{"id":"https://openalex.org/W2103640465","doi":"https://doi.org/10.1093/bioinformatics/btn155","title":"Combinatorial influence of environmental parameters on transcription factor activity","display_name":"Combinatorial influence of environmental parameters on transcription factor activity","publication_year":2008,"publication_date":"2008-06-27","ids":{"openalex":"https://openalex.org/W2103640465","doi":"https://doi.org/10.1093/bioinformatics/btn155","mag":"2103640465","pmid":"https://pubmed.ncbi.nlm.nih.gov/18586711"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn155","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn155","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://resolver.tudelft.nl/uuid:cfb27a64-b2fe-43a1-b02f-074f53d53683","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085788761","display_name":"Theo Knijnenburg","orcid":"https://orcid.org/0000-0001-6397-4222"},"institutions":[{"id":"https://openalex.org/I4210127603","display_name":"Cancer Genomics Centre","ror":"https://ror.org/02y9qjz38","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210127603"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"T.A. Knijnenburg","raw_affiliation_strings":["1 Information and Communication Theory Group, Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Kluyver Centre for Genomics of Industrial Fermentation and 3Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Information and Communication Theory Group, Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Kluyver Centre for Genomics of Industrial Fermentation and 3Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I4210127603","https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020129085","display_name":"Lodewyk F.A. Wessels","orcid":"https://orcid.org/0000-0002-1656-6995"},"institutions":[{"id":"https://openalex.org/I4210127603","display_name":"Cancer Genomics Centre","ror":"https://ror.org/02y9qjz38","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210127603"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"L.F.A. Wessels","raw_affiliation_strings":["1 Information and Communication Theory Group, Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Kluyver Centre for Genomics of Industrial Fermentation and 3Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Information and Communication Theory Group, Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Kluyver Centre for Genomics of Industrial Fermentation and 3Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I4210127603","https://openalex.org/I98358874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052699801","display_name":"Marcel Reinders","orcid":"https://orcid.org/0000-0002-1148-1562"},"institutions":[{"id":"https://openalex.org/I4210127603","display_name":"Cancer Genomics Centre","ror":"https://ror.org/02y9qjz38","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210127603"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"M.J.T. Reinders","raw_affiliation_strings":["1 Information and Communication Theory Group, Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Kluyver Centre for Genomics of Industrial Fermentation and 3Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Information and Communication Theory Group, Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Kluyver Centre for Genomics of Industrial Fermentation and 3Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I4210127603","https://openalex.org/I98358874"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085788761"],"corresponding_institution_ids":["https://openalex.org/I4210127603","https://openalex.org/I98358874"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7018,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.70734463,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"24","issue":"13","first_page":"i172","last_page":"i181"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5860999822616577,"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":0.5860999822616577,"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":0.12200000137090683,"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":0.09969999641180038,"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/chemostat","display_name":"Chemostat","score":0.5932945013046265},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.590293288230896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5264214873313904},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5237058401107788},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.48076459765434265},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.47755298018455505},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.440075159072876},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.43611517548561096},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43344414234161377},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.42485401034355164},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4197171926498413},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2973232865333557},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11212944984436035}],"concepts":[{"id":"https://openalex.org/C125111812","wikidata":"https://www.wikidata.org/wiki/Q902311","display_name":"Chemostat","level":3,"score":0.5932945013046265},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.590293288230896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5264214873313904},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5237058401107788},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.48076459765434265},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.47755298018455505},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.440075159072876},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.43611517548561096},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43344414234161377},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.42485401034355164},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4197171926498413},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2973232865333557},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11212944984436035},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004777","descriptor_name":"Environment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018929","descriptor_name":"Cell Culture Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018929","descriptor_name":"Cell Culture Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018929","descriptor_name":"Cell Culture Techniques","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn155","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn155","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18586711","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18586711","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:tud:oai:tudelft.nl:uuid:cfb27a64-b2fe-43a1-b02f-074f53d53683","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:cfb27a64-b2fe-43a1-b02f-074f53d53683","pdf_url":"http://resolver.tudelft.nl/uuid:cfb27a64-b2fe-43a1-b02f-074f53d53683","source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"Bioinformatics, 24 (13), 2008","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2718633","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2718633","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:tud:oai:tudelft.nl:uuid:cfb27a64-b2fe-43a1-b02f-074f53d53683","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:cfb27a64-b2fe-43a1-b02f-074f53d53683","pdf_url":"http://resolver.tudelft.nl/uuid:cfb27a64-b2fe-43a1-b02f-074f53d53683","source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"Bioinformatics, 24 (13), 2008","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.5}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310546","display_name":"Cancer Genomics Centre","ror":"https://ror.org/02y9qjz38"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2103640465.pdf"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1485640120","https://openalex.org/W1644724366","https://openalex.org/W1753000577","https://openalex.org/W1846192773","https://openalex.org/W1972038116","https://openalex.org/W1973260612","https://openalex.org/W1978469373","https://openalex.org/W1987075204","https://openalex.org/W2042006383","https://openalex.org/W2043370619","https://openalex.org/W2045776897","https://openalex.org/W2053126761","https://openalex.org/W2063183241","https://openalex.org/W2070340804","https://openalex.org/W2070672503","https://openalex.org/W2080498142","https://openalex.org/W2085465508","https://openalex.org/W2096037842","https://openalex.org/W2097390727","https://openalex.org/W2100771810","https://openalex.org/W2103017472","https://openalex.org/W2103733135","https://openalex.org/W2105315497","https://openalex.org/W2107465057","https://openalex.org/W2115955060","https://openalex.org/W2120376302","https://openalex.org/W2120865735","https://openalex.org/W2123812502","https://openalex.org/W2128697932","https://openalex.org/W2129265801","https://openalex.org/W2132561013","https://openalex.org/W2133446381","https://openalex.org/W2134873429","https://openalex.org/W2137446827","https://openalex.org/W2142890842","https://openalex.org/W2144710927","https://openalex.org/W2146209621","https://openalex.org/W2146513423","https://openalex.org/W2167190345","https://openalex.org/W2170989872","https://openalex.org/W4205298449","https://openalex.org/W6638863494","https://openalex.org/W6678976580"],"related_works":["https://openalex.org/W1971558040","https://openalex.org/W3156071777","https://openalex.org/W4283214369","https://openalex.org/W4296940635","https://openalex.org/W3208446472","https://openalex.org/W4281254649","https://openalex.org/W2914108095","https://openalex.org/W2791084809","https://openalex.org/W2951939896","https://openalex.org/W2560421304"],"abstract_inverted_index":{"MOTIVATION:":[0],"Cells":[1],"receive":[2],"a":[3,31,105,164,181],"wide":[4],"variety":[5],"of":[6,41,73,94,109,121,123,146,152,173,194],"environmental":[7,27,54,75,95,195],"signals,":[8],"which":[9],"are":[10,56,140,218],"often":[11,57],"processed":[12],"combinatorially":[13],"to":[14,30,36,150],"generate":[15],"specific":[16],"genetic":[17],"responses.":[18],"Changes":[19],"in":[20,38,46,148],"transcript":[21,138],"levels,":[22],"as":[23,129],"observed":[24,137],"across":[25,77],"different":[26],"conditions,":[28],"can,":[29],"large":[32],"extent,":[33],"be":[34],"attributed":[35],"changes":[37],"the":[39,52,61,74,92,116,124,144,168,174,191,210],"activity":[40,145,199],"transcription":[42,49],"factors":[43],"(TFs).":[44],"However,":[45],"unraveling":[47],"these":[48],"regulation":[50],"networks,":[51],"actual":[53],"signals":[55],"not":[58,67],"incorporated":[59],"into":[60,180],"model,":[62],"simply":[63],"because":[64],"they":[65],"have":[66],"been":[68],"measured.":[69],"The":[70,100,136,155,176,186,204],"unquantified":[71],"heterogeneity":[72],"parameters":[76,96,196],"microarray":[78,107],"experiments":[79],"frustrates":[80],"regulatory":[81,188],"network":[82,189],"inference.":[83],"RESULTS:":[84],"We":[85],"propose":[86],"an":[87],"inference":[88],"algorithm":[89],"that":[90,162],"models":[91],"influence":[93],"on":[97,104,197],"gene":[98,165,201],"expression.":[99,202],"approach":[101],"is":[102,178,207],"based":[103],"yeast":[106],"compendium":[108],"chemostat":[110],"steady-state":[111],"experiments.":[112],"Chemostat":[113],"cultivation":[114,126,153],"enables":[115],"accurate":[117],"control":[118],"and":[119,134,160,200],"measurement":[120],"many":[122],"key":[125],"parameters,":[127],"such":[128],"nutrient":[130],"concentrations,":[131],"growth":[132],"rate":[133],"temperature.":[135],"levels":[139],"explained":[141],"by":[142],"inferring":[143],"TFs":[147],"response":[149],"combinations":[151],"parameters.":[154],"interplay":[156],"between":[157],"activated":[158],"enhancers":[159],"repressors":[161],"bind":[163],"promoter":[166],"determine":[167],"possible":[169],"up-":[170],"or":[171],"downregulation":[172],"gene.":[175],"model":[177],"translated":[179],"linear":[182],"integer":[183],"optimization":[184],"problem.":[185],"resulting":[187],"identifies":[190],"combinatorial":[192],"effects":[193],"TF":[198],"AVAILABILITY:":[203],"Matlab":[205],"code":[206],"available":[208,219],"from":[209],"authors":[211],"upon":[212],"request.":[213],"SUPPLEMENTARY":[214],"INFORMATION:":[215],"Supplementary":[216],"data":[217],"at":[220],"Bioinformatics":[221],"online.":[222]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
