{"id":"https://openalex.org/W1525328068","doi":"https://doi.org/10.1371/journal.pcbi.1001099","title":"Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli","display_name":"Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli","publication_year":2011,"publication_date":"2011-03-03","ids":{"openalex":"https://openalex.org/W1525328068","doi":"https://doi.org/10.1371/journal.pcbi.1001099","mag":"1525328068","pmid":"https://pubmed.ncbi.nlm.nih.gov/21408212"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1001099","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1001099","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001099&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"book-chapter","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001099&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083112693","display_name":"Melody K. Morris","orcid":"https://orcid.org/0000-0003-2030-3466"},"institutions":[{"id":"https://openalex.org/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melody K. Morris","raw_affiliation_strings":["Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I4210143601"]}]},{"author_position":"middle","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/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"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"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America","Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062270975","display_name":"David C. Clarke","orcid":"https://orcid.org/0000-0002-1520-5426"},"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"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David C. Clarke","raw_affiliation_strings":["Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America","Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063426870","display_name":"Peter K. Sorger","orcid":"https://orcid.org/0000-0002-3364-1838"},"institutions":[{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"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":"Peter K. Sorger","raw_affiliation_strings":["Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America","Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060106170","display_name":"Douglas A. Lauffenburger","orcid":"https://orcid.org/0000-0002-0050-989X"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"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":true,"raw_author_name":"Douglas A. Lauffenburger","raw_affiliation_strings":["Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America","Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Cell Decision Processes, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5060106170"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I63966007"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.04477121,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"7","issue":"3","first_page":"e1001099","last_page":"e1001099"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9987000226974487,"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":0.9975000023841858,"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/computer-science","display_name":"Computer science","score":0.6019324660301208},{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.5906569957733154},{"id":"https://openalex.org/keywords/fuzzy-logic","display_name":"Fuzzy logic","score":0.5281457901000977},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4779767692089081},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45792990922927856},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3822202682495117},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33471134305000305},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29257047176361084}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6019324660301208},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.5906569957733154},{"id":"https://openalex.org/C58166","wikidata":"https://www.wikidata.org/wiki/Q224821","display_name":"Fuzzy logic","level":2,"score":0.5281457901000977},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4779767692089081},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45792990922927856},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3822202682495117},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33471134305000305},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29257047176361084},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018836","descriptor_name":"Inflammation Mediators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018836","descriptor_name":"Inflammation Mediators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018836","descriptor_name":"Inflammation Mediators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018836","descriptor_name":"Inflammation Mediators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","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},{"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":10,"locations":[{"id":"doi:10.1371/journal.pcbi.1001099","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1001099","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001099&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:21408212","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21408212","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:dash.harvard.edu:1/8160881","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:8160881","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"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":"","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.801.3077","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.801.3077","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/58/f7/pcbi.1001099.PMC3048376.pdf","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1001099","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001099","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:106ad181e9704e5388ae74a9bbbdd3f9","is_oa":true,"landing_page_url":"https://doaj.org/article/106ad181e9704e5388ae74a9bbbdd3f9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 7, Iss 3, p e1001099 (2011)","raw_type":"article"},{"id":"pmh:oai:dspace.mit.edu:1721.1/66218","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/66218","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":"PLoS","raw_type":"http://purl.org/eprint/type/JournalArticle"},{"id":"pmh:oai:figshare.com:article/138456","is_oa":true,"landing_page_url":"https://figshare.com/articles/Training_Signaling_Pathway_Maps_to_Biochemical_Data_with_Constrained_Fuzzy_Logic_Quantitative_Analysis_of_Liver_Cell_Responses_to_Inflammatory_Stimuli/138456","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:3048376","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3048376","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"mag:1525328068","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1001099","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1001099","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001099&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6200000047683716,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1964169749","display_name":null,"funder_award_id":"GM68762","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7124989599","display_name":null,"funder_award_id":"U54-CA112967","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8305864826","display_name":null,"funder_award_id":"CA112967","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338502","display_name":"Institute for Collaborative Biotechnologies","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W1525328068.pdf"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W121387658","https://openalex.org/W1807981783","https://openalex.org/W1970957413","https://openalex.org/W1975507400","https://openalex.org/W1989053944","https://openalex.org/W1989684700","https://openalex.org/W1992660677","https://openalex.org/W1994803330","https://openalex.org/W1998151455","https://openalex.org/W2005780170","https://openalex.org/W2011912935","https://openalex.org/W2011944491","https://openalex.org/W2015401980","https://openalex.org/W2017218687","https://openalex.org/W2018899807","https://openalex.org/W2020291168","https://openalex.org/W2023120194","https://openalex.org/W2027631876","https://openalex.org/W2027650066","https://openalex.org/W2040827479","https://openalex.org/W2041006875","https://openalex.org/W2042459594","https://openalex.org/W2045534781","https://openalex.org/W2057242313","https://openalex.org/W2061820401","https://openalex.org/W2063556121","https://openalex.org/W2065635384","https://openalex.org/W2070658593","https://openalex.org/W2086840459","https://openalex.org/W2092755129","https://openalex.org/W2095433609","https://openalex.org/W2101181377","https://openalex.org/W2102486637","https://openalex.org/W2104039751","https://openalex.org/W2106289940","https://openalex.org/W2108456065","https://openalex.org/W2109444989","https://openalex.org/W2110182592","https://openalex.org/W2110265246","https://openalex.org/W2110751128","https://openalex.org/W2115368090","https://openalex.org/W2116271446","https://openalex.org/W2121266814","https://openalex.org/W2124486107","https://openalex.org/W2135030836","https://openalex.org/W2142302575","https://openalex.org/W2143877670","https://openalex.org/W2145899141","https://openalex.org/W2146883006","https://openalex.org/W2148255564","https://openalex.org/W2151852639","https://openalex.org/W2152025725","https://openalex.org/W2157243724","https://openalex.org/W2160103276","https://openalex.org/W2160196028","https://openalex.org/W2163798887","https://openalex.org/W2166898290","https://openalex.org/W2167334954","https://openalex.org/W2171599819","https://openalex.org/W2912565176","https://openalex.org/W4211007335","https://openalex.org/W6676336203"],"related_works":["https://openalex.org/W2602750865","https://openalex.org/W188114849","https://openalex.org/W1483074639","https://openalex.org/W2953362338","https://openalex.org/W436732512","https://openalex.org/W2017715710","https://openalex.org/W1999419114","https://openalex.org/W2757839622","https://openalex.org/W2112580417","https://openalex.org/W2950749329","https://openalex.org/W2963517317","https://openalex.org/W2183092247","https://openalex.org/W2951331687","https://openalex.org/W2520019544","https://openalex.org/W1639161519","https://openalex.org/W2502745291","https://openalex.org/W35186184","https://openalex.org/W1985899955","https://openalex.org/W270036034","https://openalex.org/W2153208554"],"abstract_inverted_index":{"Predictive":[0],"understanding":[1,187],"of":[2,79,131,156,180,188,220],"cell":[3],"signaling":[4],"network":[5,42,116,141],"operation":[6],"based":[7],"on":[8,100],"general":[9],"prior":[10,114],"knowledge":[11,115],"but":[12,88],"consistent":[13],"with":[14],"empirical":[15],"data":[16,87,144,223],"in":[17,26],"a":[18,23,76,113,124,139,200,214],"specific":[19],"environmental":[20],"context":[21],"is":[22,57],"current":[24],"challenge":[25],"computational":[27],"biology.":[28],"Recent":[29],"work":[30],"has":[31],"demonstrated":[32],"that":[33,127,231],"Boolean":[34,55],"logic":[35,81,110],"can":[36],"be":[37],"used":[38],"to":[39,49,59,84,92,142,207,234],"create":[40],"context-specific":[41,208],"models":[43,95,160],"by":[44,96,149,237],"training":[45,97],"proteomic":[46],"pathway":[47,98,172,202],"maps":[48,99],"dedicated":[50,101],"biochemical":[51,209],"data;":[52],"however,":[53],"the":[54,154,157,189],"formalism":[56],"restricted":[58],"characterizing":[60],"protein":[61,132,147,181,201],"species":[62],"as":[63],"either":[64],"fully":[65,235],"active":[66],"or":[67,120],"inactive.":[68],"To":[69],"advance":[70],"beyond":[71],"this":[72],"limitation,":[73],"we":[74],"propose":[75],"novel":[77],"form":[78],"fuzzy":[80,109],"sufficiently":[82,90],"flexible":[83],"model":[85,126,216],"quantitative":[86,178],"also":[89],"simple":[91],"efficiently":[93],"construct":[94],"experimental":[102,143],"measurements.":[103],"Our":[104,194],"new":[105,221],"approach,":[106],"termed":[107],"constrained":[108],"(cFL),":[111],"converts":[112],"(obtained":[117],"from":[118],"literature":[119,206],"interactome":[121],"databases)":[122],"into":[123,228],"computable":[125,215],"describes":[128],"graded":[129],"values":[130],"activation":[133,148],"across":[134],"multiple":[135],"pathways.":[136],"We":[137],"train":[138],"cFL-converted":[140],"describing":[145],"hepatocytic":[146],"inflammatory":[150],"cytokines":[151],"and":[152,183,186,197,224],"demonstrate":[153],"application":[155],"resultant":[158],"trained":[159],"for":[161,177],"three":[162],"important":[163],"purposes:":[164],"(a)":[165],"generating":[166],"experimentally":[167],"testable":[168],"biological":[169,226],"hypotheses":[170],"concerning":[171],"crosstalk,":[173],"(b)":[174],"establishing":[175],"capability":[176],"prediction":[179,185,219],"activity,":[182],"(c)":[184],"cytokine":[190],"release":[191],"phenotypic":[192],"response.":[193],"methodology":[195],"systematically":[196],"quantitatively":[198],"trains":[199],"map":[203],"summarizing":[204],"curated":[205],"data.":[210],"This":[211],"process":[212],"generates":[213],"yielding":[217],"successful":[218],"test":[222],"offering":[225],"insight":[227],"complex":[229],"datasets":[230],"are":[232],"difficult":[233],"analyze":[236],"intuition":[238],"alone.":[239]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}