{"id":"https://openalex.org/W4411339883","doi":"https://doi.org/10.1371/journal.pcbi.1013188","title":"RIDDEN: Data-driven inference of receptor activity from transcriptomic data","display_name":"RIDDEN: Data-driven inference of receptor activity from transcriptomic data","publication_year":2025,"publication_date":"2025-06-16","ids":{"openalex":"https://openalex.org/W4411339883","doi":"https://doi.org/10.1371/journal.pcbi.1013188","pmid":"https://pubmed.ncbi.nlm.nih.gov/40522999"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013188","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013188","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1013188","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046900456","display_name":"Szilvia Barsi","orcid":"https://orcid.org/0000-0002-8779-2383"},"institutions":[{"id":"https://openalex.org/I101202996","display_name":"Semmelweis University","ror":"https://ror.org/01g9ty582","country_code":"HU","type":"education","lineage":["https://openalex.org/I101202996"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Szilvia Barsi","raw_affiliation_strings":["Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary","Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary","institution_ids":["https://openalex.org/I101202996"]},{"raw_affiliation_string":"Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary","institution_ids":["https://openalex.org/I80251312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030469165","display_name":"Eszter Varga","orcid":"https://orcid.org/0000-0002-1102-445X"},"institutions":[{"id":"https://openalex.org/I101202996","display_name":"Semmelweis University","ror":"https://ror.org/01g9ty582","country_code":"HU","type":"education","lineage":["https://openalex.org/I101202996"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Eszter Varga","raw_affiliation_strings":["Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary","institution_ids":["https://openalex.org/I101202996"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084832725","display_name":"Daniel Dimitrov","orcid":"https://orcid.org/0000-0002-5197-2112"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Daniel Dimitrov","raw_affiliation_strings":["Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005499510","display_name":"Julio S\u00e1ez-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-8552-8976"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010688747","display_name":"L\u00e1szl\u00f3 Hunyady","orcid":"https://orcid.org/0000-0002-8438-7251"},"institutions":[{"id":"https://openalex.org/I101202996","display_name":"Semmelweis University","ror":"https://ror.org/01g9ty582","country_code":"HU","type":"education","lineage":["https://openalex.org/I101202996"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"L\u00e1szl\u00f3 Hunyady","raw_affiliation_strings":["Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary","Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary","institution_ids":["https://openalex.org/I101202996"]},{"raw_affiliation_string":"Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary","institution_ids":["https://openalex.org/I80251312"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084722846","display_name":"Bence Szalai","orcid":"https://orcid.org/0000-0002-9320-5704"},"institutions":[{"id":"https://openalex.org/I101202996","display_name":"Semmelweis University","ror":"https://ror.org/01g9ty582","country_code":"HU","type":"education","lineage":["https://openalex.org/I101202996"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Bence Szalai","raw_affiliation_strings":["Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary","Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary","institution_ids":["https://openalex.org/I101202996"]},{"raw_affiliation_string":"Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary","institution_ids":["https://openalex.org/I80251312"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5005499510","https://openalex.org/A5010688747","https://openalex.org/A5030469165","https://openalex.org/A5046900456","https://openalex.org/A5084722846","https://openalex.org/A5084832725"],"corresponding_institution_ids":["https://openalex.org/I101202996","https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I80251312"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.1568,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.91691762,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"21","issue":"6","first_page":"e1013188","last_page":"e1013188"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994000196456909,"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":0.9994000196456909,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9973999857902527,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9961000084877014,"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/receptor","display_name":"Receptor","score":0.7387892603874207},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6635750532150269},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5939832925796509},{"id":"https://openalex.org/keywords/receptor-expression","display_name":"Receptor expression","score":0.5666031837463379},{"id":"https://openalex.org/keywords/immune-receptor","display_name":"Immune receptor","score":0.5113134384155273},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5111964344978333},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4806765019893646},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4129057824611664},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3968234956264496},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.39592379331588745},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3392963707447052},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.332790732383728},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23807260394096375},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.21278852224349976},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1803382933139801}],"concepts":[{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.7387892603874207},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6635750532150269},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5939832925796509},{"id":"https://openalex.org/C2993002077","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Receptor expression","level":3,"score":0.5666031837463379},{"id":"https://openalex.org/C103474210","wikidata":"https://www.wikidata.org/wiki/Q142851","display_name":"Immune receptor","level":3,"score":0.5113134384155273},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5111964344978333},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4806765019893646},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4129057824611664},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3968234956264496},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.39592379331588745},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3392963707447052},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.332790732383728},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23807260394096375},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.21278852224349976},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1803382933139801}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013188","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013188","pdf_url":null,"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:40522999","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40522999","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:35d0c61b310d4eefb41dd1ede7a348f6","is_oa":true,"landing_page_url":"https://doaj.org/article/35d0c61b310d4eefb41dd1ede7a348f6","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 21, Iss 6, p e1013188 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12193052","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12193052","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1013188","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013188","pdf_url":null,"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":[{"id":"https://metadata.un.org/sdg/3","score":0.5600000023841858,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G3790165651","display_name":null,"funder_award_id":"PharmaLab, RRF-2.3.1-21-2022-00015","funder_id":"https://openalex.org/F4320336675","funder_display_name":"National Research, Development and Innovation Office"},{"id":"https://openalex.org/G5003558051","display_name":null,"funder_award_id":"K 139231","funder_id":"https://openalex.org/F4320335908","funder_display_name":"Nemzeti Kutat\u00e1si, Fejleszt\u00e9si \u00e9s Innovaci\u00f3s Alap"},{"id":"https://openalex.org/G6844412585","display_name":null,"funder_award_id":"460044","funder_id":"https://openalex.org/F4320322192","funder_display_name":"Magyar Tudom\u00e1nyos Akad\u00e9mia"}],"funders":[{"id":"https://openalex.org/F4320322192","display_name":"Magyar Tudom\u00e1nyos Akad\u00e9mia","ror":"https://ror.org/02ks8qq67"},{"id":"https://openalex.org/F4320335908","display_name":"Nemzeti Kutat\u00e1si, Fejleszt\u00e9si \u00e9s Innovaci\u00f3s Alap","ror":null},{"id":"https://openalex.org/F4320336675","display_name":"National Research, Development and Innovation Office","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W130097387","https://openalex.org/W1973268693","https://openalex.org/W2001941062","https://openalex.org/W2016436468","https://openalex.org/W2023624246","https://openalex.org/W2043398720","https://openalex.org/W2047526240","https://openalex.org/W2085813915","https://openalex.org/W2098720608","https://openalex.org/W2118258530","https://openalex.org/W2118393858","https://openalex.org/W2141545183","https://openalex.org/W2151935175","https://openalex.org/W2158485828","https://openalex.org/W2281321365","https://openalex.org/W2557833574","https://openalex.org/W2606939149","https://openalex.org/W2612467560","https://openalex.org/W2615301036","https://openalex.org/W2791483720","https://openalex.org/W2800392236","https://openalex.org/W2817838603","https://openalex.org/W2935426292","https://openalex.org/W2952391626","https://openalex.org/W2964315448","https://openalex.org/W2965512201","https://openalex.org/W2967177832","https://openalex.org/W2972751199","https://openalex.org/W2975712044","https://openalex.org/W2988644538","https://openalex.org/W2992151131","https://openalex.org/W3003257820","https://openalex.org/W3007199577","https://openalex.org/W3007935255","https://openalex.org/W3012498554","https://openalex.org/W3029490475","https://openalex.org/W3082502100","https://openalex.org/W3099810371","https://openalex.org/W3103582283","https://openalex.org/W3109313148","https://openalex.org/W3130232612","https://openalex.org/W3132661792","https://openalex.org/W3138055079","https://openalex.org/W3138719602","https://openalex.org/W3146817258","https://openalex.org/W3167009660","https://openalex.org/W3168048358","https://openalex.org/W3198418758","https://openalex.org/W3202418805","https://openalex.org/W3209761134","https://openalex.org/W4200073170","https://openalex.org/W4200262887","https://openalex.org/W4213066726","https://openalex.org/W4214876469","https://openalex.org/W4281716326","https://openalex.org/W4283795860","https://openalex.org/W4284890877","https://openalex.org/W4294216483","https://openalex.org/W4297965106","https://openalex.org/W4310238874","https://openalex.org/W4313396397","https://openalex.org/W4319433642","https://openalex.org/W4387661643","https://openalex.org/W4388007339","https://openalex.org/W4389390583","https://openalex.org/W4390974497","https://openalex.org/W4402135155"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W4388725868","https://openalex.org/W2073305407","https://openalex.org/W2530003898","https://openalex.org/W2042937727","https://openalex.org/W1785301691","https://openalex.org/W2014023540"],"abstract_inverted_index":{"Intracellular":[0],"signaling":[1],"initiated":[2],"from":[3,121,129],"ligand-bound":[4],"receptors":[5,20,84,194],"plays":[6],"a":[7,114],"fundamental":[8],"role":[9],"in":[10,175,178,209,210,225,253],"both":[11],"physiological":[12],"regulation":[13],"and":[14,39,83,127,134,165,177,195,198,206],"development":[15],"of":[16,22,31,61,69,74,81,91,132,258],"disease":[17,40],"states,":[18],"making":[19],"one":[21],"the":[23,66,75,79,122,130,153,234,256],"most":[24,73],"frequent":[25],"drug":[26],"targets.":[27],"Systems":[28],"level":[29],"analysis":[30],"receptor":[32,42,67,119,135,160,180,201,205,237,250],"activity":[33,43,161,238,251],"can":[34,157,218,241],"help":[35],"to":[36,52,85,189,221,244],"identify":[37,222,245],"cell":[38,246],"type-specific":[41],"alterations.":[44],"While":[45],"several":[46],"computational":[47,115],"methods":[48,76],"have":[49],"been":[50],"developed":[51,107],"analyze":[53],"ligand-receptor":[54],"interactions":[55,98,192],"based":[56],"on":[57,65,173],"transcriptomics":[58,167,262],"data,":[59,150,182],"none":[60],"them":[62],"focuses":[63],"directly":[64,78],"side":[68],"these":[70,104,149],"interactions.":[71],"Also,":[72],"use":[77],"expression":[80,125,142],"ligands":[82],"infer":[86],"active":[87],"interaction,":[88],"while":[89],"co-expression":[90],"genes":[92],"does":[93],"not":[94,128],"necessarily":[95],"indicate":[96],"functional":[97],"or":[99],"activated":[100],"state.":[101],"To":[102],"address":[103],"problems,":[105],"we":[106,151],"RIDDEN":[108,154,217],"(Receptor":[109],"actIvity":[110],"Data":[111],"Driven":[112],"inferENce),":[113],"tool,":[116],"which":[117,156],"predicts":[118],"activities":[120,202],"receptor-regulated":[123],"gene":[124,141],"profiles,":[126],"expressions":[131,208],"ligand":[133,207],"genes.":[136],"We":[137,169,213],"collected":[138],"14463":[139],"perturbation":[140,181],"profiles":[143],"for":[144,162],"229":[145],"different":[146],"receptors.":[147],"Using":[148],"trained":[152],"model,":[155,240],"effectively":[158],"predict":[159],"new":[163],"bulk":[164],"single-cell":[166],"datasets.":[168,212],"validated":[170],"RIDDEN's":[171,185],"performance":[172],"independent":[174],"vitro":[176],"vivo":[179,211],"showing":[183],"that":[184,199,216],"model":[186],"weights":[187],"correspond":[188],"known":[190],"regulatory":[191],"between":[193],"transcription":[196],"factors,":[197],"predicted":[200],"correlate":[203],"with":[204,248],"also":[214],"show":[215],"be":[219,242],"used":[220,243],"mechanistic":[223],"biomarkers":[224],"an":[226],"immune":[227],"checkpoint":[228],"blockade-treated":[229],"cancer":[230],"patient":[231],"cohort.":[232],"RIDDEN,":[233],"largest":[235],"transcriptomics-based":[236],"inference":[239],"populations":[247],"altered":[249],"and,":[252],"turn,":[254],"foster":[255],"study":[257],"cell-cell":[259],"communication":[260],"using":[261],"data.":[263]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
