{"id":"https://openalex.org/W2117853146","doi":"https://doi.org/10.1186/1471-2105-11-308","title":"Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-\u03baB signaling-induced gene expression responses in inflammation","display_name":"Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-\u03baB signaling-induced gene expression responses in inflammation","publication_year":2010,"publication_date":"2010-06-08","ids":{"openalex":"https://openalex.org/W2117853146","doi":"https://doi.org/10.1186/1471-2105-11-308","mag":"2117853146","pmid":"https://pubmed.ncbi.nlm.nih.gov/20529327"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-308","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-308","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-308","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/10.1186/1471-2105-11-308","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111937781","display_name":"Shih Chi Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Shih Chi Peng","raw_affiliation_strings":["Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, ROC","[Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan ROC]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"[Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan ROC]","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046832315","display_name":"David Shan\u2010Hill Wong","orcid":"https://orcid.org/0000-0001-8574-8234"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"David Shan Hill Wong","raw_affiliation_strings":["Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan, ROC,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan, ROC,","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048065639","display_name":"Kai Che Tung","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Kai Che Tung","raw_affiliation_strings":["Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu, Taiwan, ROC"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103546820","display_name":"Yan Yu Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yan Yu Chen","raw_affiliation_strings":["Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan, ROC,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan, ROC,","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076642115","display_name":"Chun\u2010Cheih Chao","orcid":"https://orcid.org/0000-0003-4108-2658"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chun Cheih Chao","raw_affiliation_strings":["Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu, Taiwan, ROC"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109222319","display_name":"Chien-Hua Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I1296604144","display_name":"Memorial Hospital of South Bend","ror":"https://ror.org/04whfy367","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1296604144"]},{"id":"https://openalex.org/I3020100970","display_name":"Chang Gung Memorial Hospital","ror":"https://ror.org/02verss31","country_code":"TW","type":"healthcare","lineage":["https://openalex.org/I3020100970"]}],"countries":["TW","US"],"is_corresponding":false,"raw_author_name":"Chien Hua Peng","raw_affiliation_strings":["Department of Resource Center for Clinical Research, Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan, ROC","Department of Resource Center for Clinical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Resource Center for Clinical Research, Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan, ROC","institution_ids":["https://openalex.org/I3020100970"]},{"raw_affiliation_string":"Department of Resource Center for Clinical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC","institution_ids":["https://openalex.org/I1296604144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052901007","display_name":"Yung\u2010Jen Chuang","orcid":"https://orcid.org/0000-0002-6022-0107"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Yung Jen Chuang","raw_affiliation_strings":["Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu, Taiwan, ROC"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101474162","display_name":"Chuan Yi Tang","orcid":"https://orcid.org/0000-0003-0729-1624"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Chuan Yi Tang","raw_affiliation_strings":["Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","[Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan ROC]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"[Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan ROC]","institution_ids":["https://openalex.org/I25846049"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5052901007","https://openalex.org/A5101474162"],"corresponding_institution_ids":["https://openalex.org/I25846049"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0707,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.79826579,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"308","last_page":"308"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11591","display_name":"NF-\u03baB Signaling Pathways","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11591","display_name":"NF-\u03baB Signaling Pathways","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11503","display_name":"Cytokine Signaling Pathways and Interactions","score":0.008100000210106373,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10371","display_name":"Immune Response and Inflammation","score":0.0034000000450760126,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.7164679765701294},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6748650074005127},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6650866866111755},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5485870242118835},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5170814990997314},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49756672978401184},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4785333573818207},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.47156187891960144},{"id":"https://openalex.org/keywords/nfkb1","display_name":"NFKB1","score":0.4528804421424866},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.4417160451412201},{"id":"https://openalex.org/keywords/chemokine","display_name":"Chemokine","score":0.44004881381988525},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4225509464740753},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4020245671272278},{"id":"https://openalex.org/keywords/inflammation","display_name":"Inflammation","score":0.3328072428703308},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32291603088378906},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2588505744934082},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.2436995506286621}],"concepts":[{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.7164679765701294},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6748650074005127},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6650866866111755},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5485870242118835},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5170814990997314},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49756672978401184},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4785333573818207},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.47156187891960144},{"id":"https://openalex.org/C123298856","wikidata":"https://www.wikidata.org/wiki/Q15317427","display_name":"NFKB1","level":4,"score":0.4528804421424866},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4417160451412201},{"id":"https://openalex.org/C13373296","wikidata":"https://www.wikidata.org/wiki/Q421866","display_name":"Chemokine","level":3,"score":0.44004881381988525},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4225509464740753},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4020245671272278},{"id":"https://openalex.org/C2776914184","wikidata":"https://www.wikidata.org/wiki/Q101991","display_name":"Inflammation","level":2,"score":0.3328072428703308},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32291603088378906},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2588505744934082},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.2436995506286621}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007249","descriptor_name":"Inflammation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007249","descriptor_name":"Inflammation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007249","descriptor_name":"Inflammation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016328","descriptor_name":"NF-kappa B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-308","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-308","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-308","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:20529327","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20529327","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:6136fcb342014924b192be40ce5bbd57","is_oa":true,"landing_page_url":"https://doaj.org/article/6136fcb342014924b192be40ce5bbd57","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 11, Iss 1, p 308 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2889938","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2889938","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:10.1186/1471-2105-11-308","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-308","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-308","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":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2117853146.pdf","grobid_xml":"https://content.openalex.org/works/W2117853146.grobid-xml"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W184020152","https://openalex.org/W1409406454","https://openalex.org/W1481919380","https://openalex.org/W1529730227","https://openalex.org/W1573621493","https://openalex.org/W1588858818","https://openalex.org/W1641228030","https://openalex.org/W1793650522","https://openalex.org/W1955660753","https://openalex.org/W1965267927","https://openalex.org/W1970156673","https://openalex.org/W1972764318","https://openalex.org/W1979934740","https://openalex.org/W1982528660","https://openalex.org/W1985811499","https://openalex.org/W1993597798","https://openalex.org/W2004563262","https://openalex.org/W2007471837","https://openalex.org/W2007571167","https://openalex.org/W2007875429","https://openalex.org/W2009347496","https://openalex.org/W2014748042","https://openalex.org/W2016211878","https://openalex.org/W2031415436","https://openalex.org/W2037509330","https://openalex.org/W2044784465","https://openalex.org/W2045115006","https://openalex.org/W2050375893","https://openalex.org/W2052583486","https://openalex.org/W2058714321","https://openalex.org/W2064711537","https://openalex.org/W2066218635","https://openalex.org/W2069645361","https://openalex.org/W2074097004","https://openalex.org/W2080486913","https://openalex.org/W2086189875","https://openalex.org/W2095622082","https://openalex.org/W2098578848","https://openalex.org/W2100688306","https://openalex.org/W2101289679","https://openalex.org/W2106877484","https://openalex.org/W2109095035","https://openalex.org/W2109466900","https://openalex.org/W2114937915","https://openalex.org/W2116101489","https://openalex.org/W2128506325","https://openalex.org/W2131532450","https://openalex.org/W2133554538","https://openalex.org/W2133667940","https://openalex.org/W2135030836","https://openalex.org/W2137082708","https://openalex.org/W2139047628","https://openalex.org/W2139683115","https://openalex.org/W2147470531","https://openalex.org/W2147730579","https://openalex.org/W2154401739","https://openalex.org/W2155120241","https://openalex.org/W2156916138","https://openalex.org/W2157710901","https://openalex.org/W2160105565","https://openalex.org/W2160432911","https://openalex.org/W2162491638","https://openalex.org/W2162505680","https://openalex.org/W2163296727","https://openalex.org/W2163296862","https://openalex.org/W2164053161","https://openalex.org/W2234542263","https://openalex.org/W2312571711","https://openalex.org/W2335925695","https://openalex.org/W2412839122","https://openalex.org/W2417234603","https://openalex.org/W4312959532"],"related_works":["https://openalex.org/W2156421048","https://openalex.org/W2135896045","https://openalex.org/W2010571965","https://openalex.org/W3128451840","https://openalex.org/W2032799661","https://openalex.org/W2002709996","https://openalex.org/W2884256268","https://openalex.org/W2131025197","https://openalex.org/W4387092964","https://openalex.org/W2171763327"],"abstract_inverted_index":{"BACKGROUND:":[0],"Signal":[1],"transduction":[2,31,103,323,339],"is":[3,59,70,216,304],"the":[4,40,46,53,81,101,106,111,120,125,154,175,183,189,193,200,219,231,238,245,254,265,280,284,293,299,342],"major":[5,61],"mechanism":[6],"through":[7,29],"which":[8],"cells":[9],"transmit":[10],"external":[11,43],"stimuli":[12,20,44,275],"to":[13,72,79,99,136,152,164,291,309,315,335],"evoke":[14],"intracellular":[15],"biochemical":[16],"responses.":[17,108],"Diverse":[18],"cellular":[19,48],"create":[21],"a":[22,60,67,90,138,166],"wide":[23],"variety":[24],"of":[25,84,113,192,204,241,253,283,296,344,347],"transcription":[26],"factor":[27],"activities":[28],"signal":[30,102,322,338],"pathways,":[32],"resulting":[33],"in":[34,63,141,182,244],"different":[35,274],"gene":[36,107,127,167,202],"expression":[37,203],"patterns.":[38],"Understanding":[39],"relationship":[41],"between":[42],"and":[45,76,96,158,185,207,214,223,249,263],"corresponding":[47,176,266],"responses,":[49],"as":[50,52],"well":[51],"subsequent":[54],"effects":[55,235,312],"on":[56,118],"downstream":[57,345],"genes,":[58],"challenge":[62],"systems":[64,332],"biology.":[65],"Thus,":[66],"systematic":[68,91],"approach":[69,92],"needed":[71],"integrate":[73,316],"experimental":[74,190,300],"data":[75],"theoretical":[77],"hypotheses":[78],"identify":[80],"physiological":[82],"consequences":[83,295],"environmental":[85],"stimuli.":[86],"RESULTS:":[87],"We":[88,143,197,260],"proposed":[89],"that":[93,174,199],"combines":[94],"forward":[95,146],"reverse":[97,159],"engineering":[98,147,160],"link":[100,336],"cascade":[104],"with":[105,124,188,218,273,341],"To":[109],"demonstrate":[110],"feasibility":[112],"our":[114,251,278,302],"strategy,":[115],"we":[116,172],"focused":[117],"linking":[119],"NF-kappaB":[121,131,155,220,242,285],"signaling":[122,156,243,267],"pathway":[123,157],"inflammatory":[126,247,256],"regulatory":[128,168,234,286],"responses":[129,343],"because":[130],"has":[132],"long":[133],"been":[134],"recognized":[135],"play":[137],"crucial":[139,239,281],"role":[140],"inflammation.":[142,297],"first":[144],"utilized":[145],"(Hybrid":[148],"Functional":[149],"Petri":[150],"Nets)":[151],"construct":[153],"(Network":[161],"Components":[162],"Analysis)":[163],"build":[165],"network":[169,287],"(GRN).":[170],"Then,":[171],"demonstrated":[173],"IKK":[177,194],"profiles":[178,268],"can":[179],"be":[180],"identified":[181,262,290],"GRN":[184],"are":[186],"consistent":[187],"validation":[191],"kinase":[195],"assay.":[196],"found":[198],"time-lapse":[201],"several":[205],"cytokines":[206],"chemokines":[208],"(TNF-alpha,":[209],"IL-1,":[210],"IL-6,":[211],"CXCL1,":[212],"CXCL2":[213],"CCL3)":[215],"concordant":[217],"activity":[221],"profile,":[222],"these":[224],"genes":[225,282,346],"have":[226,236],"stronger":[227],"influence":[228],"strength":[229],"within":[230],"GRN.":[232],"Such":[233],"highlighted":[237],"roles":[240],"acute":[246],"response":[248,257],"enhance":[250],"understanding":[252],"systemic":[255],"syndrome.":[258],"CONCLUSION:":[259],"successfully":[261],"distinguished":[264],"among":[269],"three":[270],"microarray":[271],"datasets":[272],"strengths.":[276],"In":[277],"model,":[279],"were":[288],"also":[289,327],"reflect":[292],"biological":[294],"With":[298],"validation,":[301],"strategy":[303,326],"thus":[305],"an":[306],"effective":[307],"solution":[308],"decipher":[310],"cross-talk":[311],"when":[313],"attempting":[314],"new":[317,329],"kinetic":[318],"parameters":[319],"from":[320],"other":[321],"pathways.":[324],"The":[325],"provides":[328],"insight":[330],"for":[331],"biology":[333],"modeling":[334],"any":[337],"pathways":[340],"interest.":[348]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":6},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2016-06-24T00:00:00"}