{"id":"https://openalex.org/W2157593856","doi":"https://doi.org/10.1186/s12859-015-0728-4","title":"NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference","display_name":"NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference","publication_year":2015,"publication_date":"2015-09-29","ids":{"openalex":"https://openalex.org/W2157593856","doi":"https://doi.org/10.1186/s12859-015-0728-4","mag":"2157593856","pmid":"https://pubmed.ncbi.nlm.nih.gov/26415849"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0728-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0728-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0728-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0728-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073033661","display_name":"Pau Bellot","orcid":"https://orcid.org/0000-0001-9503-4710"},"institutions":[{"id":"https://openalex.org/I157674565","display_name":"University of Li\u00e8ge","ror":"https://ror.org/00afp2z80","country_code":"BE","type":"education","lineage":["https://openalex.org/I157674565"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES"],"is_corresponding":true,"raw_author_name":"Pau Bellot","raw_affiliation_strings":["Bioinformatics and Systems Biology (BioSys), Faculty of Sciences, Universit\u00e9 de Li\u00e8ge (ULg), 27 Blvd du Rectorat, Li\u00e8ge, 4000, Belgium. pau.bellot@upc.edu","Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. pau.bellot@upc.edu","Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology (BioSys), Faculty of Sciences, Universit\u00e9 de Li\u00e8ge (ULg), 27 Blvd du Rectorat, Li\u00e8ge, 4000, Belgium. pau.bellot@upc.edu","institution_ids":["https://openalex.org/I157674565"]},{"raw_affiliation_string":"Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. pau.bellot@upc.edu","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058483070","display_name":"Catharina Olsen","orcid":"https://orcid.org/0000-0002-6193-2296"},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["BE","IN"],"is_corresponding":false,"raw_author_name":"Catharina Olsen","raw_affiliation_strings":["Interuniversity Institute of Bioinformatics Brussels, (IB)\u00b2, Brussels, Belgium. colsen@ulb.ac.be","Machine Learning Group, Universit\u00e9 Libre de Bruxelles, Brussels, Belgium. colsen@ulb.ac.be","Machine Learning Group, Universit\u00e9 Libre de Bruxelles, Brussels, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics Brussels, (IB)\u00b2, Brussels, Belgium. colsen@ulb.ac.be","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"Machine Learning Group, Universit\u00e9 Libre de Bruxelles, Brussels, Belgium. colsen@ulb.ac.be","institution_ids":["https://openalex.org/I132053463"]},{"raw_affiliation_string":"Machine Learning Group, Universit\u00e9 Libre de Bruxelles, Brussels, Belgium","institution_ids":["https://openalex.org/I132053463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027200081","display_name":"Philippe Salembier","orcid":"https://orcid.org/0000-0001-8884-9604"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Philippe Salembier","raw_affiliation_strings":["Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. philippe.salembier@upc.edu","Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. philippe.salembier@upc.edu","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103260465","display_name":"Albert Oliveras","orcid":"https://orcid.org/0000-0003-1574-5622"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Albert Oliveras-Verg\u00e9s","raw_affiliation_strings":["Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. albert.oliveras@upc.edu","Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain. albert.oliveras@upc.edu","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Universitat Politecnica de Catalunya BarcelonaTECH, Department of Signal Theory and Communications, UPC-Campus Nord, C/ Jordi Girona, 1-3, Barcelona, 08034, Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101990038","display_name":"Patrick Meyer","orcid":"https://orcid.org/0009-0001-7238-7713"},"institutions":[{"id":"https://openalex.org/I157674565","display_name":"University of Li\u00e8ge","ror":"https://ror.org/00afp2z80","country_code":"BE","type":"education","lineage":["https://openalex.org/I157674565"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Patrick E. Meyer","raw_affiliation_strings":["Bioinformatics and Systems Biology (BioSys), Faculty of Sciences, Universit\u00e9 de Li\u00e8ge (ULg), 27 Blvd du Rectorat, Li\u00e8ge, 4000, Belgium. patrick.meyer@ulg.ac.be","Bioinformatics and Systems Biology (BioSys), Faculty of Sciences, Universit\u00e9 de Li\u00e8ge (ULg), 27 Blvd du Rectorat, Li\u00e8ge, 4000, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology (BioSys), Faculty of Sciences, Universit\u00e9 de Li\u00e8ge (ULg), 27 Blvd du Rectorat, Li\u00e8ge, 4000, Belgium. patrick.meyer@ulg.ac.be","institution_ids":["https://openalex.org/I157674565"]},{"raw_affiliation_string":"Bioinformatics and Systems Biology (BioSys), Faculty of Sciences, Universit\u00e9 de Li\u00e8ge (ULg), 27 Blvd du Rectorat, Li\u00e8ge, 4000, Belgium","institution_ids":["https://openalex.org/I157674565"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5073033661"],"corresponding_institution_ids":["https://openalex.org/I157674565","https://openalex.org/I9617848"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":3.3015,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.92973137,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"312","last_page":"312"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9229999780654907,"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":0.9229999780654907,"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":0.018699999898672104,"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":0.017899999395012856,"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/bioconductor","display_name":"Bioconductor","score":0.949303925037384},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.765627384185791},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7539222240447998},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.706824004650116},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6083039045333862},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5914536714553833},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5838156938552856},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5806514024734497},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2549358606338501},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1650591790676117},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15308406949043274},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1385073959827423}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.949303925037384},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.765627384185791},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7539222240447998},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.706824004650116},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6083039045333862},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5914536714553833},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5838156938552856},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5806514024734497},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2549358606338501},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1650591790676117},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15308406949043274},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1385073959827423},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","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":"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":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-015-0728-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0728-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0728-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26415849","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26415849","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:upcommons.upc.edu:2117/79912","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/79912","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:orbi.ulg.ac.be:2268/186414","is_oa":true,"landing_page_url":"https://orbi.uliege.be/handle/2268/186414","pdf_url":"https://orbi.uliege.be/bitstream/2268/186414/1/s12859-015-0728-4.pdf","source":{"id":"https://openalex.org/S4306400651","display_name":"Open Repository and Bibliography (University of Li\u00e8ge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I157674565","host_organization_name":"University of Li\u00e8ge","host_organization_lineage":["https://openalex.org/I157674565"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics (2015-09)","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:pubmedcentral.nih.gov:4587916","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4587916","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:dipot.ulb.ac.be:2013/220688","is_oa":true,"landing_page_url":"http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220688","pdf_url":null,"source":{"id":"https://openalex.org/S4306401063","display_name":"D\u00e9p\u00f4t institutionnel de l'Universit\u00e9 libre de Bruxelles (Universit\u00e9 Libre de Bruxelles)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I132053463","host_organization_name":"Universit\u00e9 Libre de Bruxelles","host_organization_lineage":["https://openalex.org/I132053463"],"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":"BMC bioinformatics, 16 (1","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0728-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0728-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0728-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2839630738","display_name":null,"funder_award_id":"TEC2013-43935-R","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G4248128755","display_name":null,"funder_award_id":"TEC2013-43935-R","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G528031991","display_name":null,"funder_award_id":"SFRD\u201012/03","funder_id":"https://openalex.org/F4320323329","funder_display_name":"Universit\u00e9 de Li\u00e8ge"},{"id":"https://openalex.org/G5802118512","display_name":null,"funder_award_id":"SFRD-12/04","funder_id":"https://openalex.org/F4320323329","funder_display_name":"Universit\u00e9 de Li\u00e8ge"},{"id":"https://openalex.org/G6507403436","display_name":null,"funder_award_id":"BIGGRAPH-TEC2013-43935-R","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G7256666812","display_name":null,"funder_award_id":"C-14/73","funder_id":"https://openalex.org/F4320323329","funder_display_name":"Universit\u00e9 de Li\u00e8ge"},{"id":"https://openalex.org/G7704466608","display_name":null,"funder_award_id":"23678785","funder_id":"https://openalex.org/F4320321390","funder_display_name":"Fonds De La Recherche Scientifique - FNRS"}],"funders":[{"id":"https://openalex.org/F4320310210","display_name":"Fundaci\u00f3n Cellex","ror":null},{"id":"https://openalex.org/F4320321390","display_name":"Fonds De La Recherche Scientifique - FNRS","ror":"https://ror.org/03q83t159"},{"id":"https://openalex.org/F4320321764","display_name":"Ministerio de Educaci\u00f3n, Cultura y Deporte","ror":"https://ror.org/03nc27g21"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320322852","display_name":"Innoviris","ror":"https://ror.org/04af9zr29"},{"id":"https://openalex.org/F4320323329","display_name":"Universit\u00e9 de Li\u00e8ge","ror":"https://ror.org/00afp2z80"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157593856.pdf","grobid_xml":"https://content.openalex.org/works/W2157593856.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W103650626","https://openalex.org/W1504031589","https://openalex.org/W1851422093","https://openalex.org/W1933643226","https://openalex.org/W1969761972","https://openalex.org/W1976526581","https://openalex.org/W1998544165","https://openalex.org/W2000121243","https://openalex.org/W2025320861","https://openalex.org/W2036363967","https://openalex.org/W2044525257","https://openalex.org/W2061003492","https://openalex.org/W2076513103","https://openalex.org/W2078149659","https://openalex.org/W2079517420","https://openalex.org/W2084191969","https://openalex.org/W2094558888","https://openalex.org/W2099111195","https://openalex.org/W2102471334","https://openalex.org/W2104693064","https://openalex.org/W2105129830","https://openalex.org/W2109384743","https://openalex.org/W2115108153","https://openalex.org/W2121695897","https://openalex.org/W2125904845","https://openalex.org/W2131987814","https://openalex.org/W2134586291","https://openalex.org/W2135220916","https://openalex.org/W2139997707","https://openalex.org/W2143076232","https://openalex.org/W2147440110","https://openalex.org/W2153011302","https://openalex.org/W2160697532","https://openalex.org/W2161467890","https://openalex.org/W2161922735","https://openalex.org/W2163296115","https://openalex.org/W2169053773","https://openalex.org/W2175806147","https://openalex.org/W2478708596","https://openalex.org/W2608702473","https://openalex.org/W2911964244","https://openalex.org/W2914584698","https://openalex.org/W3099289621","https://openalex.org/W4242577767","https://openalex.org/W4285719527","https://openalex.org/W6674851815"],"related_works":["https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W3156537409","https://openalex.org/W2140163842","https://openalex.org/W2747931568","https://openalex.org/W2921090651","https://openalex.org/W2133055377","https://openalex.org/W2287365612","https://openalex.org/W2121792613"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1],"the":[2,72,96,114],"last":[3],"decade,":[4],"a":[5,39,45,65,107],"great":[6],"number":[7],"of":[8,51,68,74,98],"methods":[9,100],"for":[10],"reconstructing":[11],"gene":[12],"regulatory":[13],"networks":[14],"from":[15],"expression":[16],"data":[17],"have":[18,117],"been":[19],"proposed.":[20],"However,":[21],"very":[22],"few":[23],"tools":[24,69],"and":[25,31,59,84,104],"datasets":[26,94],"allow":[27],"to":[28,43,70,112],"evaluate":[29],"accurately":[30],"reproducibly":[32],"those":[33],"methods.":[34,55],"Hence,":[35],"we":[36],"propose":[37],"here":[38],"new":[40],"tool,":[41],"able":[42],"perform":[44],"systematic,":[46],"yet":[47],"fully":[48],"reproducible,":[49],"evaluation":[50],"transcriptional":[52],"network":[53,75,102],"inference":[54,76],"RESULTS:":[56],"Our":[57],"open-source":[58],"freely":[60],"available":[61],"Bioconductor":[62],"package":[63],"aggregates":[64],"large":[66],"set":[67],"assess":[71],"robustness":[73],"algorithms":[77],"against":[78],"different":[79],"simulators,":[80],"topologies,":[81],"sample":[82],"sizes":[83],"noise":[85],"intensities.":[86],"CONCLUSIONS:":[87],"The":[88],"benchmarking":[89],"framework":[90],"that":[91,116],"uses":[92],"various":[93],"highlights":[95],"specialization":[97],"some":[99],"toward":[101],"types":[103],"data.":[105],"As":[106],"result,":[108],"it":[109],"is":[110],"possible":[111],"identify":[113],"techniques":[115],"broad":[118],"overall":[119],"performances.":[120]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3}],"updated_date":"2026-08-24T07:32:12.397491","created_date":"2025-10-10T00:00:00"}
