{"id":"https://openalex.org/W4295879679","doi":"https://doi.org/10.1371/journal.pcbi.1010468","title":"CINS: Cell Interaction Network inference from Single cell expression data","display_name":"CINS: Cell Interaction Network inference from Single cell expression data","publication_year":2022,"publication_date":"2022-09-12","ids":{"openalex":"https://openalex.org/W4295879679","doi":"https://doi.org/10.1371/journal.pcbi.1010468","pmid":"https://pubmed.ncbi.nlm.nih.gov/36095011"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010468","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010468","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010468&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.1010468&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082583182","display_name":"Ye Yuan","orcid":"https://orcid.org/0000-0002-4270-8002"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Ye Yuan","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China","Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-4270-8002","affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000567720","display_name":"Carlos Cosme","orcid":"https://orcid.org/0000-0002-2684-2615"},"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":"Carlos Cosme","raw_affiliation_strings":["Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2684-2615","affiliations":[{"raw_affiliation_string":"Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061050372","display_name":"Taylor Adams","orcid":"https://orcid.org/0000-0003-4280-9070"},"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":"Taylor Sterling Adams","raw_affiliation_strings":["Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004764468","display_name":"Jonas C. Schupp","orcid":"https://orcid.org/0000-0002-7714-8076"},"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":"Jonas Schupp","raw_affiliation_strings":["Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7714-8076","affiliations":[{"raw_affiliation_string":"Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000765342","display_name":"Koji Sakamoto","orcid":"https://orcid.org/0000-0002-1794-576X"},"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":"Koji Sakamoto","raw_affiliation_strings":["Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028586693","display_name":"Nikos Xylourgidis","orcid":null},"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":"Nikos Xylourgidis","raw_affiliation_strings":["Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091838807","display_name":"Matthew Ruffalo","orcid":"https://orcid.org/0000-0003-2222-6169"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Ruffalo","raw_affiliation_strings":["Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100357066","display_name":"Jiachen Li","orcid":"https://orcid.org/0000-0001-9137-6262"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiachen Li","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0001-9137-6262","affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088823841","display_name":"Naftali Kaminski","orcid":"https://orcid.org/0000-0001-5917-4601"},"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":"Naftali Kaminski","raw_affiliation_strings":["Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065673127","display_name":"Ziv Bar\u2010Joseph","orcid":"https://orcid.org/0000-0003-3430-6051"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ziv Bar-Joseph","raw_affiliation_strings":["Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-3430-6051","affiliations":[{"raw_affiliation_string":"Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5065673127"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.868,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.71492692,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"18","issue":"9","first_page":"e1010468","last_page":"e1010468"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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":0.9998999834060669,"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/T11266","display_name":"Neuroinflammation and Neurodegeneration Mechanisms","score":0.9912999868392944,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9907000064849854,"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/inference","display_name":"Inference","score":0.6250115036964417},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6064140200614929},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.6028625965118408},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.5768557786941528},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5454573631286621},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.4805581867694855},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4628751575946808},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4177497327327728},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36722952127456665},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3459750711917877},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32886993885040283},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13210636377334595}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6250115036964417},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6064140200614929},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.6028625965118408},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.5768557786941528},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5454573631286621},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.4805581867694855},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4628751575946808},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4177497327327728},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36722952127456665},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3459750711917877},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32886993885040283},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13210636377334595},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1010468","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010468","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010468&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:36095011","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36095011","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:doaj.org/article:ad87bd93bb924c858e01609837a47d32","is_oa":true,"landing_page_url":"https://doaj.org/article/ad87bd93bb924c858e01609837a47d32","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 9, p e1010468 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9499239","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9499239","pdf_url":null,"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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010468","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010468","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010468&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":[],"awards":[{"id":"https://openalex.org/G4640191528","display_name":null,"funder_award_id":"1R01GM122096","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5909186895","display_name":null,"funder_award_id":"1R01HL127349","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6343073573","display_name":null,"funder_award_id":"OT2OD026682","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8269204498","display_name":null,"funder_award_id":"CBET2134998","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337390","display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","ror":"https://ror.org/0471zv972"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4295879679.pdf","grobid_xml":"https://content.openalex.org/works/W4295879679.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1565400829","https://openalex.org/W1626295059","https://openalex.org/W1659961955","https://openalex.org/W1965616728","https://openalex.org/W1984069598","https://openalex.org/W2002063328","https://openalex.org/W2018116907","https://openalex.org/W2045873742","https://openalex.org/W2080658428","https://openalex.org/W2099714031","https://openalex.org/W2107210055","https://openalex.org/W2133091666","https://openalex.org/W2145456893","https://openalex.org/W2146553975","https://openalex.org/W2151013106","https://openalex.org/W2172192274","https://openalex.org/W2175832638","https://openalex.org/W2471536144","https://openalex.org/W2567951353","https://openalex.org/W2730417194","https://openalex.org/W2795624730","https://openalex.org/W2805232705","https://openalex.org/W2899224111","https://openalex.org/W2899343204","https://openalex.org/W2899948177","https://openalex.org/W2900411771","https://openalex.org/W2908139053","https://openalex.org/W2923300855","https://openalex.org/W2924067995","https://openalex.org/W2944507671","https://openalex.org/W2949177718","https://openalex.org/W2952261006","https://openalex.org/W2952383043","https://openalex.org/W2953064750","https://openalex.org/W2972445800","https://openalex.org/W2987344610","https://openalex.org/W2990349003","https://openalex.org/W2990677723","https://openalex.org/W2992151131","https://openalex.org/W2992905575","https://openalex.org/W2999977864","https://openalex.org/W3007935255","https://openalex.org/W3010692114","https://openalex.org/W3021161518","https://openalex.org/W3037544553","https://openalex.org/W3041062936","https://openalex.org/W3113349968","https://openalex.org/W4244934552","https://openalex.org/W4313343448","https://openalex.org/W6770173102"],"related_works":["https://openalex.org/W3037187668","https://openalex.org/W2055243143","https://openalex.org/W4234772502","https://openalex.org/W2380685755","https://openalex.org/W2252100032","https://openalex.org/W2963436428","https://openalex.org/W4400978025","https://openalex.org/W2918743509","https://openalex.org/W2734796617","https://openalex.org/W3083218341"],"abstract_inverted_index":{"Studies":[0],"comparing":[1],"single":[2],"cell":[3,17,34,72,101,117],"RNA-Seq":[4],"(scRNA-Seq)":[5],"data":[6],"between":[7,50],"conditions":[8,51],"mainly":[9],"focus":[10],"on":[11,20,84,90,112],"differences":[12,28],"in":[13,33,108],"the":[14,54,76,105,130],"proportion":[15],"of":[16],"types":[18],"or":[19],"differentially":[21],"expressed":[22],"genes.":[23],"In":[24,95],"many":[25],"cases":[26,97],"these":[27,109],"are":[29,37],"driven":[30],"by":[31,133],"changes":[32],"interactions":[35,47,74,103,110,131],"which":[36,127],"challenging":[38],"to":[39,69],"infer":[40],"without":[41],"spatial":[42],"information.":[43],"To":[44],"determine":[45],"cell-cell":[46],"that":[48,78],"differ":[49],"we":[52],"developed":[53],"Cell":[55],"Interaction":[56],"Network":[57],"Inference":[58],"(CINS)":[59],"pipeline.":[60],"CINS":[61,83,98],"combines":[62],"Bayesian":[63],"network":[64],"analysis":[65],"with":[66],"regression-based":[67],"modeling":[68],"identify":[70],"differential":[71],"type":[73,102],"and":[75,89,104],"proteins":[77],"underlie":[79],"them.":[80],"We":[81,120],"tested":[82],"a":[85],"disease":[86],"case":[87],"control":[88],"an":[91],"aging":[92,124],"mouse":[93,123],"dataset.":[94],"both":[96],"correctly":[99],"identifies":[100],"ligands":[106],"involved":[107],"improving":[111],"prior":[113],"methods":[114],"suggested":[115],"for":[116],"interaction":[118],"predictions.":[119],"performed":[121],"additional":[122],"scRNA-Seq":[125],"experiments":[126],"further":[128],"support":[129],"identified":[132],"CINS.":[134]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}