{"id":"https://openalex.org/W4292636457","doi":"https://doi.org/10.1371/journal.pcbi.1010383","title":"Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis","display_name":"Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis","publication_year":2022,"publication_date":"2022-08-22","ids":{"openalex":"https://openalex.org/W4292636457","doi":"https://doi.org/10.1371/journal.pcbi.1010383","pmid":"https://pubmed.ncbi.nlm.nih.gov/35994517"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010383","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010383","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010383&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":"article","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.1010383&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029116099","display_name":"Leonie Amstein","orcid":"https://orcid.org/0000-0002-9524-0343"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Leonie K. Amstein","raw_affiliation_strings":["Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101628744","display_name":"J\u00f6rg Ackermann","orcid":"https://orcid.org/0000-0002-9942-0958"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"J\u00f6rg Ackermann","raw_affiliation_strings":["Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070300562","display_name":"Jennifer Hannig","orcid":"https://orcid.org/0000-0002-2789-5540"},"institutions":[{"id":"https://openalex.org/I45155027","display_name":"Technische Hochschule Mittelhessen","ror":"https://ror.org/02qdc9985","country_code":"DE","type":"education","lineage":["https://openalex.org/I45155027"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jennifer Hannig","raw_affiliation_strings":["Cognitive Information Systems, Kompetenzzentrum f\u00fcr Informationstechnologie, Technische Hochschule Mittelhessen, Friedberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-2789-5540","affiliations":[{"raw_affiliation_string":"Cognitive Information Systems, Kompetenzzentrum f\u00fcr Informationstechnologie, Technische Hochschule Mittelhessen, Friedberg, Germany","institution_ids":["https://openalex.org/I45155027"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082730369","display_name":"Ivan \u0110iki\u0107","orcid":"https://orcid.org/0000-0001-8156-9511"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ivan \u0110iki\u0107","raw_affiliation_strings":["Goethe University Frankfurt, Institute of Biochemistry II, Medical Faculty, Frankfurt am Main, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Goethe University Frankfurt, Institute of Biochemistry II, Medical Faculty, Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080913590","display_name":"Simone Fulda","orcid":"https://orcid.org/0000-0002-0459-6417"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Simone Fulda","raw_affiliation_strings":["Goethe University Frankfurt, Institute of Biochemistry II, Medical Faculty, Frankfurt am Main, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Goethe University Frankfurt, Institute of Biochemistry II, Medical Faculty, Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015346451","display_name":"Ina Koch","orcid":"https://orcid.org/0000-0002-3621-003X"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ina Koch","raw_affiliation_strings":["Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany"],"raw_orcid":"https://orcid.org/0000-0002-3621-003X","affiliations":[{"raw_affiliation_string":"Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I114090438"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5015346451","https://openalex.org/A5029116099","https://openalex.org/A5070300562","https://openalex.org/A5080913590","https://openalex.org/A5082730369","https://openalex.org/A5101628744"],"corresponding_institution_ids":["https://openalex.org/I114090438","https://openalex.org/I45155027"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2074,"currency":"EUR","value_usd":2236},"fwci":0.7812,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.69237195,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"18","issue":"8","first_page":"e1010383","last_page":"e1010383"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9988999962806702,"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":0.9988999962806702,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.961899995803833,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9587000012397766,"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/in-silico","display_name":"In silico","score":0.828140139579773},{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.705546498298645},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.7037340402603149},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6002597808837891},{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"Pathway analysis","score":0.41858968138694763},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3944282829761505},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3690321445465088},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2591915726661682},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.13750678300857544},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13624784350395203},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11430555582046509}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.828140139579773},{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.705546498298645},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.7037340402603149},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6002597808837891},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.41858968138694763},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3944282829761505},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3690321445465088},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2591915726661682},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.13750678300857544},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13624784350395203},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11430555582046509},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0}],"mesh":[{"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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D047888","descriptor_name":"Receptors, Tumor Necrosis Factor, Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D047888","descriptor_name":"Receptors, Tumor Necrosis Factor, Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D047888","descriptor_name":"Receptors, Tumor Necrosis Factor, Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D047888","descriptor_name":"Receptors, Tumor Necrosis Factor, Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D047888","descriptor_name":"Receptors, Tumor Necrosis Factor, Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D047888","descriptor_name":"Receptors, Tumor Necrosis Factor, Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D047888","descriptor_name":"Receptors, Tumor Necrosis Factor, Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D047888","descriptor_name":"Receptors, Tumor Necrosis Factor, Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1010383","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010383","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010383&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:35994517","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35994517","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:doaj.org/article:cc3f8093f4194e55801bbdf7fea54cb6","is_oa":true,"landing_page_url":"https://doaj.org/article/cc3f8093f4194e55801bbdf7fea54cb6","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 8, p e1010383 (2022)","raw_type":"article"},{"id":"pmh:oai:publikationen.ub.uni-frankfurt.de:75522","is_oa":true,"landing_page_url":"http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/75522","pdf_url":null,"source":{"id":"https://openalex.org/S4306400432","display_name":"Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114090438","host_organization_name":"Goethe University Frankfurt","host_organization_lineage":["https://openalex.org/I114090438"],"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":"doc-type:article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9467317","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9467317","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010383","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010383","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010383&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":[],"awards":[{"id":"https://openalex.org/G2514814090","display_name":null,"funder_award_id":"ENABLE 2995/1502/11","funder_id":"https://openalex.org/F4320321961","funder_display_name":"Hessisches Ministerium f\u00fcr Wissenschaft und Kunst"},{"id":"https://openalex.org/G413934606","display_name":null,"funder_award_id":"ID 259130777","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5290293035","display_name":null,"funder_award_id":"SFB 1177","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8253053231","display_name":null,"funder_award_id":"259130777","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8859224315","display_name":null,"funder_award_id":"259130777-SFB 1177","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8971290106","display_name":null,"funder_award_id":"3212070002/TP2","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321961","display_name":"Hessisches Ministerium f\u00fcr Wissenschaft und Kunst","ror":"https://ror.org/00zd5gr55"},{"id":"https://openalex.org/F4320323366","display_name":"Goethe-Universit\u00e4t Frankfurt am Main","ror":"https://ror.org/04cvxnb49"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4292636457.pdf","grobid_xml":"https://content.openalex.org/works/W4292636457.grobid-xml"},"referenced_works_count":100,"referenced_works":["https://openalex.org/W653950636","https://openalex.org/W1500667093","https://openalex.org/W1513433586","https://openalex.org/W1542400342","https://openalex.org/W1641228030","https://openalex.org/W1642162696","https://openalex.org/W1758444021","https://openalex.org/W1778624427","https://openalex.org/W1963848568","https://openalex.org/W1965818925","https://openalex.org/W1971135164","https://openalex.org/W1975593978","https://openalex.org/W1978486653","https://openalex.org/W1980792888","https://openalex.org/W1982528660","https://openalex.org/W1985911638","https://openalex.org/W1987707979","https://openalex.org/W1993081112","https://openalex.org/W1996109622","https://openalex.org/W2005572311","https://openalex.org/W2020031294","https://openalex.org/W2020987391","https://openalex.org/W2023122823","https://openalex.org/W2035571071","https://openalex.org/W2036887984","https://openalex.org/W2041531697","https://openalex.org/W2041689838","https://openalex.org/W2046760236","https://openalex.org/W2050489710","https://openalex.org/W2075941967","https://openalex.org/W2088573055","https://openalex.org/W2088679869","https://openalex.org/W2090234862","https://openalex.org/W2091269867","https://openalex.org/W2091802222","https://openalex.org/W2094524776","https://openalex.org/W2095433609","https://openalex.org/W2096586012","https://openalex.org/W2097446858","https://openalex.org/W2097682802","https://openalex.org/W2101090646","https://openalex.org/W2102263388","https://openalex.org/W2104335693","https://openalex.org/W2109711123","https://openalex.org/W2110796758","https://openalex.org/W2114727688","https://openalex.org/W2117853146","https://openalex.org/W2117864435","https://openalex.org/W2128316422","https://openalex.org/W2129079547","https://openalex.org/W2129627069","https://openalex.org/W2133554538","https://openalex.org/W2134062610","https://openalex.org/W2134784304","https://openalex.org/W2135332272","https://openalex.org/W2136235548","https://openalex.org/W2139552156","https://openalex.org/W2141184917","https://openalex.org/W2144277227","https://openalex.org/W2147237117","https://openalex.org/W2155304845","https://openalex.org/W2157869647","https://openalex.org/W2161621619","https://openalex.org/W2164823888","https://openalex.org/W2165500494","https://openalex.org/W2166927282","https://openalex.org/W2167437179","https://openalex.org/W2169804422","https://openalex.org/W2170554156","https://openalex.org/W2192257997","https://openalex.org/W2215489389","https://openalex.org/W2229908198","https://openalex.org/W2267633848","https://openalex.org/W2288102304","https://openalex.org/W2300735552","https://openalex.org/W2411288489","https://openalex.org/W2470223656","https://openalex.org/W2474828131","https://openalex.org/W2532321522","https://openalex.org/W2558992446","https://openalex.org/W2565402466","https://openalex.org/W2613123103","https://openalex.org/W2623886837","https://openalex.org/W2739721964","https://openalex.org/W2755200731","https://openalex.org/W2757581840","https://openalex.org/W2788640168","https://openalex.org/W2789979247","https://openalex.org/W2793302414","https://openalex.org/W2851271116","https://openalex.org/W2887835835","https://openalex.org/W2890337997","https://openalex.org/W2996017884","https://openalex.org/W3046144082","https://openalex.org/W3210642915","https://openalex.org/W4211017114","https://openalex.org/W4231303787","https://openalex.org/W4242587027","https://openalex.org/W6685124837","https://openalex.org/W6697585645"],"related_works":["https://openalex.org/W1816071588","https://openalex.org/W2513589746","https://openalex.org/W2153919606","https://openalex.org/W2003194288","https://openalex.org/W2213189664","https://openalex.org/W2074002899","https://openalex.org/W2062254828","https://openalex.org/W4237480606","https://openalex.org/W2936968863","https://openalex.org/W1971792277"],"abstract_inverted_index":{"The":[0,55],"paper":[1],"describes":[2],"a":[3,35,199],"mathematical":[4],"model":[5,38,56,69],"of":[6,10,44,74,109,155,162,191],"the":[7,31,45,68,75,106,114,132,146,156,168,176],"molecular":[8,42,46],"switches":[9],"cell":[11,115],"survival,":[12,117],"apoptosis,":[13],"and":[14,52,63,80,120,126,138,151,167,182],"necroptosis":[15],"in":[16,30,82,147,160,179],"cellular":[17,103],"signaling":[18,158],"pathways":[19,112,122],"initiated":[20],"by":[21,70,81],"tumor":[22],"necrosis":[23],"factor":[24],"1.":[25],"Based":[26],"on":[27,40,172],"experimental":[28],"findings":[29],"literature,":[32],"we":[33,91,194],"constructed":[34],"Petri":[36,87,202],"net":[37,88,203],"based":[39],"detailed":[41],"reactions":[43],"players,":[47],"protein":[48],"complexes,":[49],"post-translational":[50],"modifications,":[51],"cross":[53],"talk.":[54],"comprises":[57],"118":[58],"biochemical":[59],"entities,":[60],"130":[61],"reactions,":[62],"299":[64],"edges.":[65],"We":[66,144],"verified":[67],"evaluating":[71],"invariant":[72],"properties":[73],"system":[76],"at":[77],"steady":[78],"state":[79],"silico":[83,148],"knockout":[84,149],"analysis.":[85],"Applying":[86],"analysis":[89],"techniques,":[90],"found":[92],"279":[93],"pathways,":[94,131],"which":[95,174],"describe":[96],"signal":[97],"flows":[98],"from":[99],"receptor":[100],"activation":[101],"to":[102,116,124,140],"response,":[104],"representing":[105],"combinatorial":[107],"diversity":[108],"functional":[110],"pathways.120":[111],"steered":[113],"whereas":[118],"58":[119],"35":[121],"led":[123,139],"apoptosis":[125,183],"necroptosis,":[127],"respectively.":[128],"For":[129],"65":[130],"triggered":[133],"response":[134],"was":[135],"not":[136,186],"deterministic":[137],"multiple":[141],"possible":[142],"outcomes.":[143],"investigated":[145],"behavior":[150],"identified":[152],"important":[153],"checkpoints":[154],"TNFR1":[157],"pathway":[159],"terms":[161],"ubiquitination":[163],"within":[164],"complex":[165,180],"I":[166],"gene":[169],"expression":[170],"dependent":[171],"NF-\u03baB,":[173],"controls":[175],"caspase":[177],"activity":[178],"II":[181],"induction.":[184],"Despite":[185],"knowing":[187],"enough":[188],"kinetic":[189],"data":[190],"sufficient":[192],"quality,":[193],"estimated":[195],"system's":[196],"dynamics":[197],"using":[198],"discrete,":[200],"semi-quantitative":[201],"model.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
