{"id":"https://openalex.org/W2795460076","doi":"https://doi.org/10.1186/s12859-019-2798-1","title":"WASABI: a dynamic iterative framework for gene regulatory network inference","display_name":"WASABI: a dynamic iterative framework for gene regulatory network inference","publication_year":2019,"publication_date":"2019-05-02","ids":{"openalex":"https://openalex.org/W2795460076","doi":"https://doi.org/10.1186/s12859-019-2798-1","mag":"2795460076","pmid":"https://pubmed.ncbi.nlm.nih.gov/31046682"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2798-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2798-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2798-1","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/track/pdf/10.1186/s12859-019-2798-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014325125","display_name":"Arnaud Bonnaffoux","orcid":"https://orcid.org/0000-0003-0472-0761"},"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/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"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/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"]},{"id":"https://openalex.org/I4210104796","display_name":"Institut Camille Jordan","ror":"https://ror.org/01ekw7f87","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I112936343","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210104796","https://openalex.org/I4405259976","https://openalex.org/I48430043"]},{"id":"https://openalex.org/I4210135092","display_name":"Cosmo Tech (France)","ror":"https://ror.org/037fh1278","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210135092"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Arnaud Bonnaffoux","raw_affiliation_strings":["Cosmotech, Lyon, France. a.bonnaffoux@vidium-solutions.com","Inria Team Dracula, Inria Center Grenoble Rh\u00f4ne-Alpes, Lyon, France. a.bonnaffoux@vidium-solutions.com","University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France. a.bonnaffoux@vidium-solutions.com","DRACULA - Multi-scale modelling of cell dynamics : application to hematopoiesis (Institut Camille Jordan Universit\u00e9 Claude Bernard Lyon 1 43 boulevard du 11 novembre 1918 69622 Villeurbanne cedex France - France)","Cosmo Tech (5, passage du Vercors 69007 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":"https://orcid.org/0000-0003-0472-0761","affiliations":[{"raw_affiliation_string":"Cosmotech, Lyon, France. a.bonnaffoux@vidium-solutions.com","institution_ids":["https://openalex.org/I4210135092"]},{"raw_affiliation_string":"Inria Team Dracula, Inria Center Grenoble Rh\u00f4ne-Alpes, Lyon, France. a.bonnaffoux@vidium-solutions.com","institution_ids":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"raw_affiliation_string":"University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France. a.bonnaffoux@vidium-solutions.com","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"DRACULA - Multi-scale modelling of cell dynamics : application to hematopoiesis (Institut Camille Jordan Universit\u00e9 Claude Bernard Lyon 1 43 boulevard du 11 novembre 1918 69622 Villeurbanne cedex France - France)","institution_ids":["https://openalex.org/I4210104796","https://openalex.org/I100532134"]},{"raw_affiliation_string":"Cosmo Tech (5, passage du Vercors 69007 Lyon - France)","institution_ids":["https://openalex.org/I4210135092"]},{"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/A5031719309","display_name":"Ulysse Herbach","orcid":"https://orcid.org/0000-0002-0972-385X"},"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/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"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/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"]},{"id":"https://openalex.org/I4210104796","display_name":"Institut Camille Jordan","ror":"https://ror.org/01ekw7f87","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I112936343","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210104796","https://openalex.org/I4405259976","https://openalex.org/I48430043"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ulysse Herbach","raw_affiliation_strings":["Inria Team Dracula, Inria Center Grenoble Rh\u00f4ne-Alpes, Lyon, France","Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS UMR 5208, Institut Camille Jordan, Villeurbanne, France","University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France","DRACULA - Multi-scale modelling of cell dynamics : application to hematopoiesis (Institut Camille Jordan Universit\u00e9 Claude Bernard Lyon 1 43 boulevard du 11 novembre 1918 69622 Villeurbanne cedex France - 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)","ICJ - Institut Camille Jordan (B\u00e2t. Jean Braconnier 43 bd du 11 novembre 1918 69622 VILLEURBANNE CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Team Dracula, Inria Center Grenoble Rh\u00f4ne-Alpes, Lyon, France","institution_ids":["https://openalex.org/I1326498283","https://openalex.org/I4210101348","https://openalex.org/I899635006"]},{"raw_affiliation_string":"Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS UMR 5208, Institut Camille Jordan, Villeurbanne, France","institution_ids":["https://openalex.org/I4210104796","https://openalex.org/I100532134","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"DRACULA - Multi-scale modelling of cell dynamics : application to hematopoiesis (Institut Camille Jordan Universit\u00e9 Claude Bernard Lyon 1 43 boulevard du 11 novembre 1918 69622 Villeurbanne cedex France - France)","institution_ids":["https://openalex.org/I4210104796","https://openalex.org/I100532134"]},{"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":"ICJ - Institut Camille Jordan (B\u00e2t. Jean Braconnier 43 bd du 11 novembre 1918 69622 VILLEURBANNE CEDEX - France)","institution_ids":["https://openalex.org/I4210104796"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057787642","display_name":"Ang\u00e9lique Richard","orcid":"https://orcid.org/0000-0002-5440-8656"},"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/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ang\u00e9lique Richard","raw_affiliation_strings":["University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 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":"University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590"]},{"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/A5044342058","display_name":"Anissa Guillemin","orcid":"https://orcid.org/0000-0002-7989-200X"},"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/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anissa Guillemin","raw_affiliation_strings":["University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 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":"University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590"]},{"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/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sandrine Gonin-Giraud","raw_affiliation_strings":["University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 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":"University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590"]},{"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/A5067518649","display_name":"Pierre-Alexis Gros","orcid":null},"institutions":[{"id":"https://openalex.org/I4210135092","display_name":"Cosmo Tech (France)","ror":"https://ror.org/037fh1278","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210135092"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre-Alexis Gros","raw_affiliation_strings":["Cosmotech, Lyon, France","Cosmo Tech (5, passage du Vercors 69007 Lyon - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cosmotech, Lyon, France","institution_ids":["https://openalex.org/I4210135092"]},{"raw_affiliation_string":"Cosmo Tech (5, passage du Vercors 69007 Lyon - France)","institution_ids":["https://openalex.org/I4210135092"]}]},{"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/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"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/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"]},{"id":"https://openalex.org/I4210104796","display_name":"Institut Camille Jordan","ror":"https://ror.org/01ekw7f87","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I112936343","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210104796","https://openalex.org/I4405259976","https://openalex.org/I48430043"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Olivier Gandrillon","raw_affiliation_strings":["Inria Team Dracula, Inria Center Grenoble Rh\u00f4ne-Alpes, Lyon, France","University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 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)","DRACULA - Multi-scale modelling of cell dynamics : application to hematopoiesis (Institut Camille Jordan Universit\u00e9 Claude Bernard Lyon 1 43 boulevard du 11 novembre 1918 69622 Villeurbanne cedex France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Team Dracula, Inria Center Grenoble Rh\u00f4ne-Alpes, Lyon, France","institution_ids":["https://openalex.org/I1326498283","https://openalex.org/I4210101348","https://openalex.org/I899635006"]},{"raw_affiliation_string":"University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590"]},{"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":"DRACULA - Multi-scale modelling of cell dynamics : application to hematopoiesis (Institut Camille Jordan Universit\u00e9 Claude Bernard Lyon 1 43 boulevard du 11 novembre 1918 69622 Villeurbanne cedex France - France)","institution_ids":["https://openalex.org/I4210104796","https://openalex.org/I100532134"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5014325125"],"corresponding_institution_ids":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I154526488","https://openalex.org/I4210101348","https://openalex.org/I4210104796","https://openalex.org/I4210135092"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.9919,"has_fulltext":true,"cited_by_count":63,"citation_normalized_percentile":{"value":0.92064363,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"20","issue":"1","first_page":"220","last_page":"220"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8610000014305115,"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":0.8610000014305115,"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":0.10239999741315842,"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":0.017400000244379044,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.8139712810516357},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7557461261749268},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6384236812591553},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5685334801673889},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5626529455184937},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4491002857685089},{"id":"https://openalex.org/keywords/boolean-network","display_name":"Boolean network","score":0.4483361840248108},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.44723063707351685},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.44551846385002136},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.44384831190109253},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3854700028896332},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3307075798511505},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2669047713279724},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24155232310295105},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.14459288120269775}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.8139712810516357},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7557461261749268},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6384236812591553},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5685334801673889},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5626529455184937},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4491002857685089},{"id":"https://openalex.org/C134444547","wikidata":"https://www.wikidata.org/wiki/Q585230","display_name":"Boolean network","level":3,"score":0.4483361840248108},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.44723063707351685},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.44551846385002136},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.44384831190109253},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3854700028896332},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3307075798511505},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2669047713279724},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24155232310295105},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.14459288120269775},{"id":"https://openalex.org/C187455244","wikidata":"https://www.wikidata.org/wiki/Q942353","display_name":"Boolean function","level":2,"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D041905","descriptor_name":"Erythroid Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D041905","descriptor_name":"Erythroid Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D041905","descriptor_name":"Erythroid Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-2798-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2798-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2798-1","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:31046682","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31046682","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-02159694v1","is_oa":true,"landing_page_url":"https://hal.science/hal-02159694","pdf_url":null,"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, 2019, 20 (1), pp.1-19. &#x27E8;10.1186/s12859-019-2798-1&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:51f5195ef2614a41b5b972d6f5f4f476","is_oa":true,"landing_page_url":"https://doaj.org/article/51f5195ef2614a41b5b972d6f5f4f476","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-19 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5486024","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6498543","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,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2798-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2798-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2798-1","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/G1708955491","display_name":null,"funder_award_id":"CIFRE 2015/0436","funder_id":"https://openalex.org/F4320321663","funder_display_name":"Association Nationale de la Recherche et de la Technologie"},{"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/G5673944628","display_name":null,"funder_award_id":"ANR-11-LABX-0048","funder_id":"https://openalex.org/F4320321663","funder_display_name":"Association Nationale de la Recherche et de la Technologie"},{"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"},{"id":"https://openalex.org/G8600148534","display_name":null,"funder_award_id":"ANR-IABI-3096","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320313934","display_name":"Institut national de recherche en informatique et en automatique (INRIA)","ror":"https://ror.org/02kvxyf05"},{"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/F4320326804","display_name":"Universit\u00e9 de Lyon","ror":"https://ror.org/01rk35k63"},{"id":"https://openalex.org/F4320335860","display_name":"Institut National de Physique Nucl\u00e9aire et de Physique des Particules","ror":"https://ror.org/03fd77x13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2795460076.pdf","grobid_xml":"https://content.openalex.org/works/W2795460076.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W1756428283","https://openalex.org/W1943734593","https://openalex.org/W1963522244","https://openalex.org/W1971144865","https://openalex.org/W1986397618","https://openalex.org/W1993418188","https://openalex.org/W2013714032","https://openalex.org/W2037069407","https://openalex.org/W2039745921","https://openalex.org/W2040575507","https://openalex.org/W2054286320","https://openalex.org/W2075251971","https://openalex.org/W2079777306","https://openalex.org/W2079829409","https://openalex.org/W2080878119","https://openalex.org/W2092172804","https://openalex.org/W2098086436","https://openalex.org/W2103174201","https://openalex.org/W2114402708","https://openalex.org/W2114741526","https://openalex.org/W2115108153","https://openalex.org/W2117191960","https://openalex.org/W2121793131","https://openalex.org/W2125258701","https://openalex.org/W2127403997","https://openalex.org/W2136453810","https://openalex.org/W2139997707","https://openalex.org/W2153011302","https://openalex.org/W2157121418","https://openalex.org/W2163480486","https://openalex.org/W2165247488","https://openalex.org/W2167202160","https://openalex.org/W2175406438","https://openalex.org/W2181419079","https://openalex.org/W2283951878","https://openalex.org/W2410378998","https://openalex.org/W2418830408","https://openalex.org/W2460857593","https://openalex.org/W2499065672","https://openalex.org/W2518828632","https://openalex.org/W2526724898","https://openalex.org/W2555364622","https://openalex.org/W2556247872","https://openalex.org/W2570629027","https://openalex.org/W2587784440","https://openalex.org/W2607996974","https://openalex.org/W2612568060","https://openalex.org/W2615916773","https://openalex.org/W2616279709","https://openalex.org/W2743748882","https://openalex.org/W2753908609","https://openalex.org/W2757021802","https://openalex.org/W2766512361","https://openalex.org/W2781234819","https://openalex.org/W2783975438","https://openalex.org/W2785792383","https://openalex.org/W2787865536","https://openalex.org/W2794851698","https://openalex.org/W2795093373","https://openalex.org/W2802291136","https://openalex.org/W2803394774","https://openalex.org/W2808743742","https://openalex.org/W2949513292","https://openalex.org/W2951506174","https://openalex.org/W2951850020","https://openalex.org/W2952535935","https://openalex.org/W2953280917","https://openalex.org/W4242577767"],"related_works":["https://openalex.org/W1422717320","https://openalex.org/W2330768201","https://openalex.org/W2402814600","https://openalex.org/W2794960257","https://openalex.org/W2108120899","https://openalex.org/W2158714033","https://openalex.org/W2128085946","https://openalex.org/W2063978705","https://openalex.org/W3199739261","https://openalex.org/W2156091616"],"abstract_inverted_index":{"BACKGROUND:":[0],"Inference":[1],"of":[2,65,77,123,130,148,157,177,182,223,230,269],"gene":[3,7,30,111,158,185,247],"regulatory":[4,31,186,248],"networks":[5,249],"from":[6,58],"expression":[8,159],"data":[9,24,172],"has":[10],"been":[11,26,118,139],"a":[12,54,94,100,113,144,189,209,221],"long-standing":[13],"and":[14,37,208,241],"notoriously":[15],"difficult":[16],"task":[17],"in":[18,141,169,261],"systems":[19],"biology.":[20],"Recently,":[21],"single-cell":[22,60,162,271],"transcriptomic":[23],"have":[25,117,138],"massively":[27],"used":[28],"for":[29,153,205],"network":[32,57,109,187,213],"inference,":[33],"with":[34,69],"both":[35],"successes":[36],"limitations.":[38],"RESULTS:":[39],"In":[40,199],"the":[41,66,75,82,108,128,154,161,183,193,227,231,267],"present":[42],"work":[43],"we":[44,201,218],"propose":[45],"an":[46,86,174],"iterative":[47],"algorithm":[48],"called":[49],"WASABI,":[50],"dedicated":[51],"to":[52,106,132,243,264],"inferring":[53],"causal":[55],"dynamical":[56],"time-stamped":[59,270],"data,":[61],"which":[62,79,137],"tackles":[63],"some":[64,245],"limitations":[67],"associated":[68],"current":[70],"approaches.":[71],"We":[72,125,164],"first":[73],"introduce":[74],"concept":[76,103],"waves,":[78],"posits":[80],"that":[81,220,256],"information":[83],"provided":[84],"by":[85],"external":[87],"stimulus":[88],"will":[89,258],"affect":[90],"genes":[91,116,207,224],"one-by-one":[92],"through":[93,99],"cascade,":[95],"like":[96],"waves":[97],"spreading":[98],"network.":[101],"This":[102],"allows":[104],"us":[105],"infer":[107,134],"one":[110],"at":[112,160],"time,":[114],"after":[115],"ordered":[119],"regarding":[120],"their":[121],"time":[122],"regulation.":[124],"then":[126],"demonstrate":[127,238],"ability":[129,242],"WASABI":[131,167,239,257],"correctly":[133],"small":[135],"networks,":[136],"simulated":[140],"silico":[142],"using":[143],"mechanistic":[145],"model":[146,176],"consisting":[147],"coupled":[149],"piecewise-deterministic":[150],"Markov":[151],"processes":[152],"proper":[155],"description":[156],"level.":[163],"finally":[165],"apply":[166],"on":[168,173,192],"vitro":[170],"generated":[171],"avian":[175],"erythroid":[178],"differentiation.":[179],"The":[180],"structure":[181,214],"resulting":[184],"sheds":[188],"new":[190],"light":[191],"molecular":[194],"mechanisms":[195],"controlling":[196],"this":[197],"process.":[198],"particular,":[200],"find":[202,219],"no":[203],"evidence":[204],"hub":[206],"much":[210],"more":[211],"distributed":[212],"than":[215],"expected.":[216],"Interestingly,":[217],"majority":[222],"are":[225],"under":[226],"direct":[228],"control":[229],"differentiation-inducing":[232],"stimulus.":[233],"CONCLUSIONS:":[234],"Together,":[235],"these":[236],"results":[237],"versatility":[240],"tackle":[244],"general":[246],"inference":[250],"issues.":[251],"It":[252],"is":[253],"our":[254],"hope":[255],"prove":[259],"useful":[260],"helping":[262],"biologists":[263],"fully":[265],"exploit":[266],"power":[268],"data.":[272]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
