{"id":"https://openalex.org/W2099660028","doi":"https://doi.org/10.1371/journal.pcbi.1003204","title":"Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs","display_name":"Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs","publication_year":2013,"publication_date":"2013-09-05","ids":{"openalex":"https://openalex.org/W2099660028","doi":"https://doi.org/10.1371/journal.pcbi.1003204","mag":"2099660028","pmid":"https://pubmed.ncbi.nlm.nih.gov/24039561"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003204","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003204","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003204&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.1003204&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075967151","display_name":"Ioannis N. Melas","orcid":"https://orcid.org/0000-0002-3338-5838"},"institutions":[{"id":"https://openalex.org/I174458059","display_name":"National Technical University of Athens","ror":"https://ror.org/03cx6bg69","country_code":"GR","type":"education","lineage":["https://openalex.org/I174458059"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Ioannis N. Melas","raw_affiliation_strings":["National Technical University of Athens, Athens, Greece",", National Technical University of Athens, Greece"],"affiliations":[{"raw_affiliation_string":"National Technical University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I174458059"]},{"raw_affiliation_string":", National Technical University of Athens, Greece","institution_ids":["https://openalex.org/I174458059"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087834541","display_name":"Regina Samaga","orcid":null},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"funder","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210127568","display_name":"Max Planck Institute for Dynamics of Complex Technical Systems","ror":"https://ror.org/030h7k016","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210127568"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Regina Samaga","raw_affiliation_strings":["Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany","Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany","institution_ids":["https://openalex.org/I4210127568"]},{"raw_affiliation_string":"Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society","institution_ids":["https://openalex.org/I4210127568","https://openalex.org/I149899117"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053848151","display_name":"Leonidas G. Alexopoulos","orcid":"https://orcid.org/0000-0003-0425-166X"},"institutions":[{"id":"https://openalex.org/I174458059","display_name":"National Technical University of Athens","ror":"https://ror.org/03cx6bg69","country_code":"GR","type":"education","lineage":["https://openalex.org/I174458059"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Leonidas G. Alexopoulos","raw_affiliation_strings":["National Technical University of Athens, Athens, Greece",", National Technical University of Athens, Greece"],"affiliations":[{"raw_affiliation_string":"National Technical University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I174458059"]},{"raw_affiliation_string":", National Technical University of Athens, Greece","institution_ids":["https://openalex.org/I174458059"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080707502","display_name":"Steffen Klamt","orcid":"https://orcid.org/0000-0003-2563-7561"},"institutions":[{"id":"https://openalex.org/I4210127568","display_name":"Max Planck Institute for Dynamics of Complex Technical Systems","ror":"https://ror.org/030h7k016","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210127568"]},{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"funder","lineage":["https://openalex.org/I149899117"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Steffen Klamt","raw_affiliation_strings":["Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany","Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany","institution_ids":["https://openalex.org/I4210127568"]},{"raw_affiliation_string":"Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society","institution_ids":["https://openalex.org/I4210127568","https://openalex.org/I149899117"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5080707502"],"corresponding_institution_ids":["https://openalex.org/I149899117","https://openalex.org/I4210127568"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":1914,"currency":"EUR","value_usd":2064},"fwci":1.9465,"has_fulltext":true,"cited_by_count":44,"citation_normalized_percentile":{"value":0.86119943,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"9","issue":"9","first_page":"e1003204","last_page":"e1003204"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987999796867371,"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":0.9987999796867371,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9983000159263611,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9977999925613403,"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/network-topology","display_name":"Network topology","score":0.7622566223144531},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6340993642807007},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.6010454893112183},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5929778218269348},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5157837867736816},{"id":"https://openalex.org/keywords/answer-set-programming","display_name":"Answer set programming","score":0.45210689306259155},{"id":"https://openalex.org/keywords/linear-programming","display_name":"Linear programming","score":0.4316943883895874},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.38594767451286316},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3749750852584839},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.36070871353149414},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2991989850997925},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19793134927749634},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18786391615867615},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.18737798929214478},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.13722312450408936},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11418220400810242}],"concepts":[{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.7622566223144531},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6340993642807007},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.6010454893112183},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5929778218269348},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5157837867736816},{"id":"https://openalex.org/C182620335","wikidata":"https://www.wikidata.org/wiki/Q2852531","display_name":"Answer set programming","level":3,"score":0.45210689306259155},{"id":"https://openalex.org/C41045048","wikidata":"https://www.wikidata.org/wiki/Q202843","display_name":"Linear programming","level":2,"score":0.4316943883895874},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.38594767451286316},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3749750852584839},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.36070871353149414},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2991989850997925},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19793134927749634},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18786391615867615},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.18737798929214478},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.13722312450408936},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11418220400810242},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1003204","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003204","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003204&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:24039561","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24039561","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:RePEc:plo:pcbi00:1003204","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003204","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:d05b65a77f9c41a7871591f97ddb098b","is_oa":true,"landing_page_url":"https://doaj.org/article/d05b65a77f9c41a7871591f97ddb098b","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 9, Iss 9, p e1003204 (2013)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2763839","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3764019","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/789706","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Detecting_and_Removing_Inconsistencies_between_Experimental_Data_and_Signaling_Network_Topologies_Using_Integer_Linear_Programming_on_Interaction_Graphs_/789706","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:3764019","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3764019","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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":"pmh:oai:pure.mpg.de:item_1837078","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0014-636F-6","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003204","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003204","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003204&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/G3998201246","display_name":null,"funder_award_id":"Social","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2099660028.pdf","grobid_xml":"https://content.openalex.org/works/W2099660028.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W344332445","https://openalex.org/W1762430620","https://openalex.org/W1807981783","https://openalex.org/W1857817679","https://openalex.org/W1964680470","https://openalex.org/W1978984420","https://openalex.org/W2015401980","https://openalex.org/W2016403543","https://openalex.org/W2017218687","https://openalex.org/W2033152161","https://openalex.org/W2033925647","https://openalex.org/W2069728939","https://openalex.org/W2073307618","https://openalex.org/W2075161553","https://openalex.org/W2089052780","https://openalex.org/W2104039751","https://openalex.org/W2116466534","https://openalex.org/W2124630954","https://openalex.org/W2127020923","https://openalex.org/W2130325801","https://openalex.org/W2131464440","https://openalex.org/W2134487266","https://openalex.org/W2143877670","https://openalex.org/W2145899141","https://openalex.org/W2147714160","https://openalex.org/W2156435365","https://openalex.org/W2159482845","https://openalex.org/W2164298117","https://openalex.org/W2167334954","https://openalex.org/W2167437179","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2092211394","https://openalex.org/W2086397253","https://openalex.org/W2133122801","https://openalex.org/W2140698704","https://openalex.org/W4285278887","https://openalex.org/W2995925505","https://openalex.org/W2365237642","https://openalex.org/W3116484972","https://openalex.org/W2941986668","https://openalex.org/W4232431455"],"abstract_inverted_index":{"Cross-referencing":[0],"experimental":[1,181,202],"data":[2,231],"with":[3,196],"our":[4,51],"current":[5],"knowledge":[6],"of":[7,15,18,33,68,96,100,129,149,167,180,193,201,210,222,228,262],"signaling":[8,34,41,130,224],"network":[9,42,77,170],"topologies":[10],"is":[11,266],"one":[12],"central":[13],"goal":[14],"mathematical":[16],"modeling":[17],"cellular":[19],"signal":[20],"transduction":[21],"networks.":[22,35],"We":[23,107,206],"present":[24],"a":[25,104,124,134,146,178,199,216,226,285],"new":[26,252],"methodology":[27],"for":[28,40,103,127,251,295],"data-driven":[29],"interrogation":[30],"and":[31,79,114,119,248,269],"training":[32],"While":[36],"most":[37],"published":[38],"methods":[39,237],"inference":[43],"operate":[44],"on":[45,58,64],"Bayesian,":[46],"Boolean,":[47],"or":[48],"ODE":[49],"models,":[50],"approach":[52,213,294],"uses":[53],"integer":[54],"linear":[55],"programming":[56],"(ILP)":[57],"interaction":[59,219],"graphs":[60],"to":[61,86,112,153,156,198,243],"encode":[62],"constraints":[63,72],"the":[65,69,76,88,97,101,141,164,168,191,194,204,208,211,260,270],"qualitative":[66,90],"behavior":[67],"nodes.":[70],"These":[71],"are":[73,241],"posed":[74],"by":[75,214],"topology":[78,171],"their":[80],"formulation":[81],"as":[82],"ILP":[83],"allows":[84],"us":[85],"predict":[87],"possible":[89],"changes":[91],"(up,":[92],"down,":[93],"no":[94],"effect)":[95],"activation":[98],"levels":[99],"nodes":[102,131,150],"given":[105,169],"stimulus.":[106],"provide":[108,249],"four":[109],"basic":[110],"operations":[111],"detect":[113,238],"remove":[115],"inconsistencies":[116],"between":[117],"measurements":[118,176],"predicted":[120],"behavior:":[121],"(i)":[122],"find":[123,140,184],"topology-consistent":[125],"explanation":[126],"responses":[128],"measured":[132,232],"in":[133,233,246,284],"stimulus-response":[135],"experiment":[136],"(if":[137],"none":[138],"exists,":[139],"closest":[142],"explanation);":[143],"(ii)":[144],"determine":[145,163],"minimal":[147],"set":[148,179,200],"that":[151,188,240],"need":[152],"be":[154,244],"corrected":[155],"make":[157],"an":[158,292],"inconsistent":[159],"scenario":[160],"consistent;":[161],"(iii)":[162],"optimal":[165],"subgraph":[166],"which":[172],"can":[173],"best":[174],"reflect":[175],"from":[177],"scenarios;":[182],"(iv)":[183],"possibly":[185],"missing":[186],"edges":[187],"would":[189,257],"improve":[190,259],"consistency":[192],"graph":[195,220],"respect":[197],"scenarios":[203],"most.":[205],"demonstrate":[207],"applicability":[209],"proposed":[212],"interrogating":[215],"manually":[217],"curated":[218],"model":[221,272],"EGFR/ErbB":[223],"against":[225],"library":[227],"high-throughput":[229],"phosphoproteomic":[230],"primary":[234],"hepatocytes.":[235],"Our":[236,264],"interactions":[239,253],"likely":[242],"inactive":[245],"hepatocytes":[247],"suggestions":[250],"that,":[254],"if":[255],"included,":[256],"significantly":[258],"goodness":[261],"fit.":[263],"framework":[265],"highly":[267],"flexible":[268],"underlying":[271],"requires":[273],"only":[274],"easily":[275],"accessible":[276],"biological":[277],"knowledge.":[278],"All":[279],"related":[280],"algorithms":[281],"were":[282],"implemented":[283],"freely":[286],"available":[287],"toolbox":[288],"SigNetTrainer":[289],"making":[290],"it":[291],"appealing":[293],"various":[296],"applications.":[297]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":11}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
