{"id":"https://openalex.org/W7123941645","doi":"https://doi.org/10.1038/s42003-025-09500-y","title":"Large scale compound selection guided by cell painting reveals activity cliffs and functional relationships","display_name":"Large scale compound selection guided by cell painting reveals activity cliffs and functional relationships","publication_year":2026,"publication_date":"2026-01-13","ids":{"openalex":"https://openalex.org/W7123941645","doi":"https://doi.org/10.1038/s42003-025-09500-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/41530519","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/12901981"},"language":"en","primary_location":{"id":"doi:10.1038/s42003-025-09500-y","doi":"https://doi.org/10.1038/s42003-025-09500-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42003-025-09500-y","pdf_url":"https://www.nature.com/articles/s42003-025-09500-y_reference.pdf","source":{"id":"https://openalex.org/S4210225776","display_name":"Communications Biology","issn_l":"2399-3642","issn":["2399-3642"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","doyens","jufo-1","ki-jl-2","medline","norway-1","oarl","poland-20","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.nature.com/articles/s42003-025-09500-y_reference.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111132576","display_name":"Maxime Sanchez","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Maxime Sanchez","raw_affiliation_strings":["IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France","INSERM, Paris, France","Iktos, Paris, France","Institut Curie, Universit\u00e9 PSL, Paris, France","Mines ParisTech, Universit\u00e9 PSL, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210129409"]},{"raw_affiliation_string":"INSERM, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Iktos, Paris, France","institution_ids":[]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I70768539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093367465","display_name":"Nicolas Bourriez","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Nicolas Bourriez","raw_affiliation_strings":["IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033350017","display_name":"Ihab Bendidi","orcid":"https://orcid.org/0000-0002-8080-4521","observed_orcids":["https://orcid.org/0000-0002-8080-4521"]},"institutions":[{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ihab Bendidi","raw_affiliation_strings":["IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-8080-4521","affiliations":[{"raw_affiliation_string":"IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085399801","display_name":"Ethan Cohen","orcid":"https://orcid.org/0000-0002-5019-7759","observed_orcids":["https://orcid.org/0000-0002-5019-7759"]},"institutions":[{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ethan Cohen","raw_affiliation_strings":["IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117619273","display_name":"Ivan Svatko","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210093064","display_name":"Sant\u00e9 Internationale de la m\u00e8re et de l'enfant","ror":"https://ror.org/00rd22143","country_code":"FR","type":"facility","lineage":["https://openalex.org/I204730241","https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210093064","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ivan Svatko","raw_affiliation_strings":["IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France","Universit\u00e9 Paris Cit\u00e9, IRD, Inserm, MERIT, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210129409"]},{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, IRD, Inserm, MERIT, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210093064","https://openalex.org/I4210166444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051909915","display_name":"Elaine Del Nery","orcid":"https://orcid.org/0000-0002-9654-5202","observed_orcids":["https://orcid.org/0000-0002-9654-5202"]},"institutions":[{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Elaine Del Nery","raw_affiliation_strings":["Biophenics Laboratory, Institut Curie, PSL Research University, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-9654-5202","affiliations":[{"raw_affiliation_string":"Biophenics Laboratory, Institut Curie, PSL Research University, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076358635","display_name":"Hamza Tajmouati","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hamza Tajmouati","raw_affiliation_strings":["Iktos, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iktos, Paris, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037169431","display_name":"Guillaume Bollot","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guillaume Bollot","raw_affiliation_strings":["Iktos, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iktos, Paris, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061154457","display_name":"Laurence Calzone","orcid":"https://orcid.org/0000-0002-7835-1148","observed_orcids":["https://orcid.org/0000-0002-7835-1148"]},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Laurence Calzone","raw_affiliation_strings":["INSERM, Paris, France. laurence.calzone@curie.fr","Institut Curie, Universit\u00e9 PSL, Paris, France. laurence.calzone@curie.fr","Mines ParisTech, Universit\u00e9 PSL, Paris, France. laurence.calzone@curie.fr"],"raw_orcid":"https://orcid.org/0000-0002-7835-1148","affiliations":[{"raw_affiliation_string":"INSERM, Paris, France. laurence.calzone@curie.fr","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL, Paris, France. laurence.calzone@curie.fr","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL, Paris, France. laurence.calzone@curie.fr","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I70768539"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064234141","display_name":"Auguste Genovesio","orcid":"https://orcid.org/0000-0003-1877-5595","observed_orcids":["https://orcid.org/0000-0003-1877-5595"]},"institutions":[{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Auguste Genovesio","raw_affiliation_strings":["IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France. auguste.genovesio@ens.psl.eu"],"raw_orcid":"https://orcid.org/0000-0003-1877-5595","affiliations":[{"raw_affiliation_string":"IBENS, Ecole Normale Sup\u00e9rieure, Universit\u00e9 PSL, Paris, France. auguste.genovesio@ens.psl.eu","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210129409"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5061154457","https://openalex.org/A5064234141"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210129409","https://openalex.org/I70768539","https://openalex.org/I80043"],"apc_list":{"value":4190,"currency":"USD","value_usd":4190},"apc_paid":{"value":4190,"currency":"USD","value_usd":4190},"fwci":10.7723,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.97716245,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"9","issue":"1","first_page":"225","last_page":"225"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.007499999832361937,"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/T11948","display_name":"Machine Learning in Materials Science","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cell-painting","display_name":"Cell Painting","score":0.921999990940094},{"id":"https://openalex.org/keywords/activity-cliffs","display_name":"activity cliffs","score":0.7210000157356262},{"id":"https://openalex.org/keywords/functional-convergence","display_name":"functional convergence","score":0.675000011920929},{"id":"https://openalex.org/keywords/phenotypic-profiling","display_name":"phenotypic profiling","score":0.7760000228881836},{"id":"https://openalex.org/keywords/transfer-learning","display_name":"transfer learning","score":0.8679999709129333},{"id":"https://openalex.org/keywords/compound-prioritization","display_name":"compound prioritization","score":0.6759999990463257},{"id":"https://openalex.org/keywords/batch-effect-correction","display_name":"batch effect correction","score":0.5799999833106995},{"id":"https://openalex.org/keywords/high-throughput-screening","display_name":"high-throughput screening","score":0.49799999594688416},{"id":"https://openalex.org/keywords/chemical-space-exploration","display_name":"chemical space exploration","score":0.4860000014305115}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5958999991416931},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5763000249862671},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5418000221252441},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5343000292778015},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5339999794960022},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.48179998993873596},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46459999680519104},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.40130001306533813},{"id":"https://openalex.org/C24259465","wikidata":"https://www.wikidata.org/wiki/Q2272153","display_name":"Chemical similarity","level":3,"score":0.39430001378059387},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.39419999718666077},{"id":"https://openalex.org/C6555983","wikidata":"https://www.wikidata.org/wiki/Q7181398","display_name":"Phenotypic screening","level":4,"score":0.39100000262260437},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.3783999979496002},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.36239999532699585},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3474999964237213},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3361000120639801},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.30329999327659607},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2782000005245209},{"id":"https://openalex.org/C2992918937","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Biological organism","level":3,"score":0.2775999903678894},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2766000032424927},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.27630001306533813},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2754000127315521},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2680000066757202},{"id":"https://openalex.org/C130073038","wikidata":"https://www.wikidata.org/wiki/Q1211967","display_name":"Phenotypic trait","level":4,"score":0.2671999931335449}],"mesh":[{"descriptor_ui":"D000098410","descriptor_name":"Transfer Machine Learning","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":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1038/s42003-025-09500-y","doi":"https://doi.org/10.1038/s42003-025-09500-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42003-025-09500-y","pdf_url":"https://www.nature.com/articles/s42003-025-09500-y_reference.pdf","source":{"id":"https://openalex.org/S4210225776","display_name":"Communications Biology","issn_l":"2399-3642","issn":["2399-3642"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","doyens","jufo-1","ki-jl-2","medline","norway-1","oarl","poland-20","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications Biology","raw_type":"journal-article"},{"id":"doi:10.1101/2025.05.16.654292","doi":"https://doi.org/10.1101/2025.05.16.654292","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.05.16.654292","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/21/2025.05.16.654292.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:europepmc.org:11708904","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12901981","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmid:41530519","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41530519","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,"listed_in":[],"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":"Communications biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12901981","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12901981/","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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Commun Biol","raw_type":"Text"},{"id":"pmh:oai:HAL:hal-05501580v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-05501580","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Communications Biology, 2026, 9 (1), pp.225. &#x27E8;10.1038/s42003-025-09500-y&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:c1d8d96e108043478493cb1e55df2e63","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/c1d8d96e108043478493cb1e55df2e63","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,"listed_in":[],"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":"Communications Biology, Vol 9, Iss 1 (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1038/s42003-025-09500-y","doi":"https://doi.org/10.1038/s42003-025-09500-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42003-025-09500-y","pdf_url":"https://www.nature.com/articles/s42003-025-09500-y_reference.pdf","source":{"id":"https://openalex.org/S4210225776","display_name":"Communications Biology","issn_l":"2399-3642","issn":["2399-3642"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","doyens","jufo-1","ki-jl-2","medline","norway-1","oarl","poland-20","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.46810001134872437,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1316933359","display_name":"Memory in living systems: an integrated approach","funder_award_id":"ANR-10-LABX-0054","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G1449229046","display_name":null,"funder_award_id":"10-LABX-54","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G1512583955","display_name":"INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE","funder_award_id":"ANR-11-IDEX-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G1742243815","display_name":null,"funder_award_id":"ANR11IDEX000102","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G196500007","display_name":null,"funder_award_id":"ANR\u201310\u2013LABX\u201354","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G2079521050","display_name":null,"funder_award_id":"ANR-11IDEX-0001-02 PSL","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G282959247","display_name":null,"funder_award_id":"ANR-10-LABX\u201054 MEMOLIFE","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4866930200","display_name":null,"funder_award_id":"ANR-11-IDEX","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7240651115","display_name":null,"funder_award_id":"ANR-10","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G782245399","display_name":null,"funder_award_id":"IDEX-0001-02","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320321663","display_name":"Association Nationale de la Recherche et de la Technologie","ror":"https://ror.org/00ht2ab73"},{"id":"https://openalex.org/F4320326256","display_name":"Grand \u00c9quipement National De Calcul Intensif","ror":"https://ror.org/0010d1q40"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7123941645.pdf","grobid_xml":"https://content.openalex.org/works/W7123941645.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W1185588434","https://openalex.org/W2013614403","https://openalex.org/W2023818227","https://openalex.org/W2029929739","https://openalex.org/W2044834685","https://openalex.org/W2052214665","https://openalex.org/W2060531713","https://openalex.org/W2072582769","https://openalex.org/W2096541451","https://openalex.org/W2144963196","https://openalex.org/W2151697120","https://openalex.org/W2188333210","https://openalex.org/W2194775991","https://openalex.org/W2498090354","https://openalex.org/W2584452936","https://openalex.org/W2605025138","https://openalex.org/W2728842897","https://openalex.org/W2752517304","https://openalex.org/W2794301983","https://openalex.org/W2901677030","https://openalex.org/W2919115771","https://openalex.org/W2922305141","https://openalex.org/W2942880491","https://openalex.org/W2984472267","https://openalex.org/W3030510106","https://openalex.org/W3134386172","https://openalex.org/W3177828909","https://openalex.org/W3196897371","https://openalex.org/W4226002507","https://openalex.org/W4282036924","https://openalex.org/W4286461903","https://openalex.org/W4306353209","https://openalex.org/W4310603653","https://openalex.org/W4321173085","https://openalex.org/W4323051567","https://openalex.org/W4360951525","https://openalex.org/W4362721877","https://openalex.org/W4366208220","https://openalex.org/W4379197245","https://openalex.org/W4380987341","https://openalex.org/W4385410057","https://openalex.org/W4387517389","https://openalex.org/W4388555687","https://openalex.org/W4388626060","https://openalex.org/W4389115806","https://openalex.org/W4390586937","https://openalex.org/W4391239284","https://openalex.org/W4391993840","https://openalex.org/W4395072098","https://openalex.org/W4396734615","https://openalex.org/W4399128715","https://openalex.org/W4399836800","https://openalex.org/W4399907796","https://openalex.org/W4401272991","https://openalex.org/W4401750031","https://openalex.org/W4402309394","https://openalex.org/W4402753743","https://openalex.org/W4402754164","https://openalex.org/W4403022150","https://openalex.org/W4403511080","https://openalex.org/W4403882196","https://openalex.org/W4405079632","https://openalex.org/W4407272124","https://openalex.org/W4407291617","https://openalex.org/W4409010433","https://openalex.org/W4410120149","https://openalex.org/W4410888112","https://openalex.org/W4411022275","https://openalex.org/W4412708198","https://openalex.org/W4413037989","https://openalex.org/W4413407232","https://openalex.org/W4414228986","https://openalex.org/W7115021743"],"related_works":["https://openalex.org/W4393403227","https://openalex.org/W4362721877","https://openalex.org/W7096725470","https://openalex.org/W4386766551","https://openalex.org/W4395072098","https://openalex.org/W2463929416","https://openalex.org/W2011101218","https://openalex.org/W2474801060","https://openalex.org/W4400745305","https://openalex.org/W7220357455"],"abstract_inverted_index":{"Traditional":[0],"structure-based":[1,190],"pre-screen":[2,125],"compound":[3,69,159],"selection":[4],"relies":[5],"on":[6],"the":[7,19,92,95,132,203,229,289,304,307,325],"assumption":[8],"that":[9,71,176,185,195,280],"chemical":[10,22,164,269],"similarity":[11],"implies":[12],"similar":[13,42,245],"biological":[14,105,205,273,333],"activity.":[15],"This":[16],"paradigm":[17],"narrows":[18],"exploration":[20],"of":[21,76,85,91,127,135,151,158,183,220,224,241,284,291,296,306,327],"space":[23,270],"and":[24,118,222,264,298,323],"often":[25],"fails":[26],"to":[27,40,227],"account":[28],"for":[29,66,147,267,317],"functional":[30,282],"convergence,":[31],"where":[32,162],"structurally":[33,196],"diverse":[34,197,332],"compounds":[35,48,198,243],"act":[36],"through":[37,271],"distinct":[38],"targets":[39],"produce":[41],"phenotypic":[43,74,86,172,246,252,310],"effects.":[44,110],"As":[45],"a":[46,61,148,235,257,262,272,314],"result,":[47],"with":[49,244],"therapeutic":[50],"potential":[51],"may":[52,168],"be":[53,187],"overlooked.":[54],"To":[55],"overcome":[56],"this":[57,80],"constraint,":[58],"we":[59,193,232],"introduce":[60],"training-free,":[62],"transfer":[63],"learning-based":[64],"method":[65,122],"large":[67,142],"scale":[68,305],"preselection":[70],"leverages":[72],"deep":[73],"profiling":[75,253,311],"human":[77],"cells.":[78],"Notably,":[79],"enables":[81,288],"robust":[82],"pairwise":[83],"comparison":[84],"signatures":[87,279],"across":[88,112,216,331],"any":[89],"source":[90],"entire":[93],"JUMP-CP,":[94],"largest":[96],"publicly":[97],"available":[98],"cell":[99],"painting":[100],"dataset":[101],"(112,480":[102],"compounds),":[103],"preserving":[104],"signals":[106],"while":[107],"mitigating":[108],"batch":[109],"Validated":[111],"65":[113],"high-throughput":[114],"assays-including":[115],"in":[116,119,166,170,202],"vitro":[117],"cellulo":[120],"systems-our":[121],"provides":[123],"efficient":[124],"enrichment":[126],"biologically":[128],"active":[129],"compounds,":[130,293,319],"bypassing":[131],"blind":[133],"spots":[134],"structure-centric":[136],"approaches.":[137],"Interestingly,":[138],"because":[139],"it":[140,144],"is":[141],"scale,":[143],"also":[145],"allows":[146],"comprehensive":[149],"analysis":[150],"structure-phenotypic":[152],"activity":[153,160,321],"relationships,":[154],"revealing":[155],"potentially":[156],"thousands":[157,223],"cliffs,":[161,322],"minimal":[163],"changes":[165],"structure":[167],"result":[169],"profound":[171],"shifts.":[173],"We":[174],"show":[175],"these":[177,249],"cliffs":[178],"capture":[179],"subtle,":[180],"atom-level":[181],"determinants":[182],"bioactivity":[184],"cannot":[186],"accessed":[188],"by":[189],"models.":[191],"Furthermore,":[192],"demonstrate":[194],"targeting":[199],"different":[200],"genes":[201],"same":[204],"pathway":[206],"can":[207],"induce":[208],"either":[209],"convergent":[210],"or":[211],"opposite":[212],"phenotypes-a":[213],"phenomenon":[214],"validated":[215],"30":[217],"pathways,":[218],"hundreds":[219],"genes,":[221],"compounds.":[225],"Finally,":[226],"support":[228],"broader":[230],"community,":[231],"propose":[233],"Phenoseeker,":[234],"web-based":[236],"tool":[237],"enabling":[238],"instant":[239],"retrieval":[240],"JUMP-CP":[242,308],"profiles.":[247],"Together,":[248],"findings":[250],"position":[251],"not":[254],"merely":[255],"as":[256,261,313],"complementary":[258],"tool,":[259],"but":[260],"transformative":[263],"scalable":[265],"framework":[266],"navigating":[268],"lens.":[274],"By":[275],"capturing":[276],"rich":[277],"morphological":[278],"reflect":[281],"outcomes-regardless":[283],"structural":[285],"similarity-this":[286],"approach":[287],"discovery":[290],"bioactive":[292],"novel":[294],"mechanisms":[295],"action,":[297],"unexpected":[299],"target-pathway":[300],"relationships.":[301],"Applied":[302],"at":[303],"dataset,":[309],"emerges":[312],"powerful":[315],"strategy":[316],"prioritizing":[318],"illuminating":[320],"accelerating":[324],"identification":[326],"therapeutically":[328],"relevant":[329],"candidates":[330],"contexts.":[334]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2026-01-14T00:00:00"}
