{"id":"https://openalex.org/W4400831316","doi":"https://doi.org/10.1186/s12859-024-05855-x","title":"TopoDoE: a design of experiment strategy for selection and refinement in ensembles of executable gene regulatory networks","display_name":"TopoDoE: a design of experiment strategy for selection and refinement in ensembles of executable gene regulatory networks","publication_year":2024,"publication_date":"2024-07-19","ids":{"openalex":"https://openalex.org/W4400831316","doi":"https://doi.org/10.1186/s12859-024-05855-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/39030497"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05855-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05855-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05855-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05855-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029793206","display_name":"Matteo Bouvier","orcid":"https://orcid.org/0000-0001-5793-4400"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210100775","display_name":"Laboratoire de Biologie et Mod\u00e9lisation de la Cellule","ror":"https://ror.org/01bj4fd12","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210100775"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Matteo Bouvier","raw_affiliation_strings":["Inria Grenoble, Rh\u00f4ne-Alpes Research Center, Lyon, France. matteo.bouvier@ens-lyon.fr","Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France. matteo.bouvier@ens-lyon.fr","Vidium Solutions, Lyon, France. matteo.bouvier@ens-lyon.fr","LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","Vidium [Lyon] (46 All. d'Italie, 69007 Lyon - France)","Inria Lyon (Inria de Lyon / B\u00e2timent CEI-2 / Campus La Doua - Villeurbanne / 56, Boulevard Niels Bohr / CS 52132 / 69 603 Villeurbanne - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Grenoble, Rh\u00f4ne-Alpes Research Center, Lyon, France. matteo.bouvier@ens-lyon.fr","institution_ids":["https://openalex.org/I113428412","https://openalex.org/I4210101348"]},{"raw_affiliation_string":"Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France. matteo.bouvier@ens-lyon.fr","institution_ids":["https://openalex.org/I4210100775"]},{"raw_affiliation_string":"Vidium Solutions, Lyon, France. matteo.bouvier@ens-lyon.fr","institution_ids":["https://openalex.org/I113428412"]},{"raw_affiliation_string":"LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","institution_ids":["https://openalex.org/I113428412","https://openalex.org/I100532134"]},{"raw_affiliation_string":"Vidium [Lyon] (46 All. d'Italie, 69007 Lyon - France)","institution_ids":[]},{"raw_affiliation_string":"Inria Lyon (Inria de Lyon / B\u00e2timent CEI-2 / Campus La Doua - Villeurbanne / 56, Boulevard Niels Bohr / CS 52132 / 69 603 Villeurbanne - France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058903518","display_name":"Souad Zreika","orcid":"https://orcid.org/0000-0003-3228-4258"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210100775","display_name":"Laboratoire de Biologie et Mod\u00e9lisation de la Cellule","ror":"https://ror.org/01bj4fd12","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210100775"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Souad Zreika","raw_affiliation_strings":["Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","institution_ids":["https://openalex.org/I4210100775"]},{"raw_affiliation_string":"LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","institution_ids":["https://openalex.org/I113428412","https://openalex.org/I100532134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031867652","display_name":"Elodie Vallin","orcid":null},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210100775","display_name":"Laboratoire de Biologie et Mod\u00e9lisation de la Cellule","ror":"https://ror.org/01bj4fd12","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210100775"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Elodie Vallin","raw_affiliation_strings":["Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","institution_ids":["https://openalex.org/I4210100775"]},{"raw_affiliation_string":"LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","institution_ids":["https://openalex.org/I113428412","https://openalex.org/I100532134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080652620","display_name":"Camille Fourneaux","orcid":"https://orcid.org/0000-0002-4902-2310"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210100775","display_name":"Laboratoire de Biologie et Mod\u00e9lisation de la Cellule","ror":"https://ror.org/01bj4fd12","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210100775"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Camille Fourneaux","raw_affiliation_strings":["Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","institution_ids":["https://openalex.org/I4210100775"]},{"raw_affiliation_string":"LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","institution_ids":["https://openalex.org/I113428412","https://openalex.org/I100532134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002495454","display_name":"Sandrine Gonin-Giraud","orcid":"https://orcid.org/0000-0002-4617-3674"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210100775","display_name":"Laboratoire de Biologie et Mod\u00e9lisation de la Cellule","ror":"https://ror.org/01bj4fd12","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210100775"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sandrine Gonin-Giraud","raw_affiliation_strings":["Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","institution_ids":["https://openalex.org/I4210100775"]},{"raw_affiliation_string":"LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","institution_ids":["https://openalex.org/I113428412","https://openalex.org/I100532134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014325125","display_name":"Arnaud Bonnaffoux","orcid":"https://orcid.org/0000-0003-0472-0761"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Arnaud Bonnaffoux","raw_affiliation_strings":["Vidium Solutions, Lyon, France","Vidium [Lyon] (46 All. d'Italie, 69007 Lyon - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vidium Solutions, Lyon, France","institution_ids":[]},{"raw_affiliation_string":"Vidium [Lyon] (46 All. d'Italie, 69007 Lyon - France)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089245484","display_name":"Olivier Gandrillon","orcid":"https://orcid.org/0000-0002-3676-6513"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210100775","display_name":"Laboratoire de Biologie et Mod\u00e9lisation de la Cellule","ror":"https://ror.org/01bj4fd12","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210100775"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Olivier Gandrillon","raw_affiliation_strings":["Inria Grenoble, Rh\u00f4ne-Alpes Research Center, Lyon, France","Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","Inria Grenoble - Rh\u00f4ne-Alpes (Inovall\u00e9e\r\n655 avenue de l'Europe\r\n38330 Montbonnot - France)","LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Grenoble, Rh\u00f4ne-Alpes Research Center, Lyon, France","institution_ids":["https://openalex.org/I4210101348"]},{"raw_affiliation_string":"Laboratoire de Biologie Mol\u00e9culaire de la Cellule, Lyon, France","institution_ids":["https://openalex.org/I4210100775"]},{"raw_affiliation_string":"Inria Grenoble - Rh\u00f4ne-Alpes (Inovall\u00e9e\r\n655 avenue de l'Europe\r\n38330 Montbonnot - France)","institution_ids":["https://openalex.org/I4210101348"]},{"raw_affiliation_string":"LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","institution_ids":["https://openalex.org/I113428412","https://openalex.org/I100532134"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5029793206"],"corresponding_institution_ids":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I4210100775","https://openalex.org/I4210101348"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2577},"fwci":0.4358,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.62867592,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"25","issue":"1","first_page":"245","last_page":"245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9334999918937683,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9334999918937683,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.029899999499320984,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.018200000748038292,"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/executable","display_name":"Executable","score":0.8770732879638672},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7909294366836548},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6849992871284485},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6812964081764221},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5733662843704224},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.5585174560546875},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.49274685978889465},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4433685839176178},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4276653826236725},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34959152340888977},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34810498356819153},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1580178439617157},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09835502505302429}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.8770732879638672},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7909294366836548},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6849992871284485},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6812964081764221},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5733662843704224},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.5585174560546875},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.49274685978889465},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4433685839176178},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4276653826236725},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34959152340888977},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34810498356819153},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1580178439617157},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09835502505302429},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-024-05855-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05855-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05855-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39030497","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39030497","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:hal-04678148v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04678148","pdf_url":"https://hal.science/hal-04678148/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"BMC Bioinformatics, 2024, 25 (1), pp.245. &#x27E8;10.1186/s12859-024-05855-x&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:11264509","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11264509","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11264509/pdf/12859_2024_Article_5855.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:9ad868f8016b4126a03bbf60f673194c","is_oa":false,"landing_page_url":"https://doaj.org/article/9ad868f8016b4126a03bbf60f673194c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-21 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05855-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05855-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05855-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3785575267","display_name":null,"funder_award_id":"ANR-11-LABX-0048","funder_id":"https://openalex.org/F4320330080","funder_display_name":"Laboratoire d'Excellence Ecofect"},{"id":"https://openalex.org/G4530913083","display_name":null,"funder_award_id":"ANR-17-CE12-0031","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4717252311","display_name":null,"funder_award_id":"ANR-11-LABX-0048","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5649854608","display_name":null,"funder_award_id":"ANR-11-LABX-0048","funder_id":"https://openalex.org/F4320326804","funder_display_name":"Universit\u00e9 de Lyon"},{"id":"https://openalex.org/G6803667113","display_name":null,"funder_award_id":"ANR-17","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/F4320326804","display_name":"Universit\u00e9 de Lyon","ror":"https://ror.org/01rk35k63"},{"id":"https://openalex.org/F4320330080","display_name":"Laboratoire d'Excellence Ecofect","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4400831316.pdf"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W41554520","https://openalex.org/W1937016012","https://openalex.org/W1984429906","https://openalex.org/W2004343020","https://openalex.org/W2010916267","https://openalex.org/W2016631235","https://openalex.org/W2018640006","https://openalex.org/W2037544231","https://openalex.org/W2070822442","https://openalex.org/W2074189935","https://openalex.org/W2076513103","https://openalex.org/W2078936424","https://openalex.org/W2079777306","https://openalex.org/W2100416355","https://openalex.org/W2106555403","https://openalex.org/W2110266641","https://openalex.org/W2146230717","https://openalex.org/W2163296115","https://openalex.org/W2175406438","https://openalex.org/W2181523240","https://openalex.org/W2327972292","https://openalex.org/W2395492365","https://openalex.org/W2570629027","https://openalex.org/W2608543022","https://openalex.org/W2612568060","https://openalex.org/W2621349699","https://openalex.org/W2795460076","https://openalex.org/W2803394774","https://openalex.org/W2803479625","https://openalex.org/W2908300237","https://openalex.org/W2930863966","https://openalex.org/W2971871274","https://openalex.org/W3003257820","https://openalex.org/W3004732550","https://openalex.org/W3036342146","https://openalex.org/W3081378055","https://openalex.org/W3099289621","https://openalex.org/W3103145119","https://openalex.org/W3162072975","https://openalex.org/W3174608384","https://openalex.org/W4200097400","https://openalex.org/W4283829667","https://openalex.org/W6677916085"],"related_works":["https://openalex.org/W2350278424","https://openalex.org/W2071432835","https://openalex.org/W4239401009","https://openalex.org/W4234371507","https://openalex.org/W1628824497","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"BACKGROUND:":[0],"Inference":[1],"of":[2,28,32,43,57,73,125,136,142,161,197,208,219,236,247,264,283],"Gene":[3],"Regulatory":[4],"Networks":[5],"(GRNs)":[6],"is":[7,87],"a":[8,55,71,79,118,198],"difficult":[9],"and":[10,145,175,249,279],"long-standing":[11],"question":[12],"in":[13,37,49,54,105,191],"Systems":[14],"Biology.":[15],"Numerous":[16],"approaches":[17],"have":[18],"been":[19],"proposed":[20,51,109],"with":[21,149,179],"the":[22,26,33,38,83,92,106,123,134,137,143,159,195,220,234,244,262,281],"latest":[23],"methods":[24,42],"exploring":[25],"richness":[27],"single-cell":[29],"data.":[30,152],"One":[31],"current":[34],"difficulties":[35],"lies":[36],"fact":[39],"that":[40,60,127,184],"many":[41,215],"GRN":[44,52,286],"inference":[45,84,245],"do":[46],"not":[47],"result":[48],"one":[50],"but":[53],"collection":[56],"plausible":[58],"networks":[59,186,222],"need":[61,128],"to":[62,76,97,121,129,158,172,189,259],"be":[63,130,257],"further":[64,260,275],"refined.":[65],"In":[66],"this":[67,156,269],"work,":[68],"we":[69,212,225],"present":[70],"Design":[72],"Experiment":[74],"strategy":[75,115,270],"use":[77],"as":[78,214,216],"second":[80],"stage":[81],"after":[82],"process.":[85],"It":[86],"specifically":[88],"fitted":[89],"for":[90,99,205,223],"identifying":[91],"next":[93],"most":[94],"informative":[95],"experiment":[96],"perform":[98],"deciding":[100],"between":[101],"multiple":[102],"network":[103],"topologies,":[104],"case":[107],"where":[108],"GRNs":[110,144],"are":[111],"executable":[112,252,285],"models.":[113,287],"This":[114],"first":[116],"performs":[117],"topological":[119],"analysis":[120],"reduce":[122],"number":[124],"perturbations":[126,139,174],"tested,":[131],"then":[132],"predicts":[133],"outcome":[135,196],"retained":[138],"by":[140],"simulation":[141],"finally":[146],"compares":[147],"predictions":[148,178,193],"novel":[150],"experimental":[151,180],"RESULTS:":[153],"We":[154,182,267],"apply":[155],"method":[157],"results":[160,241],"our":[162,177,185,237],"divide-and-conquer":[163],"algorithm":[164],"called":[165],"WASABI,":[166],"adapt":[167],"its":[168],"gene":[169,199,253],"expression":[170,254],"model":[171],"produce":[173,190],"compare":[176],"results.":[181],"show":[183,250],"were":[187,202],"able":[188],"silico":[192],"on":[194],"knock-out,":[200],"which":[201,224],"qualitatively":[203],"validated":[204],"48":[206],"out":[207],"49":[209],"genes.":[210],"Finally,":[211],"eliminate":[213],"two":[217],"thirds":[218],"candidate":[221],"could":[226],"identify":[227],"an":[228],"incorrect":[229],"topology,":[230],"thus":[231],"greatly":[232],"improving":[233],"accuracy":[235,246],"predictions.":[238],"CONCLUSION:":[239],"These":[240],"both":[242],"confirm":[243],"WASABI":[248],"how":[251],"models":[255],"can":[256],"leveraged":[258],"refine":[261],"topology":[263],"inferred":[265],"GRNs.":[266],"hope":[268],"will":[271],"help":[272],"systems":[273],"biologists":[274],"explore":[276],"their":[277],"data":[278],"encourage":[280],"development":[282],"more":[284]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
