{"id":"https://openalex.org/W1966667678","doi":"https://doi.org/10.1186/1471-2105-10-444","title":"IRIS: a method for reverse engineering of regulatory relations in gene networks","display_name":"IRIS: a method for reverse engineering of regulatory relations in gene networks","publication_year":2009,"publication_date":"2009-12-01","ids":{"openalex":"https://openalex.org/W1966667678","doi":"https://doi.org/10.1186/1471-2105-10-444","mag":"1966667678","pmid":"https://pubmed.ncbi.nlm.nih.gov/20030818"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-444","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-444","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-444","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/10.1186/1471-2105-10-444","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087559200","display_name":"Sandro Morganella","orcid":"https://orcid.org/0000-0003-4050-0985"},"institutions":[{"id":"https://openalex.org/I16337185","display_name":"University of Sannio","ror":"https://ror.org/04vc81p87","country_code":"IT","type":"education","lineage":["https://openalex.org/I16337185"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sandro Morganella","raw_affiliation_strings":["Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy. morganellaalx@gmail.com","Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy. morganellaalx@gmail.com","institution_ids":["https://openalex.org/I16337185"]},{"raw_affiliation_string":"Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy","institution_ids":["https://openalex.org/I16337185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009018743","display_name":"Pietro Zoppoli","orcid":"https://orcid.org/0000-0002-7860-9655"},"institutions":[{"id":"https://openalex.org/I16337185","display_name":"University of Sannio","ror":"https://ror.org/04vc81p87","country_code":"IT","type":"education","lineage":["https://openalex.org/I16337185"]},{"id":"https://openalex.org/I4210115745","display_name":"Biogem","ror":"https://ror.org/01ymr5447","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I2801626668","https://openalex.org/I4210115745"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Pietro Zoppoli","raw_affiliation_strings":["Biogem s.c.a.r.l., Ariano Irpino (Avellino), Italy","Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biogem s.c.a.r.l., Ariano Irpino (Avellino), Italy","institution_ids":["https://openalex.org/I4210115745"]},{"raw_affiliation_string":"Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy","institution_ids":["https://openalex.org/I16337185"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085527072","display_name":"Michele Ceccarelli","orcid":"https://orcid.org/0000-0002-4702-6617"},"institutions":[{"id":"https://openalex.org/I16337185","display_name":"University of Sannio","ror":"https://ror.org/04vc81p87","country_code":"IT","type":"education","lineage":["https://openalex.org/I16337185"]},{"id":"https://openalex.org/I4210115745","display_name":"Biogem","ror":"https://ror.org/01ymr5447","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I2801626668","https://openalex.org/I4210115745"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Michele Ceccarelli","raw_affiliation_strings":["Biogem s.c.a.r.l., Ariano Irpino (Avellino), Italy","Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biogem s.c.a.r.l., Ariano Irpino (Avellino), Italy","institution_ids":["https://openalex.org/I4210115745"]},{"raw_affiliation_string":"Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy","institution_ids":["https://openalex.org/I16337185"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.405,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.6190017,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"10","issue":"1","first_page":"444","last_page":"444"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9660999774932861,"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":0.9660999774932861,"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":0.019899999722838402,"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":0.004600000102072954,"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":0.7314369678497314},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6485282778739929},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6323007345199585},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5129584670066833},{"id":"https://openalex.org/keywords/reverse-engineering","display_name":"Reverse engineering","score":0.48068079352378845},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47451895475387573},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.45827317237854004},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45492616295814514},{"id":"https://openalex.org/keywords/schema","display_name":"Schema (genetic algorithms)","score":0.45233604311943054},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4492243826389313},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4285014867782593},{"id":"https://openalex.org/keywords/gene-interaction","display_name":"Gene interaction","score":0.42846623063087463},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39944326877593994},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3019416630268097},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28749680519104004},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2802901864051819},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2614029347896576},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.22739359736442566},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1834149956703186}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7314369678497314},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6485282778739929},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6323007345199585},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5129584670066833},{"id":"https://openalex.org/C207850805","wikidata":"https://www.wikidata.org/wiki/Q269608","display_name":"Reverse engineering","level":2,"score":0.48068079352378845},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47451895475387573},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.45827317237854004},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45492616295814514},{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.45233604311943054},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4492243826389313},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4285014867782593},{"id":"https://openalex.org/C2991772755","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Gene interaction","level":3,"score":0.42846623063087463},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39944326877593994},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3019416630268097},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28749680519104004},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2802901864051819},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2614029347896576},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.22739359736442566},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1834149956703186},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","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":"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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems 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}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-444","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-444","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-444","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:20030818","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20030818","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:doaj.org/article:a45387f697be4b4c9387e29bf05bbf04","is_oa":true,"landing_page_url":"https://doaj.org/article/a45387f697be4b4c9387e29bf05bbf04","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 444 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2813854","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2813854","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-444","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-444","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-444","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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1966667678.pdf","grobid_xml":"https://content.openalex.org/works/W1966667678.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W178169250","https://openalex.org/W1559547793","https://openalex.org/W1663973292","https://openalex.org/W1756428283","https://openalex.org/W1778446120","https://openalex.org/W1851422093","https://openalex.org/W1885706271","https://openalex.org/W1896341954","https://openalex.org/W1933643226","https://openalex.org/W1965555277","https://openalex.org/W1970783685","https://openalex.org/W1989921625","https://openalex.org/W2026188254","https://openalex.org/W2038716712","https://openalex.org/W2039746571","https://openalex.org/W2044542119","https://openalex.org/W2053961182","https://openalex.org/W2062319807","https://openalex.org/W2075408326","https://openalex.org/W2085903184","https://openalex.org/W2090554117","https://openalex.org/W2100603120","https://openalex.org/W2103453943","https://openalex.org/W2114140117","https://openalex.org/W2116290764","https://openalex.org/W2122342005","https://openalex.org/W2130416704","https://openalex.org/W2132434674","https://openalex.org/W2137143372","https://openalex.org/W2137813581","https://openalex.org/W2138341763","https://openalex.org/W2139584447","https://openalex.org/W2140809061","https://openalex.org/W2147225006","https://openalex.org/W2148563299","https://openalex.org/W2149191198","https://openalex.org/W2149579404","https://openalex.org/W2152603063","https://openalex.org/W2159482845","https://openalex.org/W2161409973","https://openalex.org/W2161511352","https://openalex.org/W2163296115","https://openalex.org/W2495436614","https://openalex.org/W2594639291","https://openalex.org/W2611370172","https://openalex.org/W2793957704","https://openalex.org/W2913838200","https://openalex.org/W2979006918","https://openalex.org/W3099289621","https://openalex.org/W3150936184"],"related_works":["https://openalex.org/W2106927126","https://openalex.org/W2156421048","https://openalex.org/W2135896045","https://openalex.org/W2032799661","https://openalex.org/W2884256268","https://openalex.org/W2131025197","https://openalex.org/W2171763327","https://openalex.org/W3108451992","https://openalex.org/W2511617859","https://openalex.org/W2031892952"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,324,337],"ultimate":[2],"aim":[3],"of":[4,24,31,57,74,85,123,145,181,214,281,290,296,326],"systems":[5],"biology":[6],"is":[7,21,34,67,115,152,272,329],"to":[8,16,69,104,118,130,154,191,209,234,241,248,267,304],"understand":[9],"and":[10,60,98,121,199,204,238,259,263,275,293,315,334],"describe":[11,53],"how":[12,124,153],"molecular":[13,32,96,126],"components":[14],"interact":[15],"manifest":[17],"collective":[18],"behaviour":[19],"that":[20,81,186],"the":[22,25,35,45,86,136,146,159,167,211,215,254,265,279,291,305,327],"sum":[23],"single":[26,78,137],"parts.":[27],"Building":[28],"a":[29,40,77,83,125,142,205,223,273,294,345],"network":[30,112,147,160,292,339],"interactions":[33,50,97,134],"basic":[36],"step":[37,80],"in":[38,284,344],"modelling":[39],"complex":[41],"entity":[42],"such":[43],"as":[44,302,320],"cell.":[46],"Even":[47],"if":[48],"gene-gene":[49],"only":[51],"partially":[52],"real":[54],"networks":[55,107,233],"because":[56],"post-transcriptional":[58],"modifications":[59],"protein":[61],"regulation,":[62],"using":[63],"microarray":[64,251,335],"technology":[65],"it":[66,240],"possible":[68],"combine":[70],"measurements":[71],"for":[72,133,141,253,260,278,331],"thousands":[73],"genes":[75],"into":[76,201,222],"analysis":[79],"provides":[82],"picture":[84],"cell's":[87],"gene":[88,106,193,249,285,297,309],"expression.":[89],"Several":[90],"databases":[91],"provide":[92],"information":[93,156],"about":[94],"known":[95],"various":[99],"methods":[100],"have":[101],"been":[102],"developed":[103],"infer":[105,210],"from":[108,166],"expression":[109,194,250,298,310],"data.":[110,172,336],"However,":[111],"topology":[113],"alone":[114],"not":[116],"enough":[117],"perform":[119],"simulations":[120],"predictions":[122],"system":[127],"will":[128],"respond":[129],"perturbations.":[131],"Rules":[132],"among":[135],"parts":[138],"are":[139,220,300],"needed":[140],"complete":[143],"definition":[144],"behaviour.":[148],"Another":[149],"interesting":[150],"question":[151],"integrate":[155],"carried":[157],"by":[158],"topology,":[161],"which":[162],"can":[163,340],"be":[164,342],"derived":[165],"literature,":[168],"with":[169],"large-scale":[170],"experimental":[171],"RESULTS:":[173],"Here":[174],"we":[175],"propose":[176],"an":[177,188],"algorithm,":[178],"called":[179],"inference":[180,280],"regulatory":[182,212,282,318],"interaction":[183,218],"schema":[184],"(IRIS),":[185],"uses":[187],"iterative":[189],"approach":[190],"map":[192],"profile":[195],"values":[196,314],"(both":[197],"steady-state":[198],"time-course)":[200],"discrete":[202,313],"states":[203],"simple":[206],"probabilistic":[207],"method":[208,328],"functions":[213,319],"network.":[216],"These":[217],"rules":[219],"integrated":[221],"factor":[224,346],"graph":[225,347],"model.":[226,348],"We":[227,244],"test":[228],"IRIS":[229,247,271,307],"on":[230],"two":[231],"synthetic":[232,332],"determine":[235],"its":[236],"accuracy":[237],"compare":[239,264],"other":[242],"methods.":[243],"also":[245,341],"apply":[246],"data":[252,311,333],"Saccharomyces":[255],"cerevisiae":[256],"cell":[257],"cycle":[258],"human":[261],"B-cells":[262],"results":[266],"literature":[268],"findings.":[269],"CONCLUSIONS:":[270],"rapid":[274],"efficient":[276],"tool":[277],"relations":[283],"networks.":[286],"A":[287],"topological":[288],"description":[289],"matrix":[295],"profiles":[299],"required":[301],"input":[303],"algorithm.":[306],"maps":[308],"onto":[312],"then":[316],"computes":[317],"conditional":[321],"probability":[322],"tables.":[323],"suitability":[325],"demonstrated":[330],"resulting":[338],"embedded":[343]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
