{"id":"https://openalex.org/W2328532852","doi":"https://doi.org/10.1186/s12859-016-0964-2","title":"CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction","display_name":"CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction","publication_year":2016,"publication_date":"2016-04-08","ids":{"openalex":"https://openalex.org/W2328532852","doi":"https://doi.org/10.1186/s12859-016-0964-2","mag":"2328532852","pmid":"https://pubmed.ncbi.nlm.nih.gov/27059647"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-0964-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0964-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-0964-2","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/s12859-016-0964-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078555784","display_name":"Gianfranco Politano","orcid":"https://orcid.org/0000-0001-5268-9899"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianfranco Politano","raw_affiliation_strings":["Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032327963","display_name":"Francesca Orso","orcid":"https://orcid.org/0000-0003-4706-6464"},"institutions":[{"id":"https://openalex.org/I4210096850","display_name":"Accademia Albertina delle Belle Arti","ror":"https://ror.org/00se00q44","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210096850"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesca Orso","raw_affiliation_strings":["Center for Complex Systems in Molecular Biology and Medicine, Via Accademia Albertina, 13, Torino, 10123, Italy","Dept. Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza, 52, Torino, 10126, Italy","Molecular Biotechnology Center (MBC), Via Nizza, 52, Torino, 10126, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Systems in Molecular Biology and Medicine, Via Accademia Albertina, 13, Torino, 10123, Italy","institution_ids":["https://openalex.org/I4210096850"]},{"raw_affiliation_string":"Dept. Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza, 52, Torino, 10126, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Molecular Biotechnology Center (MBC), Via Nizza, 52, Torino, 10126, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032027734","display_name":"Monica Raimo","orcid":"https://orcid.org/0000-0003-2970-3220"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Monica Raimo","raw_affiliation_strings":["Dept. Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza, 52, Torino, 10126, Italy","Molecular Biotechnology Center (MBC), Via Nizza, 52, Torino, 10126, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza, 52, Torino, 10126, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Molecular Biotechnology Center (MBC), Via Nizza, 52, Torino, 10126, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030177680","display_name":"Alfredo Benso","orcid":"https://orcid.org/0000-0003-3433-7739"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alfredo Benso","raw_affiliation_strings":["Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065582630","display_name":"Alessandro Savino","orcid":"https://orcid.org/0000-0003-0529-7950"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessandro Savino","raw_affiliation_strings":["Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012376450","display_name":"Daniela Taverna","orcid":"https://orcid.org/0000-0002-6365-527X"},"institutions":[{"id":"https://openalex.org/I4210096850","display_name":"Accademia Albertina delle Belle Arti","ror":"https://ror.org/00se00q44","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210096850"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Daniela Taverna","raw_affiliation_strings":["Center for Complex Systems in Molecular Biology and Medicine, Via Accademia Albertina, 13, Torino, 10123, Italy","Dept. Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza, 52, Torino, 10126, Italy","Molecular Biotechnology Center (MBC), Via Nizza, 52, Torino, 10126, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Systems in Molecular Biology and Medicine, Via Accademia Albertina, 13, Torino, 10123, Italy","institution_ids":["https://openalex.org/I4210096850"]},{"raw_affiliation_string":"Dept. Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza, 52, Torino, 10126, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Molecular Biotechnology Center (MBC), Via Nizza, 52, Torino, 10126, Italy","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026593274","display_name":"Stefano Di Carlo","orcid":"https://orcid.org/0000-0002-7512-5356"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Stefano Di Carlo","raw_affiliation_strings":["Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy. stefano.dicarlo@polito.it","Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy. stefano.dicarlo@polito.it","institution_ids":["https://openalex.org/I177477856"]},{"raw_affiliation_string":"Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129, Italy","institution_ids":["https://openalex.org/I177477856"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5026593274"],"corresponding_institution_ids":["https://openalex.org/I177477856"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.4428,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.81667859,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"157","last_page":"157"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.31679999828338623,"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":0.31679999828338623,"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":0.18240000307559967,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.15839999914169312,"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/signal-transduction","display_name":"Signal transduction","score":0.691368579864502},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6496134996414185},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5949939489364624},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.5703266859054565},{"id":"https://openalex.org/keywords/regulator","display_name":"Regulator","score":0.5407251715660095},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5352697372436523},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.502415657043457},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.47390520572662354},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4300926625728607},{"id":"https://openalex.org/keywords/transduction","display_name":"Transduction (biophysics)","score":0.4163843095302582},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40590494871139526},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32861465215682983},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29975879192352295},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2719312310218811}],"concepts":[{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.691368579864502},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6496134996414185},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5949939489364624},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.5703266859054565},{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.5407251715660095},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5352697372436523},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.502415657043457},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.47390520572662354},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4300926625728607},{"id":"https://openalex.org/C15152581","wikidata":"https://www.wikidata.org/wiki/Q7833966","display_name":"Transduction (biophysics)","level":2,"score":0.4163843095302582},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40590494871139526},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32861465215682983},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29975879192352295},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2719312310218811},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D008545","descriptor_name":"Melanoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008545","descriptor_name":"Melanoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008545","descriptor_name":"Melanoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-016-0964-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0964-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-0964-2","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:27059647","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27059647","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:europepmc.org:3795992","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4826505","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:iris.unito.it:2318/1596836","is_oa":true,"landing_page_url":"http://hdl.handle.net/2318/1596836","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:porto.polito.it:2641083","is_oa":true,"landing_page_url":"http://porto.polito.it/2641083/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402038","display_name":"PORTO Publications Open Repository TOrino (Politecnico di Torino)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177477856","host_organization_name":"Politecnico di Torino","host_organization_lineage":["https://openalex.org/I177477856"],"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":"ISSN:1471-2105","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-0964-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0964-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-0964-2","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/G1680515285","display_name":null,"funder_award_id":"IG2013-14201DT","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G3557565834","display_name":null,"funder_award_id":"IG-2010","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G3799009266","display_name":null,"funder_award_id":"2008.1054(DT), AIRC2010, 2013 (IG2010-10104DT; IG2013-14201DT)","funder_id":"https://openalex.org/F4320309746","funder_display_name":"Compagnia di San Paolo"},{"id":"https://openalex.org/G385539970","display_name":null,"funder_award_id":"(PRIN 2010)","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G4113219329","display_name":null,"funder_award_id":"IG 2013","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G5899702863","display_name":null,"funder_award_id":"PRIN 2010","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G8149227498","display_name":null,"funder_award_id":"2008.1054","funder_id":"https://openalex.org/F4320309746","funder_display_name":"Compagnia di San Paolo"}],"funders":[{"id":"https://openalex.org/F4320309746","display_name":"Compagnia di San Paolo","ror":"https://ror.org/00d1b1c41"},{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2328532852.pdf","grobid_xml":"https://content.openalex.org/works/W2328532852.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W37105655","https://openalex.org/W1492901739","https://openalex.org/W1518330963","https://openalex.org/W1529730227","https://openalex.org/W1530814332","https://openalex.org/W1644749979","https://openalex.org/W1926429076","https://openalex.org/W1972129511","https://openalex.org/W1975437957","https://openalex.org/W1987067655","https://openalex.org/W1992960340","https://openalex.org/W1993299801","https://openalex.org/W1994107017","https://openalex.org/W2002554381","https://openalex.org/W2005946215","https://openalex.org/W2008126077","https://openalex.org/W2010134474","https://openalex.org/W2013073774","https://openalex.org/W2014411088","https://openalex.org/W2017298826","https://openalex.org/W2019346039","https://openalex.org/W2022725285","https://openalex.org/W2027987606","https://openalex.org/W2032699123","https://openalex.org/W2040191060","https://openalex.org/W2050869737","https://openalex.org/W2053003053","https://openalex.org/W2053757597","https://openalex.org/W2053835153","https://openalex.org/W2060985970","https://openalex.org/W2061425021","https://openalex.org/W2071385561","https://openalex.org/W2073307618","https://openalex.org/W2078744455","https://openalex.org/W2081725177","https://openalex.org/W2082102894","https://openalex.org/W2083381199","https://openalex.org/W2087025873","https://openalex.org/W2096217729","https://openalex.org/W2098302826","https://openalex.org/W2101703004","https://openalex.org/W2101900454","https://openalex.org/W2102560431","https://openalex.org/W2102914855","https://openalex.org/W2103594573","https://openalex.org/W2104009289","https://openalex.org/W2108076410","https://openalex.org/W2109731329","https://openalex.org/W2119873809","https://openalex.org/W2119966479","https://openalex.org/W2120965272","https://openalex.org/W2121412124","https://openalex.org/W2123215282","https://openalex.org/W2126969584","https://openalex.org/W2127254281","https://openalex.org/W2128307263","https://openalex.org/W2131532450","https://openalex.org/W2134814029","https://openalex.org/W2139002825","https://openalex.org/W2147470531","https://openalex.org/W2152946802","https://openalex.org/W2153624566","https://openalex.org/W2158989286","https://openalex.org/W2159675211","https://openalex.org/W2161149887","https://openalex.org/W2165065179","https://openalex.org/W2170688212","https://openalex.org/W2305254786"],"related_works":["https://openalex.org/W2354064740","https://openalex.org/W2890433954","https://openalex.org/W2389923937","https://openalex.org/W2156421048","https://openalex.org/W2135896045","https://openalex.org/W2884256268","https://openalex.org/W2171763327","https://openalex.org/W3108451992","https://openalex.org/W2511617859","https://openalex.org/W2031892952"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biological":[1],"research":[2],"increasingly":[3],"relies":[4],"on":[5,98,123,147],"network":[6],"models":[7],"to":[8,26,42,49,116,139],"study":[9,163,201],"complex":[10,82],"phenomena.":[11],"Signal":[12],"Transduction":[13],"Pathways":[14],"are":[15,47,168],"molecular":[16],"circuits":[17],"that":[18,167],"model":[19],"how":[20],"cells":[21],"receive,":[22],"process,":[23],"and":[24,64,67,74,128,132,176,205,211],"respond":[25],"information":[27],"from":[28,194],"the":[29,34,40,81,152,155,181,216],"environment":[30],"providing":[31],"snapshots":[32],"of":[33,39,62,85,92,101,154,164,183,190,218],"overall":[35],"cell":[36],"dynamics.":[37],"Most":[38],"attempts":[41],"reconstruct":[43],"signal":[44,103,119,185],"transduction":[45,104,120,186],"pathways":[46,121,187],"limited":[48],"single":[50,60],"regulator":[51,63],"networks":[52,57],"including":[53,129],"only":[54],"genes/proteins.":[55],"However,":[56],"involving":[58],"a":[59,86,90,111,162,198],"type":[61,100],"neglecting":[65],"transcriptional":[66],"post-transcriptional":[68],"regulations":[69],"mediated":[70],"by":[71],"transcription":[72],"factors":[73],"microRNAs,":[75],"respectively,":[76],"may":[77],"not":[78,145],"fully":[79],"reveal":[80],"regulatory":[83,126],"mechanisms":[84],"cell.":[87],"We":[88,107],"observed":[89],"lack":[91],"computational":[93],"instruments":[94],"supporting":[95],"explorative":[96],"analysis":[97],"this":[99,219],"three-component":[102,118],"pathways.":[105],"RESULTS:":[106],"have":[108,158,202],"developed":[109],"CyTRANSFINDER,":[110],"new":[112],"Cytoscape":[113],"plugin":[114,156],"able":[115],"infer":[117],"based":[122],"user":[124],"defined":[125],"patterns":[127],"miRNAs,":[130],"TFs":[131],"genes.":[133,191],"Since":[134],"CyTRANSFINDER":[135,179],"has":[136],"been":[137,203],"designed":[138],"support":[140],"exploratory":[141,223],"analysis,":[142],"it":[143,160],"does":[144],"rely":[146],"expression":[148],"data.":[149],"To":[150],"show":[151],"potential":[153,217],"we":[157],"applied":[159],"in":[161,171,197],"two":[165],"miRNAs":[166],"particularly":[169],"relevant":[170],"human":[172],"melanoma":[173],"progression,":[174],"miR-146a":[175],"miR-214.":[177],"CONCLUSIONS:":[178],"supports":[180],"reconstruction":[182],"small":[184],"among":[188],"groups":[189],"Results":[192],"obtained":[193],"its":[195],"use":[196],"real":[199],"case":[200],"analyzed":[204],"validated":[206],"through":[207],"both":[208],"literature":[209],"data":[210],"preliminary":[212],"wet-lab":[213],"experiments,":[214],"showing":[215],"tool":[220],"when":[221],"performing":[222],"analysis.":[224]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
