{"id":"https://openalex.org/W2888151223","doi":"https://doi.org/10.3390/make1010008","title":"Inference of Genome-Scale Gene Regulatory Networks: Are There Differences in Biological and Clinical Validations?","display_name":"Inference of Genome-Scale Gene Regulatory Networks: Are There Differences in Biological and Clinical Validations?","publication_year":2018,"publication_date":"2018-08-22","ids":{"openalex":"https://openalex.org/W2888151223","doi":"https://doi.org/10.3390/make1010008","mag":"2888151223"},"language":"en","primary_location":{"id":"doi:10.3390/make1010008","is_oa":true,"landing_page_url":"https://doi.org/10.3390/make1010008","pdf_url":"https://www.mdpi.com/2504-4990/1/1/8/pdf?version=1545200908","source":{"id":"https://openalex.org/S4210213891","display_name":"Machine Learning and Knowledge Extraction","issn_l":"2504-4990","issn":["2504-4990"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning and Knowledge Extraction","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2504-4990/1/1/8/pdf?version=1545200908","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057625030","display_name":"Frank Emmert\u2010Streib","orcid":"https://orcid.org/0000-0003-0745-5641"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Frank Emmert-Streib","raw_affiliation_strings":["Institute of Biosciences and Medical Technology, 33520 Tampere, Finland","Predictive Medicine and Data Analytics Lab, Department of Signal Processing, Tampere University of Technology, 33720 Tampere, Finland"],"raw_orcid":"https://orcid.org/0000-0003-0745-5641","affiliations":[{"raw_affiliation_string":"Institute of Biosciences and Medical Technology, 33520 Tampere, Finland","institution_ids":[]},{"raw_affiliation_string":"Predictive Medicine and Data Analytics Lab, Department of Signal Processing, Tampere University of Technology, 33720 Tampere, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044244385","display_name":"Matthias Dehmer","orcid":"https://orcid.org/0000-0001-8454-5857"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]},{"id":"https://openalex.org/I4210114246","display_name":"UMIT - Private Universit\u00e4t f\u00fcr Gesundheitswissenschaften, Medizinische Informatik und Technik","ror":"https://ror.org/02d0kps43","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210114246"]},{"id":"https://openalex.org/I4210136249","display_name":"University of Applied Sciences Upper Austria","ror":"https://ror.org/03jqp6d56","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210136249"]}],"countries":["AT","CN"],"is_corresponding":false,"raw_author_name":"Matthias Dehmer","raw_affiliation_strings":["College of Computer and Control Engineering, Nankai University, Tianjin 300071, China","Department of Mechatronics and Biomedical Computer Science, University for Health Sciences, Medical Informatics and Technology (UMIT), 6060 Hall in Tyrol, Austria","Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Steyr Campus, 4400 Steyr, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Nankai University, Tianjin 300071, China","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"Department of Mechatronics and Biomedical Computer Science, University for Health Sciences, Medical Informatics and Technology (UMIT), 6060 Hall in Tyrol, Austria","institution_ids":["https://openalex.org/I4210114246"]},{"raw_affiliation_string":"Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Steyr Campus, 4400 Steyr, Austria","institution_ids":["https://openalex.org/I4210136249"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5057625030"],"corresponding_institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.2793,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.57615117,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"1","issue":"1","first_page":"138","last_page":"148"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9984999895095825,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9984999895095825,"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":0.9968000054359436,"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":0.9904000163078308,"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":0.7227659225463867},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6977472901344299},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6494619846343994},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.613241970539093},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5581331849098206},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5273191332817078},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5025370121002197},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4882948398590088},{"id":"https://openalex.org/keywords/meaning","display_name":"Meaning (existential)","score":0.42381128668785095},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4212483763694763},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4055395722389221},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35989564657211304},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3370528817176819},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.26563355326652527},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23866525292396545},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.201213538646698},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.1951521635055542}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7227659225463867},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6977472901344299},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6494619846343994},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.613241970539093},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5581331849098206},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5273191332817078},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5025370121002197},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4882948398590088},{"id":"https://openalex.org/C2780876879","wikidata":"https://www.wikidata.org/wiki/Q3054749","display_name":"Meaning (existential)","level":2,"score":0.42381128668785095},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4212483763694763},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4055395722389221},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35989564657211304},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3370528817176819},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.26563355326652527},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23866525292396545},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.201213538646698},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.1951521635055542},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/make1010008","is_oa":true,"landing_page_url":"https://doi.org/10.3390/make1010008","pdf_url":"https://www.mdpi.com/2504-4990/1/1/8/pdf?version=1545200908","source":{"id":"https://openalex.org/S4210213891","display_name":"Machine Learning and Knowledge Extraction","issn_l":"2504-4990","issn":["2504-4990"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning and Knowledge Extraction","raw_type":"journal-article"},{"id":"pmh:oai:mdpi.com:/2504-4990/1/1/8/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/make1010008","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Machine Learning and Knowledge Extraction; Volume 1; Issue 1; Pages: 138-148","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/make1010008","is_oa":true,"landing_page_url":"https://doi.org/10.3390/make1010008","pdf_url":"https://www.mdpi.com/2504-4990/1/1/8/pdf?version=1545200908","source":{"id":"https://openalex.org/S4210213891","display_name":"Machine Learning and Knowledge Extraction","issn_l":"2504-4990","issn":["2504-4990"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning and Knowledge Extraction","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.5699999928474426,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2888151223.pdf","grobid_xml":"https://content.openalex.org/works/W2888151223.grobid-xml"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W618190765","https://openalex.org/W1494192115","https://openalex.org/W1524326598","https://openalex.org/W1826377913","https://openalex.org/W1851422093","https://openalex.org/W1975032412","https://openalex.org/W1977077086","https://openalex.org/W1979200257","https://openalex.org/W1991799786","https://openalex.org/W1994127362","https://openalex.org/W2003842689","https://openalex.org/W2005588132","https://openalex.org/W2005895632","https://openalex.org/W2010615446","https://openalex.org/W2011084855","https://openalex.org/W2013156169","https://openalex.org/W2019114939","https://openalex.org/W2020541351","https://openalex.org/W2025183726","https://openalex.org/W2025498302","https://openalex.org/W2026012474","https://openalex.org/W2026341138","https://openalex.org/W2034368202","https://openalex.org/W2043409309","https://openalex.org/W2049435858","https://openalex.org/W2050559302","https://openalex.org/W2052627308","https://openalex.org/W2065515536","https://openalex.org/W2066359255","https://openalex.org/W2070030982","https://openalex.org/W2074360197","https://openalex.org/W2077350268","https://openalex.org/W2084709428","https://openalex.org/W2097255042","https://openalex.org/W2102461795","https://openalex.org/W2103903744","https://openalex.org/W2106292881","https://openalex.org/W2110699703","https://openalex.org/W2118923702","https://openalex.org/W2126038748","https://openalex.org/W2130656587","https://openalex.org/W2132245233","https://openalex.org/W2133036743","https://openalex.org/W2133984660","https://openalex.org/W2139997707","https://openalex.org/W2147566730","https://openalex.org/W2154135188","https://openalex.org/W2154947819","https://openalex.org/W2159567041","https://openalex.org/W2160317546","https://openalex.org/W2160450758","https://openalex.org/W2161409973","https://openalex.org/W2163480486","https://openalex.org/W2168909179","https://openalex.org/W2171898201","https://openalex.org/W2346811078","https://openalex.org/W2537623931","https://openalex.org/W2557154264","https://openalex.org/W2782454362","https://openalex.org/W2784588023","https://openalex.org/W2807378196","https://openalex.org/W2917375902","https://openalex.org/W2919115771","https://openalex.org/W4205408915","https://openalex.org/W4251617844","https://openalex.org/W6653050037","https://openalex.org/W6660265615"],"related_works":["https://openalex.org/W2155492529","https://openalex.org/W4252504573","https://openalex.org/W2560421304","https://openalex.org/W2950199998","https://openalex.org/W4385510321","https://openalex.org/W2101315668","https://openalex.org/W2951387065","https://openalex.org/W2134575910","https://openalex.org/W15348386","https://openalex.org/W2131550814"],"abstract_inverted_index":{"Causal":[0],"networks,":[1],"e.g.,":[2],"gene":[3,9],"regulatory":[4],"networks":[5],"(GRNs)":[6],"inferred":[7],"from":[8],"expression":[10],"data,":[11],"contain":[12],"a":[13,43,78,82],"wealth":[14],"of":[15,67,84,91],"information":[16,101],"but":[17],"are":[18],"defying":[19],"simple,":[20],"straightforward":[21],"and":[22,34,39,55,69,105],"low-budget":[23],"experimental":[24],"validations.":[25,41],"In":[26],"this":[27,32,85],"paper,":[28],"we":[29,87],"elaborate":[30],"on":[31],"problem":[33,83],"discuss":[35],"distinctions":[36],"between":[37,52],"biological":[38,54,104],"clinical":[40,56,106],"As":[42],"result,":[44],"validation":[45],"differences":[46,51],"for":[47,103],"GRNs":[48,72],"reflect":[49],"known":[50],"basic":[53],"research":[57],"questions":[58],"making":[59],"the":[60,65,89,92,100],"validations":[61,107],"context":[62],"specific.":[63],"Hence,":[64],"meaning":[66],"biologically":[68],"clinically":[70],"meaningful":[71],"can":[73],"be":[74],"very":[75],"different.":[76],"For":[77],"concerted":[79],"approach":[80],"to":[81],"size,":[86],"suggest":[88],"establishment":[90],"HUMAN":[93],"GENE":[94],"REGULATORY":[95],"NETWORK":[96],"PROJECT":[97],"which":[98],"provides":[99],"required":[102],"alike.":[108]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2018-08-31T00:00:00"}