{"id":"https://openalex.org/W2128374508","doi":"https://doi.org/10.1186/1471-2105-12-292","title":"Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study","display_name":"Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study","publication_year":2011,"publication_date":"2011-07-19","ids":{"openalex":"https://openalex.org/W2128374508","doi":"https://doi.org/10.1186/1471-2105-12-292","mag":"2128374508","pmid":"https://pubmed.ncbi.nlm.nih.gov/21771321"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-292","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-292","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-292","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/counter/pdf/10.1186/1471-2105-12-292","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075151494","display_name":"Sabrina Hempel","orcid":"https://orcid.org/0000-0002-8398-4820"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]},{"id":"https://openalex.org/I60200437","display_name":"Potsdam Institute for Climate Impact Research","ror":"https://ror.org/03e8s1d88","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I60200437"]},{"id":"https://openalex.org/I176453806","display_name":"University of Potsdam","ror":"https://ror.org/03bnmw459","country_code":"DE","type":"education","lineage":["https://openalex.org/I176453806"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Sabrina Hempel","raw_affiliation_strings":["Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, Campus Golm, Karl-Liebknecht-Str. 24, D-14476 Potsdam, Germany. sabrina.donner@pik-potsdam.de","Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, Potsdam, Germany","Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany","Department of Physics, Humboldt University of Berlin, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, Campus Golm, Karl-Liebknecht-Str. 24, D-14476 Potsdam, Germany. sabrina.donner@pik-potsdam.de","institution_ids":["https://openalex.org/I176453806"]},{"raw_affiliation_string":"Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, Potsdam, Germany","institution_ids":["https://openalex.org/I176453806"]},{"raw_affiliation_string":"Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany","institution_ids":["https://openalex.org/I60200437"]},{"raw_affiliation_string":"Department of Physics, Humboldt University of Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068624445","display_name":"Aneta Koseska","orcid":"https://orcid.org/0000-0003-4263-2340"},"institutions":[{"id":"https://openalex.org/I176453806","display_name":"University of Potsdam","ror":"https://ror.org/03bnmw459","country_code":"DE","type":"education","lineage":["https://openalex.org/I176453806"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Aneta Koseska","raw_affiliation_strings":["Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, Campus Golm, Karl-Liebknecht-Str. 24, D-14476, Potsdam, Germany","Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, Potsdam, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, Campus Golm, Karl-Liebknecht-Str. 24, D-14476, Potsdam, Germany","institution_ids":["https://openalex.org/I176453806"]},{"raw_affiliation_string":"Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, Potsdam, Germany","institution_ids":["https://openalex.org/I176453806"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059658943","display_name":"Zoran Nikoloski","orcid":"https://orcid.org/0000-0003-2671-6763"},"institutions":[{"id":"https://openalex.org/I176453806","display_name":"University of Potsdam","ror":"https://ror.org/03bnmw459","country_code":"DE","type":"education","lineage":["https://openalex.org/I176453806"]},{"id":"https://openalex.org/I4210105972","display_name":"Max Planck Institute of Molecular Plant Physiology","ror":"https://ror.org/01fbde567","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210105972"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Zoran Nikoloski","raw_affiliation_strings":["Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 25, D-14476, Potsdam, Germany","Systems Biology and Mathematical Modeling Group, Max Planck Institute for Molecular Plant Physiology, Am M\u00fchlenberg 1, D-14476, Potsdam, Germany","Systems Biology and Mathematical Modeling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany","Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 25, D-14476, Potsdam, Germany","institution_ids":["https://openalex.org/I176453806"]},{"raw_affiliation_string":"Systems Biology and Mathematical Modeling Group, Max Planck Institute for Molecular Plant Physiology, Am M\u00fchlenberg 1, D-14476, Potsdam, Germany","institution_ids":["https://openalex.org/I4210105972"]},{"raw_affiliation_string":"Systems Biology and Mathematical Modeling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany","institution_ids":["https://openalex.org/I4210105972"]},{"raw_affiliation_string":"Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany","institution_ids":["https://openalex.org/I176453806"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085207296","display_name":"J\u00fcrgen Kurths","orcid":"https://orcid.org/0000-0002-5926-4276"},"institutions":[{"id":"https://openalex.org/I195460627","display_name":"University of Aberdeen","ror":"https://ror.org/016476m91","country_code":"GB","type":"education","lineage":["https://openalex.org/I195460627"]},{"id":"https://openalex.org/I4210103223","display_name":"Ambulatory Rehabilitation Center Berlin Adlershof","ror":"https://ror.org/0196d3y13","country_code":"DE","type":"other","lineage":["https://openalex.org/I4210103223"]},{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]},{"id":"https://openalex.org/I60200437","display_name":"Potsdam Institute for Climate Impact Research","ror":"https://ror.org/03e8s1d88","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I60200437"]}],"countries":["DE","GB"],"is_corresponding":false,"raw_author_name":"J\u00fcrgen Kurths","raw_affiliation_strings":["Department of Physics, Humboldt University of Berlin, Campus Adlershof, Newtonstr. 15, D-12489, Berlin, Germany","Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB243UE, UK","Potsdam Institute for Climate Impact Research (PIK), Telegraphenberg A 31, D-14473, Potsdam, Germany","Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, UK","Department of Physics, Humboldt University of Berlin, Berlin, Germany","Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Humboldt University of Berlin, Campus Adlershof, Newtonstr. 15, D-12489, Berlin, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I4210103223"]},{"raw_affiliation_string":"Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB243UE, UK","institution_ids":["https://openalex.org/I195460627"]},{"raw_affiliation_string":"Potsdam Institute for Climate Impact Research (PIK), Telegraphenberg A 31, D-14473, Potsdam, Germany","institution_ids":["https://openalex.org/I60200437"]},{"raw_affiliation_string":"Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, UK","institution_ids":["https://openalex.org/I195460627"]},{"raw_affiliation_string":"Department of Physics, Humboldt University of Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany","institution_ids":["https://openalex.org/I60200437"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5075151494"],"corresponding_institution_ids":["https://openalex.org/I176453806","https://openalex.org/I39343248","https://openalex.org/I60200437"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.7934,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.91085879,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"292","last_page":"292"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7813000082969666,"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":0.7813000082969666,"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":0.0885000005364418,"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":0.026599999517202377,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.724621057510376},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6473814249038696},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6101706027984619},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5898695588111877},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.5474714040756226},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.4806341230869293},{"id":"https://openalex.org/keywords/time-series","display_name":"Time series","score":0.472102552652359},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47141003608703613},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.42534273862838745},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4157336950302124},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40852195024490356},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3455718457698822},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2902829051017761},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24946993589401245},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.16782993078231812},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14704978466033936}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.724621057510376},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6473814249038696},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6101706027984619},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5898695588111877},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.5474714040756226},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.4806341230869293},{"id":"https://openalex.org/C151406439","wikidata":"https://www.wikidata.org/wiki/Q186588","display_name":"Time series","level":2,"score":0.472102552652359},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47141003608703613},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.42534273862838745},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4157336950302124},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40852195024490356},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3455718457698822},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2902829051017761},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24946993589401245},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.16782993078231812},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14704978466033936},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"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/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"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":10,"locations":[{"id":"doi:10.1186/1471-2105-12-292","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-292","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-292","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:21771321","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21771321","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":null},{"id":"pmh:oai:aura.abdn.ac.uk:2164/3680","is_oa":false,"landing_page_url":"http://hdl.handle.net/2164/3680","pdf_url":null,"source":{"id":"https://openalex.org/S4306400966","display_name":"Aberdeen University Research Archive (Aberdeen University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I195460627","host_organization_name":"University of Aberdeen","host_organization_lineage":["https://openalex.org/I195460627"],"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":"Journal article"},{"id":"pmh:oai:doaj.org/article:6bec60b17a11461099441da8181d92d8","is_oa":false,"landing_page_url":"https://doaj.org/article/6bec60b17a11461099441da8181d92d8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Bioinformatics, Vol 12, Iss 1, p 292 (2011)","raw_type":"article"},{"id":"pmh:oai:edoc.mpg.de:586865","is_oa":false,"landing_page_url":"http://edoc.mpg.de/586865","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","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":"BMC Bioinformatics, v.12 (2011)","raw_type":"Article"},{"id":"pmh:oai:escidoc.org:escidoc:2341879","is_oa":false,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-002B-43D2-3","pdf_url":null,"source":{"id":"https://openalex.org/S7407052962","display_name":"Max Planck Digital Library","issn_l":null,"issn":[],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2165553","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3161045","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:kobv.de-opus4-uni-potsdam:36734","is_oa":false,"landing_page_url":"https://publishup.uni-potsdam.de/frontdoor/index/index/docId/36734","pdf_url":null,"source":{"id":"https://openalex.org/S4306400594","display_name":"publish.UP (University of Potsdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I176453806","host_organization_name":"University of Potsdam","host_organization_lineage":["https://openalex.org/I176453806"],"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":"doc-type:article"},{"id":"pmh:oai:publications.pik-potsdam.de:item_16960","is_oa":true,"landing_page_url":"https://publications.pik-potsdam.de/pubman/item/item_16960","pdf_url":null,"source":{"id":"https://openalex.org/S4306400891","display_name":"Publication Database PIK (Potsdam Institute for Climate Impact Research (PIK))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I60200437","host_organization_name":"Potsdam Institute for Climate Impact Research","host_organization_lineage":["https://openalex.org/I60200437"],"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","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.mpg.de:item_1814872","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0014-21C6-B","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":"BMC Bioinformatics","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-292","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-292","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-292","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/G1698894427","display_name":null,"funder_award_id":"0313924","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128374508.pdf","grobid_xml":"https://content.openalex.org/works/W2128374508.grobid-xml"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W1571301392","https://openalex.org/W1574019121","https://openalex.org/W1599502102","https://openalex.org/W1636081627","https://openalex.org/W1837652160","https://openalex.org/W1851422093","https://openalex.org/W1940678971","https://openalex.org/W1974183961","https://openalex.org/W1981547652","https://openalex.org/W1986092967","https://openalex.org/W1987981748","https://openalex.org/W1989037929","https://openalex.org/W1989921625","https://openalex.org/W1992165506","https://openalex.org/W1996264210","https://openalex.org/W2001983753","https://openalex.org/W2008107402","https://openalex.org/W2013160881","https://openalex.org/W2025210087","https://openalex.org/W2027607571","https://openalex.org/W2036363967","https://openalex.org/W2036543089","https://openalex.org/W2054138074","https://openalex.org/W2056780622","https://openalex.org/W2070672503","https://openalex.org/W2076927242","https://openalex.org/W2078149659","https://openalex.org/W2078450879","https://openalex.org/W2081681829","https://openalex.org/W2087039607","https://openalex.org/W2102471334","https://openalex.org/W2107092366","https://openalex.org/W2108400301","https://openalex.org/W2108675631","https://openalex.org/W2110699703","https://openalex.org/W2114518254","https://openalex.org/W2114937915","https://openalex.org/W2121695897","https://openalex.org/W2125631472","https://openalex.org/W2126602684","https://openalex.org/W2128160875","https://openalex.org/W2128937741","https://openalex.org/W2132585078","https://openalex.org/W2132663737","https://openalex.org/W2133241531","https://openalex.org/W2134239854","https://openalex.org/W2134586291","https://openalex.org/W2134923278","https://openalex.org/W2142635246","https://openalex.org/W2145068337","https://openalex.org/W2145126338","https://openalex.org/W2145590522","https://openalex.org/W2150780222","https://openalex.org/W2150926065","https://openalex.org/W2152482800","https://openalex.org/W2155205047","https://openalex.org/W2156282037","https://openalex.org/W2157121418","https://openalex.org/W2157523980","https://openalex.org/W2158698691","https://openalex.org/W2160513989","https://openalex.org/W2161920970","https://openalex.org/W2161922735","https://openalex.org/W2170040895","https://openalex.org/W2482198018","https://openalex.org/W3149745985","https://openalex.org/W3154566661"],"related_works":["https://openalex.org/W2180954594","https://openalex.org/W2052835778","https://openalex.org/W2049003611","https://openalex.org/W2156421048","https://openalex.org/W2135896045","https://openalex.org/W2884256268","https://openalex.org/W2171763327","https://openalex.org/W2511617859","https://openalex.org/W3108451992","https://openalex.org/W2031892952"],"abstract_inverted_index":{"BACKGROUND:":[0],"Inferring":[1],"regulatory":[2,14,103,144,222,262,302],"interactions":[3,104],"between":[4],"genes":[5,55],"from":[6,147,191,304],"transcriptomics":[7,168],"time-resolved":[8,62],"data,":[9,93],"yielding":[10],"reverse":[11,69,317],"engineered":[12],"gene":[13,143,301],"networks,":[15,263],"is":[16,279],"of":[17,44,53,64,79,97,101,121,124,133,242,261,291,300,314,332,342,353],"paramount":[18],"importance":[19],"to":[20,28,89,183,186,235,281,339],"systems":[21],"biology":[22],"and":[23,42,59,77,94,127,155,160,178,205,212,294,375],"bioinformatics":[24],"studies.":[25],"Accurate":[26],"methods":[27,80],"address":[29],"this":[30,274],"problem":[31,109],"can":[32,319],"ultimately":[33],"provide":[34],"a":[35,71,106,122,284,288],"deeper":[36],"insight":[37],"into":[38],"the":[39,45,50,65,68,75,99,102,117,131,134,174,202,217,226,240,247,268,330,340,350,354,361,384],"complexity,":[40],"behavior,":[41],"functions":[43],"underlying":[46],"biological":[47],"systems.":[48],"However,":[49],"large":[51],"number":[52,241],"interacting":[54],"coupled":[56],"with":[57,110,367],"short":[58,90,167,192,269,305],"often":[60],"noisy":[61],"read-outs":[63],"system":[66],"renders":[67],"engineering":[70,318],"challenging":[72],"task.":[73],"Therefore,":[74],"development":[76],"assessment":[78],"which":[81,138,162,346],"are":[82,139,163,327,383],"computationally":[83],"efficient,":[84],"robust":[85],"against":[86],"noise,":[87],"applicable":[88],"time":[91,148,169,193,270,306],"series":[92,149,194,271,307],"preferably":[95],"capable":[96],"reconstructing":[98],"directionality":[100],"remains":[105],"pressing":[107],"research":[108],"valuable":[111,237],"applications.":[112],"RESULTS:":[113],"Here":[114],"we":[115,153,358],"perform":[116],"largest":[118],"systematic":[119],"analysis":[120],"set":[123],"similarity":[125,292,344],"measures":[126,159,177,215,293,325,345,370,378],"scoring":[128,180,228,295,364],"schemes":[129,161,181,296],"within":[130],"scope":[132],"relevance":[135],"network":[136,145],"approach":[137],"commonly":[140],"used":[141,258],"for":[142,166,286,298,316],"reconstruction":[146,299],"data.":[150,308,356],"In":[151,224],"addition,":[152,225],"define":[154],"analyze":[156],"several":[157],"novel":[158],"particularly":[164],"suitable":[165,297,386],"series.":[170],"We":[171,309],"also":[172],"compare":[173],"considered":[175],"21":[176],"6":[179],"according":[182],"their":[184],"ability":[185],"correctly":[187],"reconstruct":[188],"such":[189],"networks":[190,303],"data":[195],"by":[196,230],"calculating":[197],"summary":[198],"statistics":[199],"based":[200,214,369,377],"on":[201,267],"corresponding":[203],"specificity":[204],"sensitivity.":[206],"Our":[207,277],"results":[208],"demonstrate":[209],"that":[210,311,326,360],"rank":[211,376],"symbol":[213,368],"have":[216],"highest":[218],"performance":[219,266],"in":[220,238,259,273,329,337],"inferring":[221],"interactions.":[223,245],"proposed":[227],"scheme":[229,365],"asymmetric":[231,362],"weighting":[232,363],"has":[233],"shown":[234],"be":[236,320],"reducing":[239],"false":[243],"positive":[244],"On":[246],"other":[248],"hand,":[249],"Granger":[250],"causality":[251],"as":[252,254,283],"well":[253],"information-theoretic":[255],"measures,":[256],"frequently":[257],"inference":[260],"show":[264,310],"low":[265,372],"analyzed":[272],"study.":[275],"CONCLUSIONS:":[276],"study":[278,331],"intended":[280],"serve":[282],"guide":[285],"choosing":[287],"particular":[289],"combination":[290],"further":[312],"improvement":[313],"algorithms":[315],"obtained":[321],"if":[322],"one":[323],"considers":[324],"rooted":[328],"symbolic":[333],"dynamics":[334],"or":[335],"ranks,":[336],"contrast":[338],"application":[341],"common":[343],"do":[347],"not":[348],"consider":[349],"temporal":[351],"character":[352],"employed":[355],"Moreover,":[357],"establish":[359],"together":[366],"(for":[371,379],"noise":[373,381],"level)":[374,382],"high":[380],"most":[385],"choices.":[387]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":9}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}