092","display_name":"Hannah Cevasco","orcid":"https://orcid.org/0000-0002-5466-0181"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hannah Cevasco","raw_affiliation_strings":["Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-5466-0181","affiliations":[{"raw_affiliation_string":"Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012454723","display_name":"Yucheng Yang","orcid":"https://orcid.org/0000-0002-6873-5279"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210085920","display_name":"Shanghai Institute for Science of Science","ror":"https://ror.org/004srxn73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210085920"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yucheng T. Yang","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China","MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China","MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I4210085920","https://openalex.org/I24943067"]},{"raw_affiliation_string":"MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Gerstein","raw_affiliation_strings":["Department of Biomedical Informatics & Data Science, Yale University, New Haven, Connecticut, United States of America","Department of Computer Science, Yale University, New Haven, Connecticut, United States of America","Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America","Department of Statistics & Data Science Yale University, New Haven, Connecticut, United States of America","Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9746-3719","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics & Data Science, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Computer Science, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Statistics & Data Science Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5042321575"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.3378,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.76048941,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"19","issue":"7","first_page":"e1011222","last_page":"e1011222"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9843999743461609,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9843999743461609,"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"}},{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9803000092506409,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10041","display_name":"COVID-19 Clinical Research Studies","score":0.9689000248908997,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.9477578401565552},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6618780493736267},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6349421739578247},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5462616682052612},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5060941576957703},{"id":"https://openalex.org/keywords/crosstalk","display_name":"Crosstalk","score":0.45769768953323364},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.4537633955478668},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.44877681136131287},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.4379368722438812},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4219357967376709},{"id":"https://openalex.org/keywords/pandemic","display_name":"Pandemic","score":0.4181543290615082},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.4155951738357544},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.3335988521575928},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32100358605384827},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.1980394721031189},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.14527124166488647}],"concepts":[{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.9477578401565552},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6618780493736267},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6349421739578247},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5462616682052612},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5060941576957703},{"id":"https://openalex.org/C169822122","wikidata":"https://www.wikidata.org/wiki/Q230187","display_name":"Crosstalk","level":2,"score":0.45769768953323364},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.4537633955478668},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.44877681136131287},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.4379368722438812},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4219357967376709},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.4181543290615082},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.4155951738357544},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.3335988521575928},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32100358605384827},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.1980394721031189},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.14527124166488647},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000094024","descriptor_name":"Post-Acute COVID-19 Syndrome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000094024","descriptor_name":"Post-Acute COVID-19 Syndrome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000094024","descriptor_name":"Post-Acute COVID-19 Syndrome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000094024","descriptor_name":"Post-Acute COVID-19 Syndrome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000094024","descriptor_name":"Post-Acute COVID-19 Syndrome","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":"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":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":"Q000517","qualifier_name":"prevention & control","is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":"Q000517","qualifier_name":"prevention & control","is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":"Q000517","qualifier_name":"prevention & control","is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":"Q000517","qualifier_name":"prevention & control","is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":"Q000517","qualifier_name":"prevention & control","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011222","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011222","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011222&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37410793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37410793","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10325097","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10325097","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10325097/pdf/pcbi.1011222.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d695763806e0400b833124b01159cec7","is_oa":true,"landing_page_url":"https://doaj.org/article/d695763806e0400b833124b01159cec7","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 7, p e1011222 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011222","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011222","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011222&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8399999737739563}],"awards":[{"id":"https://openalex.org/G2074609328","display_name":null,"funder_award_id":"R01DA051906","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G4816937021","display_name":null,"funder_award_id":"R01DA051906","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4383314212.pdf","grobid_xml":"https://content.openalex.org/works/W4383314212.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W2036134896","https://openalex.org/W2057841587","https://openalex.org/W2092795568","https://openalex.org/W2151350595","https://openalex.org/W2154867378","https://openalex.org/W2159954944","https://openalex.org/W2169456326","https://openalex.org/W2497207463","https://openalex.org/W2618503740","https://openalex.org/W2922273006","https://openalex.org/W2928729781","https://openalex.org/W2972250108","https://openalex.org/W2988353404","https://openalex.org/W3003217347","https://openalex.org/W3003518864","https://openalex.org/W3009109635","https://openalex.org/W3017680297","https://openalex.org/W3022248657","https://openalex.org/W3022285953","https://openalex.org/W3033192367","https://openalex.org/W3041733494","https://openalex.org/W3043868614","https://openalex.org/W3044391874","https://openalex.org/W3045645692","https://openalex.org/W3047549677","https://openalex.org/W3048884493","https://openalex.org/W3092904880","https://openalex.org/W3093213262","https://openalex.org/W3097702668","https://openalex.org/W3100904172","https://openalex.org/W3109293685","https://openalex.org/W3110054816","https://openalex.org/W3112860625","https://openalex.org/W3126904753","https://openalex.org/W3128961456","https://openalex.org/W3131015235","https://openalex.org/W3132529333","https://openalex.org/W3134844657","https://openalex.org/W3138252766","https://openalex.org/W3156713432","https://openalex.org/W3164741267","https://openalex.org/W3171906465","https://openalex.org/W3173861184","https://openalex.org/W3207416197","https://openalex.org/W3208934579","https://openalex.org/W4221013931","https://openalex.org/W4221107345","https://openalex.org/W4225134020","https://openalex.org/W4242729757","https://openalex.org/W4254656873","https://openalex.org/W4280587540","https://openalex.org/W4282580030","https://openalex.org/W4283732018","https://openalex.org/W4301372179","https://openalex.org/W4307232282","https://openalex.org/W4316014106"],"related_works":["https://openalex.org/W4292634579","https://openalex.org/W2964314049","https://openalex.org/W2022326234","https://openalex.org/W1531941329","https://openalex.org/W4388694323","https://openalex.org/W3215098729","https://openalex.org/W4243081378","https://openalex.org/W1979330259","https://openalex.org/W2951532861","https://openalex.org/W2063905494"],"abstract_inverted_index":{"The":[0,15],"COVID-19":[1],"pandemic":[2],"caused":[3],"by":[4,43,250],"the":[5,34,45,54,61,81,111,125,220],"SARS-CoV-2":[6,64,85,164,186,245],"virus":[7],"has":[8],"resulted":[9],"in":[10,24,103,120,219],"millions":[11],"of":[12,36,47,63,80,84,113,173,209,252],"deaths":[13],"worldwide.":[14],"disease":[16],"presents":[17],"with":[18,165,244],"various":[19],"manifestations":[20],"that":[21,58,162,225,233],"can":[22],"vary":[23],"severity":[25],"and":[26,41,96,116,155,167,187,191,211,222,236,241],"long-term":[27],"outcomes.":[28],"Previous":[29],"efforts":[30],"have":[31],"contributed":[32],"to":[33,70,76,107,182,202,228],"development":[35],"effective":[37],"strategies":[38],"for":[39],"treatment":[40],"prevention":[42],"uncovering":[44],"mechanism":[46],"viral":[48],"infection.":[49],"We":[50,178,193,230],"now":[51],"know":[52],"all":[53],"direct":[55],"protein-protein":[56,157],"interactions":[57,75],"occur":[59],"during":[60],"lifecycle":[62],"infection,":[65,86],"but":[66],"it":[67],"is":[68],"critical":[69],"move":[71],"beyond":[72],"these":[73,180,196],"known":[74],"a":[77,130,206,247],"comprehensive":[78],"understanding":[79],"\"full":[82],"interactome\"":[83],"which":[87],"incorporates":[88],"human":[89,93,151,156],"microRNAs":[90],"(miRNAs),":[91],"additional":[92],"protein-coding":[94,152,188],"genes,":[95,153,189],"exogenous":[97],"microbes.":[98,192],"Potentially,":[99],"this":[100],"will":[101],"help":[102],"developing":[104],"new":[105],"drugs":[106],"treat":[108],"COVID-19,":[109],"differentiating":[110],"nuances":[112],"long":[114],"COVID,":[115],"identifying":[117],"histopathological":[118],"signatures":[119],"SARS-CoV-2-infected":[121],"organs.":[122],"To":[123],"construct":[124],"full":[126],"interactome,":[127],"we":[128,216],"developed":[129],"statistical":[131],"modeling":[132],"approach":[133],"called":[134],"MLCrosstalk":[135,143],"(multiple-layer":[136],"crosstalk)":[137],"based":[138,169],"on":[139,170],"latent":[140],"Dirichlet":[141],"allocation.":[142],"integrates":[144],"data":[145],"from":[146],"multiple":[147],"sources,":[148],"including":[149],"microbes,":[150],"miRNAs,":[154,190],"interactions.":[158],"It":[159],"constructs":[160],"\"topics\"":[161],"group":[163],"genes":[166,218],"microbes":[168],"similar":[171],"patterns":[172],"co-occurrence":[174],"across":[175],"patient":[176],"samples.":[177],"use":[179],"topics":[181],"infer":[183],"linkages":[184,198],"between":[185],"then":[194],"refine":[195],"initial":[197],"using":[199],"network":[200,210],"propagation":[201],"contextualize":[203],"them":[204],"within":[205],"larger":[207],"framework":[208],"pathway":[212],"structures.":[213],"Using":[214],"MLCrosstalk,":[215],"identified":[217],"IL1-processing":[221],"VEGFA-VEGFR2":[223],"pathways":[224],"are":[226,239],"linked":[227],"SARS-CoV-2.":[229],"also":[231],"found":[232],"Rothia":[234],"mucilaginosa":[235],"Prevotella":[237],"melaninogenica":[238],"positively":[240],"negatively":[242],"correlated":[243],"abundance,":[246],"finding":[248],"corroborated":[249],"analysis":[251],"single-cell":[253],"sequencing":[254],"data.":[255]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}