{"id":"https://openalex.org/W1506161505","doi":"https://doi.org/10.1186/1752-0509-6-133","title":"CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms","display_name":"CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms","publication_year":2012,"publication_date":"2012-10-18","ids":{"openalex":"https://openalex.org/W1506161505","doi":"https://doi.org/10.1186/1752-0509-6-133","mag":"1506161505","pmid":"https://pubmed.ncbi.nlm.nih.gov/23079107"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-133","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-133","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-133","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-133","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062204579","display_name":"Camille Terfve","orcid":"https://orcid.org/0000-0001-7930-280X"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Camille Terfve","raw_affiliation_strings":["European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026372984","display_name":"Thomas Cokelaer","orcid":"https://orcid.org/0000-0001-6286-1138"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Thomas Cokelaer","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051590122","display_name":"David Henriques","orcid":"https://orcid.org/0000-0002-9477-292X"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David Henriques","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064631396","display_name":"Aidan MacNamara","orcid":"https://orcid.org/0000-0001-5958-2429"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Aidan MacNamara","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065746791","display_name":"Emanuel Gon\u00e7alves","orcid":"https://orcid.org/0000-0002-9967-5205"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emanuel Goncalves","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083112693","display_name":"Melody K. Morris","orcid":"https://orcid.org/0000-0003-2030-3466"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melody K Morris","raw_affiliation_strings":["Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058353197","display_name":"Martijn van Iersel","orcid":"https://orcid.org/0000-0002-5877-4338"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Martijn van Iersel","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060106170","display_name":"Douglas A. Lauffenburger","orcid":"https://orcid.org/0000-0002-0050-989X"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas A Lauffenburger","raw_affiliation_strings":["Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005499510","display_name":"Julio S\u00e1ez-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-8552-8976"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5005499510"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":null,"apc_paid":null,"fwci":0.2688,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.56362133,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"6","issue":"1","first_page":"133","last_page":"133"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7267000079154968,"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":0.7267000079154968,"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":0.1307000070810318,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.046799998730421066,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/rotation-formalisms-in-three-dimensions","display_name":"Rotation formalisms in three dimensions","score":0.8327239155769348},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6133127808570862},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.32457566261291504},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14027142524719238}],"concepts":[{"id":"https://openalex.org/C171018156","wikidata":"https://www.wikidata.org/wiki/Q7370306","display_name":"Rotation formalisms in three dimensions","level":2,"score":0.8327239155769348},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6133127808570862},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.32457566261291504},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14027142524719238},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-6-133","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-133","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-133","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:23079107","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23079107","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 systems biology","raw_type":null},{"id":"pmh:oai:dspace.mit.edu:1721.1/77960","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/77960","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioMed Central Ltd","raw_type":"http://purl.org/eprint/type/JournalArticle"},{"id":"pmh:oai:europepmc.org:2604272","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3605281","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"},{"id":"mag:1506161505","is_oa":false,"landing_page_url":"http://dspace.mit.edu/handle/1721.1/77960","pdf_url":null,"source":{"id":"https://openalex.org/S4306504412","display_name":"BioMed Central Ltd","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"BioMed Central Ltd","raw_type":null}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-133","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-133","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-133","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3284194659","display_name":null,"funder_award_id":"W911NF-09-D-0001","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"},{"id":"https://openalex.org/G4365921341","display_name":null,"funder_award_id":"W911NF-09-D-0001","funder_id":"https://openalex.org/F4320338502","funder_display_name":"Institute for Collaborative Biotechnologies"},{"id":"https://openalex.org/G7452299184","display_name":null,"funder_award_id":"W911NF","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"}],"funders":[{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"},{"id":"https://openalex.org/F4320338502","display_name":"Institute for Collaborative Biotechnologies","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1506161505.pdf","grobid_xml":"https://content.openalex.org/works/W1506161505.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W166533788","https://openalex.org/W1807981783","https://openalex.org/W1970957413","https://openalex.org/W1971224531","https://openalex.org/W1978177843","https://openalex.org/W1985911638","https://openalex.org/W2004322850","https://openalex.org/W2006777504","https://openalex.org/W2008633581","https://openalex.org/W2015401980","https://openalex.org/W2027631876","https://openalex.org/W2042459594","https://openalex.org/W2069233518","https://openalex.org/W2069728939","https://openalex.org/W2075941967","https://openalex.org/W2090020814","https://openalex.org/W2096766502","https://openalex.org/W2100980426","https://openalex.org/W2102486637","https://openalex.org/W2103454055","https://openalex.org/W2103723044","https://openalex.org/W2104039751","https://openalex.org/W2112580417","https://openalex.org/W2114140117","https://openalex.org/W2115108153","https://openalex.org/W2124082948","https://openalex.org/W2125886217","https://openalex.org/W2127808973","https://openalex.org/W2129388048","https://openalex.org/W2132450464","https://openalex.org/W2142302575","https://openalex.org/W2143877670","https://openalex.org/W2144501202","https://openalex.org/W2152482800","https://openalex.org/W2153316724","https://openalex.org/W2153747194","https://openalex.org/W2155142785","https://openalex.org/W2163500926","https://openalex.org/W2164298117","https://openalex.org/W2167334954","https://openalex.org/W2167909734","https://openalex.org/W2172102555"],"related_works":["https://openalex.org/W2253747480","https://openalex.org/W2944001281","https://openalex.org/W2121525062","https://openalex.org/W2162094872","https://openalex.org/W2293412076","https://openalex.org/W2540253713","https://openalex.org/W1987535580","https://openalex.org/W3015697860","https://openalex.org/W3090510404","https://openalex.org/W2159809982"],"abstract_inverted_index":{"BACKGROUND:":[0],"Cells":[1],"process":[2],"signals":[3,210],"using":[4,188],"complex":[5],"and":[6,17,30,117,137,171,180,215,236],"dynamic":[7],"networks.":[8],"Studying":[9],"how":[10,209,216],"this":[11,147,217],"is":[12,22,41,218],"performed":[13],"in":[14,28,106,127,177,220,234],"a":[15,107],"context":[16,170],"cell":[18,172,249],"type":[19,250],"specific":[20],"way":[21],"essential":[23],"to":[24,45,56,90,103,134,165,207,226,238],"understand":[25,208],"signaling":[26,60,81,91],"both":[27],"physiological":[29],"diseased":[31],"situations.":[32],"Context-specific":[33],"medium/high":[34],"throughput":[35],"proteomic":[36],"data":[37],"measured":[38],"upon":[39],"perturbation":[40],"now":[42],"relatively":[43],"easy":[44],"obtain":[46],"but":[47,163],"formalisms":[48,191],"that":[49,241],"can":[50,185,223],"take":[51],"advantage":[52],"of":[53,59,80,123,196,230],"these":[54],"features":[55,96],"build":[57],"models":[58,79,102],"are":[61,155,168,204,211],"still":[62],"comparatively":[63],"scarce.":[64],"RESULTS:":[65],"Here":[66],"we":[67],"present":[68],"CellNOptR,":[69],"an":[70,129],"open-source":[71],"R":[72],"software":[73],"package":[74],"for":[75],"building":[76],"predictive":[77,179],"logic":[78,98,112,190],"networks":[82,85],"by":[83,157,213],"training":[84],"derived":[86],"from":[87,100],"prior":[88,158],"knowledge":[89,159],"(typically":[92],"phosphoproteomic)":[93],"data.":[94,166,199],"CellNOptR":[95,203],"different":[97,111,189],"formalisms,":[99],"Boolean":[101],"differential":[104,243],"equations,":[105],"common":[108],"framework.":[109],"These":[110],"model":[113],"representations":[114],"accommodate":[115],"state":[116],"time":[118],"values":[119],"with":[120,139,146,202],"increasing":[121],"levels":[122],"detail.":[124],"We":[125],"provide":[126],"addition":[128],"interface":[130],"via":[131],"Cytoscape":[132,140],"(CytoCopteR)":[133],"facilitate":[135],"use":[136],"integration":[138],"network-based":[141],"capabilities.":[142],"CONCLUSIONS:":[143],"Models":[144,200],"generated":[145],"pipeline":[148],"have":[149,242],"two":[150],"key":[151],"features.":[152],"First,":[153],"they":[154,184],"constrained":[156],"about":[160],"the":[161,194,197,228,248],"network":[162],"trained":[164],"They":[167,222],"therefore":[169],"line":[173],"specific,":[174],"which":[175],"results":[176],"enhanced":[178],"mechanistic":[181],"insights.":[182],"Second,":[183],"be":[186,224],"built":[187,201],"depending":[192,246],"on":[193,247],"richness":[195],"available":[198],"useful":[205],"tools":[206],"processed":[212],"cells":[214],"altered":[219],"disease.":[221],"used":[225],"predict":[227],"effect":[229],"perturbations":[231],"(individual":[232],"or":[233,251],"combinations),":[235],"potentially":[237],"engineer":[239],"therapies":[240],"effects/side":[244],"effects":[245],"context.":[252]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
