{"id":"https://openalex.org/W3033403590","doi":"https://doi.org/10.1093/bioinformatics/btaa561","title":"Converting networks to predictive logic models from perturbation signalling data with CellNOpt","display_name":"Converting networks to predictive logic models from perturbation signalling data with CellNOpt","publication_year":2020,"publication_date":"2020-06-03","ids":{"openalex":"https://openalex.org/W3033403590","doi":"https://doi.org/10.1093/bioinformatics/btaa561","mag":"3033403590","pmid":"https://pubmed.ncbi.nlm.nih.gov/32516357"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa561","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa561","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4523/33965427/btaa561.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4523/33965427/btaa561.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051832409","display_name":"Enio Gjerga","orcid":"https://orcid.org/0000-0001-8042-0395"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Enio Gjerga","raw_affiliation_strings":["Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany","Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)"],"raw_orcid":"https://orcid.org/0000-0001-8042-0395","affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]},{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008563172","display_name":"Panuwat Trairatphisan","orcid":"https://orcid.org/0000-0001-9015-5855"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Panuwat Trairatphisan","raw_affiliation_strings":["Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050239570","display_name":"Attila G\u00e1bor","orcid":"https://orcid.org/0000-0002-0776-1182"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Attila Gabor","raw_affiliation_strings":["Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079948362","display_name":"Hermann Koch","orcid":null},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hermann Koch","raw_affiliation_strings":["Aachener Verfahrenstechnik, Process Systems Engineering, RWTH Aachen University , Aachen, Germany","Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aachener Verfahrenstechnik, Process Systems Engineering, RWTH Aachen University , Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113912569","display_name":"C\u00e9line Chevalier","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Celine Chevalier","raw_affiliation_strings":["Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)","University Paris-Saclay, Espace Technologique Bat. Discovery ,91190 Saint-Aubin, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)","institution_ids":[]},{"raw_affiliation_string":"University Paris-Saclay, Espace Technologique Bat. Discovery ,91190 Saint-Aubin, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013429566","display_name":"Franceco Ceccarelli","orcid":null},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Franceco Ceccarelli","raw_affiliation_strings":["Computer Laboratory, University of Cambridge , Cambridge CB2 1TN, UK","Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge , Cambridge CB2 1TN, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019269764","display_name":"Aur\u00e9lien Dugourd","orcid":"https://orcid.org/0000-0002-0714-028X"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Aurelien Dugourd","raw_affiliation_strings":["Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany","Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]},{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045091643","display_name":"Alexander Mitsos","orcid":"https://orcid.org/0000-0003-0335-6566"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alexander Mitsos","raw_affiliation_strings":["Aachener Verfahrenstechnik, Process Systems Engineering, RWTH Aachen University , Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aachener Verfahrenstechnik, Process Systems Engineering, RWTH Aachen University , Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"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/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany","Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)"],"raw_orcid":"https://orcid.org/0000-0002-8552-8976","affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]},{"raw_affiliation_string":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5005499510"],"corresponding_institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.4928,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.82178526,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"36","issue":"16","first_page":"4523","last_page":"4524"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7160999774932861,"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":0.7160999774932861,"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":0.12359999865293503,"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":0.05609999969601631,"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/signalling","display_name":"Signalling","score":0.6138274073600769},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6138140559196472},{"id":"https://openalex.org/keywords/perturbation","display_name":"Perturbation (astronomy)","score":0.4752649664878845},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3201502561569214},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17278897762298584},{"id":"https://openalex.org/keywords/mathematical-economics","display_name":"Mathematical economics","score":0.1571197807788849},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07217651605606079}],"concepts":[{"id":"https://openalex.org/C39743133","wikidata":"https://www.wikidata.org/wiki/Q3262595","display_name":"Signalling","level":2,"score":0.6138274073600769},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6138140559196472},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.4752649664878845},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3201502561569214},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17278897762298584},{"id":"https://openalex.org/C144237770","wikidata":"https://www.wikidata.org/wiki/Q747534","display_name":"Mathematical economics","level":1,"score":0.1571197807788849},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07217651605606079},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa561","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa561","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4523/33965427/btaa561.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32516357","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32516357","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7575044","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7575044","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"Bioinformatics","raw_type":"Text"},{"id":"doi:10.18154/rwth-2020-07443","is_oa":true,"landing_page_url":"https://doi.org/10.18154/rwth-2020-07443","pdf_url":null,"source":{"id":"https://openalex.org/S4306401033","display_name":"RWTH Publications (RWTH Aachen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887968799","host_organization_name":"RWTH Aachen University","host_organization_lineage":["https://openalex.org/I887968799"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa561","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa561","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4523/33965427/btaa561.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G190043295","display_name":null,"funder_award_id":"675585","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G3766693508","display_name":null,"funder_award_id":"116030","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320307771","display_name":"Bayer","ror":"https://ror.org/04hmn8g73"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3033403590.pdf","grobid_xml":"https://content.openalex.org/works/W3033403590.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2015401980","https://openalex.org/W2073903631","https://openalex.org/W2129325583","https://openalex.org/W2153316724","https://openalex.org/W2157947216","https://openalex.org/W2557833574"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2105336199","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4386783876","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"SUMMARY:":[0],"The":[1],"molecular":[2],"changes":[3],"induced":[4],"by":[5,39],"perturbations":[6],"such":[7],"as":[8],"drugs":[9],"and":[10,68,80,130],"ligands":[11],"are":[12,148],"highly":[13],"informative":[14],"of":[15,47,57,71,92,114],"the":[16,36,82,89,112],"intracellular":[17],"wiring.":[18],"Our":[19],"capacity":[20],"to":[21,31,49,85,122,135],"generate":[22],"large":[23,94],"datasets":[24],"is":[25,38,54],"increasing":[26],"steadily.":[27],"A":[28],"useful":[29],"way":[30],"extract":[32],"mechanistic":[33],"insight":[34],"from":[35,65],"data":[37,67,147],"integrating":[40],"them":[41],"with":[42,88],"a":[43,55,104,115,120],"prior":[44,69],"knowledge":[45,70],"network":[46],"signalling":[48,72],"obtain":[50],"dynamic":[51],"models.":[52],"CellNOpt":[53,137],"collection":[56],"Bioconductor":[58],"R":[59],"packages":[60],"for":[61,108],"building":[62],"logic":[63,106],"models":[64],"perturbation":[66],"networks.":[73],"We":[74],"have":[75],"recently":[76],"developed":[77],"new":[78],"components":[79],"refined":[81],"existing":[83],"ones":[84],"keep":[86],"up":[87],"computational":[90],"demand":[91],"increasingly":[93],"datasets,":[95,110],"including":[96],"(i)":[97],"an":[98,132],"efficient":[99],"integer":[100],"linear":[101],"programming,":[102],"(ii)":[103],"probabilistic":[105],"implementation":[107],"semi-quantitative":[109],"(iii)":[111],"integration":[113],"stochastic":[116],"Boolean":[117],"simulator,":[118],"(iv)":[119],"tool":[121,134],"identify":[123],"missing":[124],"links,":[125],"(v)":[126],"systematic":[127],"post-hoc":[128],"analyses":[129],"(vi)":[131],"R-Shiny":[133],"run":[136],"interactively.":[138],"AVAILABILITY":[139],"AND":[140],"IMPLEMENTATION:":[141],"R-package(s):":[142],"https://github.com/saezlab/cellnopt.":[143],"SUPPLEMENTARY":[144],"INFORMATION:":[145],"Supplementary":[146],"available":[149],"at":[150],"Bioinformatics":[151],"online.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":3}],"updated_date":"2026-08-10T07:06:39.071514","created_date":"2020-06-12T00:00:00"}
