{"id":"https://openalex.org/W2153316724","doi":"https://doi.org/10.1093/bioinformatics/bts363","title":"Integrating literature-constrained and data-driven inference of signalling networks","display_name":"Integrating literature-constrained and data-driven inference of signalling networks","publication_year":2012,"publication_date":"2012-06-25","ids":{"openalex":"https://openalex.org/W2153316724","doi":"https://doi.org/10.1093/bioinformatics/bts363","mag":"2153316724","pmid":"https://pubmed.ncbi.nlm.nih.gov/22734019"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2311/48883699/bioinformatics_28_18_2311.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2311/48883699/bioinformatics_28_18_2311.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016886168","display_name":"Federica Eduati","orcid":"https://orcid.org/0000-0002-7822-3867"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I4210138819","display_name":"Centro de Investigaci\u00f3n del C\u00e1ncer","ror":"https://ror.org/04rxrdv16","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I184999862","https://openalex.org/I4210138819"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Federica Eduati","raw_affiliation_strings":["1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I4210138819","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090598948","display_name":"Javier De Las Rivas","orcid":"https://orcid.org/0000-0002-0984-9946"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I4210138819","display_name":"Centro de Investigaci\u00f3n del C\u00e1ncer","ror":"https://ror.org/04rxrdv16","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I184999862","https://openalex.org/I4210138819"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Javier De Las Rivas","raw_affiliation_strings":["1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I4210138819","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077821068","display_name":"Barbara Di Camillo","orcid":"https://orcid.org/0000-0001-8415-4688"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I4210138819","display_name":"Centro de Investigaci\u00f3n del C\u00e1ncer","ror":"https://ror.org/04rxrdv16","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I184999862","https://openalex.org/I4210138819"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Barbara Di Camillo","raw_affiliation_strings":["1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I4210138819","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019053602","display_name":"Gianna Toffolo","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I4210138819","display_name":"Centro de Investigaci\u00f3n del C\u00e1ncer","ror":"https://ror.org/04rxrdv16","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I184999862","https://openalex.org/I4210138819"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Gianna Toffolo","raw_affiliation_strings":["1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I4210138819","https://openalex.org/I87048295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005499510","display_name":"Julio S\u00e1ez-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-8552-8976"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I4210138819","display_name":"Centro de Investigaci\u00f3n del C\u00e1ncer","ror":"https://ror.org/04rxrdv16","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I184999862","https://openalex.org/I4210138819"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["ES","GB"],"is_corresponding":true,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Information Engineering, University of Padova, Padova, 31050, Italy, 2European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK and 3Bioinformatics & Functional Genomics Group, Cancer Research Center (CSIC/USAL), Salamanca, E37007, Spain","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I4210138819","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005499510"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I4210138819","https://openalex.org/I87048295"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":2.6196,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.90599354,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"28","issue":"18","first_page":"2311","last_page":"2317"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.652400016784668,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.652400016784668,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.23430000245571136,"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/T10885","display_name":"Gene expression and cancer classification","score":0.022600000724196434,"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/interpretability","display_name":"Interpretability","score":0.8315775990486145},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7819870710372925},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7433952689170837},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.7110413312911987},{"id":"https://openalex.org/keywords/signalling","display_name":"Signalling","score":0.4833957254886627},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4818378686904907},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4740426540374756},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4343542158603668},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38961073756217957},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.324690043926239},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.14888378977775574},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07886385917663574}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8315775990486145},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7819870710372925},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7433952689170837},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.7110413312911987},{"id":"https://openalex.org/C39743133","wikidata":"https://www.wikidata.org/wiki/Q3262595","display_name":"Signalling","level":2,"score":0.4833957254886627},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4818378686904907},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4740426540374756},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4343542158603668},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38961073756217957},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.324690043926239},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.14888378977775574},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07886385917663574},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"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":"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":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/bts363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2311/48883699/bioinformatics_28_18_2311.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22734019","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22734019","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pure.tue.nl:openaire/562d53af-12fa-453d-be25-c3a299b13b03","is_oa":true,"landing_page_url":"https://research.tue.nl/en/publications/562d53af-12fa-453d-be25-c3a299b13b03","pdf_url":null,"source":{"id":"https://openalex.org/S4406922641","display_name":"TU/e Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Eduati, F, De Las Rivas, J, Di Camillo, B, Toffolo, G & Saez-Rodriguez, J 2012, 'Integrating literature-constrained and data-driven inference of signalling networks', Bioinformatics, vol. 28, no. 18, pp. 2311-2317. https://doi.org/10.1093/bioinformatics/bts363","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2440668","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3436796","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:digital.csic.es:10261/52730","is_oa":true,"landing_page_url":"http://hdl.handle.net/10261/52730","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"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":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:library.tue.nl:871375","is_oa":false,"landing_page_url":"http://repository.tue.nl/871375","pdf_url":null,"source":{"id":"https://openalex.org/S4406922641","display_name":"TU/e Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN:1367-4803","raw_type":"Article / Letter to the editor"},{"id":"pmh:oai:library.tue.nl:877852","is_oa":false,"landing_page_url":"http://repository.tue.nl/877852","pdf_url":null,"source":{"id":"https://openalex.org/S4406922641","display_name":"TU/e Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN:1367-4803","raw_type":"Article / Letter to the editor"},{"id":"pmh:tue:oai:pure.tue.nl:publications/562d53af-12fa-453d-be25-c3a299b13b03","is_oa":true,"landing_page_url":"https://research.tue.nl/nl/publications/562d53af-12fa-453d-be25-c3a299b13b03","pdf_url":null,"source":{"id":"https://openalex.org/S4406922641","display_name":"TU/e Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Bioinformatics, 28(18), 2311 - 2317. Oxford University Press","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2311/48883699/bioinformatics_28_18_2311.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2153316724.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W166533788","https://openalex.org/W229097380","https://openalex.org/W1599207601","https://openalex.org/W1976937534","https://openalex.org/W1985911638","https://openalex.org/W1995008770","https://openalex.org/W2010502047","https://openalex.org/W2027631876","https://openalex.org/W2042431901","https://openalex.org/W2044525257","https://openalex.org/W2047265332","https://openalex.org/W2067803871","https://openalex.org/W2071344383","https://openalex.org/W2095433609","https://openalex.org/W2100025044","https://openalex.org/W2104039751","https://openalex.org/W2115108153","https://openalex.org/W2118128448","https://openalex.org/W2121851657","https://openalex.org/W2137304236","https://openalex.org/W2140116490","https://openalex.org/W2145899141","https://openalex.org/W2146883006","https://openalex.org/W2147714160","https://openalex.org/W2150627960","https://openalex.org/W2154293840","https://openalex.org/W2159482845","https://openalex.org/W2161868542","https://openalex.org/W2161922735","https://openalex.org/W2163296115","https://openalex.org/W2164298117","https://openalex.org/W2167334954","https://openalex.org/W3099289621","https://openalex.org/W6608852248"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2135678793","https://openalex.org/W2011682793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W2978247079","https://openalex.org/W2140163842","https://openalex.org/W2148708580","https://openalex.org/W3037604406","https://openalex.org/W249159571"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"developments":[2],"in":[3,69,138,152,161],"experimental":[4],"methods":[5,46,56,79],"facilitate":[6],"increasingly":[7],"larger":[8],"signal":[9],"transduction":[10],"datasets.":[11],"Two":[12],"main":[13],"approaches":[14],"can":[15],"be":[16],"taken":[17],"to":[18,33,74,80,111,122,158],"derive":[19],"a":[20,27,90,123,132],"mathematical":[21],"model":[22,133],"from":[23,31,40,84,96],"these":[24],"data:":[25],"training":[26],"network":[28,39,92,124],"(obtained,":[29],"e.g.,":[30],"literature)":[32],"the":[34,38,41,70,97,115,139,153,162],"data,":[35],"or":[36],"inferring":[37],"data":[42,98,136,172],"alone.":[43],"Purely":[44],"data-driven":[45,78],"scale":[47],"up":[48],"poorly":[49],"and":[50,77,103,113,127,144,160],"have":[51],"limited":[52],"interpretability,":[53],"whereas":[54],"literature-constrained":[55,76],"cannot":[57],"deal":[58],"with":[59,93,134],"incomplete":[60],"networks.":[61],"RESULTS:":[62],"We":[63,119,130],"present":[64],"an":[65],"efficient":[66],"approach,":[67],"implemented":[68],"R":[71],"package":[72],"CNORfeeder,":[73],"integrate":[75],"infer":[81],"signalling":[82],"networks":[83],"perturbation":[85],"experiments.":[86],"Our":[87],"method":[88],"extends":[89],"given":[91],"links":[94],"derived":[95],"via":[99],"various":[100],"inference":[101],"methods,":[102],"uses":[104],"information":[105],"on":[106],"physical":[107],"interactions":[108],"of":[109,117,125,155],"proteins":[110],"guide":[112],"validate":[114],"integration":[116],"links.":[118],"apply":[120],"CNORfeeder":[121,150],"growth":[126],"inflammatory":[128],"signalling.":[129],"obtain":[131],"superior":[135],"fit":[137],"human":[140],"liver":[141],"cancer":[142],"HepG2":[143],"propose":[145],"potential":[146],"missing":[147],"pathways.":[148],"AVAILABILITY:":[149],"is":[151],"process":[154],"being":[156],"submitted":[157],"Bioconductor":[159],"meantime":[163],"available":[164,174],"at":[165,175],"www.cellnopt.org.":[166],"CONTACT:":[167],"saezrodriguez@ebi.ac.uk":[168],"SUPPLEMENTARY":[169],"INFORMATION:":[170],"Supplementary":[171],"are":[173],"Bioinformatics":[176],"online.":[177]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-30T07:30:35.949966","created_date":"2025-10-10T00:00:00"}
